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Phys Rev E. 2016 Jan;93(1):012417. doi: 10.1103/PhysRevE.93.012417. Epub 2016 Jan 28.

Nonuniform elastic properties of macromolecules and effect of prestrain on their continuum nature.

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Zienkiewicz Centre for Computational Engineering, Swansea University, Swansea SA1 8EN, United Kigdom.
Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269, USA.
Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109, USA.
Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, California 90095, USA.


Many experimental and theoretical methods have been developed to calculate the coarse-grained continuum elastic properties of macromolecules. However, all of those methods assume uniform elastic properties. Following the continuum mechanics framework, we present a systematic way of calculating the nonuniform effective elastic properties from atomic thermal fluctuations obtained from molecular dynamics simulation at any coarse-grained scale using a potential of the mean-force approach. We present the results for a mutant of Sesbania mosaic virus capsid, where we calculate the elastic moduli at different scales and observe an apparent problem with the chosen reference configuration in some cases. We present a possible explanation using an elastic network model, where inducing random prestrain results in a similar behavior. This phenomenon provides a novel insight into the continuum nature of macromolecules and defines the limits on details that the elasticity theory can capture. Further investigation into prestrains could elucidate important aspects of conformational dynamics of macromolecules.

[Indexed for MEDLINE]

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