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Molecular mechanism of VDE-initiated intein homing in yeast nuclear genome.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: Fukuda T, Nagai Y, Ohya Y In Saccharomyces cerevisiae, VMA1 intein encodes a homing endonuclease termed VDE which is produced by an autocatalytic protein splicing reaction. VDE introduces a DSB at its recognition sequence on intein-minus allele, resulting in the lateral transfer of VMA1 intein. In this review, we summarize a decade of in vitro study on VDE and describe our recent study on the in vivo behavior of both VDE and host proteins involved in intein mobility. Meiotic DSBs caused by VDE are repaired in the similar pathway to that working in meiotic recombination induced by Spo11p-mediated DSBs. Meiosis-...
Source: Advances in Biophysics - January 22, 2007 Category: Physics Source Type: journals

Structure and function of the shufflon in plasmid R64.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: Gyohda A, Furuya N, Ishiwa A, Zhu S, Komano T Conservative site-specific recombination plays key roles in creating biological diversity in prokaryotes. Most site-specific inversion systems consist of two recombination sites and a recombinase gene. In contrast, the shufflon multiple inversion system of plasmid R64 consists of seven sfx recombination sites, which separate four invertible DNA segments, and the rci gene encoding a site-specific recombinase of the integrase family. The rci product mediates recombination between any two inverted sfx sites, resulting in the inversion of four DNA segments independentl...
Source: Advances in Biophysics - January 22, 2007 Category: Physics Source Type: journals

Transposition mechanisms and biotechnology applications of the medaka fish Tol2 transposable element.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: Koga A The Tol2 element of the medaka fish is a member of the hAT (hobo/Activator/ Tam3) transposable element family. About 20 copies are present in the medaka fish genome and, unlike many other hAT family elements, virtually all the copies are autonomous or potentially autonomous, containing an intact transposase gene. Excision of Tol2 is not precise at the nucleotide sequence level, excision foot-prints being heterogeneous. In more than half of excision events, however, breakage and rejoining of DNA molecules occur within the 8-bp target site duplication region, removing the entire Tol2 sequence and retainin...
Source: Advances in Biophysics - January 22, 2007 Category: Physics Source Type: journals

Genetics and epigenetics in flower pigmentation associated with transposable elements in morning glories.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: Iida S, Morita Y, Choi JD, Park KI, Hoshino A Among the genus Ipomoea, three morning glories, I. nil (the Japanese morning glory), I. purpurea (the common morning glory), and I. tricolor, were domesticated well for floricultural plants, and many spontaneous mutants displaying various flower pigmentation patterns were isolated. Most of these spontaneous mutations were found to be caused by the insertion of DNA transposable elements in the genes for the anthocyanin pigmentation in flowers, and many of them exhibited variegated flowers, such as white flowers with pigmented spots and sectors. Here, we describe the...
Source: Advances in Biophysics - January 22, 2007 Category: Physics Source Type: journals

Intermediate molecules generated by transposase in the pathways of transposition of bacterial insertion element IS3.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: Ohtsubo E, Minematsu H, Tsuchida K, Ohtsubo H, Sekine Y PMID: 15493331 [PubMed - indexed for MEDLINE]
Source: Advances in Biophysics - January 22, 2007 Category: Physics Source Type: journals

Gpt delta transgenic mouse: a novel approach for molecular dissection of deletion mutations in vivo.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: Nohmi T, Masumura K Human genome is continuously exposed to various DNA damaging agents including reactive oxygen species. Of various forms of DNA damage, double-strand breaks (DSBs) in DNA are the most detrimental because of the mutagenicity and cytotoxicity. To combat the serious threats posed by DSBs, cells evolved various homologous and non-homologous recombination repair mechanisms. However, some repair mechanisms appear to be involved in the induction of genome rearrangements such as deletions. To analyze the deletion mutations in a whole body system, gpt delta mice were established. In this mouse model,...
Source: Advances in Biophysics - January 22, 2007 Category: Physics Source Type: journals

