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Title: Computational exploration of single-protein mechanics by steered molecular dynamics

Hair cell mechanotransduction happens in tens of microseconds, involves forces of a few picoNewtons, and is mediated by nanometer-scale molecular conformational changes. As proteins involved in this process become identified and their high resolution structures become available, multiple tools are being used to explore their “single-molecule responses” to force. Optical tweezers and atomic force microscopy offer exquisite force and extension resolution, but cannot reach the high loading rates expected for high frequency auditory stimuli. Molecular dynamics (MD) simulations can reach these fast time scales, and also provide a unique view of the molecular events underlying protein mechanics, but its predictions must be experimentally verified. Thus a combination of simulations and experiments might be appropriate to study the molecular mechanics of hearing. Here I review the basics of MD simulations and the different methods used to apply force and study protein mechanics in silico. Simulations of tip link proteins are used to illustrate the advantages and limitations of this method.
Authors:
 [1]
  1. Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio (United States)
Publication Date:
OSTI Identifier:
22494500
Resource Type:
Journal Article
Resource Relation:
Journal Name: AIP Conference Proceedings; Journal Volume: 1703; Journal Issue: 1; Conference: 12. international workshop on the mechanics of hearing, Cape Sounio (Greece), 23-29 Jun 2014; Other Information: (c) 2015 AIP Publishing LLC; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
United States
Language:
English
Subject:
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS; ATOMIC FORCE MICROSCOPY; CONFORMATIONAL CHANGES; HAIR; HEARINGS; MOLECULAR DYNAMICS METHOD; MOLECULES; PROTEINS; RESOLUTION; SIMULATION