Literature DB >> 18172203

Origins of barriers and barrierless folding in BBL.

Samuel S Cho1, Patrick Weinkam, Peter G Wolynes.   

Abstract

In contrast to classical chemical phenomenology, theory suggests that proteins may undergo downhill folding without an activation barrier under certain thermodynamic conditions. Recently, the BBL protein was proposed to fold by such a downhill scenario, but discrepancies between experimental results found in different groups argue against this. After briefly reviewing the major experimental studies of the BBL folding mechanism, we show that simulations of both coarse-grained and atomistic models can reconcile the seemingly conflicting observations.

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Year:  2008        PMID: 18172203      PMCID: PMC2224170          DOI: 10.1073/pnas.0709376104

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


  25 in total

1.  Folding at the speed limit.

Authors:  Wei Yuan Yang; Martin Gruebele
Journal:  Nature       Date:  2003-05-08       Impact factor: 49.962

Review 2.  Theory of protein folding.

Authors:  José Nelson Onuchic; Peter G Wolynes
Journal:  Curr Opin Struct Biol       Date:  2004-02       Impact factor: 6.809

Review 3.  The experimental survey of protein-folding energy landscapes.

Authors:  Mikael Oliveberg; Peter G Wolynes
Journal:  Q Rev Biophys       Date:  2006-06-19       Impact factor: 5.318

4.  Atom-by-atom analysis of global downhill protein folding.

Authors:  Mourad Sadqi; David Fushman; Victor Muñoz
Journal:  Nature       Date:  2006-06-14       Impact factor: 49.962

5.  Criteria for downhill protein folding: calorimetry, chevron plot, kinetic relaxation, and single-molecule radius of gyration in chain models with subdued degrees of cooperativity.

Authors:  Michael Knott; Hue Sun Chan
Journal:  Proteins       Date:  2006-11-01

6.  Folding with downhill behavior and low cooperativity of proteins.

Authors:  Guanghong Zuo; Jun Wang; Wei Wang
Journal:  Proteins       Date:  2006-04-01

7.  Tuning lambda6-85 towards downhill folding at its melting temperature.

Authors:  Feng Liu; Martin Gruebele
Journal:  J Mol Biol       Date:  2007-04-19       Impact factor: 5.469

8.  Protein folding kinetics: barrier effects in chemical and thermal denaturation experiments.

Authors:  Athi N Naganathan; Urmi Doshi; Victor Muñoz
Journal:  J Am Chem Soc       Date:  2007-04-10       Impact factor: 15.419

9.  Excluded volume, local structural cooperativity, and the polymer physics of protein folding rates.

Authors:  Xianghong Qi; John J Portman
Journal:  Proc Natl Acad Sci U S A       Date:  2007-06-14       Impact factor: 11.205

10.  Designed protein tetramer zipped together with a hydrophobic Alzheimer homology: a structural clue to amyloid assembly.

Authors:  D E Otzen; O Kristensen; M Oliveberg
Journal:  Proc Natl Acad Sci U S A       Date:  2000-08-29       Impact factor: 11.205

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  45 in total

1.  Single-molecule observation of helix staggering, sliding, and coiled coil misfolding.

Authors:  Zhiqun Xi; Ying Gao; George Sirinakis; Honglian Guo; Yongli Zhang
Journal:  Proc Natl Acad Sci U S A       Date:  2012-03-26       Impact factor: 11.205

2.  Folding without charges.

Authors:  Martin Kurnik; Linda Hedberg; Jens Danielsson; Mikael Oliveberg
Journal:  Proc Natl Acad Sci U S A       Date:  2012-03-27       Impact factor: 11.205

3.  The origin of nonmonotonic complex behavior and the effects of nonnative interactions on the diffusive properties of protein folding.

Authors:  Ronaldo J Oliveira; Paul C Whitford; Jorge Chahine; Jin Wang; José N Onuchic; Vitor B P Leite
Journal:  Biophys J       Date:  2010-07-21       Impact factor: 4.033

4.  Folding simulations of a de novo designed protein with a betaalphabeta fold.

Authors:  Yifei Qi; Yongqi Huang; Huanhuan Liang; Zhirong Liu; Luhua Lai
Journal:  Biophys J       Date:  2010-01-20       Impact factor: 4.033

5.  A natural missing link between activated and downhill protein folding scenarios.

Authors:  Feng Liu; Caroline Maynard; Gregory Scott; Artem Melnykov; Kathleen B Hall; Martin Gruebele
Journal:  Phys Chem Chem Phys       Date:  2010-02-11       Impact factor: 3.676

Review 6.  Molecular dynamics simulations of protein dynamics and their relevance to drug discovery.

Authors:  Freddie R Salsbury
Journal:  Curr Opin Pharmacol       Date:  2010-12       Impact factor: 5.547

7.  An experimental survey of the transition between two-state and downhill protein folding scenarios.

Authors:  Feng Liu; Deguo Du; Amelia A Fuller; Jennifer E Davoren; Peter Wipf; Jeffery W Kelly; Martin Gruebele
Journal:  Proc Natl Acad Sci U S A       Date:  2008-02-11       Impact factor: 11.205

8.  Exploiting the downhill folding regime via experiment.

Authors:  Victor Muñoz; Mourad Sadqi; Athi N Naganathan; David de Sancho
Journal:  HFSP J       Date:  2008-10-13

9.  Quantitative criteria for native energetic heterogeneity influences in the prediction of protein folding kinetics.

Authors:  Samuel S Cho; Yaakov Levy; Peter G Wolynes
Journal:  Proc Natl Acad Sci U S A       Date:  2008-12-15       Impact factor: 11.205

10.  The fast-folding HP35 double mutant has a substantially reduced primary folding free energy barrier.

Authors:  Hongxing Lei; Xiaojian Deng; Zhixiang Wang; Yong Duan
Journal:  J Chem Phys       Date:  2008-10-21       Impact factor: 3.488

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