Literature DB >> 27166801

Meandering Down the Energy Landscape of Protein Folding: Are We There Yet?

Rachel M Abaskharon1, Feng Gai2.   

Abstract

As judged by a single publication metric, the activity in the protein folding field has been declining over the past 5 years, after enjoying a decade-long growth. Does this development indicate that the field is sunsetting or is this decline only temporary? Upon surveying a small territory of its landscape, we find that the protein folding field is still quite active and many important findings have emerged from recent experimental studies. However, it is also clear that only continued development of new techniques and methods, especially those enabling dissection of the fine details and features of the protein folding energy landscape, will fuel this old field to move forward.
Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Mesh:

Year:  2016        PMID: 27166801      PMCID: PMC4940508          DOI: 10.1016/j.bpj.2016.03.030

Source DB:  PubMed          Journal:  Biophys J        ISSN: 0006-3495            Impact factor:   4.033


  84 in total

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Authors:  Eilon Sherman; Gilad Haran
Journal:  Chemphyschem       Date:  2011-01-26       Impact factor: 3.102

2.  Alpha-helix formation in a photoswitchable peptide tracked from picoseconds to microseconds by time-resolved IR spectroscopy.

Authors:  Jens Bredenbeck; Jan Helbing; Janet R Kumita; G Andrew Woolley; Peter Hamm
Journal:  Proc Natl Acad Sci U S A       Date:  2005-02-07       Impact factor: 11.205

3.  Transient two-dimensional IR spectrometer for probing nanosecond temperature-jump kinetics.

Authors:  Hoi Sung Chung; Munira Khalil; Adam W Smith; Andrei Tokmakoff
Journal:  Rev Sci Instrum       Date:  2007-06       Impact factor: 1.523

Review 4.  Biomolecular simulation: a computational microscope for molecular biology.

Authors:  Ron O Dror; Robert M Dirks; J P Grossman; Huafeng Xu; David E Shaw
Journal:  Annu Rev Biophys       Date:  2012       Impact factor: 12.981

5.  Single-molecule fluorescence experiments determine protein folding transition path times.

Authors:  Hoi Sung Chung; Kevin McHale; John M Louis; William A Eaton
Journal:  Science       Date:  2012-02-24       Impact factor: 47.728

6.  Protein hydrogen exchange at residue resolution by proteolytic fragmentation mass spectrometry analysis.

Authors:  Zhong-Yuan Kan; Benjamin T Walters; Leland Mayne; S Walter Englander
Journal:  Proc Natl Acad Sci U S A       Date:  2013-09-09       Impact factor: 11.205

7.  Differential ordering of the protein backbone and side chains during protein folding revealed by site-specific recombinant infrared probes.

Authors:  Sureshbabu Nagarajan; Humeyra Taskent-Sezgin; Dzmitry Parul; Isaac Carrico; Daniel P Raleigh; R Brian Dyer
Journal:  J Am Chem Soc       Date:  2011-11-28       Impact factor: 15.419

Review 8.  Everything you wanted to know about Markov State Models but were afraid to ask.

Authors:  Vijay S Pande; Kyle Beauchamp; Gregory R Bowman
Journal:  Methods       Date:  2010-06-04       Impact factor: 3.608

9.  Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles.

Authors:  Robert B Best; Xiao Zhu; Jihyun Shim; Pedro E M Lopes; Jeetain Mittal; Michael Feig; Alexander D Mackerell
Journal:  J Chem Theory Comput       Date:  2012-07-18       Impact factor: 6.006

10.  Single-molecule chemo-mechanical unfolding reveals multiple transition state barriers in a small single-domain protein.

Authors:  Emily J Guinn; Bharat Jagannathan; Susan Marqusee
Journal:  Nat Commun       Date:  2015-04-17       Impact factor: 14.919

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  5 in total

1.  The case for defined protein folding pathways.

Authors:  S Walter Englander; Leland Mayne
Journal:  Proc Natl Acad Sci U S A       Date:  2017-06-19       Impact factor: 11.205

Review 2.  Hypothesis: structural heterogeneity of the unfolded proteins originating from the coupling of the local clusters and the long-range distance distribution.

Authors:  Satoshi Takahashi; Aya Yoshida; Hiroyuki Oikawa
Journal:  Biophys Rev       Date:  2018-02-14

Review 3.  Unraveling co-translational protein folding: Concepts and methods.

Authors:  Anton A Komar
Journal:  Methods       Date:  2017-12-06       Impact factor: 3.608

4.  Microscopic nucleation and propagation rates of an alanine-based α-helix.

Authors:  Chun-Wei Lin; Feng Gai
Journal:  Phys Chem Chem Phys       Date:  2017-02-15       Impact factor: 3.676

5.  Transition path times of coupled folding and binding reveal the formation of an encounter complex.

Authors:  Flurin Sturzenegger; Franziska Zosel; Erik D Holmstrom; Karin J Buholzer; Dmitrii E Makarov; Daniel Nettels; Benjamin Schuler
Journal:  Nat Commun       Date:  2018-11-09       Impact factor: 14.919

  5 in total

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