Literature DB >> 15869383

How well can simulation predict protein folding kinetics and thermodynamics?

Christopher D Snow1, Eric J Sorin, Young Min Rhee, Vijay S Pande.   

Abstract

Simulation of protein folding has come a long way in five years. Notably, new quantitative comparisons with experiments for small, rapidly folding proteins have become possible. As the only way to validate simulation methodology, this achievement marks a significant advance. Here, we detail these recent achievements and ask whether simulations have indeed rendered quantitative predictions in several areas, including protein folding kinetics, thermodynamics, and physics-based methods for structure prediction. We conclude by looking to the future of such comparisons between simulations and experiments.

Mesh:

Substances:

Year:  2005        PMID: 15869383     DOI: 10.1146/annurev.biophys.34.040204.144447

Source DB:  PubMed          Journal:  Annu Rev Biophys Biomol Struct        ISSN: 1056-8700


  64 in total

1.  Structure and stability of the lamin A tail domain and HGPS mutant.

Authors:  Zhao Qin; Agnieszka Kalinowski; Kris Noel Dahl; Markus J Buehler
Journal:  J Struct Biol       Date:  2011-05-24       Impact factor: 2.867

2.  Dominant folding pathways of a WW domain.

Authors:  Silvio A Beccara; Tatjana Škrbić; Roberto Covino; Pietro Faccioli
Journal:  Proc Natl Acad Sci U S A       Date:  2012-01-26       Impact factor: 11.205

3.  The folding transition-state ensemble of a four-helix bundle protein: helix propensity as a determinant and macromolecular crowding as a probe.

Authors:  Harianto Tjong; Huan-Xiang Zhou
Journal:  Biophys J       Date:  2010-05-19       Impact factor: 4.033

4.  Modeling the self-assembly of the cellulosome enzyme complex.

Authors:  Yannick J Bomble; Gregg T Beckham; James F Matthews; Mark R Nimlos; Michael E Himmel; Michael F Crowley
Journal:  J Biol Chem       Date:  2010-11-22       Impact factor: 5.157

5.  An information theoretic approach to macromolecular modeling: II. Force fields.

Authors:  Tiba Aynechi; Irwin D Kuntz
Journal:  Biophys J       Date:  2005-11       Impact factor: 4.033

6.  Kinetic definition of protein folding transition state ensembles and reaction coordinates.

Authors:  Christopher D Snow; Young Min Rhee; Vijay S Pande
Journal:  Biophys J       Date:  2006-04-14       Impact factor: 4.033

7.  Similarity and difference in the unfolding of thermophilic and mesophilic cold shock proteins studied by molecular dynamics simulations.

Authors:  Xiaoqin Huang; Huan-Xiang Zhou
Journal:  Biophys J       Date:  2006-07-14       Impact factor: 4.033

8.  P versus Q: structural reaction coordinates capture protein folding on smooth landscapes.

Authors:  Samuel S Cho; Yaakov Levy; Peter G Wolynes
Journal:  Proc Natl Acad Sci U S A       Date:  2006-01-09       Impact factor: 11.205

9.  A finite element framework for studying the mechanical response of macromolecules: application to the gating of the mechanosensitive channel MscL.

Authors:  Yuye Tang; Guoxin Cao; Xi Chen; Jejoong Yoo; Arun Yethiraj; Qiang Cui
Journal:  Biophys J       Date:  2006-05-26       Impact factor: 4.033

10.  Speed of conformational change: comparing explicit and implicit solvent molecular dynamics simulations.

Authors:  Ramu Anandakrishnan; Aleksander Drozdetski; Ross C Walker; Alexey V Onufriev
Journal:  Biophys J       Date:  2015-03-10       Impact factor: 4.033

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.