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Partially Folded Conformations Of E Coli Ribonuclease H
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Book Synopsis Partially Folded Conformations of E. Coli Ribonuclease H by : Aaron K. Chamberlain
Download or read book Partially Folded Conformations of E. Coli Ribonuclease H written by Aaron K. Chamberlain and published by . This book was released on 1997 with total page 256 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Folding of Ribonuclease H from Escherichia Coli by : Tanya Marie Raschke
Download or read book Folding of Ribonuclease H from Escherichia Coli written by Tanya Marie Raschke and published by . This book was released on 1999 with total page 308 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Beyond the Native State by : Katelyn Blair Connell
Download or read book Beyond the Native State written by Katelyn Blair Connell and published by . This book was released on 2010 with total page 242 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins can sample a variety of partially folded conformations during the transition between the unfolded and native states. The role of such intermediates is a matter of considerable debate, but it is clear that characterization of these partially folded species is crucial for understanding protein folding and function. A single amino acid change can convert E. coli ribonuclease H from a three-state folder that populates a kinetic intermediate to one that folds in an apparent two-state fashion. We have compared the folding trajectories of the three-state and two-state RNases H, proteins with the same native state topology but altered regional stability, using a protein engineering approach. Our data indicate that that both versions of RNase H fold through a similar trajectory with similar high-energy conformations. This suggests that formation of specific partially folded conformations may be a general feature of protein folding that can promote, rather than hinder, efficient folding. To better understand the robust role this high-energy species plays in folding, we set out to trap the transient intermediate of RNase H at equilibrium by selectively destabilizing the region of the protein known to be unfolded in this species. We find that the intermediate is undetectable in a series of HSQC's, revealing the dynamic nature of this partially folded form on the timescale of NMR detection. This result is in contrast to studies in which the structures of trapped intermediates are solved by NMR, indicating that the they are well-packed and native-like. The dynamic nature of the RNase H intermediate may be important for its role as an on-pathway, productive species that promotes efficient folding. An analogous intermediate is populated on the kinetic trajectory of RNase H from T. thermophilus, an organism that grows optimally at a temperature 30 oC higher than E. coli. To understand how two proteins that share identical structures can function in such different environments, we looked for differences in their energetics by comparing equilibrium mimics of their high-energy intermediates. We find potential differences in the dynamic properties of the intermediates, which may provide insight into how proteins with the same native structure can exhibit vastly different biophysical behavior. In contrast to globular proteins such as RNase H, repeat proteins are tandem arrays of repeating structural units that have no long-range contacts. In these modular domains, the majority of native contacts could be maintained in the face of partial unfolding. Repeat proteins therefore offer a unique architecture for exploring the extent of cooperativity and roughness on the energy landscape. To understand how a modular system builds cooperativity into its energetics, and to explore the origins and limits of this cooperativity, we studied the behavior of the Notch ankyrin domain in the optical tweezers, a single molecule mechanical tool. The forced unfolding of the Notch ankyrin domain occurs in one or two steps when manipulated in the optical tweezers. Though the unfolding pathway is heterogenous compared to that observed in bulk studies, there is a limit to the degree of uncoupling of individual repeats. We compare these results to the unfolding behavior of the Notch ankyrin domain in the atomic force microscope obtained by our collaborators for this project. This offers some insight into the apparent difference in solution and AFM unfolding of ankyrin repeat proteins.
