Literature DB >> 21081274

Taming the complexity of protein folding.

Gregory R Bowman1, Vincent A Voelz, Vijay S Pande.   

Abstract

Protein folding is an important problem in structural biology with significant medical implications, particularly for misfolding disorders like Alzheimer's disease. Solving the folding problem will ultimately require a combination of theory and experiment, with theoretical models providing a comprehensive view of folding and experiments grounding these models in reality. Here we review progress towards this goal over the past decade, with an emphasis on recent theoretical advances that are empowering chemically detailed models of folding and the new results these technologies are providing. In particular, we discuss new insights made possible by Markov state models (MSMs), including the role of non-native contacts and the hub-like character of protein folded states.
Copyright © 2010 Elsevier Ltd. All rights reserved.

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Year:  2011        PMID: 21081274      PMCID: PMC3042729          DOI: 10.1016/j.sbi.2010.10.006

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  64 in total

1.  Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing.

Authors:  Vijay S Pande; Ian Baker; Jarrod Chapman; Sidney P Elmer; Siraj Khaliq; Stefan M Larson; Young Min Rhee; Michael R Shirts; Christopher D Snow; Eric J Sorin; Bojan Zagrovic
Journal:  Biopolymers       Date:  2003-01       Impact factor: 2.505

2.  Computing time scales from reaction coordinates by milestoning.

Authors:  Anton K Faradjian; Ron Elber
Journal:  J Chem Phys       Date:  2004-06-15       Impact factor: 3.488

3.  Exploring the helix-coil transition via all-atom equilibrium ensemble simulations.

Authors:  Eric J Sorin; Vijay S Pande
Journal:  Biophys J       Date:  2005-01-21       Impact factor: 4.033

4.  Heterogeneity even at the speed limit of folding: large-scale molecular dynamics study of a fast-folding variant of the villin headpiece.

Authors:  Daniel L Ensign; Peter M Kasson; Vijay S Pande
Journal:  J Mol Biol       Date:  2007-09-29       Impact factor: 5.469

5.  Coarse master equations for peptide folding dynamics.

Authors:  Nicolae-Viorel Buchete; Gerhard Hummer
Journal:  J Phys Chem B       Date:  2008-01-31       Impact factor: 2.991

6.  Folding of chymotrypsin inhibitor 2. 1. Evidence for a two-state transition.

Authors:  S E Jackson; A R Fersht
Journal:  Biochemistry       Date:  1991-10-29       Impact factor: 3.162

Review 7.  Intermediates in the folding reactions of small proteins.

Authors:  P S Kim; R L Baldwin
Journal:  Annu Rev Biochem       Date:  1990       Impact factor: 23.643

8.  Enhanced modeling via network theory: Adaptive sampling of Markov state models.

Authors:  Gregory R Bowman; Daniel L Ensign; Vijay S Pande
Journal:  J Chem Theory Comput       Date:  2010       Impact factor: 6.006

9.  Order of steps in the cytochrome C folding pathway: evidence for a sequential stabilization mechanism.

Authors:  Mallela M G Krishna; Haripada Maity; Jon N Rumbley; Yan Lin; S Walter Englander
Journal:  J Mol Biol       Date:  2006-05-02       Impact factor: 5.469

10.  The unfolded state of the C-terminal domain of the ribosomal protein L9 contains both native and non-native structure.

Authors:  Bing Shan; David Eliezer; Daniel P Raleigh
Journal:  Biochemistry       Date:  2009-06-09       Impact factor: 3.162

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  57 in total

1.  Sequence-dependent stability test of a left-handed β-helix motif.

Authors:  Natha R Hayre; Rajiv R P Singh; Daniel L Cox
Journal:  Biophys J       Date:  2012-03-20       Impact factor: 4.033

2.  Visualizing transient protein-folding intermediates by tryptophan-scanning mutagenesis.

Authors:  Alexis Vallée-Bélisle; Stephen W Michnick
Journal:  Nat Struct Mol Biol       Date:  2012-06-10       Impact factor: 15.369

3.  Mapping L1 ligase ribozyme conformational switch.

Authors:  George M Giambaşu; Tai-Sung Lee; William G Scott; Darrin M York
Journal:  J Mol Biol       Date:  2012-07-03       Impact factor: 5.469

4.  How long does it take to equilibrate the unfolded state of a protein?

Authors:  Ronald M Levy; Wei Dai; Nan-Jie Deng; Dmitrii E Makarov
Journal:  Protein Sci       Date:  2013-09-17       Impact factor: 6.725

5.  Comparing a simple theoretical model for protein folding with all-atom molecular dynamics simulations.

Authors:  Eric R Henry; Robert B Best; William A Eaton
Journal:  Proc Natl Acad Sci U S A       Date:  2013-10-15       Impact factor: 11.205

6.  Millisecond dynamics of RNA polymerase II translocation at atomic resolution.

Authors:  Daniel-Adriano Silva; Dahlia R Weiss; Fátima Pardo Avila; Lin-Tai Da; Michael Levitt; Dong Wang; Xuhui Huang
Journal:  Proc Natl Acad Sci U S A       Date:  2014-04-21       Impact factor: 11.205

7.  Intrinsic α-helical and β-sheet conformational preferences: a computational case study of alanine.

Authors:  Diego Caballero; Jukka Määttä; Alice Qinhua Zhou; Maria Sammalkorpi; Corey S O'Hern; Lynne Regan
Journal:  Protein Sci       Date:  2014-05-09       Impact factor: 6.725

8.  Extracting intrinsic dynamic parameters of biomolecular folding from single-molecule force spectroscopy experiments.

Authors:  Gi-Moon Nam; Dmitrii E Makarov
Journal:  Protein Sci       Date:  2015-07-14       Impact factor: 6.725

9.  Cooperative folding of a polytopic α-helical membrane protein involves a compact N-terminal nucleus and nonnative loops.

Authors:  Wojciech Paslawski; Ove K Lillelund; Julie Veje Kristensen; Nicholas P Schafer; Rosanna P Baker; Sinisa Urban; Daniel E Otzen
Journal:  Proc Natl Acad Sci U S A       Date:  2015-06-08       Impact factor: 11.205

10.  Competing Pathways and Multiple Folding Nuclei in a Large Multidomain Protein, Luciferase.

Authors:  Zackary N Scholl; Weitao Yang; Piotr E Marszalek
Journal:  Biophys J       Date:  2017-05-09       Impact factor: 4.033

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