Literature DB >> 12876329

Fast protein folding on downhill energy landscape.

Andrea Cavalli1, Urs Haberthür, Emanuele Paci, Amedeo Caflisch.   

Abstract

Proteins fold in a time range of microseconds to minutes despite the large amount of possible conformers. Molecular dynamics simulations of a three-stranded antiparallel beta-sheet peptide (for a total of 12.6 microsec and 72 folding events) show that at the melting temperature the unfolded state ensemble contains many more conformers than those sampled during a folding event.

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Year:  2003        PMID： 12876329      PMCID： PMC2323966          DOI： 10.1110/ps.0366103

Source DB:  PubMed          Journal:  Protein Sci        ISSN： 0961-8368            Impact factor:   6.725


  18 in total

Review 1.  From folding theories to folding proteins: a review and assessment of simulation studies of protein folding and unfolding.

Authors:  J E Shea; C L Brooks
Journal:  Annu Rev Phys Chem       Date:  2001       Impact factor: 12.703

2.  The Key to Solving the Protein-Folding Problem Lies in an Accurate Description of the Denatured State Financial support from the Schweizerischer Nationalfonds (Project no. 21-50929.97) is gratefully acknowledged.

Authors:  Wilfred F. van Gunsteren; Roland Bürgi; Christine Peter; Xavier Daura
Journal:  Angew Chem Int Ed Engl       Date:  2001-01-19       Impact factor: 15.336

Review 3.  Fast kinetics and mechanisms in protein folding.

Authors:  W A Eaton; V Muñoz; S J Hagen; G S Jas; L J Lapidus; E R Henry; J Hofrichter
Journal:  Annu Rev Biophys Biomol Struct       Date:  2000

Review 4.  Understanding protein folding via free-energy surfaces from theory and experiment.

Authors:  A R Dinner; A Sali; L J Smith; C M Dobson; M Karplus
Journal:  Trends Biochem Sci       Date:  2000-07       Impact factor: 13.807

5.  Evaluation of a fast implicit solvent model for molecular dynamics simulations.

Authors:  Philippe Ferrara; Joannis Apostolakis; Amedeo Caflisch
Journal:  Proteins       Date:  2002-01-01

6.  Molecular dynamics simulations of protein folding from the transition state.

Authors:  Jörg Gsponer; Amedeo Caflisch
Journal:  Proc Natl Acad Sci U S A       Date:  2002-04-30       Impact factor: 11.205

7.  Comment on the Communication "The Key to Solving the Protein-Folding Problem Lies in an Accurate Description of the Denatured State" by van Gunsteren et al. We thank Eugene Shakhnovich (Harvard University) for pointing out the references on lattice polymer simulations and very helpful discussions. We also thank Wilfred van Gunsteren for comments on the manuscript. A.R.D. is a Burroughs Wellcome Fund Hitchings-Elion Postdoctoral Fellow. The work done at Harvard was supported in part by the National Institutes of Health.

Authors:  Aaron R. Dinner; Martin Karplus
Journal:  Angew Chem Int Ed Engl       Date:  2001-12-17       Impact factor: 15.336

8.  Reply.

Authors:  Wilfred F. Van Gunsteren; Roland Bürgi; Christine Peter; Xavier Daura
Journal:  Angew Chem Int Ed Engl       Date:  2001-12-17       Impact factor: 15.336

9.  Protein folding funnels: a kinetic approach to the sequence-structure relationship.

Authors:  P E Leopold; M Montal; J N Onuchic
Journal:  Proc Natl Acad Sci U S A       Date:  1992-09-15       Impact factor: 11.205

Review 10.  From Levinthal to pathways to funnels.

Authors:  K A Dill; H S Chan
Journal:  Nat Struct Biol       Date:  1997-01
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  10 in total

1.  Formation of the folding nucleus of an SH3 domain investigated by loosely coupled molecular dynamics simulations.

Authors:  G Settanni; J Gsponer; A Caflisch
Journal:  Biophys J       Date:  2004-03       Impact factor: 4.033

2.  Comparison of sequence-based and structure-based energy functions for the reversible folding of a peptide.

Authors:  Andrea Cavalli; Michele Vendruscolo; Emanuele Paci
Journal:  Biophys J       Date:  2005-03-04       Impact factor: 4.033

3.  Barrier-limited, microsecond folding of a stable protein measured with hydrogen exchange: Implications for downhill folding.

Authors:  W Kevin Meisner; Tobin R Sosnick
Journal:  Proc Natl Acad Sci U S A       Date:  2004-10-25       Impact factor: 11.205

Review 4.  CHARMM: the biomolecular simulation program.

Authors:  B R Brooks; C L Brooks; A D Mackerell; L Nilsson; R J Petrella; B Roux; Y Won; G Archontis; C Bartels; S Boresch; A Caflisch; L Caves; Q Cui; A R Dinner; M Feig; S Fischer; J Gao; M Hodoscek; W Im; K Kuczera; T Lazaridis; J Ma; V Ovchinnikov; E Paci; R W Pastor; C B Post; J Z Pu; M Schaefer; B Tidor; R M Venable; H L Woodcock; X Wu; W Yang; D M York; M Karplus
Journal:  J Comput Chem       Date:  2009-07-30       Impact factor: 3.376

5.  Behind the folding funnel diagram.

Authors:  Martin Karplus
Journal:  Nat Chem Biol       Date:  2011-06-17       Impact factor: 15.040

6.  Crowding effects on the small, fast-folding protein lambda6-85.

Authors:  Sharlene Denos; Apratim Dhar; Martin Gruebele
Journal:  Faraday Discuss       Date:  2012       Impact factor: 4.008

7.  Probing the folding of mini-protein Beta3s by two-dimensional infrared spectroscopy; simulation study.

Authors:  Christopher Nj Marai; Shaul Mukamel; Jin Wang
Journal:  PMC Biophys       Date:  2010-03-19

8.  Combination of Markov state models and kinetic networks for the analysis of molecular dynamics simulations of peptide folding.

Authors:  Isolde H Radford; Alan R Fersht; Giovanni Settanni
Journal:  J Phys Chem B       Date:  2011-05-09       Impact factor: 2.991

9.  Downhill, Ultrafast and Fast Folding Proteins Revised.

Authors:  Mateusz Banach; Katarzyna Stapor; Leszek Konieczny; Piotr Fabian; Irena Roterman
Journal:  Int J Mol Sci       Date:  2020-10-15       Impact factor: 5.923

10.  Conformational transitions and glycation of serum albumin in patients with minimal-change glomerulopathy.

Authors:  Sae Yong Hong; Eun Young Lee; Jong Oh Yang; Tae Yeong Kim; Eun Hee Kim; Mi Young Cheong; Soo Hyun Kim; Chae Joon Cheong
Journal:  Korean J Intern Med       Date:  2004-09       Impact factor: 2.884
  10 in total

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