Cell death promoted by homologous DNA interaction from bacteria to humans.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: Kusano K Pairing between homologous DNA controls cellular functions including double-strand break repair, mitotic recombination, and progression of DNA replication forks, as well as chiasma formation during meiosis. Here I summarize that homologous interaction could promote the cell killing in bacteria, yeast, and multicellular organisms. The mechanisms of cell killing are categorized into two types: (1) the killing due to the accumulation of extrachromosomal DNA; (2) the killing induced by Holliday junction structures. I propose that the mechanisms of such killing function as novel apoptotic pathways in the c...
Source: Advances in Biophysics - January 22, 2007 Category: Physics Source Type: journals

Nijmegen breakage syndrome and DNA double strand break repair by NBS1 complex.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: Matsuura S, Kobayashi J, Tauchi H, Komatsu K The isolation of the NBS1 gene revealed the molecular mechanisms of DSB repair. In response to DNA damage, histone H2AX in the vicinity of DSBs is phosphorylated by ATM. NBS1 then targets the MRE11/RAD50 complex to the sites of DSBs through interaction of the FHA/BRCT domain with gamma-H2AX. NBS1 complex binds to damaged-DNA directly, and HR repair is initiated. To collaborate DSB repair, ATM also regulates cell cycle checkpoints at G1, G2, and intra-S phases via phosphorylation of SMC, CHK2 and FANCD2. The phosphorylation of these proteins require NBS1 complex. Thu...
Source: Advances in Biophysics - January 22, 2007 Category: Physics Source Type: journals

The function of RecQ helicase gene family (especially BLM) in DNA recombination and joining.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: Kaneko H, Fukao T, Kondo N Bloom syndrome is a rare autosomal recessive genetic disorder characterized by lupus-like erythematous telangiectasias of the face, sun sensitivity, stunted growth, and immunodeficiency. Chromosome instability syndromes have a common feature, being associated at high frequency with neoplasia. BS is considered as one of the chromosome instability syndromes since the fibroblasts or lymphocytes of BS patients show excessive spontaneous chromosome instability. The causative gene of BS (BLM) was identified as a RecQ helicase homologue. In this review, we showed the characteristic phenotyp...
Source: Advances in Biophysics - January 22, 2007 Category: Physics Source Type: journals

Genetic and physiological regulation of non-homologous end-joining in mammalian cells.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: Tachibana A Repair of DSBs is important to prevent chromosomal fragmentation, translocations and deletions. To investigate the process in NHEJ, we have established an in vitro system to clarify the measurement and analysis of the efficiency and the fidelity of rejoining of DSBs, and applied the method to investigate NHEJ in human cells derived from patients suffering from cancer-prone hereditary diseases. A DSB was introduced in plasmid pZErO-2 at a specific site within the ccdB gene that is lethal to E. coli cells, and treated with nuclear extracts from human cells. The efficiency of rejoining in the nuclear ...
Source: Advances in Biophysics - January 22, 2007 Category: Physics Source Type: journals

Illegitimate recombination mediated by double-strand break and end-joining in Escherichia coli.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: Ikeda H, Shiraishi K, Ogata Y The frequency of illegitimate recombination has been measured by a lambda bio transducing phage assay during the induction of the E. coli lambda cI857 lysogen. Illegitimate recombination falls into two classes, short homology-independent and short homology-dependent illegitimate recombination. The former involves sequences with virtually no homology, and is mediated by DNA topoisomerases and controlled by the DNA binding protein HU. The latter is induced by UV irradiation or other DNA damaging agents and requires short regions of homology, usually contain 4 to 13 base pairs, at si...
Source: Advances in Biophysics - January 22, 2007 Category: Physics Source Type: journals

Molecular mechanism of vde-initiated intein homing in yeast nuclear genome.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: Fukuda T, Nagai Y, Ohya Y In Saccharomyces cerevisiae, VMAI intein encodes a homing endonuclease termed VDE which is produced by an autocatalytic protein splicing reaction. VDE introduces a DSB at its recognition sequence on intein-minus allele, resulting in the lateral transfer of VMAI intein. In this review, we summarize a decade of in vitro study on VDE and describe our recent study on the in vivo behavior of both VDE and host proteins involved in intein mobility. Meiotic DSBs caused by VDE are repaired in the similar pathway to that working in meiotic recombination induced by Spollp-mediated DSBs. Meiosis-...
Source: Advances in Biophysics - January 22, 2007 Category: Physics Source Type: journals

