Literature DB >> 21952221

Capturing the essence of folding and functions of biomolecules using coarse-grained models.

Changbong Hyeon1, D Thirumalai.   

Abstract

The distances over which biological molecules and their complexes can function range from a few nanometres, in the case of folded structures, to millimetres, for example, during chromosome organization. Describing phenomena that cover such diverse length, and also time, scales requires models that capture the underlying physics for the particular length scale of interest. Theoretical ideas, in particular, concepts from polymer physics, have guided the development of coarse-grained models to study folding of DNA, RNA and proteins. More recently, such models and their variants have been applied to the functions of biological nanomachines. Simulations using coarse-grained models are now poised to address a wide range of problems in biology.

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Year:  2011        PMID: 21952221     DOI: 10.1038/ncomms1481

Source DB:  PubMed          Journal:  Nat Commun        ISSN: 2041-1723            Impact factor:   14.919


  81 in total

1.  High resolution structure of the large ribosomal subunit from a mesophilic eubacterium.

Authors:  J Harms; F Schluenzen; R Zarivach; A Bashan; S Gat; I Agmon; H Bartels; F Franceschi; A Yonath
Journal:  Cell       Date:  2001-11-30       Impact factor: 41.582

Review 2.  Chaperonin-mediated protein folding.

Authors:  D Thirumalai; G H Lorimer
Journal:  Annu Rev Biophys Biomol Struct       Date:  2001

3.  Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways.

Authors:  Paul C Whitford; Peter Geggier; Roger B Altman; Scott C Blanchard; José N Onuchic; Karissa Y Sanbonmatsu
Journal:  RNA       Date:  2010-04-28       Impact factor: 4.942

4.  Promoter melting triggered by bacterial RNA polymerase occurs in three steps.

Authors:  Jie Chen; Seth A Darst; D Thirumalai
Journal:  Proc Natl Acad Sci U S A       Date:  2010-07-01       Impact factor: 11.205

Review 5.  RNA and protein folding: common themes and variations.

Authors:  D Thirumalai; Changbong Hyeon
Journal:  Biochemistry       Date:  2005-04-05       Impact factor: 3.162

Review 6.  Protein folding thermodynamics and dynamics: where physics, chemistry, and biology meet.

Authors:  Eugene Shakhnovich
Journal:  Chem Rev       Date:  2006-05       Impact factor: 60.622

7.  Mechanical control of the directional stepping dynamics of the kinesin motor.

Authors:  Changbong Hyeon; José N Onuchic
Journal:  Proc Natl Acad Sci U S A       Date:  2007-10-24       Impact factor: 11.205

Review 8.  The protein folding problem.

Authors:  Ken A Dill; S Banu Ozkan; M Scott Shell; Thomas R Weikl
Journal:  Annu Rev Biophys       Date:  2008       Impact factor: 12.981

Review 9.  Entropy as the driver of chromosome segregation.

Authors:  Suckjoon Jun; Andrew Wright
Journal:  Nat Rev Microbiol       Date:  2010-08       Impact factor: 60.633

10.  Multiscale simulations of protein landscapes: using coarse-grained models as reference potentials to full explicit models.

Authors:  Benjamin M Messer; Maite Roca; Zhen T Chu; Spyridon Vicatos; Alexandra Vardi Kilshtain; Arieh Warshel
Journal:  Proteins       Date:  2010-04
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  65 in total

1.  A structural perspective on the dynamics of kinesin motors.

Authors:  Changbong Hyeon; José N Onuchic
Journal:  Biophys J       Date:  2011-12-07       Impact factor: 4.033

2.  Denaturant-dependent folding of GFP.

Authors:  Govardhan Reddy; Zhenxing Liu; D Thirumalai
Journal:  Proc Natl Acad Sci U S A       Date:  2012-07-09       Impact factor: 11.205

3.  Communication over the network of binary switches regulates the activation of A2A adenosine receptor.

Authors:  Yoonji Lee; Sun Choi; Changbong Hyeon
Journal:  PLoS Comput Biol       Date:  2015-02-09       Impact factor: 4.475

4.  Simulating movement of tRNA through the ribosome during hybrid-state formation.

Authors:  Paul C Whitford; Karissa Y Sanbonmatsu
Journal:  J Chem Phys       Date:  2013-09-28       Impact factor: 3.488

5.  Denaturants Alter the Flux through Multiple Pathways in the Folding of PDZ Domain.

Authors:  Zhenxing Liu; D Thirumalai
Journal:  J Phys Chem B       Date:  2018-01-22       Impact factor: 2.991

6.  Capturing transition paths and transition states for conformational rearrangements in the ribosome.

Authors:  Jeffrey K Noel; Jorge Chahine; Vitor B P Leite; Paul Charles Whitford
Journal:  Biophys J       Date:  2014-12-16       Impact factor: 4.033

7.  Dissecting the role of the γ-subunit in the rotary-chemical coupling and torque generation of F1-ATPase.

Authors:  Shayantani Mukherjee; Arieh Warshel
Journal:  Proc Natl Acad Sci U S A       Date:  2015-02-17       Impact factor: 11.205

8.  Fast Protein Translation Can Promote Co- and Posttranslational Folding of Misfolding-Prone Proteins.

Authors:  Fabio Trovato; Edward P O'Brien
Journal:  Biophys J       Date:  2017-05-09       Impact factor: 4.033

9.  Kinematics of the lever arm swing in myosin VI.

Authors:  Mauro L Mugnai; D Thirumalai
Journal:  Proc Natl Acad Sci U S A       Date:  2017-05-16       Impact factor: 11.205

10.  Coarse-grained model for colloidal protein interactions, B(22), and protein cluster formation.

Authors:  Marco A Blanco; Erinc Sahin; Anne S Robinson; Christopher J Roberts
Journal:  J Phys Chem B       Date:  2013-12-10       Impact factor: 2.991

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