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On Hydrogen Bonds and Mobility of Protein Molecules

[+] Author Affiliations
Zahra Shahbazi, Horea T. Ilieş, Kazem Kazerounian

University of Connecticut, Storrs, CT

Paper No. DETC2009-87470, pp. 1123-1137; 15 pages
doi:10.1115/DETC2009-87470
From:
  • ASME 2009 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference
  • Volume 7: 33rd Mechanisms and Robotics Conference, Parts A and B
  • San Diego, California, USA, August 30–September 2, 2009
  • Conference Sponsors: Design Engineering Division and Computers in Engineering Division
  • ISBN: 978-0-7918-4904-0 | eISBN: 978-0-7918-3856-3
  • Copyright © 2009 by ASME

abstract

Modeling protein molecules as kinematic chains provides the foundation for developing powerful approaches to the design, manipulation and fabrication of peptide based molecules and devices. Nevertheless, these models possess a high number of degrees of freedom (DOF) with considerable computational implications. On the other hand, real protein molecules appear to exhibits a much lower mobility during the folding process than what is suggested by existing kinematic models. The key contributor to the lower mobility of real proteins is the formation of Hydrogen bonds during the folding process. In this paper we explore the pivotal role of Hydrogen bonds in determining the structure and function of the proteins from the point of view of mechanical mobility. The existing geometric criteria on the formation of Hydrogen bonds are reviewed and a new set of geometric criteria are proposed. We show that the new criteria better correlate the number of predicted Hydrogen bonds with those established by biological principles than other existing criteria. Furthermore, we employ established tools in kinematics mobility analysis to evaluate the internal mobility of protein molecules, and to identify the rigid and flexible segments of the proteins. Our results show that the developed procedure significantly reduces the DOF of the protein models, with an average reduction of 94%. Such a dramatic reduction in the number of DOF can have has enormous computational implications in protein folding simulations.

Copyright © 2009 by ASME

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