The effect of box shape on the dynamic properties of proteins simulated under periodic boundary conditions

Wassenaar, T. A. and Mark, A. E. (2006) The effect of box shape on the dynamic properties of proteins simulated under periodic boundary conditions. Journal of Computational Chemistry, 27 3: 316-325. doi:10.1002/jcc.20341


Author Wassenaar, T. A.
Mark, A. E.
Title The effect of box shape on the dynamic properties of proteins simulated under periodic boundary conditions
Journal name Journal of Computational Chemistry   Check publisher's open access policy
ISSN 0192-8651
Publication date 2006-01-01
Sub-type Article (original research)
DOI 10.1002/jcc.20341
Volume 27
Issue 3
Start page 316
End page 325
Total pages 10
Place of publication Hoboken
Publisher John Wiley & Sons Inc
Collection year 2006
Subject C1
250699 Theoretical and Computational Chemistry not elsewhere classified
780103 Chemical sciences
Abstract The effect of the box shape on the dynamic behavior of proteins simulated under periodic boundary conditions is evaluated. In particular, the influence of simulation boxes defined by the near-densest lattice packing (NDLP) in conjunction with rotational constraints is compared to that of standard box types without these constraints. Three different proteins of varying size, shape, and secondary structure content were examined in the study. The statistical significance of differences in RMSD, radius of gyration, solvent-accessible surface, number of hydrogen bonds, and secondary structure content between proteins, box types, and the application or not of rotational constraints has been assessed. Furthermore, the differences in the collective modes for each protein between different boxes and the application or not of rotational constraints have been examined. In total 105 simulations were performed, and the results compared using a three-way multivariate analysis of variance (MANOVA) for properties derived from the trajectories and a three-way univariate analysis of variance (ANOVA) for collective modes. It is shown that application of roto-translational constraints does not have a statistically significant effect on the results obtained from the different simulations. However, the choice of simulation box was found to have a small (5-10%), but statistically significant effect on the behavior of two of the three proteins included in the study. (c) 2005 Wiley Periodicals, Inc.
Keyword Periodic Boundary Conditions
Near-densest Lattice Packing
Molecular Dynamics
Simulation
Manova
Chemistry, Multidisciplinary
Molecular-dynamics
N-alkanes
Constraints
Forms
Q-Index Code C1

 
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Created: Wed, 15 Aug 2007, 19:19:59 EST