Literature DB >> 16227442

Hairpin folding rates reflect mutations within and remote from the turn region.

Katherine A Olsen1, R Matthew Fesinmeyer, James M Stewart, Niels H Andersen.   

Abstract

Hairpins play a central role in numerous protein folding and misfolding scenarios. Prior studies of hairpin folding, many conducted with analogs of a sequence from the B1 domain of protein G, suggest that faster folding can be achieved only by optimizing the turn propensity of the reversing loop. Based on studies using dynamic NMR, the native GB1 sequence is a slow folding hairpin (k(F)(278)=1.5 x 10(4)/s). GB1 hairpin analogs spanning a wide range of thermodynamic stabilities (DeltaG(U)(298)=-3.09 to+3.25 kJ/mol) were examined. Fold-stabilizing changes in the reversing loop can act either by accelerating folding or retarding unfolding; we present examples of both types. The introduction of an attractive side-chain/side-chain Coulombic interaction at the chain termini further stabilizes this hairpin. The 1.9-fold increase in folding rate constant observed for this change at the chain termini implies that this Coulombic interaction contributes before or at the transition state. This observation is difficult to rationalize by "zipper" folding pathways that require native turn formation as the sole nucleating event; it also suggests that Coulombic interactions should be considered in the design of systems intended to probe the protein folding speed limit.

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Mesh:

Year:  2005        PMID: 16227442      PMCID: PMC1266093          DOI: 10.1073/pnas.0504392102

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


  31 in total

1.  Understanding beta-hairpin formation.

Authors:  A R Dinner; T Lazaridis; M Karplus
Journal:  Proc Natl Acad Sci U S A       Date:  1999-08-03       Impact factor: 11.205

2.  Molecular dynamics simulations of unfolding and refolding of a beta-hairpin fragment of protein G.

Authors:  V S Pande; D S Rokhsar
Journal:  Proc Natl Acad Sci U S A       Date:  1999-08-03       Impact factor: 11.205

3.  Accurate computer-based design of a new backbone conformation in the second turn of protein L.

Authors:  Brian Kuhlman; Jason W O'Neill; David E Kim; Kam Y J Zhang; David Baker
Journal:  J Mol Biol       Date:  2002-01-18       Impact factor: 5.469

4.  Computer-based redesign of a protein folding pathway.

Authors:  S Nauli; B Kuhlman; D Baker
Journal:  Nat Struct Biol       Date:  2001-07

Review 5.  Protein aggregation in disease: a role for folding intermediates forming specific multimeric interactions.

Authors:  Arthur Horwich
Journal:  J Clin Invest       Date:  2002-11       Impact factor: 14.808

6.  Nanosecond temperature jump relaxation dynamics of cyclic beta-hairpin peptides.

Authors:  Shelia J Maness; Stefan Franzen; Alan C Gibbs; Timothy P Causgrove; R Brian Dyer
Journal:  Biophys J       Date:  2003-06       Impact factor: 4.033

7.  Turn stability in beta-hairpin peptides: Investigation of peptides containing 3:5 type I G1 bulge turns.

Authors:  Tamas Blandl; Andrea G Cochran; Nicholas J Skelton
Journal:  Protein Sci       Date:  2003-02       Impact factor: 6.725

8.  Understanding the key factors that control the rate of beta-hairpin folding.

Authors:  Deguo Du; Yongjin Zhu; Cheng-Yen Huang; Feng Gai
Journal:  Proc Natl Acad Sci U S A       Date:  2004-11-01       Impact factor: 11.205

9.  Extending the folding nucleus of ubiquitin with an independently folding beta-hairpin finger: hurdles to rapid folding arising from the stabilisation of local interactions.

Authors:  Roger Bofill; Emma R Simpson; Geoffrey W Platt; Maria D Crespo; Mark S Searle
Journal:  J Mol Biol       Date:  2005-04-07       Impact factor: 5.469

Review 10.  Protein aggregation: folding aggregates, inclusion bodies and amyloid.

Authors:  A L Fink
Journal:  Fold Des       Date:  1998
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  30 in total

1.  Stabilizing capping motif for beta-hairpins and sheets.

Authors:  Brandon L Kier; Irene Shu; Lisa A Eidenschink; Niels H Andersen
Journal:  Proc Natl Acad Sci U S A       Date:  2010-05-19       Impact factor: 11.205

2.  Transient β-hairpin formation in α-synuclein monomer revealed by coarse-grained molecular dynamics simulation.

Authors:  Hang Yu; Wei Han; Wen Ma; Klaus Schulten
Journal:  J Chem Phys       Date:  2015-12-28       Impact factor: 3.488

3.  PRIMO: A Transferable Coarse-grained Force Field for Proteins.

Authors:  Parimal Kar; Srinivasa Murthy Gopal; Yi-Ming Cheng; Alexander Predeus; Michael Feig
Journal:  J Chem Theory Comput       Date:  2013-08-13       Impact factor: 6.006

4.  13C structuring shifts for the analysis of model β-hairpins and β-sheets in proteins: diagnostic shifts appear only at the cross-strand H-bonded residues.

Authors:  Irene Shu; Michele Scian; James M Stewart; Brandon L Kier; Niels H Andersen
Journal:  J Biomol NMR       Date:  2013-07-14       Impact factor: 2.835

5.  Microscopic events in β-hairpin folding from alternative unfolded ensembles.

Authors:  Robert B Best; Jeetain Mittal
Journal:  Proc Natl Acad Sci U S A       Date:  2011-06-20       Impact factor: 11.205

6.  Solution state structures of human pancreatic amylin and pramlintide.

Authors:  John R Cort; Zhihong Liu; Gregory M Lee; K N L Huggins; Susan Janes; Kathryn Prickett; Niels H Andersen
Journal:  Protein Eng Des Sel       Date:  2009-07-12       Impact factor: 1.650

7.  Optimization of a β-sheet-cap for long loop closure.

Authors:  Jordan M Anderson; Alexander A Shcherbakov; Brandon L Kier; Jackson Kellock; Irene Shu; Aimee L Byrne; Lisa A Eidenschink; Niels H Andersen
Journal:  Biopolymers       Date:  2017-03       Impact factor: 2.505

8.  The Trp-cage: optimizing the stability of a globular miniprotein.

Authors:  Bipasha Barua; Jasper C Lin; Victoria D Williams; Phillip Kummler; Jonathan W Neidigh; Niels H Andersen
Journal:  Protein Eng Des Sel       Date:  2008-01-18       Impact factor: 1.650

9.  Mutational effects on the folding dynamics of a minimized hairpin.

Authors:  Michele Scian; Irene Shu; Katherine A Olsen; Khalil Hassam; Niels H Andersen
Journal:  Biochemistry       Date:  2013-04-05       Impact factor: 3.162

10.  Protein GB1 folding and assembly from structural elements.

Authors:  Mikael C Bauer; Wei-Feng Xue; Sara Linse
Journal:  Int J Mol Sci       Date:  2009-04-08       Impact factor: 6.208

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