Literature DB >> 23361200

Microsecond folding experiments and simulations: a match is made.

M B Prigozhin1, M Gruebele.   

Abstract

For the past two decades, protein folding experiments have been speeding up from the second or millisecond time scale to the microsecond time scale, and full-atom simulations have been extended from the nanosecond to the microsecond and even millisecond time scale. Where the two meet, it is now possible to compare results directly, allowing force fields to be validated and refined, and allowing experimental data to be interpreted in atomistic detail. In this perspective we compare recent experiments and simulations on the microsecond time scale, pointing out the progress that has been made in determining native structures from physics-based simulations, refining experiments and simulations to provide more quantitative underlying mechanisms, and tackling the problems of multiple reaction coordinates, downhill folding, and complex underlying structure of unfolded or misfolded states.

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Year:  2013        PMID: 23361200      PMCID: PMC3632410          DOI: 10.1039/c3cp43992e

Source DB:  PubMed          Journal:  Phys Chem Chem Phys        ISSN: 1463-9076            Impact factor:   3.676


  147 in total

Review 1.  Molecular dynamics simulations of biomolecules.

Authors:  Martin Karplus; J Andrew McCammon
Journal:  Nat Struct Biol       Date:  2002-09

2.  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

3.  Low barrier kinetics: dependence on observables and free energy surface.

Authors:  Hairong Ma; Martin Gruebele
Journal:  J Comput Chem       Date:  2006-01-30       Impact factor: 3.376

4.  Reaction coordinates and rates from transition paths.

Authors:  Robert B Best; Gerhard Hummer
Journal:  Proc Natl Acad Sci U S A       Date:  2005-04-06       Impact factor: 11.205

5.  Picosecond dynamics of a membrane protein revealed by 2D IR.

Authors:  Prabuddha Mukherjee; Itamar Kass; Isaiah T Arkin; Isaiah Arkin; Martin T Zanni
Journal:  Proc Natl Acad Sci U S A       Date:  2006-02-27       Impact factor: 11.205

6.  Solvent-tuning the collapse and helix formation time scales of lambda(6-85)*.

Authors:  Charles Dumont; Yoshitaka Matsumura; Seung Joong Kim; Jinsong Li; Elena Kondrashkina; Hiroshi Kihara; Martin Gruebele
Journal:  Protein Sci       Date:  2006-11       Impact factor: 6.725

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Authors:  H Frauenfelder; S G Sligar; P G Wolynes
Journal:  Science       Date:  1991-12-13       Impact factor: 47.728

8.  Local conformational dynamics in alpha-helices measured by fast triplet transfer.

Authors:  Beat Fierz; Andreas Reiner; Thomas Kiefhaber
Journal:  Proc Natl Acad Sci U S A       Date:  2009-01-08       Impact factor: 11.205

Review 9.  Biomolecular simulation: a computational microscope for molecular biology.

Authors:  Ron O Dror; Robert M Dirks; J P Grossman; Huafeng Xu; David E Shaw
Journal:  Annu Rev Biophys       Date:  2012       Impact factor: 12.981

10.  The transition state transit time of WW domain folding is controlled by energy landscape roughness.

Authors:  Feng Liu; Marcelo Nakaema; Martin Gruebele
Journal:  J Chem Phys       Date:  2009-11-21       Impact factor: 3.488

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  16 in total

1.  Perspective: Computer simulations of long time dynamics.

Authors:  Ron Elber
Journal:  J Chem Phys       Date:  2016-02-14       Impact factor: 3.488

2.  Probing the origins of two-state folding.

Authors:  Thomas J Lane; Christian R Schwantes; Kyle A Beauchamp; Vijay S Pande
Journal:  J Chem Phys       Date:  2013-10-14       Impact factor: 3.488

3.  Mapping fast protein folding with multiple-site fluorescent probes.

Authors:  Maxim B Prigozhin; Shu-Han Chao; Shahar Sukenik; Taras V Pogorelov; Martin Gruebele
Journal:  Proc Natl Acad Sci U S A       Date:  2015-06-15       Impact factor: 11.205

4.  A molecular interpretation of 2D IR protein folding experiments with Markov state models.

Authors:  Carlos R Baiz; Yu-Shan Lin; Chunte Sam Peng; Kyle A Beauchamp; Vincent A Voelz; Vijay S Pande; Andrei Tokmakoff
Journal:  Biophys J       Date:  2014-03-18       Impact factor: 4.033

5.  Fast pressure-jump all-atom simulations and experiments reveal site-specific protein dehydration-folding dynamics.

Authors:  Maxim B Prigozhin; Yi Zhang; Klaus Schulten; Martin Gruebele; Taras V Pogorelov
Journal:  Proc Natl Acad Sci U S A       Date:  2019-03-05       Impact factor: 11.205

6.  Ultrafast hydrogen exchange reveals specific structural events during the initial stages of folding of cytochrome c.

Authors:  Hossein Fazelinia; Ming Xu; Hong Cheng; Heinrich Roder
Journal:  J Am Chem Soc       Date:  2013-12-31       Impact factor: 15.419

7.  Fast single-molecule FRET spectroscopy: theory and experiment.

Authors:  Hoi Sung Chung; Irina V Gopich
Journal:  Phys Chem Chem Phys       Date:  2014-09-21       Impact factor: 3.676

Review 8.  Advances in free-energy-based simulations of protein folding and ligand binding.

Authors:  Alberto Perez; Joseph A Morrone; Carlos Simmerling; Ken A Dill
Journal:  Curr Opin Struct Biol       Date:  2016-01-07       Impact factor: 6.809

Review 9.  Fast-folding proteins under stress.

Authors:  Kapil Dave; Martin Gruebele
Journal:  Cell Mol Life Sci       Date:  2015-08-01       Impact factor: 9.261

10.  pH-Dependent cooperativity and existence of a dry molten globule in the folding of a miniprotein BBL.

Authors:  Zhi Yue; Jana Shen
Journal:  Phys Chem Chem Phys       Date:  2018-01-31       Impact factor: 3.676

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