Book Synopsis Detection and Characterization of Partially Folded Forms on the Protein Energy Landscape by : Rachel Simma Bernstein
Download or read book Detection and Characterization of Partially Folded Forms on the Protein Energy Landscape written by Rachel Simma Bernstein and published by . This book was released on 2011 with total page 220 pages. Available in PDF, EPUB and Kindle. Book excerpt: Most proteins spend the majority of their time in their folded native state. Adopting this conformation, however, involves passing through various partially folded forms, including transition states and potentially kinetic intermediates. Furthermore, even under conditions favoring the folded conformation, a protein will take excursions away from the native state, populating partially and fully unfolded conformations. All of these states together constitute the protein energy landscape, and exploration of this complete landscape is crucial for a complete understanding of protein folding behavior, as well as potentially function. This work discusses a variety of methods applied to various model proteins, elucidating novel details about the folding landscapes. Kinetic investigations were conducted with both T4 lysozyme and E. coli ribonuclease H (RNase H). The lysozyme study revealed a "hidden" unfolding intermediate in addition to the previously characterized folding intermediate, resolving a long-standing discrepancy between kinetic and native-state hydrogen exchange experiments. The RNase H study, on the other hand, focused on the nature of the transition state. This protein is known to fold through an intermediate, which has been investigated by various methods, including kinetic hydrogen exchange and kinetic analysis; however, the post-intermediate transition state had not previously been thoroughly investigated. The results from the study in this thesis suggest that the protein traverses the rate-limiting transition state through a highly localized nucleation-condensation process involving part of the protein that is unfolded in the kinetic intermediate. E. coli RNase H was further investigated using a novel technique called native-state thiol alkyl-proton exchange (NSSX), a method analogous to native-state hydrogen exchange that takes advantage of the unique reactivity of cysteine to monitor exchange at the side chain, rather than the amide position of the backbone that is the target of hydrogen exchange experiments. Initial studies indicated that the wild-type protein was not amenable for these studies, but introduction of a stabilizing mutation allowed for investigation of the folding landscape under native conditions, with probes exposed on the folded and unfolded sides of the rate-limiting barrier exchanging in different kinetic regimes. This kinetic partitioning allowed for identification and characterization of novel partially folded species on the native side of the barrier and revealed structural and kinetic data for probes that are only exposed on unfolded side of the barrier. Interestingly, some of the probes involved in the rate-limiting nucleation step, as identified in the kinetic analysis, are also shown to be structured in the transition state by the NSSX experiments. These in vitro studies are complemented by in vivo translational misincorporation experiments with two pairs of homologous proteins. A library of mutant tRNAs was developed for NSSX to introduce cysteines in the place of a given amino acid during translation; however, it was found that E. coli RNase H was refractory to the misincorporation method. A highly similar protein from a thermophilic organism, Thermus thermophilus, on the other hand, shows robust misincorporation. Similarly, E. coli phosphoglycerate kinase (PGK) shows essentially no misincorporation, while yeast PGK misincorporates well. There is some in vitro evidence that those proteins that show significant misincorporate - T. thermophilus RNase H and yeast PGK - adopt partially folded conformations that are not accessible to their homologs. Therefore, it is plausible that misincorporation efficiency may report on the existence of partially folded forms in vivo; specifically, the absence of such conformations may result in degradation of the nascent chain on the ribosome, while adopting a protected conformation may allow for translation of the full-length misincorporated protein. While these results are preliminary and the hypothesis must be verified by further experiments, they provide an intriguing suggestion for a new in vivo probe of partially folded structure.
