Literature DB >> 16116080

A funneled energy landscape for cytochrome c directly predicts the sequential folding route inferred from hydrogen exchange experiments.

Patrick Weinkam1, Chenghang Zong, Peter G Wolynes.   

Abstract

Proteins fold through a variety of mechanisms. For a given protein, folding routes largely depend on the protein's stability and its native-state geometry, because the landscape is funneled. These ideas are corroborated for cytochrome c by using a coarse-grained topology-based model with a perfect funnel landscape that includes explicit modeling of the heme. The results show the importance of the heme as a nucleation site and explain the observed hydrogen exchange patterns of cytochrome c within the context of energy landscape theory.

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Year:  2005        PMID： 16116080      PMCID： PMC1194935          DOI： 10.1073/pnas.0505274102

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN： 0027-8424            Impact factor:   11.205


  35 in total

1.  A theoretical search for folding/unfolding nuclei in three-dimensional protein structures.

Authors:  O V Galzitskaya; A V Finkelstein
Journal:  Proc Natl Acad Sci U S A       Date:  1999-09-28       Impact factor: 11.205

2.  Exploring structures in protein folding funnels with free energy functionals: the transition state ensemble.

Authors:  B A Shoemaker; J Wang; P G Wolynes
Journal:  J Mol Biol       Date:  1999-04-02       Impact factor: 5.469

3.  Roles of native topology and chain-length scaling in protein folding: a simulation study with a Go-like model.

Authors:  N Koga; S Takada
Journal:  J Mol Biol       Date:  2001-10-12       Impact factor: 5.469

4.  Unifying features in protein-folding mechanisms.

Authors:  Stefano Gianni; Nicholas R Guydosh; Faaizah Khan; Teresa D Caldas; Ugo Mayor; George W N White; Mari L DeMarco; Valerie Daggett; Alan R Fersht
Journal:  Proc Natl Acad Sci U S A       Date:  2003-10-31       Impact factor: 11.205

5.  Scanning malleable transition state ensembles: comparing theory and experiment for folding protein U1A.

Authors:  Tongye Shen; Christoph P Hofmann; Mikael Oliveberg; Peter G Wolynes
Journal:  Biochemistry       Date:  2005-05-03       Impact factor: 3.162

6.  Toward protein tertiary structure recognition by means of associative memory hamiltonians.

Authors:  M S Friedrichs; P G Wolynes
Journal:  Science       Date:  1989-10-20       Impact factor: 47.728

7.  Protein folding mechanisms and the multidimensional folding funnel.

Authors:  N D Socci; J N Onuchic; P G Wolynes
Journal:  Proteins       Date:  1998-08-01

8.  On the origin of the cooperativity of protein folding: implications from model simulations.

Authors:  A Kolinski; W Galazka; J Skolnick
Journal:  Proteins       Date:  1996-11

9.  Protein folding intermediates: native-state hydrogen exchange.

Authors:  Y Bai; T R Sosnick; L Mayne; S W Englander
Journal:  Science       Date:  1995-07-14       Impact factor: 47.728

10.  Kinetics of cytochrome C folding: atomically detailed simulations.

Authors:  Alfredo E Cárdenas; Ron Elber
Journal:  Proteins       Date:  2003-05-01
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  48 in total

1.  Vaccinia virus virulence factor N1L is a novel promising target for antiviral therapeutic intervention.

Authors:  Anton V Cheltsov; Mika Aoyagi; Alexander Aleshin; Eric Chi-Wang Yu; Taylor Gilliland; Dayong Zhai; Andrey A Bobkov; John C Reed; Robert C Liddington; Ruben Abagyan
Journal:  J Med Chem       Date:  2010-05-27       Impact factor: 7.446

2.  Snapshots of cytochrome c folding.

Authors:  Ekaterina V Pletneva; Harry B Gray; Jay R Winkler
Journal:  Proc Natl Acad Sci U S A       Date:  2005-12-12       Impact factor: 11.205

3.  Flexibly varying folding mechanism of a nearly symmetrical protein: B domain of protein A.

Authors:  Kazuhito Itoh; Masaki Sasai
Journal:  Proc Natl Acad Sci U S A       Date:  2006-04-28       Impact factor: 11.205

4.  Site-specific collapse dynamics guide the formation of the cytochrome c' four-helix bundle.

Authors:  Tetsunari Kimura; Jennifer C Lee; Harry B Gray; Jay R Winkler
Journal:  Proc Natl Acad Sci U S A       Date:  2006-12-19       Impact factor: 11.205

Review 5.  A backbone-based theory of protein folding.

Authors:  George D Rose; Patrick J Fleming; Jayanth R Banavar; Amos Maritan
Journal:  Proc Natl Acad Sci U S A       Date:  2006-10-30       Impact factor: 11.205

6.  A unified mechanism for protein folding: predetermined pathways with optional errors.

Authors:  Mallela M G Krishna; S Walter Englander
Journal:  Protein Sci       Date:  2007-03       Impact factor: 6.725

7.  Mapping the structure of folding cores in TIM barrel proteins by hydrogen exchange mass spectrometry: the roles of motif and sequence for the indole-3-glycerol phosphate synthase from Sulfolobus solfataricus.

Authors:  Zhenyu Gu; Jill A Zitzewitz; C Robert Matthews
Journal:  J Mol Biol       Date:  2007-02-20       Impact factor: 5.469

8.  Branching in the sequential folding pathway of cytochrome c.

Authors:  Mallela M G Krishna; Haripada Maity; Jon N Rumbley; S Walter Englander
Journal:  Protein Sci       Date:  2007-07-27       Impact factor: 6.725

9.  Impact of mutations on the allosteric conformational equilibrium.

Authors:  Patrick Weinkam; Yao Chi Chen; Jaume Pons; Andrej Sali
Journal:  J Mol Biol       Date:  2012-12-07       Impact factor: 5.469

10.  The foldon substructure of staphylococcal nuclease.

Authors:  Sabrina Bédard; Leland C Mayne; Ronald W Peterson; A Joshua Wand; S Walter Englander
Journal:  J Mol Biol       Date:  2007-12-15       Impact factor: 5.469
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