MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'Current Protein and Peptide Science' source. Thu, 09 Feb 2012 13:38:34 +0100 http://www.medworm.com/index.php?rid=5636655&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22264127%26dopt%3DAbstract Authors: Zhang Y, Rao R Abstract The ubiquitous and essential V-ATPase is a worthy chemotherapeutic target in the escalating battle against invasive fungal infections. Pathogenic fungi require optimum V-ATPase function for secretion of virulence factors, induction of stress response pathways, hyphal morphology and homeostasis of pH and other cations in order to successfully survive within and colonize the host. This review discusses why impairment of V-ATPase activity confers multidrug sensitivity and loss of virulence. Recent evidence points to the V-ATPase as a novel downstream target of the azole class of antifungals that inhibit the biogenesis of ergosterol. Depletion of ergosterol from vacuolar membranes led to progressive alkalization of yeast vacuoles, loss of V-ATPase activ... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=5636655 Mon, 16 Jan 2012 05:00:00 +0100 5636655 http://www.medworm.com/index.php?rid=5525463&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22182249%26dopt%3DAbstract Authors: Du QS, Huang RB Abstract For quite a long period of time in history, many intense efforts have been made to determine the 3D (three-dimensional) structure of the M2 proton channel. The reason why the M2 proton channel has attracted so many attentions is because (1) it is the key for really understanding the life cycle of influenza viruses, and (2) it is indispensable for conducting rational drug design against the flu viruses. Recently, the long-sough 3D structures of the M2 proton channels for both influenza A and B viruses were consecutively successfully determined by the high-resolution NMR spectroscopy (Schnell J.R. and Chou, J.J., Nature, 2008, 451: 591-595; Wang, J., Pielak, R.M., McClintock, M.A., and Chou, J.J., Nature Structural & Molecular Biology, 2009,16: 1... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=5525463 Mon, 28 Nov 2011 05:00:00 +0100 5525463 http://www.medworm.com/index.php?rid=5525462&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22182250%26dopt%3DAbstract Authors: Xuan J, Feng Y Abstract Here we review the present state of structural and functional studies of the Sac10b protein family, a class of highly conserved 10 kDa nucleic acid-binding proteins in archaea. Based on biochemical and structural studies, these proteins were originally assigned a role in the structural organization of chromatin; Sac10b proteins of hyperthermophilic archaea, for example, showed tight, unspecific DNA binding. More recently, however, Sac10b proteins of mesophilic archaea were found to interact preferentially with specific DNA sequences thereby affecting the expression of distinct genes. Furthermore, Sac10b proteins of hyperthermophilic, thermophilic and mesophilic archaea were also shown to bind to RNA with distinct affinities and specificities but fun... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=5525462 Mon, 28 Nov 2011 05:00:00 +0100 5525462 http://www.medworm.com/index.php?rid=5525461&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22182251%26dopt%3DAbstract Authors: Chen Q, Chen B PMID: 22182251 [PubMed - as supplied by publisher] (Source: Current Protein and Peptide Science) Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=5525461 Mon, 28 Nov 2011 05:00:00 +0100 5525461 http://www.medworm.com/index.php?rid=5525460&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22182252%26dopt%3DAbstract Authors: Carrer DC PMID: 22182252 [PubMed - as supplied by publisher] (Source: Current Protein and Peptide Science) Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=5525460 Mon, 28 Nov 2011 05:00:00 +0100 5525460 http://www.medworm.com/index.php?rid=5525464&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22181021%26dopt%3DAbstract Authors: Chen Q, Chen B PMID: 22181021 [PubMed - in process] (Source: Current Protein and Peptide Science) Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=5525464 Tue, 01 Nov 2011 04:00:00 +0100 5525464 http://www.medworm.com/index.php?rid=5376520&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22044140%26dopt%3DAbstract Authors: Hohlweg W, Kosol S, Zangger K Abstract Many naturally occurring bioactive peptides bind to biological membranes. Studying and elucidating the mode of interaction is often an essential step to understand their molecular and biological functions. To obtain the complete orientation and immersion depth of such compounds in the membrane or a membrane-mimetic system, a number of methods are available, which are separated in this review into four main classes: solution NMR, solid-state NMR, EPR and other methods. Solution NMR methods include the Nuclear Overhauser Effect (NOE) between peptide and membrane signals, residual dipolar couplings and the use of paramagnetic probes, either within the membrane-mimetic or in the solvent. The vast array of solid state NMR methods to study ... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=5376520 Tue, 25 Oct 2011 04:00:00 +0100 5376520 http://www.medworm.com/index.php?rid=5376519&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22044141%26dopt%3DAbstract Authors: Clausen MP, Lagerholm BC Abstract Single particle tracking (SPT) enables light microscopy at a sub-diffraction limited spatial resolution by a combination of imaging at low molecular labeling densities and computational image processing. SPT and related single molecule imaging techniques have found a rapidly expanded use within the life sciences. This expanded use is due to an increased demand and requisite for developing a comprehensive understanding of the spatial dynamics of bio-molecular interactions at a spatial scale that is equivalent to the size of the molecules themselves, as well as by the emergence of new imaging techniques and probes that have made historically very demanding and specialized bio-imaging techniques more easily accessible and achievable. SPT has ... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=5376519 Tue, 25 Oct 2011 04:00:00 +0100 5376519 http://www.medworm.com/index.php?rid=5376518&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22044142%26dopt%3DAbstract Authors: Cybulski LE, de Mendoza D Abstract The influence of the lipid environment on the function of membrane proteins is increasingly recognized as crucial. Nevertheless, the molecular mechanisms underlying protein-lipid interactions remain obscure. Membrane lipid composition has a regulatory effect on membrane protein activity, and for a number of membrane proteins a clear correlation was found between protein activity and properties of the membrane bilayer such as fluidity. Membrane thickness is an important property of a lipid bilayer. It is expected that hydrophobic thickness match the hydrophobic thickness of transmembrane segments of integral membrane proteins. Any mismatch between the hydrophobic thicknesses of the lipid bilayer and the protein would lead to some modificat... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=5376518 Tue, 25 Oct 2011 04:00:00 +0100 5376518 http://www.medworm.com/index.php?rid=5376517&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22044143%26dopt%3DAbstract Authors: Bleicken S, Otsuki M, García-Sáez AJ Abstract The characterization of interactions between membrane proteins as they take place within the lipid bilayer poses a technical challenge, which is currently very difficult and, in many cases, impossible to overcome. The recent development of a method based in the combination two-color fluorescence cross-correlation spectroscopy with scanning of the focal volume allows the detection and quantification of interactions between biomolecules inserted in biological membranes. This powerful strategy has allowed the quantitative analysis of diverse systems, such as the association between proteins of the Bcl-2 family involved in apoptosis regulation or the binding between a growth factor and its receptor during signaling. Here, we revi... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=5376517 Tue, 25 Oct 2011 04:00:00 +0100 5376517 http://www.medworm.com/index.php?rid=5376516&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22044144%26dopt%3DAbstract Authors: Leckband DE Abstract Cell surface carbohydrates are important targets for many cell surface receptors, and they mediate crucial biological processes ranging from pathogen infectivity to neutrophil adhesion to drug targeting. A central challenge is to identify relationships between lectin architecture and function that influence the adhesion strength, avidity, and kinetics of receptor-glycan bonds. This information is central both to understanding recognition mechanisms and to developing effective therapeutic agents for drug targeting or for preventing infection. Increasingly, force probes are used to assess structure activity relationships of both the glycan ligands and the receptors that bind them, as well as molecular mechanisms underlying binding and adhesion. This revi... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=5376516 Tue, 25 Oct 2011 04:00:00 +0100 5376516 http://www.medworm.com/index.php?rid=5376515&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22044145%26dopt%3DAbstract We describe the new method in detail, and show the applicability on two specific examples: firstly, kinetic rate constants can be derived for the transient interaction of mobile membrane proteins; secondly, residence time and corral size can be extracted for confined diffusion. PMID: 22044145 [PubMed - as supplied by publisher] (Source: Current Protein and Peptide Science) Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=5376515 Tue, 25 Oct 2011 04:00:00 +0100 5376515 http://www.medworm.com/index.php?rid=5376514&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22044146%26dopt%3DAbstract Authors: Csermely P, Sandhu KS, Hazai E, Hoksza Z, Kiss HJ, Veres DV, Piazza F, Nussinov R Abstract During the last decade, network approaches became a powerful tool to describe protein structure and dynamics. Here we review the links between disordered proteins and the associated networks, and describe the consequences of local, mesoscopic and global network disorder on changes in protein structure and dynamics. We introduce a new classification of protein networks into 'cumulus-type', i.e., those similar to puffy (white) clouds, and 'stratus-type', i.e., those similar to flat, dense (dark) low-lying clouds, and relate these network types to protein disorder dynamics and to differences in energy transmission processes. In the first class, there is limited overlap between the modul... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=5376514 Tue, 25 Oct 2011 04:00:00 +0100 5376514 http://www.medworm.com/index.php?rid=5376513&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22044147%26dopt%3DAbstract THE ROLE OF INTRINSICALLY DISORDERED REGIONS IN THE STRUCTURE AND FUNCTIONING OF SMALL HEAT SHOCK PROTEINS. Curr Protein Pept Sci. 2011 Oct 25; Authors: Gusev NB Abstract Small heat shock proteins (sHsp) form a large ubiquitous family of proteins expressed in all fila of living organisms. The members of this family have low molecular masses (13-43 kDa) and contain a conservative α-crystallin domain. This domain (about 90 residues) consists of several β-strands forming two β-sheets packed in immunoglobulin-like manner. The α-crystallin domain plays an important role in formation of stable sHsp dimers, which are the building blocks of the large sHsp oligomers. A large N-terminal domain and a short C-terminal extension flank the α-crystallin domain. Both the N-terminal do... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=5376513 Tue, 25 Oct 2011 04:00:00 +0100 5376513 http://www.medworm.com/index.php?rid=5376512&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22044148%26dopt%3DAbstract Authors: Lee SH, Kim DH, Lee SH, Han JJ, Cha EJ, Lim JE, Cho YJ, Lee C, Han KH Abstract Intrinsically unfolded proteins (IUPs) do not obey the golden rule of structural biology, 3D structure = function, as they manifest their inherent functions without resorting to three-dimensional structures. Absence of a compact globular topology in these proteins strongly implies that their ligand recognition processes should involve factors other than spatially well-defined binding pockets. Heteronuclear multidimensional (HetMulD) NMR spectroscopy assisted with a stable isotope labeling technology is a powerful tool for quantitatively investigating detailed structural features in IUPs. In particular, it allows us to delineate the presence and locations of pre-structured motifs (PreSMos) on a p... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=5376512 Tue, 25 Oct 2011 04:00:00 +0100 5376512 http://www.medworm.com/index.php?rid=5376511&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22044149%26dopt%3DAbstract Authors: Peng ZL, Kurgan L Abstract The intrinsic disorder is relatively common in proteins, plays important roles in numerous cellular activities, and its prevalence was implicated in various human diseases. However, annotations of the disorder lag behind the rapidly increasing number of known protein chains. Last decade observed development of a relatively large number of in-silico methods that predict the disorder using the protein sequence as their input. We perform a first-of-its kind comprehensive empirical evaluation of the disorder predictors which is characterized by three novel aspects, (1) we evaluate the quality of the disorder predictions at the residue, segment, and chain levels; (2) we consider a large number of published and accessible to the end user predictors tha... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=5376511 Tue, 25 Oct 2011 04:00:00 +0100 5376511 http://www.medworm.com/index.php?rid=5376510&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22044150%26dopt%3DAbstract Authors: Receveur-Bréchot V, Durand D Abstract While the crucial role of intrinsically disordered proteins (IDPs) in the cell cycle is now recognized, deciphering their molecular mode of action at the structural level still remains highly challenging and requires a combination of many biophysical approaches. Among them, small angle X-ray scattering (SAXS) has been extremely successful in the last decade and has become an indispensable technique for addressing many of the fundamental questions regarding the activities of IDPs. After introducing some experimental issues specific to IDPs and in relation to the latest technical developments, this article presents the interest of the theory of polymer physics to evaluate the flexibility of fully disordered proteins. The different strat... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=5376510 Tue, 25 Oct 2011 04:00:00 +0100 5376510 http://www.medworm.com/index.php?rid=5376509&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22044151%26dopt%3DAbstract Authors: Westerheide SD, Raynes R, Powell C, Xue B, Uversky VN Abstract Intrinsically disordered proteins are highly abundant in all kingdoms of life, and several protein functional classes, such as transcription factors, transcriptional regulators, hub and scaffold proteins, signaling proteins, and chaperones are especially enriched in intrinsic disorder. One of the unique cellular reactions to protein damaging stress is the so-called heat shock response that results in the upregulation of heat shock proteins including molecular chaperones. This molecular protective mechanism is conserved from prokaryotes to eukaryotes and allows an organism to respond to various proteotoxic stressors, such as heat shock, oxidative stress, exposure to heavy metals, and drugs. The heat shock respon... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=5376509 Tue, 25 Oct 2011 04:00:00 +0100 5376509 http://www.medworm.com/index.php?rid=5376508&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22044152%26dopt%3DAbstract Authors: Cs T, Vk J, Ma K, K H Abstract The unique ability of the osteoclasts to resorb the calcified bone matrix is dependent on secretion of hydrochloric acid. This process is mediated by a vacuolar H+ ATPase (V-ATPase) and a chloride-proton antiporter. The structural subunit of the V-ATPase, a3, is highly specific for osteoclasts, and mutations in a3 lead to infantile malignant osteopetrosis, a phenomenon characterized by increased bone mass, an increased number of non-resorbing osteoclasts, and a complete lack of bone resorption. Importantly, these individuals have normal or even increased osteoblast numbers and bone formation suggesting that the osteoclasts, but not their resorptive capability, relay an anabolic signal, and, hence, that bone formation can be uncoupled from bon... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=5376508 Tue, 25 Oct 2011 04:00:00 +0100 5376508 http://www.medworm.com/index.php?rid=5376507&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22044153%26dopt%3DAbstract Authors: Kane PM Abstract Vacuolar proton-translocating ATPases (V-ATPases) are highly conserved proton pumps consisting of a peripheral membrane subcomplex called V(1), which contains the sites of ATP hydrolysis, attached to an integral membrane subcomplex called V(o), which encompasses the proton pore. V-ATPase regulation by reversible dissociation, characterized by release of assembled V(1) sectors into the cytosol and inhibition of both ATPase and proton transport activities, was first identified in tobacco hornworm and yeast. It has since become clear that modulation of V-ATPase assembly level is also a regulatory mechanism in mammalian cells. In this review, the implications of reversible disassembly for V-ATPase structure are discussed, along with insights into underlying su... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=5376507 Tue, 25 Oct 2011 04:00:00 +0100 5376507 http://www.medworm.com/index.php?rid=5376506&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22044154%26dopt%3DAbstract Authors: Lee BS Abstract Vacuolar ATPases (V-ATPases) are large multisubunit complexes that actively transport protons across cellular membranes to acidify intracellular compartments, thereby serving a critical housekeeping function. In addition, V-ATPases are also expressed on the plasma membrane of cell types such as kidney epithelia and osteoclasts, which require high levels of proton secretion to perform their specialized activities. This multiplicity of function is achieved by the expression of numerous V-ATPase subunit isoforms that are mixed and matched to produce complexes required for each cellular activity. Multiple regulatory mechanisms are necessary to allow coordinated expression of V-ATPase subunit proteins involved in both housekeeping and specialized functions. This... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=5376506 Tue, 25 Oct 2011 04:00:00 +0100 5376506 http://www.medworm.com/index.php?rid=5376505&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22044155%26dopt%3DAbstract Authors: Kartner N, Manolson MF Abstract Over the last three decades, V-ATPases have emerged from the obscurity of poorly understood membrane proton transport phenomena to being recognized as ubiquitous proton pumps that underlie vital cellular processes in all eukaryotic and many prokaryotic cells. These exquisitely complex molecular motors also engage in diverse specialized roles contributing to development, tissue function and pH homeostasis within complex organisms. Increasingly, mutations and misappropriation of V-ATPase function have been linked to diseases, ranging from sclerosing bone pathologies and renal tubular acidosis to bone-loss disorders and cancer metastasis. Much remains to be learned about the details of V-ATPase cell and molecular biology; nevertheless, interest... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=5376505 Tue, 25 Oct 2011 04:00:00 +0100 5376505 http://www.medworm.com/index.php?rid=5376504&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22044156%26dopt%3DAbstract Authors: Jansen EJ, Martens GJ Abstract The vacuolar (H(+))-ATPase (V-ATPase) is a universal proton pump and its activity is required for a variety of cell-biological processes such as membrane trafficking, receptor-mediated endocytosis, lysosomal protein degradation, osteoclastic bone resorption and maintenance of acid-base homeostasis by renal intercalated cells. In neuronal and neuroendocrine cells, the V-ATPase is the major regulator of intragranular acidification which is indispensable for correct prohormone processing and neurotransmitter uptake. In these specialized cells, the V-ATPase is equipped with the accessory subunits ATP6AP1/Ac45 and ATP6AP2/(pro)renin receptor. Recent studies have shown that Ac45 interacts with the V(0)-sector of the V-ATPase complex, thereby regula... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=5376504 Tue, 25 Oct 2011 04:00:00 +0100 5376504 http://www.medworm.com/index.php?rid=5376503&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22044157%26dopt%3DAbstract Authors: Sennoune SR, Martínez-Zaguilán R Abstract Up-regulated aerobic glycolysis is a hallmark of malignant cancers. Little is understood about the reasons why malignant tumors up-regulate glycolysis and acidify their microenvironment. Signaling pathways involved in glucose changes are numerous. However, the identity of the internal glucose signal remains obscure. In this review we address the question of the significance of vacuolar proton ATPase (V-ATPase) and its relationship to up-regulated glycolysis in tumors. We know that glycolysis is extremely sensitive to changes in pH. Importantly, the V-ATPase activity is sensitive to glucose availability. Therefore, we propose that pH acts as the glucose signal via the V-ATPase that responds to changes in intracellular pH and acts ... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=5376503 Tue, 25 Oct 2011 04:00:00 +0100 5376503 http://www.medworm.com/index.php?rid=5376502&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22044158%26dopt%3DAbstract Authors: Toro EJ, Ostrov DA, Wronski TJ, Holliday LS Abstract Binding between vacuolar H(+)-ATPases (V-ATPases) and microfilaments is mediated by an actin binding domain in the B-subunit. Both isoforms of mammalian B-subunit and that of yeast bind microfilaments with a high affinity. A similar actin-binding activity has been demonstrated in the B-subunit of yeast. A conserved "profilin-like" domain in the B-subunit mediates this actin-binding activity, named due to its sequence and structural similarity to an actin-binding surface of the canonical actin binding protein profilin. Subtle mutations in the "profilin-like" domain eliminate actin binding activity without disrupting the ability of the altered protein to associate with the other subunits of V-ATPase to form a functional pr... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=5376502 Tue, 25 Oct 2011 04:00:00 +0100 5376502 http://www.medworm.com/index.php?rid=5147351&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21827421%26dopt%3DAbstract Authors: Xuan J, Feng Y Here we review the present state of structural and functional studies of the Sac10b protein family, a class of highly conserved 10 kDa nucleic acid-binding proteins in archaea. Based on biochemical and structural studies, these proteins were originally assigned a role in the structural organization of chromatin; Sac10b proteins of hyperthermophilic archaea, for example, showed tight, unspecific DNA binding. More recently, however, Sac10b proteins of mesophilic archaea were found to interact preferentially with specific DNA sequences thereby affecting the expression of distinct genes. Furthermore, Sac10b proteins of hyperthermophilic, thermophilic and mesophilic archaea were also shown to bind to RNA with distinct affinities and specificities but functional conse... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=5147351 Mon, 08 Aug 2011 23:00:00 +0100 5147351 http://www.medworm.com/index.php?rid=5147350&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21827422%26dopt%3DAbstract Authors: Suda S, Cotter PD, Hill C, Ross RP The continuing problem of the emergence of multidrug resistance in pathogens has resulted in renewed efforts to identify novel antimicrobials that could be used in clinical settings. Lantibiotics are bacterially produced gene encoded antimicrobial peptides which have been the focus of extensive investigation in recent years because of their broad spectrum of activity. Lantibiotics (lanthionine-containing antibiotics), which have traditionally been regarded as antimicrobials for use in food or veterinary medicine, may provide at least part of the solution to these problems. Lacticin 3147 is a two peptide lantibiotic (consisting of the peptides Ltnα and Ltnβ) which is active at low concentrations against many pathogens. It has been the subjec... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=5147350 Mon, 08 Aug 2011 23:00:00 +0100 5147350 http://www.medworm.com/index.php?rid=5147349&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21827423%26dopt%3DAbstract Authors: Papaleo E, Tiberti M, Invernizzi G, Pasi M, Ranzani V The identification of molecular mechanisms underlying enzyme cold adaptation is a hot-topic both for fundamental research and industrial applications. In the present contribution, we review the last decades of structural computational investigations on cold-adapted enzymes in comparison to their warm-adapted counterparts. Comparative sequence and structural studies allow the definition of a multitude of adaptation strategies. Different enzymes carried out diverse mechanisms to adapt to low temperatures, so that a general theory for enzyme cold adaptation cannot be formulated. However, some common features can be traced in dynamic and flexibility properties of these enzymes, as well as in their intra- and inter-molecular int... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=5147349 Mon, 08 Aug 2011 23:00:00 +0100 5147349 http://www.medworm.com/index.php?rid=5147348&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21827424%26dopt%3DAbstract Authors: Ren J, Gao X, Liu Z, Cao J, Ma Q, Xue Y Phosphorylation is one of the most essential post-translational modifications (PTMs) of proteins, regulates a variety of cellular signaling pathways, and at least partially determines the biological diversity. Recent progresses in phosphoproteomics have identified more than 100,000 phosphorylation sites, while this number will easily exceed one million in the next decade. In this regard, how to extract useful information from flood of phosphoproteomics data has emerged as a great challenge. In this review, we summarized the leading edges on computational analysis of phosphoproteomics, including discovery of phosphorylation motifs from phosphoproteomics data, systematic modeling of phosphorylation network, analysis of genetic variation th... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=5147348 Mon, 08 Aug 2011 23:00:00 +0100 5147348 http://www.medworm.com/index.php?rid=5138918&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21827425%26dopt%3DAbstract Authors: Liu Q, Yang Y, Li Y, Zhang Z Inferring transcriptional regulatory networks from high-throughput biological data is a major challenge to bioinformatics today. To address this challenge, we developed TReNGO (Transcriptional Regulatory Networks reconstruction based on Global Optimization), a global and threshold-free algorithm with simulated annealing for inferring regulatory networks by the integration of ChIP-chip and expression data. Superior to existing methods, TReNGO was expected to find the optimal structure of transcriptional regulatory networks without any arbitrary thresholds or predetermined number of transcriptional modules (TMs). TReNGO was applied to both synthetic data and real yeast data in the rapamycin response. In these applications, we demonstrated an improved... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=5138918 Mon, 08 Aug 2011 23:00:00 +0100 5138918 http://www.medworm.com/index.php?rid=5138861&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21827426%26dopt%3DAbstract In this study, a new approach for Oryza sativa proteome annotation based on the 2D-gel maps was developed. Based on the publicly available 2D-PAGE data of rice, 11,201 gel spots were annotated accounting for 87.2% of the total spots on the gel maps. Gel spot alignments were performed for the annotated gel maps belonging to 23 rice tissues or organelles. In summary, 253 alignments between 23 tissues or organelles were performed, and 26,207 co-expressed proteins were identified using our analytical strategy. Large-scale bi-cluster analysis of 23 tissues/organelles proteomes of rice was carried out to detect novel functional proteins. Function and pathway analysis identified a number of common gene products with great potential in regulating specific physiological and biochemical events withi... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=5138861 Mon, 08 Aug 2011 23:00:00 +0100 5138861 http://www.medworm.com/index.php?rid=5138819&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21827427%26dopt%3DAbstract Authors: Marinil S, Xu Q, Yang Q Protein-Protein Interaction (PPI) prediction is a well known problem in Bioinformatics, for which a large number of techniques have been proposed in the past. However, prediction results have not been sufficiently satisfactory for guiding biologists in web-lab experiments. One reason is that not all useful information, such as pairwise protein interaction information based on sequence alignment, has been integrated together in PPI prediction. Alignment is a basic concept to measure sequence similarity in Proteomics that has been used in a number of applications ranging from protein recognition to protein subcellular localization. In this article, we propose a novel integrated approach to predicting PPI based on sequence alignment by jointly using a k-Ne... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=5138819 Mon, 08 Aug 2011 23:00:00 +0100 5138819 http://www.medworm.com/index.php?rid=5138811&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21827428%26dopt%3DAbstract Authors: Kido EA, de Araújo Barbosa PK, Costa Ferreira Neto JR, Pandolfi V, Houllou-Kido LM, Crovella S, Molina C, Kahl G, Benko-Iseppon AM Plants are sessile organisms subjected to many environmental adversities. For their survival they must sense and respond to biotic and abiotic stresses efficiently. During this process, protein kinases are essential in the perception of environmental stimuli, triggering signaling cascades. Kinases are among the largest and most important gene families for biotechnological purposes, bringing many challenges to the bioinformaticians due to the combination of conserved domains besides diversified regions. Cowpea [Vigna unguiculata (L.) Walp.] is an important legume that is adapted to different agroclimatic conditions, including drought, humidity and ... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=5138811 Mon, 08 Aug 2011 23:00:00 +0100 5138811 http://www.medworm.com/index.php?rid=5138778&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21827429%26dopt%3DAbstract A Closer Look at "Social" Boundary Genes Reveals Knowledge to Gene Expression Profiles. Curr Protein Pept Sci. 2011 Aug 9; Authors: Gao S, Zeng J, Elsheikh AM, Naji G, Alhajj R, Rokne J, Demetrick D As social network analysis is gaining popularity in modeling real world problems, the task of applying the social network model concepts and notions to biological data is still one of the most attractive research problems to be addressed. According, our work described in this paper focuses on a particular set of genes that reside on the community boundaries in gene co-expression networks. Stemmed from community mining problem in social networks, peripheries of communities (i.e., boundaries) can be used to aid certain biological analysis. The proposed method consists of three parts: ... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=5138778 Mon, 08 Aug 2011 23:00:00 +0100 5138778 http://www.medworm.com/index.php?rid=5089277&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21787297%26dopt%3DAbstract Authors: Xin F, Radivojac P The recent accumulation of experimentally determined protein 3D structures combined with our ability to computationally model structure from amino acid sequence has resulted in an increased importance of structure-based methods for protein function prediction. Two types of methods for function prediction have been proposed: those that can accurately predict overall biochemical or biological roles of a protein and those that predict its functional residues. Here, we review approaches used for the computational identification of functional residues in protein structures and summarize their applications to a wide variety of problems in functional proteomics, such as the prediction of catalytic residues, posttranslational modifications, or nucleic acid-binding s... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=5089277 Sun, 24 Jul 2011 23:00:00 +0100 5089277 http://www.medworm.com/index.php?rid=5089276&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21787298%26dopt%3DAbstract Authors: Xiao X, Wang P, Chou KC With the explosion of protein sequences generated in the postgenomic era, it is highly desirable to develop high-throughput tools for rapidly and reliably identifying various attributes of uncharacterized proteins based on their sequence information alone. The knowledge thus obtained can help us timely utilize these newly found protein sequences for both basic research and drug discovery. Many bioinformatics tools have been developed by means of machine learning methods. This review is focused on the applications of a new kind of science (cellular automata) in protein bioinformatics. A cellular automaton (CA) is an open, flexible and discrete dynamic model that holds enormous potentials in modeling complex systems, in spite of the simplicity of the mode... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=5089276 Sun, 24 Jul 2011 23:00:00 +0100 5089276 http://www.medworm.com/index.php?rid=5089275&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21787299%26dopt%3DAbstract Authors: Kurgan L, Disfani FM The last few decades observed an increasing interest in development and application of 1-dimansional (1D) descriptors of protein structure. These descriptors project 3D structural features onto 1D strings of residue-wise structural assignments. They cover a wide-range of structural aspects including conformation of the backbone, burying depth/solvent exposure and flexibility of residues, and inter-chain residue-residue contacts. We perform first-of-its-kind comprehensive comparative review of the existing 1D structural descriptors. We define, review and categorize ten structural descriptors and we also describe, summarize and contrast over eighty computational models that are used to predict these descriptors from the protein sequences. We show that the ma... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=5089275 Sun, 24 Jul 2011 23:00:00 +0100 5089275 http://www.medworm.com/index.php?rid=5089274&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21787300%26dopt%3DAbstract Authors: Cheng H, Chan WS, Li Z, Wang D, Liu S, Zhou Y Evidence is accumulating that small open reading frames (sORF, <100 codons) play key roles in many important biological processes. Yet, they are generally ignored in gene annotation despite they are far more abundant than the genes with more than 100 codons. Here, we demonstrate that popular homolog search and codon-index techniques perform poorly for small genes relative to that for larger genes, while a method dedicated to sORF discovery has a similar level of accuracy as homology search. The result is largely due to the small dataset of experimentally verified sORF available for homology search and for training ab initio techniques. It highlights the urgent need for both experimental and computational studies in order to furt... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=5089274 Sun, 24 Jul 2011 23:00:00 +0100 5089274 http://www.medworm.com/index.php?rid=5089273&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21787301%26dopt%3DAbstract Authors: Gromiha MM, Huang LT Machine learning algorithms have wide range of applications in bioinformatics and computational biology such as prediction of protein secondary structures, solvent accessibility, binding site residues in protein complexes, protein folding rates, stability of mutant proteins, discrimination of proteins based on their structure and function. In this work, we focus on two aspects of predications: (i) protein folding rates and (ii) stability of proteins upon mutations. We briefly introduce the concepts of protein folding rates and stability along with available databases, features for prediction methods and measures for prediction performance. Subsequently, the development of structure based parameters and their relationship with protein folding rates will be ... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=5089273 Sun, 24 Jul 2011 23:00:00 +0100 5089273 http://www.medworm.com/index.php?rid=5089272&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21787302%26dopt%3DAbstract Authors: Phatak M, Adamczak R, Cao B, Wagner M, Meller J On-going efforts to improve protein structure prediction stimulate the development of scoring functions and methods for model quality assessment (MQA) that can be used to rank and select the best protein models for further refinement. In this work, sequence-based prediction of relative solvent accessibility (RSA) is employed as a basis for a simple MQA method for soluble proteins, and subsequently extended to the much less explored case of (alpha-helical) membrane proteins. In analogy to soluble proteins, the level of exposure to the lipid of amino acid residues in transmembrane (TM) domains is captured in terms of the relative lipid accessibility (RLA), which is predicted from sequence using lowcomplexity Support Vector Regressi... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=5089272 Sun, 24 Jul 2011 23:00:00 +0100 5089272 http://www.medworm.com/index.php?rid=5089271&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21787303%26dopt%3DAbstract In this report, we analyze the weighted contact-number profiles of both catalytic residues and non-catalytic residues for a dataset of 760 structures. We found that catalytic residues have distinct distributions of weighted contact numbers from those of non-catalytic residues. Using this feature, we are able to effectively differentiate catalytic residues from other residues with a single optimized threshold value. Our method is simple to implement and compares favourably with other more sophisticated methods. In addition, we discuss the physics behind the relationship between catalytic residues and their contact numbers as well as other features (such as residue centrality or Bfactors) associated with catalytic residues. PMID: 21787303 [PubMed - as supplied by publisher] (Source: Curr... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=5089271 Sun, 24 Jul 2011 23:00:00 +0100 5089271 http://www.medworm.com/index.php?rid=5089270&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21787304%26dopt%3DAbstract Authors: Qin S, Zhou HX Protein-DNA interactions are the physical basis of gene expression and DNA modification. Structural models that reveal these interactions are essential for their understanding. As only a limited number of structures for protein-DNA complexes have been determined by experimental methods, computation methods provide a potential way to fill the need. We have developed the DISPLAR method to predict DNA binding sites on proteins. Predicted binding sites have been used to assist the building of structural models by docking, either by guiding the docking or by selecting near-native candidates from the docked poses. Here we applied the DISPLAR method to predict the DNA binding sites for 20 DNAbinding proteins, which have had their DNA binding sites characterized by NMR ... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=5089270 Sun, 24 Jul 2011 23:00:00 +0100 5089270 http://www.medworm.com/index.php?rid=5089269&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21787305%26dopt%3DAbstract In this study, a novel method, named dHKNN, is developed to predict conotoxin superfamily. Firstly, we extract the protein's sequential features composed of physicochemical properties, evolutionary information, predicted secondary structures and amino acid composition. Secondly, we use the diffusion maps for dimensionality reduction, which interpret the eigenfunctions of Markov matrices as a system of coordinates on the original data set in order to obtain efficient representation of data geometric descriptions. Finally, an improved K-local hyperplane distance nearest neighbor subspace classifier method called dHKNN is proposed for predicting conotoxin superfamilies by considering the local density information in the diffusion space. An overall accuracy of 91.90% is obtained through the ja... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=5089269 Sun, 24 Jul 2011 23:00:00 +0100 5089269 http://www.medworm.com/index.php?rid=5089268&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21787306%26dopt%3DAbstract Authors: Kihara D, Sael L, Chikhi R, Esquivel-Rodriguez J The tertiary structures of proteins have been solved in an increasing pace in recent years. To capitalize the enormous efforts paid for accumulating the structure data, efficient and effective computational methods need to be developed for comparing, searching, and investigating interactions of protein structures. We introduce the 3D Zernike descriptor (3DZD), an emerging technique to describe molecular surfaces. The 3DZD is a series expansion of mathematical three-dimensional function, and thus a tertiary structure is represented compactly by a vector of coefficients of terms in the series. A strong advantage of the 3DZD is that it is invariant to rotation of target object to be represented. These two characteristics of the 3DZ... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=5089268 Sun, 24 Jul 2011 23:00:00 +0100 5089268 http://www.medworm.com/index.php?rid=5089267&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21787307%26dopt%3DAbstract We present a new knowledge-based MQAP which evaluates single protein structure models. We use a tree representation of the C trace to train a novel Neural Network Pairwise Interaction Field (NN-PIF) to predict the global quality of a model. NN-PIF allows fast evaluation of multiple structure models for a single sequence. In our tests on a large set of structures, our networks outperform most other methods based on different and more complex protein structure representations in global model quality prediction. Moreover, given NNPIF can evaluate protein conformations very fast, we train a separate version of the model to gauge its ability to fold protein structures ab initio. We show that the resulting system, which relies only on basic information about the sequence and the C trace of a con... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=5089267 Sun, 24 Jul 2011 23:00:00 +0100 5089267 http://www.medworm.com/index.php?rid=5089266&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21787308%26dopt%3DAbstract In this study, we developed a sampling-based machine-learning method to rank protein structural models by integrating multiple scores and features. First, features such as predicted secondary structure, solvent accessibility and residue-residue contact information are integrated by two Radial Basis Function (RBF) models trained from different datasets. Then, the two RBF scores and five selected scoring functions developed by others, i.e., Opus-CA, Opus-PSP, DFIRE, RAPDF, and Cheng Score are synthesized by a sampling method. At last, another integrated RBF model ranks the structural models according to the features of sampling distribution. We tested the proposed method by using two different datasets, including the CASP server prediction models of all CASP8 targets and a set of models gene... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=5089266 Sun, 24 Jul 2011 23:00:00 +0100 5089266 http://www.medworm.com/index.php?rid=5089265&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21787309%26dopt%3DAbstract Authors: Kurgan L, Zhou Y PMID: 21787309 [PubMed - as supplied by publisher] (Source: Current Protein and Peptide Science) Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=5089265 Sun, 24 Jul 2011 23:00:00 +0100 5089265 http://www.medworm.com/index.php?rid=4851183&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21574952%26dopt%3DAbstract Authors: Shido O, Sugimoto N Anapyrexia, which is a regulated fall in core temperature, is beneficial for animals and humans when the oxygen supply is limited, e.g., hypoxic, ischemic, or histotoxic hypoxia, since at low body temperature the tissues require less oxygen due to Q10. Besides hypoxia, anapyrexia can be induced various exogenous and endogenous substances, named cryogens. However, there are only a few reports investigating endogenous cryogens in mammals. We have experienced one patient who suffered from severe hypothermia. The patient seemed to be excessively producing endogenous peptidergic cryogenic substances the molecular weight of which may be greater than 30 kDa. In animal studies, the patient's cryogen appeared to affect metabolic functions, including thermogenic thre... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4851183 Mon, 16 May 2011 23:00:00 +0100 4851183 http://www.medworm.com/index.php?rid=4851182&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21574953%26dopt%3DAbstract Authors: Carrascosa JM, Andrés A, Ros M, Bogónez E, Arribas C, Fernández-Agulló T, De Solís AJ, Gallardo N, Martínez C Aging in mammals associates with the development of peripheral insulin resistance. Additionally, adiposity usually increases with aging and this could play a relevant role in the gradual impairment of insulin action. In fact, fat accretion leads to changes in the expression and circulating concentrations of factors originated in adipose tissue like leptin, resistin and inflammatory cytokines which have been shown to modulate insulin signaling in insulin target tissues acting both, directly or through the central nervous system. Even insulin action on peripheral target tissues has been recently demonstrated to be partially mediated by its central action, suggestin... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4851182 Mon, 16 May 2011 23:00:00 +0100 4851182 http://www.medworm.com/index.php?rid=4851181&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21574954%26dopt%3DAbstract Authors: Hashimoto H, Ueta Y Ghrelin is a stomach-derived peptide discovered as a ligand of the orphan G-protein coupled receptor. Ghrelin is now recognized as a major orexigenic neuropeptide. Immunohistochemical studies demonstrated that centrally administered ghrelin induced c-fos protein expression in many areas in the brain. Indeed, centrally administered ghrelin has various effects such as stimulating feeding, arousal, increasing gastric acid secretion, release of hormones from the pituitary, and inhibition of water intake. In particular, we recently showed that ghrelin was an antidipsogenic peptide with a simultaneous orexigenic effect. This may be of important, because most spontaneous daily water intake is temporally associated with feeding. Here, we summarise recent findings o... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4851181 Mon, 16 May 2011 23:00:00 +0100 4851181 http://www.medworm.com/index.php?rid=4851180&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21574955%26dopt%3DAbstract Authors: Pétervári E, Soós S, Székely M, Balaskó M With advancing age most aspects of the peptidergic regulation of energy balance are altered. The alteration involves both the peripheral peptides derived from the adipose tissue or the gastrointestinal tract and the peptides of the central nervous system (brainstem and hypothalamus). In general, the expression of orexigenic peptides and their receptors decreases with age, while that of the anorexic ones rather increases, but not simultaneously and not in a linear fashion. Apart from such quantitative changes, the efficacy of the related peptides may also change with age. These changes are not necessarily linear, either: instead of continuous decline or increase of its effects, the effects of a peptide may become less pronounced in... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4851180 Mon, 16 May 2011 23:00:00 +0100 4851180 http://www.medworm.com/index.php?rid=4851179&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21574956%26dopt%3DAbstract Authors: Kmiec Z Aging affects energy homeostasis and fuel metabolism in a form of either an increased body mass and glucose intolerance that may lead to obesity and type 2 diabetes or loss of appetite that also may seriously compromise health status. The data, obtained mainly in rat, suggest that aging suppresses the expression and action of potent orexigenic peptides such as predominantly neuropeptides NPY and orexins as peripheral hormone, ghrelin. Senescent animals show over-responsiveness to αMSH, the major anorexigenic neuropeptide. However, central anorexigenic action of leptin is clearly diminished in aging, most likely due to the impaired leptin signal transduction. The age-related central resistance to leptin and insulin does not reduce their inhibitory effects on the activi... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4851179 Mon, 16 May 2011 23:00:00 +0100 4851179 http://www.medworm.com/index.php?rid=4633409&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21428875%26dopt%3DAbstract Authors: Taché Y, Stengel A Several peptides are produced and released from endocrine cells scattered within the gastric oxyntic and the small intestinal mucosa. These peptide hormones are crucially involved in the regulation of gastrointestinal functions and food intake by conveying their information to central regulatory sites located in the brainstem as well as in the forebrain, such as hypothalamic nuclei. So far, ghrelin is the only known hormone that is peripherally produced in gastric X/A-like cells and centrally acting to stimulate food intake, whereas the suppression of feeding seems to be much more redundantly controlled by a number of gut peptides. Cholecystokinin produced in the duodenum is a well established anorexigenic hormone that interacts with ghrelin to modulate foo... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4633409 Thu, 24 Mar 2011 00:00:00 +0100 4633409 http://www.medworm.com/index.php?rid=4633408&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21428876%26dopt%3DAbstract Authors: Székely M PMID: 21428876 [PubMed - as supplied by publisher] (Source: Current Protein and Peptide Science) Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4633408 Thu, 24 Mar 2011 00:00:00 +0100 4633408 http://www.medworm.com/index.php?rid=4633432&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21418016%26dopt%3DAbstract Authors: Pearce G Systemin, an 18-amino acid signaling peptide isolated from tomato leaves, has been found to be an integral component of the jasmine acid signaling pathway, leading to the synthesis of protease inhibitors (PIs). The discovery of systemin has led to a search for other peptide signals involved in defense in the Solanaceae and in other plant families. A new class of peptides having similar signaling properties but little sequence homology to systemin have been found and termed hydroxyproline-rich glycopeptide systemins (HypSys). These small (18-20 amino acids) glycopeptides, like systemin, are derived from larger precursor proteins (proHypSys) and until recently were thought to function only in protection from herbivore attack. However, HypSys peptides isolated from petun... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4633432 Tue, 22 Mar 2011 00:00:00 +0100 4633432 http://www.medworm.com/index.php?rid=4633431&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21418017%26dopt%3DAbstract Authors: Volpicella M, Leoni C, Costanza A, De Leo F, Gallerani R, Ceci LR Plant protease inhibitors (PIs) are generally small proteins present in high concentrations in storage tissues (tubers and seeds), and to a lower level in leaves. Even if most of them are active against serine and cysteine proteases, PIs active against aspartic proteases and carboxypeptidases have also been identified. Inhibitors of serine proteases are further classifiable in several families on the basis of their structural features. They comprise the families known as Bowman-Birk, Kunitz, Potato I and Potato II, which are the subject of review articles included in this special issue. In the present article we aim to give an overview of other families of plant PIs, active either against serine proteases or oth... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4633431 Tue, 22 Mar 2011 00:00:00 +0100 4633431 http://www.medworm.com/index.php?rid=4633430&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21418018%26dopt%3DAbstract Authors: Gomes MT, Oliva ML, Lopes MT, Salas CE Proteinases play a fundamental metabolic role during the life cycle in the plant kingdom. By interacting with endogenous or exogenous inhibitors, the proteolytic activity is modulated to meet metabolic requirements. By probing proteolytic enzymes with their inhibitors, it is possible to identify novel functions unrelated to their proteolytic activity. A group of plant proteolytic enzymes stands as a line of defence against environmental changes as their activation is triggered following various types of stress. On the other hand, plants also contain proteinase inhibitors as countermeasures for their protection against insects and pests. Both proteinases and inhibitors emerge as useful tools to combat human diseases. This review focuses on... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4633430 Tue, 22 Mar 2011 00:00:00 +0100 4633430 http://www.medworm.com/index.php?rid=4633429&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21418019%26dopt%3DAbstract Authors: Oliva ML, da Silva Ferreira R, Ferreira JG, de Paula CA, Salas CE, Sampai MU Seed proteins that inhibit proteinases are classified in families based on amino acid sequence similarity, nature of reactive site and mechanism of action, and are used as tools for investigating proteinases in physiological and pathological events. More recently, the plant Kunitz family of inhibitors with two disulphide bridges was enlarged with members containing variable number of cysteine residues, ranging from no cysteine at all to more than four residues. The characteristic of these proteins, as well the interactions with their target proteinases, are briefly discussed. PMID: 21418019 [PubMed - as supplied by publisher] (Source: Current Protein and Peptide Science) Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4633429 Tue, 22 Mar 2011 00:00:00 +0100 4633429 http://www.medworm.com/index.php?rid=4633428&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21418020%26dopt%3DAbstract Authors: Turra D, Lorito M Serine protease inhibitors (PIs) are a large and complex group of plant proteins. Members of the Potato type I (Pin1) and II (Pin2) proteinase inhibitor families are among the first and most extensively characterized plant PIs. Many insects and phytopathogenic microorganisms use intracellular and extracellular serine proteases playing important roles in pathogenesis. Plants, however, are able to fight these pathogens through the activation of an intricate defence system that leads to the accumulation of various PIs, including Pin1 and Pin2. Several transgenic plants over-expressing members of the Pin1 and Pin2 families have been obtained in the last twenty years and their enhanced defensive capabilities demonstrated against insects, fungi and bacteria. Furthe... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4633428 Tue, 22 Mar 2011 00:00:00 +0100 4633428 http://www.medworm.com/index.php?rid=4633427&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21418021%26dopt%3DAbstract Authors: Beekwilder J, Jongsma MA Plants are at the basis of the food chain, but there is no such thing as a "free lunch" for herbivores. To promote reproductive success, plants evolved multi-layered defensive tactics to avoid or discourage herbivory. To the detriment of plants, herbivores, in turn, evolved intricate strategies to find, eat, and successfully digest essential plant parts to raise their own offspring. In this battle the digestive tract is the arena determining final victory or defeat as measured by growth or starvation of the herbivore. Earlier, specific molecular opponents were identified as proteases and inhibitors: digestive proteases of herbivores evolved structural motifs to occlude plant protease inhibitors, or alternatively, the insects evolved proteases capable o... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4633427 Tue, 22 Mar 2011 00:00:00 +0100 4633427 http://www.medworm.com/index.php?rid=4633421&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21418022%26dopt%3DAbstract Authors: Bateman KS, James MN This review outlines known examples of the three-dimensional structures of protein proteinase inhibitors from plants. Three families of enzymes, serine proteinases, carboxypeptidases and cysteine proteinases, are targeted by at least a dozen inhibitor families, with the majority of them adopting the standard mechanism of inhibition towards the serine proteinases. All of the inhibitors discussed maintain compact and stable inhibitory domains that bind to the active site of their target proteinases and prevent access to the substrate molecules. One interesting highlight is the knottin group. Three separate inhibitor families utilize the overall knottin fold in a different way. This fold can accommodate extensive sequence variation and for each of the squash,... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4633421 Tue, 22 Mar 2011 00:00:00 +0100 4633421 http://www.medworm.com/index.php?rid=4633413&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21418023%26dopt%3DAbstract Authors: Gatehouse JA Proteinase inhibitors which act on the digestive enzymes of insect herbivores are a basic mechanism of plant defence. Attempts to exploit this defence mechanism in plant genetic engineering have used over-expression of both endogenous and exogenous inhibitors. While significant protection against insect pests has been routinely achieved, the engineered plants do not show levels of resistance considered commercially viable. As a result of selective pressures, insect herbivores have developed multiple mechanisms of adaptation to overcome the defensive effects of plant proteinase inhibitors. Common polyphagous crop pests are well adapted to deal with a range of different inhibitors, which have only limited effects on fitness as a result. A range of strategies have be... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4633413 Tue, 22 Mar 2011 00:00:00 +0100 4633413 http://www.medworm.com/index.php?rid=4633412&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21418024%26dopt%3DAbstract Authors: Consiglio A, Grillo G, Licciulli F, Ceci LR, Liuni S, Losito N, Volpicella M, Gallerani R, De Leo F PlantPIs is a web querying system for a database collection of plant protease inhibitors data. Protease inhibitors in plants are naturally occurring proteins that inhibit the function of endogenous and exogenous proteases. In this paper the design and development of a web framework providing a clear and very flexible way of querying plant protease inhibitors data is reported. The web resource is based on a relational database, containing data of plants protease inhibitors publicly accessible, and a graphical user interface providing all the necessary browsing tools, including a data exporting function. PlantPIs contains information extracted principally from MEROPS database, fil... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4633412 Tue, 22 Mar 2011 00:00:00 +0100 4633412 http://www.medworm.com/index.php?rid=4633411&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21418025%26dopt%3DAbstract Authors: Clemente A, Sonnante G, Domoney C Bowman-Birk inhibitors and their variants (BBI) from legumes, such as soybean, pea, lentil and chickpea, are a class of naturally-occurring protease inhibitors which have potential health-promoting properties within the gastrointestinal tract. BBI can resist both acidic conditions and the action of proteolytic enzymes, and transit through the stomach and small intestine without major degradation, permitting significant amounts to reach the large intestine in active form to exert their reported anti-carcinogenic and anti-inflammatory properties. These potential pharmacological benefits have been linked recently to the intrinsic ability of BBI to inhibit serine proteases, and the data suggest that both trypsin- and chymotrypsin-like proteases in... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4633411 Tue, 22 Mar 2011 00:00:00 +0100 4633411 http://www.medworm.com/index.php?rid=4633410&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21418026%26dopt%3DAbstract Authors: Ceci LR PMID: 21418026 [PubMed - as supplied by publisher] (Source: Current Protein and Peptide Science) Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4633410 Tue, 22 Mar 2011 00:00:00 +0100 4633410 http://www.medworm.com/index.php?rid=4633433&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21401523%26dopt%3DAbstract This article summarizes recent findings on the structural and energetic impact of cation binding to different proteins. A general framework can be envisaged in which cations can be considered as a special type of allosteric effectors able to modulate the functional properties of proteins, in particular the ability to interact with biological targets, by altering their conformational equilibrium. PMID: 21401523 [PubMed - as supplied by publisher] (Source: Current Protein and Peptide Science) Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4633433 Tue, 15 Mar 2011 00:00:00 +0100 4633433 http://www.medworm.com/index.php?rid=4571327&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21348834%26dopt%3DAbstract Authors: Orcellet ML, Fernández CO The misfolding of proteins into a toxic conformation is proposed to be at the molecular foundation of a number of neurodegenerative disorders including Alzheimer's and Parkinson's diseases. Evidence that α-synuclein amyloidogenesis plays a causative role in the development of Parkinson's disease is furnished by a variety of genetic, neuropathological and biochemical studies. There is a major interest in understanding the structural and toxicity features of the various species populated along the aggregation pathway of this protein. The development of multidimensional nuclear magnetic resonance (NMR) spectroscopy in liquid and solid state over the last decade has significantly increased the scope of molecules that are amenable for structural studies.... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4571327 Thu, 24 Feb 2011 00:00:00 +0100 4571327 http://www.medworm.com/index.php?rid=4571326&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21348835%26dopt%3DAbstract Authors: Dulc PG, Christophe M, Bao HM, Fernando S, Ludmilla S, Elisa SD, Rita RV A number of neurodegenerative diseases, as Parkinson, prion, and Alzheimer's diseases, has been directly associated with altered conformations of certain peptides or proteins that assemble to form highly organized aggregates, also called amyloid fibers. Glycosaminoglycans have shown to play important roles on fibrils formation, stability and resistance to proteolysis. This manuscript reviews from basic concepts on the biochemistry and biology of glycosaminoglycans to their implications in neurodegeneration with particular emphasis in pathologic protein aggregation. Prion protein, Aβ42, Tau, and α-synuclein, are all proteins that can interact with glycosaminoglycans. We document here how these interactio... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4571326 Thu, 24 Feb 2011 00:00:00 +0100 4571326 http://www.medworm.com/index.php?rid=4571325&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21348836%26dopt%3DAbstract Authors: Avila CL, Drechsel NJ, Alcántara R, Villè-Freixa J The 60's gave birth to the practical implementation of classical mechanics to unravel the dynamics and energetics of biomolecules. In the 70's the use of generalized force fields and more advanced integrative solutions to the microscopic understanding of nature (like hybrid QM/MM) were introduced. During the 80's, algorithms to obtain free energy values were further developed and in the 90's practical integration schemes of molecular mechanics force fields with other levels of detail (QM on one extreme and advances in implicit solvation on the other) were implemented in widely spread software. In the first decade of the XXIst century a considerable effort has been put in two seemingly discordant models for the simulation of ... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4571325 Thu, 24 Feb 2011 00:00:00 +0100 4571325 http://www.medworm.com/index.php?rid=4571324&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21348837%26dopt%3DAbstract Authors: Mohamed A, Cortez L, de Chaves EP Alzheimer's disease (AD) represents the most common form of senile dementia and represents a tremendous health problem as the world population is aging. AD is characterized by the accumulation of amyloid β-peptide (Aβ) in the brain and the loss of cholinergic neurons in the basal forebrain. Accumulation of soluble and insoluble assemblies of Aβ in the brain is a crucial event in AD pathogenesis and the presence of amyloid plaques in the brain is required for definitive identification of AD. Yet, there is no correlation between amyloid plaques and the degree of dementia. In the past two decades researchers have devoted their effort to study and explain the mechanisms involved in the pathology of this devastating disease. Studies from differe... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4571324 Thu, 24 Feb 2011 00:00:00 +0100 4571324 http://www.medworm.com/index.php?rid=4571323&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21348838%26dopt%3DAbstract Authors: Torres-Bugeau CM, Borsarelli CD, Minhak CJ, Chehín RN Even though our knowledge of how proteins misfold and aggregate is deeper nowadays, the mechanisms driving this process are still poorly understood. Among the factors involved, membranes should be taken into account. Indeed, convincing evidence suggests that membranes may influence protein folding, misfolding and aggregation. In fact, membrane lipid composition of different cellular types may attenuate or intensify the environmental pressure over protein folding equilibrium. In the present review the aim is to make an up-to-date analysis of the membrane influence on protein aggregation from a biophysical point of view in order to provide useful tools for researchers from other fields. In particular, we discuss how membrane... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4571323 Thu, 24 Feb 2011 00:00:00 +0100 4571323 http://www.medworm.com/index.php?rid=4571322&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21348839%26dopt%3DAbstract Authors: Bertoncini CW, Celej MS The misfolding and aggregation of amyloidogenic polypeptides are characteristics of many neurodegenerative syndromes including Alzheimer's and Parkinson's disease. There is a major interest in the availability of amyloid-specific probes that exhibit fluorescence properties, for its use as reporters of protein aggregation in spectroscopy and microscopy methodologies. In this review, we intend to provide an overview of novel fluorescence-based probes and procedures applied for addressing fundamental aspects of amyloid self-assembly in vitro and in vivo. We highlight the utilization in vitro of several small-molecule fluorescent probes as extrinsic and site-specific reporters of amyloid formation, including single-molecule determinations. Detection of amyl... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4571322 Thu, 24 Feb 2011 00:00:00 +0100 4571322 http://www.medworm.com/index.php?rid=4571321&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21348840%26dopt%3DAbstract Authors: de la Arada I, Andraka N, Pacios MG, Arrondo JL Cell viability depends on the correct folding of the proteins involved in metabolism. Proteins are synthesized on the endoplasmic reticulum and must follow a pathway to a correct, metastable, tridimensional structure. Changes in structure or in environmental conditions can drive an instability of the folding conditions and produce non-active aggregates that in principle are proteolysed by the cellular mechanisms. However, these aggregates can be even more stable than the native proteins, escaping the cellular control. They can be classified as amorphous, if there is not a well-organized structural pattern, or ordered if a repetitive pattern is produced. These ordered structures, known as fibrils, are involved in many diseases. In... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4571321 Thu, 24 Feb 2011 00:00:00 +0100 4571321 http://www.medworm.com/index.php?rid=4571320&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21348841%26dopt%3DAbstract Authors: Chehin RN PMID: 21348841 [PubMed - as supplied by publisher] (Source: Current Protein and Peptide Science) Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4571320 Thu, 24 Feb 2011 00:00:00 +0100 4571320 http://www.medworm.com/index.php?rid=4571319&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21348842%26dopt%3DAbstract Authors: Perrine-Walker F, Gherbi H, Imanishi L, Hocher V, Ghodhbane-Gtari F, Lavenus J, Benabdoun FM, Nambiar-Veeti M, Svistoonoff S, Laplaze L Actinorhizal symbioses are mutualistic associations between plants belonging to eight angiosperm families and soil bacteria of the genus Frankia. These interactions lead to the formation of new root organs, actinorhizal nodules, where the bacteria are hosted and fix atmospheric nitrogen thus providing the plant with an almost unlimited source of nitrogen for its nutrition. It involves an elaborate signaling between both partners of the symbiosis. In recent years, our knowledge of this signaling pathway has increased tremendously thanks to a series of technical breakthroughs including the sequencing of three Frankia genomes [1] and the implemen... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4571319 Thu, 24 Feb 2011 00:00:00 +0100 4571319 http://www.medworm.com/index.php?rid=4571318&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21348843%26dopt%3DAbstract Authors: Malínská K, Zažímalová E Current models of the plasma membrane (PM) organization focus on the lateral heterogeneity of the membrane and its relation to the cell function. Increasing evidence in mammals and yeast supports the direct relationship between PM lateral microdomains and specific cell processes and functions (nutrient transport, signaling, protein and lipid sorting, endocytosis, pathogen entry etc.). However, for the present the functional significance of an enrichment of specific proteins and possibly lipids in plant PM domains as well as the underlying molecular mechanism driving the lateral PM segregation remain unaddressed. Here we summarize recent findings on the plant PM organization and its role in signaling pathways, with the special emphasis on auxin tra... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4571318 Thu, 24 Feb 2011 00:00:00 +0100 4571318 http://www.medworm.com/index.php?rid=4571317&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21348844%26dopt%3DAbstract Authors: Pernisová M, Kuderová A, Hejátko J Auxin and cytokinins have been identified as key regulators of plant development. Recently, these phytohormones have been shown to interact during important developmental processes, including positioning, identity acquisition and maintenance of meristem organizing centres, regulation of balance between cell division and differentiation, and postembryonic de novo organogenesis. Here, we discuss recent advances in our understanding of the underlying molecular mechanisms at the levels of regulating metabolism, signalling, gene expression and protein stability. PMID: 21348844 [PubMed - as supplied by publisher] (Source: Current Protein and Peptide Science) Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4571317 Thu, 24 Feb 2011 00:00:00 +0100 4571317 http://www.medworm.com/index.php?rid=4571316&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21348845%26dopt%3DAbstract Authors: Horák J, Janda L, Pekárová B, Hejátko J Multistep phosphorelay (MSP) pathways mediate a wide spectrum of adaptive responses in plants, including hormonal and abiotic stress regulations. Recent genetic evidence suggests both partial redundancy and possible functional cross-talk on the one hand and a certain level of specificity on the other. Here, we discuss recent achievements improving our understanding of possible molecular mechanisms of specificity in MSP. We consider a certain evolutionary conservation of ancestral two-component signalling systems from bacteria in a process of molecular recognition that, as we have recently shown, could be applied also to a certain extent in the case of plant MSP. Furthermore, we discuss possible roles of kinase and phosphatase activit... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4571316 Thu, 24 Feb 2011 00:00:00 +0100 4571316 http://www.medworm.com/index.php?rid=4571315&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21348846%26dopt%3DAbstract Authors: Nováková K, Sedo O, Zdráhal Z Protein phosphorylation constitutes a major type of post-translational modifications mobilizing a high number of genes. It is involved in many crucial cell processes and largely participates in the features of the proteome. For several biological and technical reasons, the characterization of protein phosphorylation requires a combination of distinct procedures. In this review, a special emphasis is given to analytical strategies connected with the determination of the presence of phosphorylation sites and their localization by mass spectrometry (MS). The feasibility of selected combinations of analytical approaches for diverse objectives of phosphoproteomic research is discussed. PMID: 21348846 [PubMed - as supplied by publisher] (Source: ... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4571315 Thu, 24 Feb 2011 00:00:00 +0100 4571315 http://www.medworm.com/index.php?rid=4571314&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21348847%26dopt%3DAbstract Authors: Schrumpfová PP, Fojtová M, Mokroš P, Grasser KD, Fajkus J Chromosome stability is conditioned by functional chromatin structure of chromosome ends - telomeres. Organisation and regulation of telomere maintenance represent a complex process whose details still remain enigmatic, especially in plants. Several telomere-binding or telomere-associated proteins and distinct epigenetic marks have been shown to influence telomere length and telomerase activity. HMGB proteins play important role in dynamic changes of chromatin structure and are involved in regulation of cellular processes of key importance, such as replication, transcription, recombination and DNA-repair. HMGB proteins in plants are more diversified than in other eukaryotes. Here, we summarise the roles of plant HMGB... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4571314 Thu, 24 Feb 2011 00:00:00 +0100 4571314 http://www.medworm.com/index.php?rid=4571313&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21348848%26dopt%3DAbstract Authors: Yuan L, Yang X, Makaroff CA Cohesin complexes are critical for holding sister chromatids together during nuclear division. They also play important roles in the compaction of chromosomes and their bipolar attachment to the spindle, DNA double strand break repair, and the regulation of gene expression. Studies on sister chromatid cohesion in a wide range of organisms have shown that the proteins involved, and the general events of this important process are conserved between yeast, plants and animals. However, species-specific differences have been identified. In this review a general overview of cohesins, their roles and mechanisms of action is presented, followed by a review of our current state of knowledge on plant cohesins. While plants utilize the same general set of cohe... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4571313 Thu, 24 Feb 2011 00:00:00 +0100 4571313 http://www.medworm.com/index.php?rid=4571312&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21348849%26dopt%3DAbstract Authors: Amiard S, White C, Gallego ME Repair of DNA damage is essential for the maintenance of the integrity and transmission of the genome in development and reproduction. Telomeres are nucleoprotein structures which protect the ends of (linear) eukaryotic chromosomes. Telomere dysfunction results in loss of this protection and the telomeres being recognised as DNA damage by the cellular DNA Damage Repair and Response (DDR) machinery, leading to senescence or cell death. Telomeric homeostasis is thus tightly controlled and many specific and non-specific proteins are involved in its regulation. Among these, DNA damage and Repair proteins contribute both to the recognition of telomere dysfunction and more surprisingly, are directly implicated in telomere homeostasis itself. Plants offe... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4571312 Thu, 24 Feb 2011 00:00:00 +0100 4571312 http://www.medworm.com/index.php?rid=4571311&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21348850%26dopt%3DAbstract Authors: Peška V, Schrumpfová PP, Fajkus J Telobox is a Myb-related DNA-binding domain which is present in a number of yeast, plant and animal proteins. Its capacity to bind preferentially double-stranded telomeric DNA has been used in numerous studies to search for candidate telomeric proteins in various organisms, including plants. Here we provide an overview of these studies with a special emphasis on plants, where a specific subfamily of the proteins possessing the N-terminally positioned telobox is present in addition to more common C-terminal telobox proteins. We further demonstrate the presence of a telobox protein (CpTBP1) in Cestrum parqui, a plant lacking typical telomeres and telomerase. The protein shows nuclear localisation and association with chromatin. The role of thi... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4571311 Thu, 24 Feb 2011 00:00:00 +0100 4571311 http://www.medworm.com/index.php?rid=4571310&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21348851%26dopt%3DAbstract Authors: Fajkus J PMID: 21348851 [PubMed - as supplied by publisher] (Source: Current Protein and Peptide Science) Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4571310 Thu, 24 Feb 2011 00:00:00 +0100 4571310 http://www.medworm.com/index.php?rid=4305688&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21190525%26dopt%3DAbstract Authors: Soung YH, Gil HJ, Clifford JL, Chung J Integrin a644 is the receptor for the laminin family of extracellular matrix proteins and is widely expressed in most epithelial tissues and Schwann cells. The expression of this integrin is up-regulated in most epithelial tumors, suggesting the role of a6b4 in their progression. The tumor microenvironment is also known to enhance the signaling competence of a6b4 through functional and physical interactions with other receptors. In this review, we discuss the biological mechanisms by which integrin a6b4 promotes carcinoma cell motility and invasion that leads to mammary tumor progression. PMID: 21190525 [PubMed - as supplied by publisher] (Source: Current Protein and Peptide Science) Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4305688 Wed, 29 Dec 2010 00:00:00 +0100 4305688 http://www.medworm.com/index.php?rid=4305680&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21190526%26dopt%3DAbstract Authors: Peng X, Guan JL Focal adhesion kinase (FAK) is a non-receptor tyrosine kinase that has been shown to have key roles in cell migration, proliferation and survival. FAK activity can be stimulated in response to several types of extracellular ligands, including components of the extracellular matrix and growth factors, suggesting that FAK is an important integrator of multiple cues in the extracellular milieu. Recently, major progress has been made in understanding the molecular mechanisms regulating FAK activity. In particular, several novel proteins have been identified that can bind to FAK and inhibit its activity and associated cellular functions, including cell motility and invasion. Consistent with its critical functions in signal transduction, FAK also plays a pivotal role... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4305680 Wed, 29 Dec 2010 00:00:00 +0100 4305680 http://www.medworm.com/index.php?rid=4305677&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21190527%26dopt%3DAbstract Authors: Basu S Cell motility is a very critical phenomenon that plays an important role in the development of eukaryotic organisms. One of the well studied cell motility phenomena is chemotaxis, which is described as a directional movement of cell in response to changes in external chemotactic gradient. Numerous studies conducted both in unicellular organism and in mammalian cells have demonstrated the importance of phosphatidylionositol-3 kinase (PI3K) in this process. In addition, it is now well established that although PI3K plays an activation role in chemotaxis, the role of phosphatases is also critical to maintain this dynamic cyclical process. Protein phosphatase 2A (PP2A) is a major serine/threonine phosphatase that is a key player in regulating PI3K signaling. PP2A is abundan... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4305677 Wed, 29 Dec 2010 00:00:00 +0100 4305677 http://www.medworm.com/index.php?rid=4305672&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21190528%26dopt%3DAbstract Authors: Huang S PMID: 21190528 [PubMed - as supplied by publisher] (Source: Current Protein and Peptide Science) Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4305672 Wed, 29 Dec 2010 00:00:00 +0100 4305672 http://www.medworm.com/index.php?rid=4392763&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21235500%26dopt%3DAbstract Authors: de la Torre-Ruiz MA PMID: 21235500 [PubMed - in process] (Source: Current Protein and Peptide Science) Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4392763 Wed, 01 Dec 2010 00:00:00 +0100 4392763 http://www.medworm.com/index.php?rid=4392762&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21235501%26dopt%3DAbstract Authors: Irazusta V, Moreno-Cermeño A, Cabiscol E, Tamarit J, Ros J Oxidative stress is caused by an imbalance between formation and destruction of reactive oxygen species. Analysis of the reaction products of reactive oxygen species in biomolecules is an indirect way of determining the existence of oxidative stress. In this context, the formation of carbonyl groups in proteins has been one of the most studied oxidative stress markers because of its stability and easy detection. Various proteomic tools offer great potential for the discovery of new proteins susceptible to oxidative stress, determination of quantitative changes in the profile of these modifications under different biological conditions, and characterization of the type of modification it has suffered a particular prote... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4392762 Wed, 01 Dec 2010 00:00:00 +0100 4392762 http://www.medworm.com/index.php?rid=4392761&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21235502%26dopt%3DAbstract Authors: Herrero E, Bellí G, Casa C Glutaredoxins are defined as thiol disulfide oxidoreductases that reduce disulfide bonds employing reduced glutathione as electron donor. They constitute a complex family of proteins with a diversity of enzymatic and functional properties. Thus, dithiol glutaredoxins are able to reduce disulfide bonds and deglutathionylate mixed disulfides between glutathione and cysteine protein residues. They could act regulating the redox state of sulfhydryl residues of specific proteins, while thioredoxins (another family of thiol disulfide oxidoreductases which employ NADPH as electron donor) would be the general sulfhydryl reductants. Some dithiol glutaredoxins such as human Grx2 form dimers bridged by one iron-sulfur cluster, which acts as a sensor of oxidati... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4392761 Wed, 01 Dec 2010 00:00:00 +0100 4392761 http://www.medworm.com/index.php?rid=4392760&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21235503%26dopt%3DAbstract Authors: de la Torre-Ruiz MA, Mozo-Villarías A, Pujol N, Petkova MI The eukaryotic microorganism Saccharomyces cerevisiae is a current model system in which to study the signal transduction pathways involved in the oxidative stress response. In this review we present the current evidence demonstrating that in S. cerevisiae several MAPK and signalling routes participate in this response (PKC1-MAPK, TOR, RAS-PKA-cAMP). The signalling processes converge in the activation of a number of transcription factors (Yap1, Skn7, Rlm1, Msn2/Msn4, Sfp1, among others) required for the expression of certain genes involved in the oxidative stress response. Another important output of these signalling pathways is the actin cytoskeleton, a known target for oxidation and whose organisation needs to be ti... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4392760 Wed, 01 Dec 2010 00:00:00 +0100 4392760 http://www.medworm.com/index.php?rid=4392759&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21235504%26dopt%3DAbstract Authors: Pérez P, Cansado J Cellular responses to external signals are regulated by conserved mitogen-activated protein (MAP) kinase signaling cascades. These pathways are triggered by a vast range of stimuli. They phosphorylate numerous proteins, produce significant changes in the gene expression, and regulate diverse processes ranging from proliferation and differentiation to apoptosis in all eukaryotic cells. Three conserved MAP kinase signaling pathways have been identified in the fission yeast Schizosaccharomyces pombe. In this article, we present an overview of two of those pathways that regulate the response of fission yeast to stress and maintain cell integrity. The structure of these signaling modules and the function of the pathways, including the regulation by endogenous in... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4392759 Wed, 01 Dec 2010 00:00:00 +0100 4392759 http://www.medworm.com/index.php?rid=4392758&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21235505%26dopt%3DAbstract Authors: de Dios CH, Román E, Monge RA, Pla J In recent years, Mitogen-Activated Protein Kinase (MAPK) pathways have emerged as major regulators of cellular physiology. In the fungal pathogen Candida albicans, three different MAPK pathways have been characterized in the last years. The HOG pathway is mainly a stress response pathway that is activated in response to osmotic and oxidative stress and also participates regulating other pathways. The SVG pathway (or mediated by the Cek1 MAPK) is involved in cell wall formation under vegetative and filamentous growth, while the Mkc1-mediated pathway is involved in cell wall integrity. Oxidative stress is one of the types of stress that every fungal cell has to face during colonization of the host, where the cell encounters both hypoxia nich... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4392758 Wed, 01 Dec 2010 00:00:00 +0100 4392758 http://www.medworm.com/index.php?rid=4392757&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21235506%26dopt%3DAbstract Authors: Etxebeste O, Ugalde U, Espeso EA Development in the ascomycete A. nidulans is principally determined by environmental signals. Adaptability to oxidative stimuli can derive in changes of growth patterns and /or the activation of sexual or asexual reproductive cycles but this model fungus might also respond to high osmotic or salt concentrations, the redox state, the availability and quantity of carbon or nitrogen sources and the degree or quality of illumination. Since each cell within the colony follows a single morphogenetic program at a time, all these environmental cues might be sensed and integrated into a limited number of intracellular signals which, finally, would activate the required morphogenetic program and repress the others. This signaling mainly occurs through st... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4392757 Wed, 01 Dec 2010 00:00:00 +0100 4392757 http://www.medworm.com/index.php?rid=4392756&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21235507%26dopt%3DAbstract Authors: Hossain MA, Wade JD Two members of the human insulin/relaxin superfamily, relaxins-2 and 3 (H2 and H3 respectively), are separated by nearly 75 years in terms of chronological identification but are both the subject of intense recent biological study. The physiological effects of H2 relaxin include vasodilatory, anti-inflammatory, extracellular matrix remodeling, and angiogenic and anti-ischemic. Because of its potent systemic and renal vasodilatory effects, it is currently undergoing phase III clinical trial for the treatment of acute heart failure. In contrast, H3 relaxin is a highly conserved neuropeptide that has rapidly emerged as an important regulator of homeostatic physiology and complex behaviors. Because of their immense clinical potential, an understanding of the st... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4392756 Wed, 01 Dec 2010 00:00:00 +0100 4392756 http://www.medworm.com/index.php?rid=4392755&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21235508%26dopt%3DAbstract Authors: Toh EC, Huq NL, Dashper SG, Reynolds EC Cysteine proteases are one of the largest groups of proteases and are involved in many important biological functions in all kingdoms of life. They are virulence factors of a range of eukaryotic, bacterial and viral pathogens and are involved in host invasion, pathogen replication and disruption of the host immune response. Their activity is regulated by a range of protease inhibitors. This review discusses the various families of cysteine protease inhibitors, their different modes of inhibition and their evolutionary relationships. These inhibitors as well as the recent discovery of propeptide and propeptide-like inhibitors provide insights into the structures that are important for particular inhibitory mechanisms, thus forming the fou... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4392755 Wed, 01 Dec 2010 00:00:00 +0100 4392755 http://www.medworm.com/index.php?rid=4392754&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21235509%26dopt%3DAbstract Authors: Melo EP, Estrela N, Lopes C, Matias AC, Tavares E, Ochoa-Mendes V Biomedical applications of osmolytes, including stabilization of protein-based pharmaceutics, preservation of living biological material and potential therapeutic prescription in vivo, are intimately related to the fact that osmolytes favour the native structure of proteins. The shift towards the native structure is associated to the compaction of the protein by a non-specific mechanism. This compaction is observed mostly for the unfolded state but also for the transition state ensemble and even for the native state. In addition, more stable three-dimensional structures are more stabilized by osmolytes if the overall protein fold is the same indicating that point mutations and osmolytes should share a similar me... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4392754 Wed, 01 Dec 2010 00:00:00 +0100 4392754 http://www.medworm.com/index.php?rid=4392753&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21235510%26dopt%3DAbstract Authors: Zhang Y, Fang H, Xu W Tic, short for 1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid, is a kind of unnatural α-amino acids. Due to its distinct geometrical conformation and biological activity, the structure of Tic, regarded as the surrogate of proline and the rigid analogue of phenylalanine or tyrosine, has been introduced into many compounds, which target diverse enzymes or receptors. The most successful example is that substituting the Tic residue for the proline residue of enalapril led to an approved drug quinapril. In this review, we will summarize the applications and modifications of Tic in peptides and peptidomimetics design and discovery, and hope to spark medicinal researchers' inspiration in the field of protein and peptide drug design and optimization. PMID:... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4392753 Wed, 01 Dec 2010 00:00:00 +0100 4392753 http://www.medworm.com/index.php?rid=4392752&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21235511%26dopt%3DAbstract Authors: Dan L, Shi M, Duan H, Han C, Guo N Erbin belongs to the LAP protein family. It represents a novel type of adaptor protein that features targeting of basolateral localization of the Her2 receptor through direct binding to the Her2 C terminus. Recent studies demonstrated that Erbin could inhibit the Ras-mediated activation of the mitogen-activated protein kinase (MAPK), nuclear factor-κB (NF-κB) and transforming growth factor β (TGF-β) signaling pathways. It suggests that Erbin may function as a signaling molecule. The functions of Erbin in determining cell polarity and cell adhesion have been well described. This review mainly focuses on the recent findings in regulation of signaling pathways by Erbin. PMID: 21235511 [PubMed - in process] (Source: Current Protein and Pe... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4392752 Wed, 01 Dec 2010 00:00:00 +0100 4392752 http://www.medworm.com/index.php?rid=4040313&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20887249%26dopt%3DAbstract Authors: Dan L, Shi M, Duan H, Han C, Guo N Erbin belongs to the LAP protein family. It represents a novel type of adaptor protein that features targeting of basolateral localization of the Her2 receptor through direct binding to the Her2 C terminus. Recent studies demonstrated that Erbin could inhibit the Ras-mediated activation of the mitogen-activated protein kinase (MAPK), nuclear factor-κB (NF-κB) and transforming growth factor β (TGF-β) signaling pathways. It suggests that Erbin may function as a signaling molecule. The functions of Erbin in determining cell polarity and cell adhesion have been well described. This review mainly focuses on the recent findings in regulation of signaling pathways by Erbin. PMID: 20887249 [PubMed - as supplied by publisher] (Source: Current ... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4040313 Thu, 07 Oct 2010 22:46:08 +0100 4040313 http://www.medworm.com/index.php?rid=4040312&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20887250%26dopt%3DAbstract Authors: Toh EC, Huq NL, Dashper SG, Reynolds EC Cysteine proteases are one of the largest groups of proteases and are involved in many important biological functions in all kingdoms of life. They are virulence factors of a range of eukaryotic, bacterial and viral pathogens and are involved in host invasion, pathogen replication and disruption of the host immune response. Their activity is regulated by a range of protease inhibitors. This review discusses the various families of cysteine protease inhibitors, their different modes of inhibition and their evolutionary relationships. These inhibitors as well as the recent discovery of propeptide and propeptide-like inhibitors provide insights into the structures that are important for particular inhibitory mechanisms, thus forming the fou... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4040312 Thu, 07 Oct 2010 22:46:05 +0100 4040312 http://www.medworm.com/index.php?rid=4040311&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20887251%26dopt%3DAbstract Authors: Hossain MA, Wade JD Two members of the human insulin/relaxin superfamily, relaxins-2 and 3 (H2 and H3 respectively), are separated by nearly 75 years in terms of chronological identification but are both the subject of intense recent biological study. The physiological effects of H2 relaxin include vasodilatory, anti-inflammatory, extracellular matrix remodeling, and angiogenic and anti-ischemic. Because of its potent systemic and renal vasodilatory effects, it is currently undergoing phase III clinical trial for the treatment of acute heart failure. In contrast, H3 relaxin is a highly conserved neuropeptide that has rapidly emerged as an important regulator of homeostatic physiology and complex behaviors. Because of their immense clinical potential, an understanding of the st... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4040311 Thu, 07 Oct 2010 22:46:01 +0100 4040311 http://www.medworm.com/index.php?rid=4040310&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20887252%26dopt%3DAbstract Authors: Zhang Y, Fang H, Xu W Tic, short for 1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid, is a kind of unnatural α-amino acids. Due to its distinct geometrical conformation and biological activity, the structure of Tic, regarded as the surrogate of proline and the rigid analogue of phenylalanine or tyrosine, has been introduced into many compounds, which target diverse enzymes or receptors. The most successful example is that substituting the Tic residue for the proline residue of enalapril led to an approved drug quinapril. In this review, we will summarize the applications and modifications of Tic in peptides and peptidomimetics design and discovery, and hope to spark medicinal researchers' inspiration in the field of protein and peptide drug design and optimization. PMID:... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4040310 Thu, 07 Oct 2010 22:45:57 +0100 4040310 http://www.medworm.com/index.php?rid=4040309&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20887253%26dopt%3DAbstract Authors: Melo EP, Estrela N, Lopes C, Matias AC, Tavares E, Ochoa-Mendes V Biomedical applications of osmolytes, including stabilization of protein-based pharmaceutics, preservation of living biological material and potential therapeutic prescription in vivo, are intimately related to the fact that osmolytes favour the native structure of proteins. The shift towards the native structure is associated to the compaction of the protein by a non-specific mechanism. This compaction is observed mostly for the unfolded state but also for the transition state ensemble and even for the native state. In addition, more stable three-dimensional structures are more stabilized by osmolytes if the overall protein fold is the same indicating that point mutations and osmolytes should share a similar me... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4040309 Thu, 07 Oct 2010 22:45:54 +0100 4040309 http://www.medworm.com/index.php?rid=4040308&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20887254%26dopt%3DAbstract Authors: Djinovic-Carugo K, Carugo O We review the most recent findings on human filamin structure, with particular emphasis on the relationships between structure, function, and interaction. Filamin is a cytoskeletal actin-binding protein and it is therefore crucial in providing cells with the necessary mechanical and dynamical properties. Filamentous actin cross-linking by filamin is regulated by a number of other proteins and the molecular mechanisms of this complex interaction network can be understood by highlighting the structural features of isolated filamin moieties and of their complexes with several partners. Here we describe first the structure-function relationships of the isolated filamin, its flexibility, and its dimerization mechanism. Secondly, we illustrate the structu... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4040308 Thu, 07 Oct 2010 22:45:50 +0100 4040308 http://www.medworm.com/index.php?rid=4040307&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20887255%26dopt%3DAbstract Authors: Gromiha MM, Yokota K, Fukui K Protein-RNA interactions perform diverse functions within the cell. Understanding the recognition mechanism of protein-RNA complexes is a challenging task in molecular and computational biology. In this work, we have developed an energy based approach for identifying the binding sites and important residues for binding in protein-RNA complexes. The new approach considers the repulsive interactions as well as the effect of distance between the atoms in protein and RNA in terms of interaction energy, which are not considered in traditional distance based methods to identify the binding sites. We found that the positively charged, polar and aromatic residues are important for binding. These residues influence to form electrostatic, hydrogen bonding a... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4040307 Thu, 07 Oct 2010 22:45:47 +0100 4040307 http://www.medworm.com/index.php?rid=4040306&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20887256%26dopt%3DAbstract Authors: Zhang T, Zhang H, Chen K, Ruan J, Shen S, Kurgan L Identification and prediction of RNA-binding residues (RBRs) provides valuable insights into the mechanisms of protein-RNA interactions. We analyzed the contributions of a wide range of factors including amino acid sequence, evolutionary conservation, secondary structure and solvent accessibility, to the prediction/characterization of RBRs. Five feature sets were designed and feature selection was performed to find and investigate relevant features. We demonstrate that (1) interactions with positively charged amino acids Arg and Lys are preferred by the egatively charged nucleotides; (2) Gly provides flexibility for the RNA binding sites; (3) Glu with negatively charged side chain and several hydrophobic residues such as Leu, ... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4040306 Thu, 07 Oct 2010 22:45:43 +0100 4040306 http://www.medworm.com/index.php?rid=4040305&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20887257%26dopt%3DAbstract Authors: Bartoli L, Martelli PL, Rossi I, Fariselli P, Casadio R In this paper we aim at investigating possible correlations between the number of putative interaction patches of a given protein, as inferred by an algorithm that we have developed, and its degree (number of edges of the protein node in a protein interaction network). We focus on the human cell cycle that, as compared with other biological processes, comprises the largest number of proteins whose structure is known at atomic resolution both as monomers and as interacting complexes. For predicting interaction patches we specifically develop a HM-SVM based method reaching 71% overall accuracy with a correlation coefficient value equal to 0.43 on a non redundant set of protein complexes. To test the biological meaning of ou... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4040305 Thu, 07 Oct 2010 22:45:39 +0100 4040305 http://www.medworm.com/index.php?rid=4040304&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20887258%26dopt%3DAbstract Authors: Rashid M, Ramasamy S, Raghava GP The availability of an increased number of fully sequenced genomes demands functional interpretation of the genomic information. Despite high throughput experimental techniques and in silico methods of predicting protein-protein interaction (PPI); the interactome of most organisms is far from completion. Thus, predicting the interactome of an organism is one of the major challenges in the post-genomic era. This manuscript describes Support Vector Machine (SVM) based models that have been developed for discriminating interacting and non-interacting pairs of proteins from their amino acid sequence. We have developed SVM models using various types of sequence compositions e.g. amino acid, dipeptide, biochemical property, split amino acid and pseud... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4040304 Thu, 07 Oct 2010 22:45:36 +0100 4040304 http://www.medworm.com/index.php?rid=4040303&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20887259%26dopt%3DAbstract Authors: Horst JA, Wang K, Horst OV, Cunningham ML, Samudrala R Advancements in sequencing techniques place personalized genomic medicine upon the horizon, bringing along the responsibility of clinicians to understand the likelihood for a mutation to cause disease, and of scientists to separate etiology from nonpathologic variability. Pathogenicity is discernable from patterns of interactions between a missense mutation, the surrounding protein structure, and intermolecular interactions. Physicochemical stability calculations are not accessible without structures, as is the case for the vast majority of human proteins, so diagnostic accuracy remains in infancy. To model the effects of missense mutations on functional stability without structure, we combine novel protein sequence analys... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4040303 Thu, 07 Oct 2010 22:45:32 +0100 4040303 http://www.medworm.com/index.php?rid=4040302&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20887260%26dopt%3DAbstract Authors: Verma D, Jacobs DJ, Livesay DR A complete understanding of the relationships between protein structure and stability remains an open problem. Much of our insight comes from laborious experimental analyses that perturb structure via directed mutation. The glycolytic enzyme lysozyme is among the most well characterized proteins under this paradigm, due to its abundance and ease of manipulation. To speed up such analyses, efficient computational models that can accurately predict mutation effects are needed. We employ a minimal Distance Constraint Model (mDCM) to predict the stability of a series of lysozyme mutants (specifically, human wild-type C-type lysozyme and 14 point mutations). With three phenomenological parameters that characterize microscopic interactions, the mDCM pa... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4040302 Thu, 07 Oct 2010 22:45:28 +0100 4040302 http://www.medworm.com/index.php?rid=4040301&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20887261%26dopt%3DAbstract Authors: Tusnády GE, Simon I Transmembrane protein topology prediction methods play important roles in structural biology, because the structure determination of these types of proteins is extremely difficult by the common biophysical, biochemical and molecular biological methods. The need for accurate prediction methods is high, as the number of known membrane protein structures fall far behind the estimated number of these proteins in various genomes. The accuracy of these prediction methods appears to be higher than most prediction methods applied on globular proteins, however it decreases slightly with the increasing number of structures. Unfortunately, most prediction algorithms use common machine learning techniques, and they do not reveal why topologies are predicted with such ... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4040301 Thu, 07 Oct 2010 22:45:24 +0100 4040301 http://www.medworm.com/index.php?rid=4040300&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20887262%26dopt%3DAbstract This article gives an overview of the project history as well as of the concepts and principles developed within this the project. PMID: 20887262 [PubMed - as supplied by publisher] (Source: Current Protein and Peptide Science) Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4040300 Thu, 07 Oct 2010 22:45:21 +0100 4040300 http://www.medworm.com/index.php?rid=4040299&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20887263%26dopt%3DAbstract Authors: Galzitskaya OV The problem of protein self-organization is one of the most important problems of molecular biology nowadays. Despite the recent success in the understanding of general principles of protein folding, details of this process are yet to be elucidated. Moreover, the prediction of protein folding rates has its own practical value due to the fact that aggregation directly depends on the rate of protein folding. The time of folding has been calculated for 67 proteins with known experimental data at the point of thermodynamic equilibrium between unfolded and native states using a Monte Carlo model where each residue is considered to be either folded as in the native state or completely disordered. The times of folding for 67 proteins which reach the native state within... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4040299 Thu, 07 Oct 2010 22:45:17 +0100 4040299 http://www.medworm.com/index.php?rid=4040298&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20887264%26dopt%3DAbstract Authors: Gáspári Z, Angyán AF, Dhir S, Franklin D, Perczel A, Pintar A, Pongor S The emerging role of internal dynamics in protein fold and function requires new avenues of structure analysis. We analyzed the dynamically restrained conformational ensemble of ubiquitin generated from residual dipolar coupling data, in terms of protruding and buried atoms as well as interatomic distances, using four proximity-based algorithms, CX, DPX, PRIDE and PRIDE-NMR (http://hydra.icgeb.trieste.it/protein/). We found that Ubiquitin, this relatively rigid molecule has a highly diverse dynamic ensemble. The environment of protruding atoms is highly variable across conformers, on the other hand, only a part of buried atoms tends to fluctuate. The variability of the ensemble cautions against the use ... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4040298 Thu, 07 Oct 2010 22:45:13 +0100 4040298 http://www.medworm.com/index.php?rid=4040297&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20887265%26dopt%3DAbstract Authors: Shenoy SR, Jayaram B In an era that has been dominated by Structural Biology for the last 30-40 years, a dramatic change of focus towards sequence analysis has spurred the advent of the genome projects and the resultant diverging sequence/structure deficit. The central challenge of Computational Structural Biology is therefore to rationalize the mass of sequence information into biochemical and biophysical knowledge and to decipher the structural, functional and evolutionary clues encoded in the language of biological sequences. In investigating the meaning of sequences, two distinct analytical themes have emerged: in the first approach, pattern recognition techniques are used to detect similarity between sequences and hence to infer related structures and functions; in the se... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4040297 Thu, 07 Oct 2010 22:45:09 +0100 4040297 http://www.medworm.com/index.php?rid=4040296&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20887266%26dopt%3DAbstract Curr Protein Pept Sci. 2010 Nov 4; Authors: Gromiha MM PMID: 20887266 [PubMed - as supplied by publisher] (Source: Current Protein and Peptide Science) Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=4040296 Thu, 07 Oct 2010 22:45:06 +0100 4040296 http://www.medworm.com/index.php?rid=3851014&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20690897%26dopt%3DAbstract Authors: Jelinek R PMID: 20690897 [PubMed - in process] (Source: Current Protein and Peptide Science) Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=3851014 Sat, 31 Jul 2010 23:00:00 +0100 3851014 http://www.medworm.com/index.php?rid=3596399&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20491621%26dopt%3DAbstract Authors: Xue Y, Gao X, Cao J, Liu Z, Jin C, Wen L, Yao X, Ren J Protein phosphorylation is the most ubiquitous post-translational modification (PTM), and plays important roles in most of biological processes. Identification of site-specific phosphorylated substrates is fundamental for understanding the molecular mechanisms of phosphorylation. Besides experimental approaches, prediction of potential candidates with computational methods has also attracted great attention for its convenience, fast-speed and low-cost. In this review, we present a comprehensive but brief summarization of computational resources of protein phosphorylation, including phosphorylation databases, prediction of non-specific or organism-specific phosphorylation sites, prediction of kinase-specific phosphorylation... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=3596399 Sun, 23 May 2010 23:00:00 +0100 3596399 http://www.medworm.com/index.php?rid=3596398&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20491622%26dopt%3DAbstract Merlin, a "Magic" Linker between Extracellular Cues and Intracellular Signaling Pathways that Regulate Cell Motility, Proliferation, and Survival. Curr Protein Pept Sci. 2010 May 24; Authors: Stamenkovic I, Yu Q Genetic alterations of neurofibromatosis type 2 (NF2) gene lead to the development of schwannomas, meningiomas, and ependymomas. Mutations of NF2 gene were also found in thyroid cancer, mesothelioma, and melanoma, suggesting that it functions as a tumor suppressor in a wide spectrum of cells. The product of NF2 gene is merlin (moesin-ezrin-radixin-like protein), a member of the Band 4.1 superfamily proteins. Merlin shares significant sequence homology with the ERM (Ezrin-Radixin-Moesin) family proteins and serves as a linker between transmembrane proteins and the actin-... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=3596398 Sun, 23 May 2010 23:00:00 +0100 3596398 http://www.medworm.com/index.php?rid=3596397&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20491623%26dopt%3DAbstract Authors: Chen D, Dou QP Proteasomes are large multicatalytic proteinase complexes located in the cytosol and the nucleus of eukaryotic cells. The ubiquitin-proteasome system is responsible for the degradation of most intracellular proteins and therefore plays an essential regulatory role in critical cellular processes including cell cycle progression, proliferation, differentiation, angiogenesis and apoptosis. Besides involving in normal cellular functions and homeostasis, the alteration of proteasomal activity contributes to the pathological states of several clinical disorders including inflammation, neurodegeneration and cancer. It has been reported that human cancer cells possess elevated level of proteasome activity and are more sensitive to proteasome inhibitors than normal cells... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=3596397 Sun, 23 May 2010 23:00:00 +0100 3596397 http://www.medworm.com/index.php?rid=3596396&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20491624%26dopt%3DAbstract Authors: Sivanandam A, Murthy S, Kim SH, Barrack ER, Veer Reddy GP The androgen receptor (AR) plays a critical role in proliferation and viability of prostate cancer cells. Therefore, suppressing AR activity by androgen deprivation or anti-androgen treatment has been the frontline therapy for over six decades. However, these treatment strategies are not curative and patients succumb to castration-resistant disease. Although AR is evidently critical for proliferation of prostate cancer cells, very little is known about its mechanism of action in this process. Over the years, the role of AR in prostate cancer cell proliferation and viability has been studied by focusing primarily on its role as a transcription factor. However, recent observations indicate that besides its role as a trans... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=3596396 Sun, 23 May 2010 23:00:00 +0100 3596396 http://www.medworm.com/index.php?rid=3596395&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20491625%26dopt%3DAbstract Authors: Nautiyal J, Kanwar SS, Majumdar AP Cells of the gastrointestinal (GI) mucosa are subject to a constant process of renewal which, in normal adults, reflects a balance between the rates of cell production and cell loss. Detailed knowledge of these events is, therefore, essential for a better understanding of the normal aging processes as well as many GI diseases, particularly malignancy, that represent disorders of tissue growth. In general, many GI dysfunctions, including malignancy, increase with advancing age, and aging itself is associated with alterations in structural and functional integrity of the GI tract. Although the regulatory mechanisms for age-related increase in the incidence of GI-cancers are yet to be fully delineated, recent evidence suggests a role for epiderm... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=3596395 Sun, 23 May 2010 23:00:00 +0100 3596395 http://www.medworm.com/index.php?rid=3596394&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20491626%26dopt%3DAbstract Authors: Wu G Phosphatidylinositol 3-kinases (PI3Ks) are a group of lipid kinases that coordinate various fundamental cellular responses including mitogenic signaling, cell survival and proliferation, vesicular trafficking, cytoskeletal rearrangement and metabolism. Overexpression caused by genetic alterations such as the amplification or gain of copy numbers was frequently observed for various PI3Ks in different human cancers. In recent years, the high-frequency somatic mutations of PIK3CA observed in different human cancers further strengthen the notion that PI3Ks are optimal targets for therapeutic intervention. In this review, I summarize current experimental evidence about the transformation capability and oncogenic properties of different PIK3CA mutations identified in human canc... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=3596394 Sun, 23 May 2010 23:00:00 +0100 3596394 http://www.medworm.com/index.php?rid=3596393&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20491627%26dopt%3DAbstract Authors: Zhou H, Huang S The mammalian target of rapamycin (mTOR) has attracted substantial attention because of its involvement in a variety of diseases, such as cancer, cardiac hypertrophy, diabetes and obesity. Current knowledge indicates that mTOR functions as two distinct multiprotein complexes, mTORC1 and mTORC2. mTORC1 phosphorylates p70 S6 kinase (S6K1) and eukaryotic initiation factor 4E (eIF4E) binding protein 1 (4E-BP1), and regulates cell growth, proliferation, and survival by integrating hormones, growth factors, nutrients, stressors and energy signals. In contrast, mTORC2 is insensitive to nutrients or energy conditions. However, in response to hormones or growth factors, mTORC2 phosphorylates Akt, and regulates actin cytoskeleton and cell survival. These findings not onl... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=3596393 Sun, 23 May 2010 23:00:00 +0100 3596393 http://www.medworm.com/index.php?rid=3596392&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20491628%26dopt%3DAbstract Authors: Wang Z, Li Y, Sarkar FH Proteins and small peptides (growth factors and hormones) are key molecules in maintaining cellular homeostasis. To that end, Notch signaling pathway proteins are known to play critical roles in maintaining the balance between cell proliferation, differentiation and apoptosis, and thus it has been suggested that Notch may be responsible for the development and progression of human malignancies. Therefore, the Notch signaling pathway proteins may present novel therapeutic targets, which could have promising therapeutic impact on eradicating human malignancies. This review describes the role of Notch signaling pathway proteins in cancer and how its deregulation is involved in tumor development and progression leading to metastasis and the ultimate demise ... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=3596392 Sun, 23 May 2010 23:00:00 +0100 3596392 http://www.medworm.com/index.php?rid=3596391&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20491629%26dopt%3DAbstract Authors: Dou QP PMID: 20491629 [PubMed - as supplied by publisher] (Source: Current Protein and Peptide Science) Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=3596391 Sun, 23 May 2010 23:00:00 +0100 3596391 http://www.medworm.com/index.php?rid=3520465&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20426733%26dopt%3DAbstract Authors: Hagen SJ The famous Kramers rate theory for diffusion-controlled reactions has been extended in numerous ways and successfully applied to many types of reactions. Its application to protein folding reactions has been of particular interest in recent years, as many researchers have performed experiments and simulations to test whether folding reactions are diffusion-controlled, whether the solvent is the source of the reaction friction, and whether the friction-dependence of folding rates generally can provide insight into folding dynamics. These experiments involve many practical difficulties, however. They have also produced some unexpected results. Here we briefly review the Kramers theory for reactions in the presence of strong friction and summarize some of the subtle prob... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=3520465 Tue, 27 Apr 2010 23:00:00 +0100 3520465 http://www.medworm.com/index.php?rid=3512379&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20423294%26dopt%3DAbstract Authors: van Rooijen BD, Claessens MM, Subramaniam V alpha-Synuclein is a small neuronal protein that has been implicated to play an important role in Parkinson's disease. Genetic mutations and multiplications in the alpha-synuclein gene can cause familial forms of the disease. In aggregated fibrillar form, alpha-synuclein is the main component of Lewy bodies, the intraneuronal inclusion bodies characteristic of Parkinson's disease. The loss of functional dopaminergic neurons in Parkinson's disease may be caused by a gain in toxic function of the protein. Elucidating if this gain of toxic function is related to the aggregation of alpha-synuclein may be vital in understanding Parkinson's disease. Although there are many ideas on how alpha-synuclein could be involved in the disease, this... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=3512379 Sun, 25 Apr 2010 23:00:00 +0100 3512379 http://www.medworm.com/index.php?rid=3512378&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20423295%26dopt%3DAbstract Authors: Stefani M The past fifteen years have led to a profound re-consideration of the molecular and cellular basis of amyloid diseases. Since the formulation of the amyloid hypothesis in 1991-1992, increasing interest was initially focused at amyloid fibrils and, subsequently, at their precursors, oligomers and pre-fibrillar aggregates as main culprits of cell impairment and demise, particularly in neurodegenerative diseases with amyloid deposition. In 2002, this concept was generalized by the demonstration that pre-fibrillar aggregates were toxic even when they were grown from proteins not associated with amyloid disease. Presently, the general structural features and polymorphism of amyloid fibrils grown from a range of different peptides and proteins are rather well known; howeve... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=3512378 Sun, 25 Apr 2010 23:00:00 +0100 3512378 http://www.medworm.com/index.php?rid=3512377&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20423296%26dopt%3DAbstract Authors: Otzen DE Attempts to understand the biophysical foundations and biochemical consequences of protein aggregation process are greatly aided by conditions which provide either robust and reliable reaction conditions or constitute mimics of the physiological conditions. While both anionic surfactants such as SDS and fluorinated alcohols such as TFE are often championed as membrane mimics in one way or another, it is probably fair to say that their greatest advantage is to facilitate protein aggregation under simple and well-defined solvent conditions which are compatible with a plethora of biophysical techniques. In contrast to the biological membrane, whose chemical complexity and physical heterogeneity gives rise to a multitude of possible interactions with proteins, SDS and TFE... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=3512377 Sun, 25 Apr 2010 23:00:00 +0100 3512377 http://www.medworm.com/index.php?rid=3512376&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20423297%26dopt%3DAbstract Authors: Jelinek R, Sheynis T The growing interest in membrane interactions of amyloidogenic peptides and proteins emanates from the realization that lipids and membranes play important, potentially central, roles in the toxicity and pathological pathways of amyloid diseases. Expanding body of evidence indicates that lipid binding of amyloidogenic peptides and amyloid peptide association with cellular membranes is critical in the onset and progression of amyloid diseases. Advancing the understanding in this field goes hand in hand with application of varied biophysical and biological techniques designed to probe the characteristics and underlying mechanisms of membrane-peptide interactions. This review summarizes experimental approaches and technical aspects employed in recent years fo... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=3512376 Sun, 25 Apr 2010 23:00:00 +0100 3512376 http://www.medworm.com/index.php?rid=3512375&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20423298%26dopt%3DAbstract Authors: Henriques ST, Castanho MA Prion diseases are a class of fatal neurodegenerative disorders that affect mammals and are characterized by their unique transmissibility and the nature of the infectious agent. When the physiological prion protein (PrP(C)) become corrupted (PrP(Sc)) it accumulates in the brain, promoting infection and self-propagation via recruitment of PrP(C). Although with identical sequence, PrP(C) and PrP(Sc) differ in their physicochemical properties: PrP(C) is soluble, has an alpha-helical structure and is sensitive to enzymatic degradation, whereas PrP(Sc) is insoluble, forms beta-aggregates and is resistant to proteolysis. The fragment PrP(16-126) possess similar physicochemical and pathological properties to PrP(sc), and therefore is commonly used as a mode... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=3512375 Sun, 25 Apr 2010 23:00:00 +0100 3512375 http://www.medworm.com/index.php?rid=3512374&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20423299%26dopt%3DAbstract Authors: Eckert GP, Wood WG, Müller WE Gradual changes in steady-state levels of beta amyloid peptides (Abeta) in the brain are considered as initial step in the amyloid cascade hypothesis of Alzheimer's disease (AD). Abeta is a product of the secretase cleavage of the amyloid precursor protein and there is evidence that the membrane lipid environment may modulate secretase activity and alters its function. Abeta disturbs membrane properties of artificial and isolated biological membranes and of plasma membranes in living cells. Abeta induced changes in membrane fluidity could be explained by physico-chemical interactions of the peptide with membrane components such as cholesterol, phospholipids and gangliosides. Thus, cell membranes may be the location where the neurotoxic cascade ... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=3512374 Sun, 25 Apr 2010 23:00:00 +0100 3512374 http://www.medworm.com/index.php?rid=3433523&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20353382%26dopt%3DAbstract Authors: Benko-Iseppon AM, Crovella S Despite of the high biological diversity and traditional use of medicinal plants in Brazil, no comprehensive ethnobotanic review of plants with potential antimicrobial effects is available. In the present work own field information is aggregated with a literature review, identifying 433 Brazilian plant species potentially useful for identification of antimicrobial peptides. They included mainly woody species, distributed on 100 plant families (93 angiosperms and 7 pteridophytes) and 266 genera, covering all Brazilian regions and ecosystems. Main plant parts and indications for their use are presented and discussed, revealing the high potential that these plants present for the future planning strategies regarding the future development of antimicro... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=3433523 Tue, 30 Mar 2010 23:00:00 +0100 3433523 http://www.medworm.com/index.php?rid=3361080&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20222865%26dopt%3DAbstract Authors: Varca GH, Andréo-Filho N, Lopes PS, Ferraz HG Cyclodextrins are oligosaccharides, specifically cyclic alpha-1,4-D-glucose oligomers, that possess a cone-like shape resulting in a hydrophobic inner cavity capable of forming complexes with several guest molecules in a hydrophilic matrix. This capability has led to an extensive investigation into cyclodextrin applications in several different substrates with the purpose of overcoming limitations, such as solubility issues, physical degradation and sensitivity to solvents, in guest substances. Researchers have recently described successful interactions between cyclodextrins and proteins, such as enzymes, peptides and amino acids. These complex biomolecules consist of potent active ingredients and are employed in several indus... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=3361080 Fri, 12 Mar 2010 00:00:00 +0100 3361080 http://www.medworm.com/index.php?rid=3339921&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20201794%26dopt%3DAbstract Authors: Baccari MC Orexin A (OXA) and orexin B (OXB) are recently discovered neuropeptides that appear to play a role in various distinct functions such as arousal and the sleep-wake cycle as well as on appetite and regulation of feeding and energy homeostasis. Orexins were first described as neuropeptides expressed by a specific population of neurons in the lateral hypothalamic area, a region classically implicated in feeding behaviour. Orexin neurons project to numerous brain regions, where orexin receptors have been shown to be widely distributed: both OXA and OXB act through two subtypes of receptors (OX1R and OX2R) that belong to the G protein-coupled superfamily of receptors. Growing evidence indicates that orexins act in the central nervous system also to regulate gastrointesti... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=3339921 Thu, 04 Mar 2010 00:00:00 +0100 3339921 http://www.medworm.com/index.php?rid=3284533&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20158453%26dopt%3DAbstract Authors: Sakudo A, Xue G, Kawashita N, Ano Y, Takagi T, Shintani H, Tanaka Y, Onodera T, Ikuta K Prion protein (PrP) gene encodes cellular PrP (PrPC), a glycosylphosphatidylinositol (GPI)-anchored cell membrane protein indispensable for infections of prion, which causes Creutzfeldt-Jakob disease (CJD) in humans, bovine spongiform encephalopathy (BSE) in cattle, and scrapie in sheep. Although PrPC is known to be converted into an abnormal isoform (PrPSc) upon prion infection and play an important role in prion diseases, the mechanisms involved remain unclear, partly due to the insolubility of PrPSc, which prevents experimental biochemical and biophysical analyses. Recently, with improvements in computer power and methods, computer analyses have been contributing more to prion studies. A... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=3284533 Tue, 16 Feb 2010 00:00:00 +0100 3284533 http://www.medworm.com/index.php?rid=3200933&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20088767%26dopt%3DAbstract Authors: Pestana-Calsa MC, Ribeiro IL, Calsa T As eukaryotes, plants include in innate defense antimicrobial peptides (AMP), usually small cysteine or glycine-rich peptides effective against a wide range of pathogens. The main classes of AMPs are represented by alpha/beta-defensins, lipid-transfer proteins, thionins, cyclotides, snakins and hevein-like, according to amino acid sequence homology. In spite of increasing number of described AMPs from plants, last decade advances in methodologies for gene expression and the huge amounts of genomic, proteomic and other "-omics" data lead to new prospection strategies of novel potential candidates. Organised user-friendly databases are available to be searched and enlarged with newly discovered plant-derived AMPs. Bioinformatics has allowed ... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=3200933 Thu, 21 Jan 2010 00:00:00 +0100 3200933 http://www.medworm.com/index.php?rid=3200932&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20088768%26dopt%3DAbstract Authors: da Rocha Pitta MG, da Rocha Pitta MG, Galdino SL All living organisms, ranging from microorganisms to plants and mammals, have evolved mechanisms to actively defend themselves against pathogen attack. A wide range of biological activities have been attributed to plant antimicrobial peptides (AMPs) including growth inhibitory effects on a broad range of fungi, Gram-positive and Gram-negative bacteria, viruses, neoplasic cells and parasitic protozoa. Classes of AMPs, their mechanisms of action, biological activity, and cytotoxicity towards host cells are discussed. A particular focus regards AMP candidates with potential for use in defense against biological warfare agents. This field is young, but provides additional stimulus to consideration of these molecules as a new class o... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=3200932 Thu, 21 Jan 2010 00:00:00 +0100 3200932 http://www.medworm.com/index.php?rid=3200931&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20088769%26dopt%3DAbstract Authors: Padovan L, Scocchi M, Tossi A EST (Expressed Sequence Tags) databases are increasing in number and size, especially regarding cultivated plants. Sugarcane is one of the most important tropical and subtropical crops, presenting a complex polyploid genome of hybrid origin, bearing a challenge for the understanding of genetic processes in higher plants. In the present work a general search was carried out on the largest Sugarcane EST Database (SUCEST) that includes 237,954 ESTs aiming to identify defensin antimicrobial peptides - a class of small, basic, cysteine-rich peptides distributed throughout the kingdoms. Using a computational approach 17 new defensin isoforms could be identified. Main steps for the search, characterization and evaluation of the defensin expression profil... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=3200931 Thu, 21 Jan 2010 00:00:00 +0100 3200931 http://www.medworm.com/index.php?rid=3200930&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20088770%26dopt%3DAbstract Authors: Padovan L, Crovella S, Tossi A, Segat L To defend themselves from attack by pathogens, plants can rely only on their innate defense systems. Defensins are antimicrobial peptides that contribute to plant immunity by displaying a direct cidal activity against various pathogens, some of which are responsible for plant diseases. These determine a significant decrease in the quality and safety of agricultural products, especially among food crops, and cause significant economic losses. There is consequently an increasing interest for antimicrobial compounds such as the defensins, which might be applied in different ways to protect important food or bio-fuel crops. In this review we analyse the techniques that have been reported in the literature for the production of isolated plant... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=3200930 Thu, 21 Jan 2010 00:00:00 +0100 3200930 http://www.medworm.com/index.php?rid=3200929&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20088771%26dopt%3DAbstract Authors: Kido EA, Pandolfi V, Houllou-Kido LM, Andrade PP, Marcelino FC, Nepomuceno AL, Abdelnoor RV, Burnquist WL, Benko-Iseppon AM Defensin, thionin and lipid transfer protein (LTP) gene families, which antimicrobial activity has an attractive use in protein engineering and transgenic production of agronomical important plants, have been here functionally reviewed. Also, a transcriptional overview of a set of plant SuperSAGE libraries and analysis looking for 26 bp tags possibly annotated for those families is presented. Tags differentially expressed (p = 0.05) or constitutively transcribed were identified from leaves or roots SuperSAGE libraries from important Brazilian plant species [cowpea (Vigna unguiculata (L.) Walp.), soybean (Glycine max (L.) Merr.) and modern sugarcane hybrid... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=3200929 Thu, 21 Jan 2010 00:00:00 +0100 3200929 http://www.medworm.com/index.php?rid=3200928&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20088772%26dopt%3DAbstract Authors: Benko-Iseppon AM, Galdino SL, Calsa T, Kido EA, Tossi A, Belarmino LC, Crovella S Mechanisms related to biotic interactions, such as pathogen attack, herbivory and symbiosis are important challenges to higher plants and have been widely studied especially for breeding purposes. The present review focuses on a special category of defense molecules, the plant antimicrobial peptides, providing an overview of their main molecular features and structures. PMID: 20088772 [PubMed - as supplied by publisher] (Source: Current Protein and Peptide Science) Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=3200928 Thu, 21 Jan 2010 00:00:00 +0100 3200928 http://www.medworm.com/index.php?rid=3200927&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20088773%26dopt%3DAbstract Authors: Belarmino C, Capriles PV, Crovella S, Dardene LE, Benko-Iseppon AM EST (Expressed Sequence Tags) databases are increasing in number and size, especially regarding cultivated plants. Sugarcane is one of the most important tropical and subtropical crops, presenting a complex polyploid genome of hybrid origin, bearing a challenge for the understanding of genetic processes in higher plants. In the present work a general search was carried out on the largest Sugarcane EST Database (SUCEST) that includes 237,954 ESTs aiming to identify defensin antimicrobial peptides - a class of small, basic, cysteine-rich peptides distributed throughout the kingdoms. Using a computational approach 17 new defensin isoforms could be identified. Main steps for the search, characterization and evaluat... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=3200927 Thu, 21 Jan 2010 00:00:00 +0100 3200927 http://www.medworm.com/index.php?rid=3200926&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20088774%26dopt%3DAbstract Authors: Belarmino LC, Benko-Iseppon AM The expressive amount of nucleotide sequences from diverse plant species in databanks enables the use of computational approaches to discovery still unidentified genes and to infer about their function, structure and role in some biological processes. Of special interest are the antimicrobial peptides (AMP), whose functionalities have a very important role in defense against microbial infection in multicellular eukaryotes, being considered less susceptible to bacterial resistance than traditional antibiotics, with potential to develop a new class of therapeutic agents. Recent computational developments have provided various algorithms and resources to profit from the overwhelming information in data banks for biomining such peptides. This review ... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=3200926 Thu, 21 Jan 2010 00:00:00 +0100 3200926 http://www.medworm.com/index.php?rid=3200925&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20088775%26dopt%3DAbstract Authors: Alguel Y, Leung J, Singh S, Rana R, Civiero L, Alves C, Byrne B The last five years have seen a dramatic increase in the number of membrane protein structures. The vast majority of these 191 unique structures are of membrane proteins from prokaryotic sources. Whilst these have provided unprecedented insight into the mechanism of action of these important molecules our understanding of many clinically important eukaryotic membrane proteins remains limited by a lack of high resolution structural data. It is clear that novel approaches are required to facilitate the structural characterization of eukaryotic membrane proteins. Here we review some of the techniques developed recently which are having a major impact on the way in which structural studies of eukaryotic membrane prote... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=3200925 Thu, 21 Jan 2010 00:00:00 +0100 3200925 http://www.medworm.com/index.php?rid=3200924&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20088776%26dopt%3DAbstract Authors: Vas M, Varga A, Graczer E Coupling of structural flexibility and biological function is an essential feature of proteins. The role of relative domain movements in enzyme function has been evidenced in many cases. However, the way of communication between protein domains and its manifestation in their movements as well as in the biological function are rarely delineated. In this review we summarize comprehensive studies with a typical hinge-bending two-domain enzyme, 3-phosphoglycerate kinase. A possible mechanism is proposed by which the two substrates that bind to different domains trigger the operation of the molecular hinges, located in the interdomain region. Various crystal structures of the enzyme have been determined with different relative domain positions, suggesting ... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=3200924 Thu, 21 Jan 2010 00:00:00 +0100 3200924 http://www.medworm.com/index.php?rid=2546342&cid=s_37257_60_f&fid=37257&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19538139%26dopt%3DAbstract Authors: Kuznetsov IB Conformational flexibility is an inherent property of the protein structure. Large scale changes in the protein conformation play a key role in a variety of fundamental biological activities and have been implicated in a number of diseases. The time scales of functionally relevant dynamic processes in proteins generally do not allow the researchers to study them by the means of detailed atomic level simulations. Therefore, less computationally demanding methods based on the coarse grained models of protein structure and bioinformatics approaches are particularly important for the flexibility-related studies. This review is focused on two broad categories of protein flexibility - protein disorder and conformational switches. In the case of protein disorder, a flexi... Current Protein and Peptide Science journals http://www.medworm.com/rss/comments.php?id=2546342 Sun, 28 Jun 2009 03:42:39 +0100 2546342