Structure and function of the shufflon in plasmid r64.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: Gyohda A, Furuya N, Ishiwa A, Zhu S, Komano T Conservative site-specific recombination plays key roles in creating biological diversity in prokaryotes. Most site-specific inversion systems consist of two recombination sites and a recombinase gene. In contrast, the shufflon multiple inversion system of plasmid R64 consists of seven sfx recombination sites, which separate four invertible DNA segments, and the rci gene encoding a site-specific recombinase of the integrase family. The rci product mediates recombination between any two inverted sfx sites, resulting in the inversion of four DNA segments independentl...
Source: Advances in Biophysics - January 22, 2007 Category: Physics Source Type: journals

Transposition mechanisms and biothechnology applications of the medaka fish tol2 transposable element.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: Koga A The Tol2 element of the medaka fish is a member of the hAT (hobo/Activator/Tam3) transposable element family. About 20 copies are present in the medaka fish genome and, unlike many other hAT family elements, virtually all the copies are autonomous or potentially autonomous, containing an intact transposase gene. Excision of Tol2 is not precise at the nucleotide sequence level, excision footprints being heterogeneous. In more than half of excision events, however, breakage and rejoining of DNA molecules occur within the 8-bp target site duplication region, removing the entire Tol2 sequence and retaining ...
Source: Advances in Biophysics - January 22, 2007 Category: Physics Source Type: journals

Genetics and epigenetics in flower pigmentation associated with transposable elements in morning glories.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: Iida S, Morita Y, Choi JD, Park KI, Hoshino A Among the genus Ipomoea, three morning glories, I. nil the Japanese morning glory), I. purpurea (the common morning glory), and I. tricolor, were domesticated well for floricultural plants, and many spontaneous mutants displaying various flower pigmentation patterns were isolated. Most of these spontaneous mutations were found to be caused by the insertion of DNA transposable elements in the genes for the anthocyanin pigmentation in flowers, and many of them exhibited variegated flowers, such as white flowers with pigmented spots and sectors. Here, we describe the ...
Source: Advances in Biophysics - January 22, 2007 Category: Physics Source Type: journals

Intermediate molecules generated by transposase in the pathways of transposition of bacterial insertion element 1S3.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: Ohtsubo E, Minematsu H, Tsuchida K, Ohtsubo H, Sekine Y PMID: 15476896 [PubMed - as supplied by publisher]
Source: Advances in Biophysics - January 22, 2007 Category: Physics Source Type: journals

Gpt delta transgenic mouse: A novel approach for molecular dissection of deletion mutations in vivo.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: Nohmi T, Masumura KI Human genome is continuously exposed to various DNA damaging agents including reactive oxygen species. Of various forms of DNA damage, double-strand breaks (DSBs) in DNA are the most detrimental because of the mutagenicity and cytotoxicity. To combat the serious threats posed by DSBs, cells evolved various homologous and non-homologous recombination repair mechanisms. However, some repair mechanisms appear to be involved in the induction of genome rearrangements such as deletions. To analyze the deletion mutations in a whole body system, gpt delta mice were established. In this mouse model...
Source: Advances in Biophysics - January 22, 2007 Category: Physics Source Type: journals

Nijmegen breakage syndrome and DNA double strand break repair by NBS1 complex.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: Matsuura S, Kobayashi J, Tauchi H, Komatsu K The isolation of the NBS1 gene revealed the molecular mechanisms of DSB repair. In response to DNA damage, histone H2AX in the vicinity of DSBs is phosphorylated by ATM. NBS1 then targets the MRE11/RAD50 complex to the sites of DSBs through interaction of the FHA/BRCT domain with gamma-H2AX. NBSI complex binds to damaged-DNA directly, and HR repair is initiated. To collaborate DSB repair, ATM also regulates cell cycle checkpoints at GI, G2, and intra-S phases via phosphorylation of SMC, CHK2 and FANCD2. The phosphorylation of these proteins require NBS1 complex. Thu...
Source: Advances in Biophysics - January 22, 2007 Category: Physics Source Type: journals

Illegitimate recombination mediated by double-strand break and end-joining in Escherichia coli.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: Ikeda H, Shiraishi K, Ogata Y The frequency of illegitimate recombination has been measured by a lambdabio transducing phage assay during the induction of the E. coli lambda c1857 lysogen. Illegitimate recombination falls into two classes, short homology-independent and short homology-dependent illegitimate recombination. The former involves sequences with virtually no homology, and is mediated by DNA topoisomerases and controlled by the DNA binding protein HU. The latter is induced by UV irradiation or other DNA damaging agents and requires short regions of homology, usually contain 4 to 13 base pairs, at sit...
Source: Advances in Biophysics - January 22, 2007 Category: Physics Source Type: journals

Preface to volume 38.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: Ikeda H, Iida S, Ohtsubo E PMID: 15476889 [PubMed - as supplied by publisher]
Source: Advances in Biophysics - January 22, 2007 Category: Physics Source Type: journals

Preface.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: Ebashi S, Noda H PMID: 15476888 [PubMed - as supplied by publisher]
Source: Advances in Biophysics - January 22, 2007 Category: Physics Source Type: journals

Studies and perspectives of calponin in smooth muscle regulation and cancer gene therapy.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: Takahashi K, Yamamura H PMID: 12954553 [PubMed - indexed for MEDLINE]
Source: Advances in Biophysics - January 22, 2007 Category: Physics Source Type: journals

Fertilization and development initiation in orthodox and unorthodox ways: from normal fertilization to cloning.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: Yanagimachi R PMID: 12954552 [PubMed - indexed for MEDLINE]
Source: Advances in Biophysics - January 22, 2007 Category: Physics Source Type: journals

Brain neurosteroids are 4th generation neuromessengers in the brain: cell biophysical analysis of steroid signal transduction.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: Kawato S, Yamada M, Kimoto T PMID: 12954551 [PubMed - indexed for MEDLINE]
Source: Advances in Biophysics - January 22, 2007 Category: Physics Source Type: journals

Multiple sequence alignment: algorithms and applications.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: Gotoh O Elucidation of interrelationships among sequence, structure, function, and evolution (FESS relationships) of a family of genes or gene products is a central theme of modern molecular biology. Multiple sequence alignment has been proven to be a powerful tool for many fields of studies such as phylogenetic reconstruction, illumination of functionally important regions, and prediction of higher order structures of proteins and RNAs. However, it is far too trivial to automatically construct a multiple alignment from a set of related sequences. A variety of methods for solving this computationally difficult...
Source: Advances in Biophysics - January 22, 2007 Category: Physics Source Type: journals

Induced potential model of muscular contraction mechanism and myosin molecular structure.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: Mitsui T The proposed model is characterized by the constant r (Eq. 2-1), the induced potential (Fig. 1), two attached states of a myosin head (Fig. 1), the nonlinear elastic property of the crossbridge (Eq. 2-7), and the expression of U* (Eqs. 3-8 and 3-9), which led us to the following conclusions. 1. The following various magnitudes of myosin head motion are compatible with each other: about 2 nm of the quantity called power stroke by Irving (27), which is the mean moving distance of myosin head in the isometric tension in our model, 4-5 nm of the displacement of a single myosin head during one ATP hydrolys...
Source: Advances in Biophysics - January 22, 2007 Category: Physics Source Type: journals

Evolution of the carabid ground beetles.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: Osawa S, Su ZH, Kim CG, Okamoto M, Tominaga O, Imura Y The phylogenetic relationships of the carabid ground beetles have been estimated by analysing a large part of the ND5 gene sequences of more than 1,000 specimens consisting of the representative species and geographic races covering most of the genera and subgenera known in the world. From the phylogenetic analyses in conjunction with the mtDNA-based dating, a scenario of the establishment of the present habitats of the respective Japanese carabids has been constructed. The carabid diversification took place ca. 40 MYA as an explosive radiation of the majo...
Source: Advances in Biophysics - January 22, 2007 Category: Physics Source Type: journals

Ryanodine receptor isoforms in excitation-contraction coupling.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: Ogawa Y, Kurebayashi N, Murayama T Three genomically distinct isoforms of RyR are now known. RyR1 homologue is the primary isoform in skeletal muscles, whereas in cardiac muscles it is RyR2 homologue. RyR3 homologue occurs ubiquitously in many cells, but the biological function is little known, partly because of its minuscule amount in mammalian cells. The difference among RyR isoforms may not be so great in CICR activity, in other words, in the interaction of RyR isoforms with Ca2+, adenine nucleotides and caffeine. Species specificity among RyR1 homologues may be more important in the apparent difference bet...
Source: Advances in Biophysics - January 22, 2007 Category: Physics Source Type: journals

Biophysical studies on ATP synthase.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: Kagawa Y The isolation of ATP synthase (F0F1) (82) and F0 (83) 34 years ago finally revealed that F0F1 is a motor composed of F0 (ion-motor, abc subunits) and F1 (ATP-motor, alpha 3 beta 3 gamma delta epsilon subunits) (Fig. 1). The single molecule videotape (4, 5, 65, 66) revealed that gamma epsilon axis of F1 rotates counterclockwise, proceeds by each 2 pi/3 step, and is driven by torque of 42 pN.nm (12) with nearly 100% efficiency (5) (Fig. 4). The motor is composed of a rotor (gamma epsilon-F0-c) and a stator (alpha 3 beta 3 delta-F0-ab), and the rotor is connected to a shaft (gamma epsilon). Since F0F1 is...
Source: Advances in Biophysics - January 22, 2007 Category: Physics Source Type: journals

Design of protein function by physical perturbation method.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: Kidokoro S Based on three-dimensional structure of proteins, a rational strategy to design the protein function by physical perturbation method was proposed and tested on one of the well-examined enzymes, thermolysin for higher catalytic activity. An attempt was made to change the electrostatic potential and the dynamic property of three-dimensional structure around the active sites by single-amino-acid mutations, and the physical property of the mutants was then evaluated. Several mutants were found to have remarkably higher enzymatic activity than wild type. The multiple mutation was introduced and the logar...
Source: Advances in Biophysics - January 22, 2007 Category: Physics Source Type: journals

The neuronal basis of visual memory and imagery in the primate: a neurophysiological approach.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: Nakahara K, Ohbayashi M, Tomita H, Miyashita Y To understand the biological basis of memory is one of the most exciting frontiers of science. Single unit recording is a powerful method to investigate neuronal correlates of various brain functions such as memory in awake animals. Anatomical, neuropsychological, and neurophysiological evidence indicates that the IT has an important role not only for synthesizing the analyzed visual attribute into a unique configuration, but also for the storehouse of visual memory in humans and primates. We performed single unit recordings in the primate IT, and found neuronal c...
Source: Advances in Biophysics - January 22, 2007 Category: Physics Source Type: journals

Neural systems for control of voluntary action--a hypothesis.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: Hikosaka O Action is the means by which we and animals survive. It consists of a complex combination of movements which are either innately endowed or acquired by learning. In this article, I propose a hypothesis on the relationship between the organization of action and the organization of the brain. Innate and learned actions are controlled by different levels of neural networks: innate actions are controlled by reflex mechanisms and pattern generators in the spinal cord and brainstem, while learned actions are controlled by the cerebral cortex, basal ganglia, and cerebellum. However, these mechanisms are by...
Source: Advances in Biophysics - January 22, 2007 Category: Physics Source Type: journals

The structural study of membrane proteins by electron crystallography.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: Fujiyoshi Y A high-resolution electron cryo-microscope equipped with a top-entry specimen stage has been refined by modifying a previously described superfluid helium stage. Instruments equipped with such a cryo-stage achieve a resolution of better than 2.0 A and have proved extremely powerful in the high-resolution structure analysis of membrane proteins. Improvement of the electron microscopic system in combination with improved specimen preparation techniques allowed the structure of bR to be analyzed to a resolution of 3.0 A. The 3D structure of bR, especially the surface features, revealed the structural ...
Source: Advances in Biophysics - January 22, 2007 Category: Physics Source Type: journals

Structure-mutation analysis of the ATPase site of Dictyostelium discoideum myosin II.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: Sasaki N, Sutoh K Three loop structures called the P-loop, switch I loop and switch II loop of myosin are major components of its ATPase site, and share structural and functional homology with the loop structures in other ATPases and GTPases such as kinesin and G-protein. Using the alanine scanning mutagenesis, structure-function relationship of the switch I and switch II loops in Dictyostelium myosin II was examined. Based on crystal structures of Dictyostelium myosin motor domain, functions of each residue in those loops are discussed. PMID: 9949764 [PubMed - indexed for MEDLINE]
Source: Advances in Biophysics - January 22, 2007 Category: Physics Source Type: journals

Natural and artificial carbohydrate-glued protein aggregates.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: Matsubara K, Ebina S Carbohydrate gluing (which may have a carbohydrate-lectin binding mechanism) was first recognized as a major contributor in the supramolecular assembly of annelid giant Hb from the marine-worm P. aibuhitensis. Although this assembly obviously also relies on protein-protein interactions, the authors tested the application of carbohydrate gluing in the assembly of a protein aggregate using a lectin and a carbohydrate-containing protein. The resultant aggregate was a mixture of the protein aggregate and the ingredient proteins. The significance of the method is that the assembly of the aggreg...
Source: Advances in Biophysics - January 22, 2007 Category: Physics Source Type: journals

Supramolecular architectures for the functionalization of solid surfaces.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: Knoll W, Liley M, Piscevic D, Spinke J, Tarlov MJ Surface plasmon optical techniques are described as sensitive tools that allow for the on-line characterization of supramolecular biofunctional architectures at solid/solution interfaces. After a short introduction into the fundamentals of surface plasmon optics the observation of the build up of a functional bio-interface by the self-assembly process of long chain thiolates at an Au surface is described. Criteria are developed for tailoring the SAM architectures optimized for maximum protein binding from solution by specific bio-recognition reactions. SPM is e...
Source: Advances in Biophysics - January 22, 2007 Category: Physics Source Type: journals

Novel biosensoric devices based on molecular protein hetero-multilayer films.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: Diederich A, Lösche M We have developed a novel concept for the modification of technical surfaces with molecularly well-organized layers of bioorganic components. A molecular construction set has been used to implement this concept which is based on molecularly stratified polyelectrolyte films as a structure decoupling protein layers from solid substrates. Utilizing this technology, one can start from a number of different substrates to obtain the same surface structures, on which protein hetero-multilayer films can be prepared to functionalize the interface for (potentially very different) purposes. We have...
Source: Advances in Biophysics - January 22, 2007 Category: Physics Source Type: journals

Single molecular functional assay of ferritin arrays.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: Yamaki M In situ functional assay of each ferritin molecule in single-layer 2D arrays for horse spleen apoferritin and recombinant horse L- and human H-apoferritins was conducted by observing the iron-cores formed in the arrays by TEM. The study of the time-course, pH-dependence, and temperature-dependence of the function confirmed the iron-core formation to be due to the native function of apoferritins in array. Dark-field TEM imaging revealed that there was crystallinity in the cores in the array of recombinant human H-apoferritin. This iron-core formation was perfectly preserved in the array even after 3 mo...
Source: Advances in Biophysics - January 22, 2007 Category: Physics Source Type: journals

The influence of protein and interfacial structure on the self-assembly of oriented protein arrays.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: Leckband DE These results demonstrate the complexity of factors that impact the self-assembly of protein arrays via the specific binding to receptor-functionalized interfaces. Both the composition and colloidal properties of the protein and target membrane surfaces will affect the protein-surface interactions. However, different structural features control the interactions over different distance regimes and with different consequences. The long-range interactions that control the adsorption kinetics are sensitive not only to the charge on the target surface but also by the topological charge distribution on t...
Source: Advances in Biophysics - January 22, 2007 Category: Physics Source Type: journals

Electron crystallography of macromolecular periodic arrays on phospholipid monolayers.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: Chiu W, Avila-Sakar AJ, Schmid MF Electron crystallography has the potential of yielding structural information equivalent to x-ray diffraction. The major difficulty has been preparing specimens with the required structural order and size for diffraction and imaging in the electron microscope. 2D crystallization on phospholipid monolayers is capable of fulfilling both of these requirements. Crystals can form as a result of specific interactions with a protein's ligand or an analog, suitably linked to a lipid tail; or on a surface of complementary head-group charge. With such choices, the availability of a suit...
Source: Advances in Biophysics - January 22, 2007 Category: Physics Source Type: journals

Assembly of protein structures on liposomes by non-specific and specific interactions.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: Velev OD We investigate different schemes for fabrication of nanometer sized assemblies that consist of a liposome core over which a shell of ferritin is attached. Three distinct interactions were used for this assembly: (i) Electrostatic attraction. The liposomes are charged by the presence of cationic surfactant (HTAB) and at an appropriate pH collect the ferritin molecules into a 2D-ordered ferritin shell. The protein shells can be fixed by glutaraldehyde. Next, the liposomes can be removed by solubilisation, leaving behind ordered ferritin clusters. (ii) Specific avidin-biotin or streptavidin-biotin bindin...
Source: Advances in Biophysics - January 22, 2007 Category: Physics Source Type: journals

Supramolecular assembly using helical peptides.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: Fujita K, Kimura S, Imanishi Y, Rump E, Ringsdorf H We investigated supramolecular assemblies of various hydrophobic helical peptides. The assemblies were formed at the air/water interface or in aqueous medium. The hexadecapeptide, Boc-(Ala-Aib)s-OMe (BA16M), was reported to take alpha-helical structure by X-ray analysis. Several derivatives were prepared, which have the repeating sequence of Ala-Aib, Lys(Z)-Aib or Leu-Aib, or have the terminal chemically modified. CD spectra of the peptides indicated helical conformation in ethanol solution. The surface pressure-area isotherms of the peptide monolayers showed...
Source: Advances in Biophysics - January 22, 2007 Category: Physics Source Type: journals

Molecular handling of photosynthetic proteins for molecular assembly construction.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: Miyake J, Hara M Methods of constructing proteins were examined with special reference to the molecular assembly using photosynthetic RCs as membrane proteins. Molecular assemblies at the interfaces were studied by LB films, adsorption to the surface and reconstitution into liposomes and bilayer lipid membranes. The applications of biological specific ligands (recognition and binding), combinatorial chemical method, 2-D and 3-D order array assemblies and modification of protein molecules to make fusion proteins, as well as physical methods of manipulation of molecules by AFM tips and electric fields were revie...
Source: Advances in Biophysics - January 22, 2007 Category: Physics Source Type: journals

Two-dimensional crystals of apoferritin.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: Yoshimura H A simple 2D crystallization method using unfolded protein film as a supporting film of crystals was described, which allows modification of protein surfaces by injecting chemical reagents into the subphase after the crystal formation. As an example, glutaraldehyde was used to cross-link adjacent proteins and then stabilize protein crystals. The second layer of other proteins can also be formed on the apoferritin array using cross-linkers. The array of apoferritin is not only beneficial for electron crystallography but also for practical applications. For example, apoferritin produces a mineral core...
Source: Advances in Biophysics - January 22, 2007 Category: Physics Source Type: journals

Assembly process of 2D protein arrays in wetting films.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: Adachi E, Nagayama K We were successful in developing a technique to form protein array developed directly on solid surfaces. This promising array formation revealed two new concepts of the ordering mechanism: the lifetime of a secondary minimum and secondary films. These concepts are not limited to our film formation technique. Any electrolytic thin film on a solid surfaces or any free film may contain a secondary film. If the secondary film can be retained in an electrolytic thin film for a sufficient period, a large single domain of small colloidal particles, such as proteins, fine metal particles, fine sem...
Source: Advances in Biophysics - January 22, 2007 Category: Physics Source Type: journals

Advances in S-layer nanotechnology and biomimetics.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: Sleytr UB, Pum D, Sára M Two-dimensional crystalline bacterial S-layers composed of identical protein or glycoprotein subunits turned out to be ideal materials for the development of biomimetic membranes and new approaches in molecular nanotechnology. These isoporous protein lattices have already been used as (i) structure for producing isoporous ultrafiltration membranes with very precisely defined molecular sieving properties, (ii) matrices for immobilizing monolayers of functional molecules, (iii) stabilizing structure for LB-films and liposomes, and (iv) patterning elements in molecular nanotechnology. ...
Source: Advances in Biophysics - January 22, 2007 Category: Physics Source Type: journals

Criticality found in a model for orientational ordering of protein arrays.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: Hogyoku M MC-PSRG analysis allowed us to reduce criticalities A, B, and C found in the poker chip model, respectively, to ones of the Ising universality, of the 3-state Potts universality, and of the KT-like phase. We note that not only the KT-like phase but also the Ising and 3-state Potts universality have been predicted to appear in the generalized 6-state clock model. We expect that the criticality inherent in actual protein array systems, whose Hamiltonians might be more complex than those of the poker chip model, can also be reduced to the criticality clarified with the aid of the naive models. However, ...
Source: Advances in Biophysics - January 22, 2007 Category: Physics Source Type: journals