Phase separation and mechanical properties of an elastomeric biomaterial from spider wrapping silk and elastin block copolymers
This study describes the biophysical characterization of recombinant polypeptides designed by combining spider wrapping silk and elastin‐like sequences as a strategy to rationally increase the strength of elastin‐based materials while maintaining extensibility. We demonstrate a thermo‐responsive phase separation and spontaneous colloid‐like droplet formation from silk‐elastin block copolymers, and from a thirty‐four residue disordered region of Argiope trifasciata wrapping silk alone, and measure a comprehensive suite of tensile mechanical properties from cross‐linked materials. Silk‐elastin materials exhib...
Source: Biopolymers - June 8, 2016 Category: Biochemistry Authors: Lisa D. Muiznieks, Fred W. Keeley Tags: Original Article Source Type: research
High‐resolution, hybrid optical trapping methods and their application to nucleic acid processing proteins
This article is protected by copyright. All rights reserved. (Source: Biopolymers)
Source: Biopolymers - May 27, 2016 Category: Biochemistry Authors: Yann R. Chemla Tags: Review Source Type: research
High ‐resolution, hybrid optical trapping methods and their application to nucleic acid processing proteins
This article is protected by copyright. All rights reserved. (Source: Biopolymers)
Source: Biopolymers - May 25, 2016 Category: Biochemistry Authors: Yann R. Chemla Tags: Review Source Type: research
Review: The HSP90 molecular chaperone—an enigmatic ATPase
ABSTRACT
The HSP90 molecular chaperone is involved in the activation and cellular stabilization of a range of ‘client’ proteins, of which oncogenic protein kinases and nuclear steroid hormone receptors are of particular biomedical significance. Work over the last two decades has revealed a conformational cycle critical to the biological function of HSP90, coupled to an inherent ATPase activity that is regulated and manipulated by many of the co‐chaperones proteins with which it collaborates. Pharmacological inhibition of HSP90 ATPase activity results in degradation of client proteins in vivo, and is a promising targe...
Source: Biopolymers - May 19, 2016 Category: Biochemistry Authors: Laurence H. Pearl Tags: Article Source Type: research
Invited review: Mechanisms of GTP hydrolysis and conformational transitions in the dynamin superfamily
ABSTRACT
Dynamin superfamily proteins are multidomain mechano‐chemical GTPases which are implicated in nucleotide‐dependent membrane remodeling events. A prominent feature of these proteins is their assembly‐ stimulated mechanism of GTP hydrolysis. The molecular basis for this reaction has been initially clarified for the dynamin‐related guanylate binding protein 1 (GBP1) and involves the transient dimerization of the GTPase domains in a parallel head‐to‐head fashion. A catalytic arginine finger from the phosphate binding (P‐) loop is repositioned toward the nucleotide of the same molecule to stabilize the tr...
Source: Biopolymers - May 19, 2016 Category: Biochemistry Authors: Oliver Daumke, Gerrit J. K. Praefcke Tags: Article Source Type: research
Invited review: MnmE, a GTPase that drives a complex tRNA modification reaction
ABSTRACT
MnmE is a multi‐domain GTPase that is conserved from bacteria to man. Together with its partner protein MnmG it is involved in the synthesis of a tRNA wobble uridine modification. The orthologues of these proteins in eukaryotes are targeted to mitochondria and mutations in the encoding genes are associated with severe mitochondrial diseases. While classical small GTP‐binding proteins are regulated via auxiliary GEFs and GAPs, the GTPase activity of MnmE is activated via potassium‐dependent homodimerization of its G domains. In this review we focus on the catalytic mechanism of GTP hydrolysis by MnmE and the ...
Source: Biopolymers - May 19, 2016 Category: Biochemistry Authors: Marcus Fislage, Lina Wauters, Wim Versées Tags: Article Source Type: research
Review: Structure and mechanism of the dynein motor ATPase
ABSTRACT
Dyneins are multiprotein complexes that move cargo along microtubules in the minus end direction. The largest individual component of the dynein complex is the heavy chain. Its C‐terminal 3500 amino‐acid residues form the motor domain, which hydrolyses ATP in its ring of AAA+ (ATPases associated with diverse cellular activities) domains to generate the force for movement. The production of force is synchronized with cycles of microtubule binding and release, another important prerequisite for efficient motility along the microtubule. Although the large scale conformational changes that lead to force production...
Source: Biopolymers - May 19, 2016 Category: Biochemistry Authors: Helgo Schmidt, Andrew P. Carter Tags: Article Source Type: research
Invited review: Microtubule severing enzymes couple atpase activity with tubulin GTPase spring loading
We present a list of challenges regarding the mechanism of severing, which require development of experimental and modeling approaches to shed light as to how severing enzymes can act to regulate microtubule dynamics in cells. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 547–556, 2016. (Source: Biopolymers)
Source: Biopolymers - May 19, 2016 Category: Biochemistry Authors: Megan E. Bailey, Nan Jiang, Ruxandra I. Dima, Jennifer L. Ross Tags: Article Source Type: research
Review: The lord of the rings: Structure and mechanism of the sliding clamp loader
ABSTRACT
Sliding clamps are ring‐shaped polymerase processivity factors that act as master regulators of cellular replication by coordinating multiple functions on DNA to ensure faithful transmission of genetic and epigenetic information. Dedicated AAA+ ATPase machines called clamp loaders actively place clamps on DNA, thereby governing clamp function by controlling when and where clamps are used. Clamp loaders are also important model systems for understanding the basic principles of AAA+ mechanism and function. After nearly 30 years of study, the ATP‐dependent mechanism of opening and loading of clamps is now becomin...
Source: Biopolymers - May 19, 2016 Category: Biochemistry Authors: Brian A. Kelch Tags: Article Source Type: research
Review: Progresses in understanding N‐ethylmaleimide sensitive factor (NSF) mediated disassembly of SNARE complexes
ABSTRACT
N‐ethylmaleimide sensitive factor (NSF) is a key protein of intracellular membrane traffic. NSF is a highly conserved protein belonging to the ATPases associated with other activities (AAA+ proteins). AAA+ share common domains and all transduce ATP hydrolysis into major conformational movements that are used to carry out conformational work on client proteins. Together with its cofactor SNAP, NSF is specialized on disassembling highly stable SNARE complexes that form after each membrane fusion event. Although essential for all eukaryotic cells, however, the details of this reaction have long been enigmatic. Rece...
Source: Biopolymers - May 19, 2016 Category: Biochemistry Authors: Je-Kyung Ryu, Reinhard Jahn, Tae‐Young Yoon Tags: Article Source Type: research
Mini review: ATP‐dependent proteases in bacteria
ABSTRACT
AAA+ proteases are universal barrel‐like and ATP‐fueled machines preventing the accumulation of aberrant proteins and regulating the proteome according to the cellular demand. They are characterized by two separate operating units, the ATPase and peptidase domains. ATP‐dependent unfolding and translocation of a substrate into the proteolytic chamber is followed by ATP‐independent degradation. This review addresses the structure and function of bacterial AAA+ proteases with a focus on the ATP‐driven mechanisms and the coordinated movements in the complex mainly based on the knowledge of ClpXP. We conclude...
Source: Biopolymers - May 19, 2016 Category: Biochemistry Authors: Lisa‐Marie Bittner, Jan Arends, Franz Narberhaus Tags: Article Source Type: research
Invited review: Architectures and mechanisms of ATP binding cassette proteins
ABSTRACT
ATP binding cassette (ABC) ATPases form chemo‐mechanical engines and switches that function in a broad range of biological processes. Most prominently, a very large family of integral membrane NTPases—ABC transporters—catalyzes the import or export of a diverse molecules across membranes. ABC proteins are also important components of the chromosome segregation, recombination, and DNA repair machineries and regulate or catalyze critical steps of ribosomal protein synthesis. Recent structural and mechanistic studies draw interesting architectural and mechanistic parallels between diverse ABC proteins. Here, I ...
Source: Biopolymers - May 19, 2016 Category: Biochemistry Authors: Karl‐Peter Hopfner Tags: Article Source Type: research
Review: The ATPase mechanism of myosin and actomyosin
ABSTRACT
Myosins are a large family of molecular motors that use the common P‐loop, Switch 1 and Switch 2 nucleotide binding motifs to recognize ATP, to create a catalytic site than can efficiently hydrolyze ATP and to communicate the state of the nucleotide pocket to other allosteric binding sites on myosin. The energy of ATP hydrolysis is used to do work against an external load. In this short review I will outline current thinking on the mechanism of ATP hydrolysis and how the energy of ATP hydrolysis is coupled to a series of protein conformational changes that allow a myosin, with the cytoskeleton track actin, to op...
Source: Biopolymers - May 19, 2016 Category: Biochemistry Authors: Michael A. Geeves Tags: Article Source Type: research
Review: Mechanochemistry of the kinesin‐1 ATPase
ABSTRACT
Kinesins are P‐loop NTPases that can do mechanical work. Like small G‐proteins, to which they are related, kinesins execute a program of active site conformational changes that cleaves the terminal phosphate from an NTP substrate. But unlike small G‐proteins, kinesins can amplify and harness these conformational changes in order to exert force. In this short review I summarize current ideas about how the kinesin active site works and outline how the active site chemistry is coupled to the larger‐scale structural cycle of the kinesin motor domain. Focusing largely on kinesin‐1, the best‐studied kinesin,...
Source: Biopolymers - May 19, 2016 Category: Biochemistry Authors: R. A. Cross Tags: Article Source Type: research
Review: Translational GTPases
ABSTRACT
Translational GTPases (trGTPases) play key roles in facilitating protein synthesis on the ribosome. Despite the high degree of evolutionary conservation in the sequences of their GTP‐binding domains, the rates of GTP hydrolysis and nucleotide exchange vary broadly between different trGTPases. EF‐Tu, one of the best‐characterized model G proteins, evolved an exceptionally rapid and tightly regulated GTPase activity, which ensures rapid and accurate incorporation of amino acids into the nascent chain. Other trGTPases instead use the energy of GTP hydrolysis to promote movement or to ensure the forward commitme...
Source: Biopolymers - May 19, 2016 Category: Biochemistry Authors: Cristina Maracci, Marina V. Rodnina Tags: Article Source Type: research