Book Synopsis Interactions in the Folding of Escherichia Coli RNase H by : Giulietta Marie Spudich
Download or read book Interactions in the Folding of Escherichia Coli RNase H written by Giulietta Marie Spudich and published by . This book was released on 2002 with total page 234 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Comprehensive Biophysics written by and published by Academic Press. This book was released on 2012-04-12 with total page 3533 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biophysics is a rapidly-evolving interdisciplinary science that applies theories and methods of the physical sciences to questions of biology. Biophysics encompasses many disciplines, including physics, chemistry, mathematics, biology, biochemistry, medicine, pharmacology, physiology, and neuroscience, and it is essential that scientists working in these varied fields are able to understand each other's research. Comprehensive Biophysics, Nine Volume Set will help bridge that communication gap. Written by a team of researchers at the forefront of their respective fields, under the guidance of Chief Editor Edward Egelman, Comprehensive Biophysics, Nine Volume Set provides definitive introductions to a broad array of topics, uniting different areas of biophysics research - from the physical techniques for studying macromolecular structure to protein folding, muscle and molecular motors, cell biophysics, bioenergetics and more. The result is this comprehensive scientific resource - a valuable tool both for helping researchers come to grips quickly with material from related biophysics fields outside their areas of expertise, and for reinforcing their existing knowledge. Biophysical research today encompasses many areas of biology. These studies do not necessarily share a unique identifying factor. This work unites the different areas of research and allows users, regardless of their background, to navigate through the most essential concepts with ease, saving them time and vastly improving their understanding The field of biophysics counts several journals that are directly and indirectly concerned with the field. There is no reference work that encompasses the entire field and unites the different areas of research through deep foundational reviews. Comprehensive Biophysics fills this vacuum, being a definitive work on biophysics. It will help users apply context to the diverse journal literature offering, and aid them in identifying areas for further research Chief Editor Edward Egelman (E-I-C, Biophysical Journal) has assembled an impressive, world-class team of Volume Editors and Contributing Authors. Each chapter has been painstakingly reviewed and checked for consistent high quality. The result is an authoritative overview which ties the literature together and provides the user with a reliable background information and citation resource
Book Synopsis Comparisons of the Thermodynamics and Foldings of Thermophilic and Mesophilic Ribonucleases H by : Julie Elizabeth Hollien
Download or read book Comparisons of the Thermodynamics and Foldings of Thermophilic and Mesophilic Ribonucleases H written by Julie Elizabeth Hollien and published by . This book was released on 2001 with total page 254 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Class 3.1 Hydrolases VI by : Dietmar Schomburg
Download or read book Class 3.1 Hydrolases VI written by Dietmar Schomburg and published by Springer Science & Business Media. This book was released on 2002-10-10 with total page 668 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Springer Handbook of Enzymes provides concise data on some 5,000 enzymes sufficiently well characterized – and here is the second, updated edition. Their application in analytical, synthetic and biotechnology processes as well as in food industry, and for medicinal treatments is added. Data sheets are arranged in their EC-Number sequence. The new edition reflects considerable progress in enzymology: the total material has more than doubled, and the complete 2nd edition consists of 39 volumes plus Synonym Index. Starting in 2009, all newly classified enzymes are treated in Supplement Volumes.
Book Synopsis Thermodynamic Characterization and Folding of a Moderately Thermophilic RNase H by : Kathleen Ratcliff
Download or read book Thermodynamic Characterization and Folding of a Moderately Thermophilic RNase H written by Kathleen Ratcliff and published by . This book was released on 2009 with total page 288 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis An Investigation of the Single Molecule Behavior of RNase H by : Elizabeth Anne Shank
Download or read book An Investigation of the Single Molecule Behavior of RNase H written by Elizabeth Anne Shank and published by . This book was released on 2004 with total page 460 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis The Role of Subdomains and Intermediates in the Folding and Unfolding of T4 Lysozyme by : Jason Frederick Cellitti
Download or read book The Role of Subdomains and Intermediates in the Folding and Unfolding of T4 Lysozyme written by Jason Frederick Cellitti and published by . This book was released on 2006 with total page 344 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Cumulated Index Medicus written by and published by . This book was released on 2000 with total page 1844 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Studies of the Mechanical Unfolding and Refolding of RNase H and T4 Lysozyme by : Ciro Cecconi
Download or read book Studies of the Mechanical Unfolding and Refolding of RNase H and T4 Lysozyme written by Ciro Cecconi and published by . This book was released on 2003 with total page 316 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Dissertation Abstracts International by :
Download or read book Dissertation Abstracts International written by and published by . This book was released on 2004 with total page 882 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Breaking Down the Protein Folding Problem by : Jonathan Marc Dabora
Download or read book Breaking Down the Protein Folding Problem written by Jonathan Marc Dabora and published by . This book was released on 1996 with total page 288 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Energy Research Abstracts written by and published by . This book was released on 1978 with total page 1510 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Ribonucleases H by : Robert J.. Crouch
Download or read book Ribonucleases H written by Robert J.. Crouch and published by . This book was released on 1998-01-01 with total page 265 pages. Available in PDF, EPUB and Kindle. Book excerpt: