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Analyzing Internal Motion of Proteins From Viewpoint of Robot Kinematics: Formulation of Group Forced Response Method

[+] Author Affiliations
Keisuke Arikawa

Kanagawa Institute of Technology, