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Kinematic Motion Constraints of the Protein Molecule Chains

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

University of Connecticut, Storrs, CT

Paper No. DETC2011-48519, pp. 535-542; 8 pages
doi:10.1115/DETC2011-48519
From:
  • ASME 2011 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference
  • Volume 6: 35th Mechanisms and Robotics Conference, Parts A and B
  • Washington, DC, USA, August 28–31, 2011
  • Conference Sponsors: Design Engineering Division and Computers and Information in Engineering Division
  • ISBN: 978-0-7918-5483-9
  • Copyright © 2011 by ASME

abstract

The function of protein molecules is defined by their 3-D geometry, as well as their internal mobility, which is heavily influenced by the internal hydrogen bonds. The correct identification of these hydrogen bonds and the prediction of their effect on the mobility of protein molecules can provide an invaluable mechanism to understand protein behavior. Applications of this study ranges from nano-engineering to new drug design. We are extending our recent approach from identifying main-chain main-chain hydrogen bonds to all types of hydrogen bonds that occur in protein structures, such as α-helices and β-sheets. We use the Grübler-Kutzbach kinematic mobility criterion to determine the degrees of freedom of all closed loops (rigid loops as well as closed loops of one or more degrees of freedom) formed by Hydrogen bonds. Furthermore, we systematically develop constraint equations for non-rigid closed loops. Several examples of protein molecules from PDB are used to show that these additions both improve the accuracy of mobility analysis and enable us to study a broader range of the motion of protein molecules. This approach offers theoretical insight as well as extensive numerical efficiencies in protein simulations.

Copyright © 2011 by ASME
Topics: Motion , Chain , Proteins

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