Literature DB >> 17161367

Stability and dynamics of virus capsids described by coarse-grained modeling.

Anton Arkhipov1, Peter L Freddolino, Klaus Schulten.   

Abstract

We report a study of the structural dynamics of viral capsids, simulated on a microsecond timescale, by employing a coarse-graining molecular dynamics method. The method was calibrated against an all-atom simulation of one complete virus. Among the studied capsids, some collapsed rapidly, while others were found to be stable. Interlocking between coat proteins is found to be a key factor determining the stability of the capsids.

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Year:  2006        PMID: 17161367     DOI: 10.1016/j.str.2006.10.003

Source DB:  PubMed          Journal:  Structure        ISSN: 0969-2126            Impact factor:   5.006


  76 in total

1.  Hierarchical Order Parameters for Macromolecular Assembly Simulations I: Construction and Dynamical Properties of Order Parameters.

Authors:  Abhishek Singharoy; Yuriy Sereda; Peter J Ortoleva
Journal:  J Chem Theory Comput       Date:  2012-03-13       Impact factor: 6.006

2.  Langevin dynamics simulation of polymer-assisted virus-like assembly.

Authors:  J P Mahalik; M Muthukumar
Journal:  J Chem Phys       Date:  2012-04-07       Impact factor: 3.488

3.  Squeezing protein shells: how continuum elastic models, molecular dynamics simulations, and experiments coalesce at the nanoscale.

Authors:  W H Roos; M M Gibbons; A Arkhipov; C Uetrecht; N R Watts; P T Wingfield; A C Steven; A J R Heck; K Schulten; W S Klug; G J L Wuite
Journal:  Biophys J       Date:  2010-08-09       Impact factor: 4.033

4.  Tabulation as a high-resolution alternative to coarse-graining protein interactions: Initial application to virus capsid subunits.

Authors:  Justin Spiriti; Daniel M Zuckerman
Journal:  J Chem Phys       Date:  2015-12-28       Impact factor: 3.488

5.  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

6.  Modeling Viral Capsid Assembly.

Authors:  Michael F Hagan
Journal:  Adv Chem Phys       Date:  2014       Impact factor: 1.000

7.  Improved siRNA delivery efficiency via solvent-induced condensation of micellar nanoparticles.

Authors:  Juan Wu; Wei Qu; John-Michael Williford; Yong Ren; Xuesong Jiang; Xuan Jiang; Deng Pan; Hai-Quan Mao; Erik Luijten
Journal:  Nanotechnology       Date:  2017-03-07       Impact factor: 3.874

8.  Vibrational dynamics of icosahedrally symmetric biomolecular assemblies compared with predictions based on continuum elasticity.

Authors:  Zheng Yang; Ivet Bahar; Michael Widom
Journal:  Biophys J       Date:  2009-06-03       Impact factor: 4.033

9.  Effects of the binding of calcium ions on the structure and dynamics of the ΦX174 virus investigated using molecular dynamics.

Authors:  Jason E Pina; Kuo Hao Lee; F Marty Ytreberg
Journal:  J Biol Phys       Date:  2012-01-21       Impact factor: 1.365

10.  PRIMO/PRIMONA: a coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy.

Authors:  Srinivasa M Gopal; Shayantani Mukherjee; Yi-Ming Cheng; Michael Feig
Journal:  Proteins       Date:  2010-04
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