Literature DB >> 22873643

Raising the speed limit for β-hairpin formation.

Caitlin M Davis1, Shifeng Xiao, Daniel P Raleigh, R Brian Dyer.   

Abstract

Understanding the folding of the β-hairpin is a crucial step in studying how β-rich proteins fold. We have studied CLN025, an optimized ten residue synthetic peptide, which adopts a compact, well-structured β-hairpin conformation. Formation of the component β-sheet and β-turn structures of CLN025 was probed independently using a combination of equilibrium Fourier transform infrared spectroscopy and laser-induced temperature jump coupled with time-resolved infrared and fluorescence spectroscopies. We find that CLN025 is an ultrafast folder due to its small free energy barrier to folding and that it exceeds the predicted speed limit for β-hairpin formation by an order of magnitude. We also find that the folding mechanism cannot be described by a simple two-state model, but rather is a heterogeneous process involving two independent parallel processes. Formation of stabilizing cross-strand hydrophobic interactions and turn alignment occur competitively, with relaxation lifetimes of 82 ± 10 and 124 ± 10 ns, respectively, at the highest probed temperature. The ultrafast and heterogeneous folding kinetics observed for CLN025 provide evidence for folding on a nearly barrierless free energy landscape, and recalibrate the speed limit for the formation of a β-hairpin.

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Year:  2012        PMID: 22873643      PMCID: PMC3443077          DOI: 10.1021/ja3046734

Source DB:  PubMed          Journal:  J Am Chem Soc        ISSN: 0002-7863            Impact factor:   15.419


  30 in total

1.  Mechanisms and kinetics of beta-hairpin formation.

Authors:  D K Klimov; D Thirumalai
Journal:  Proc Natl Acad Sci U S A       Date:  2000-03-14       Impact factor: 11.205

2.  Thermodynamics of a beta-hairpin structure: evidence for cooperative formation of folding nucleus.

Authors:  S Honda; N Kobayashi; E Munekata
Journal:  J Mol Biol       Date:  2000-01-14       Impact factor: 5.469

3.  How fast-folding proteins fold.

Authors:  Kresten Lindorff-Larsen; Stefano Piana; Ron O Dror; David E Shaw
Journal:  Science       Date:  2011-10-28       Impact factor: 47.728

Review 4.  Ultrafast and downhill protein folding.

Authors:  R Brian Dyer
Journal:  Curr Opin Struct Biol       Date:  2007-01-12       Impact factor: 6.809

5.  Folding dynamics of 10-residue beta-hairpin peptide chignolin.

Authors:  Atsushi Suenaga; Tetsu Narumi; Noriyuki Futatsugi; Ryoko Yanai; Yousuke Ohno; Noriaki Okimoto; Makoto Taiji
Journal:  Chem Asian J       Date:  2007-05-04

6.  Crystal structure of a ten-amino acid protein.

Authors:  Shinya Honda; Toshihiko Akiba; Yusuke S Kato; Yoshito Sawada; Masakazu Sekijima; Miyuki Ishimura; Ayako Ooishi; Hideki Watanabe; Takayuki Odahara; Kazuaki Harata
Journal:  J Am Chem Soc       Date:  2008-10-25       Impact factor: 15.419

7.  Transform and relax sampling for highly anisotropic systems: application to protein domain motion and folding.

Authors:  Akio Kitao
Journal:  J Chem Phys       Date:  2011-07-28       Impact factor: 3.488

8.  Exploring the folding free energy landscape of a β-hairpin miniprotein, chignolin, using multiscale free energy landscape calculation method.

Authors:  Ryuhei Harada; Akio Kitao
Journal:  J Phys Chem B       Date:  2011-06-22       Impact factor: 2.991

9.  Folding dynamics and mechanism of beta-hairpin formation.

Authors:  V Muñoz; P A Thompson; J Hofrichter; W A Eaton
Journal:  Nature       Date:  1997-11-13       Impact factor: 49.962

10.  Development and validation of transferable amide I vibrational frequency maps for peptides.

Authors:  L Wang; C T Middleton; M T Zanni; J L Skinner
Journal:  J Phys Chem B       Date:  2011-03-15       Impact factor: 2.991

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  15 in total

1.  Tracing primordial protein evolution through structurally guided stepwise segment elongation.

Authors:  Hideki Watanabe; Kazuhiko Yamasaki; Shinya Honda
Journal:  J Biol Chem       Date:  2013-12-19       Impact factor: 5.157

2.  Influence of Glu/Arg, Asp/Arg, and Glu/Lys Salt Bridges on α-Helical Stability and Folding Kinetics.

Authors:  Heleen Meuzelaar; Jocelyne Vreede; Sander Woutersen
Journal:  Biophys J       Date:  2016-06-07       Impact factor: 4.033

3.  Modeling the mechanism of CLN025 beta-hairpin formation.

Authors:  Keri A McKiernan; Brooke E Husic; Vijay S Pande
Journal:  J Chem Phys       Date:  2017-09-14       Impact factor: 3.488

4.  Dynamics of an ultrafast folding subdomain in the context of a larger protein fold.

Authors:  Caitlin M Davis; R Brian Dyer
Journal:  J Am Chem Soc       Date:  2013-12-13       Impact factor: 15.419

5.  Early turn formation and chain collapse drive fast folding of the major cold shock protein CspA of Escherichia coli.

Authors:  Dung M Vu; Scott H Brewer; R Brian Dyer
Journal:  Biochemistry       Date:  2012-11-01       Impact factor: 3.162

6.  ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB.

Authors:  James A Maier; Carmenza Martinez; Koushik Kasavajhala; Lauren Wickstrom; Kevin E Hauser; Carlos Simmerling
Journal:  J Chem Theory Comput       Date:  2015-07-23       Impact factor: 6.006

7.  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

8.  Microsecond folding experiments and simulations: a match is made.

Authors:  M B Prigozhin; M Gruebele
Journal:  Phys Chem Chem Phys       Date:  2013-01-29       Impact factor: 3.676

Review 9.  Fast protein folding kinetics.

Authors:  Hannah Gelman; Martin Gruebele
Journal:  Q Rev Biophys       Date:  2014-03-18       Impact factor: 5.318

10.  How quickly can a β-hairpin fold from its transition state?

Authors:  Beatrice N Markiewicz; Lijiang Yang; Robert M Culik; Yi Qin Gao; Feng Gai
Journal:  J Phys Chem B       Date:  2014-03-17       Impact factor: 2.991

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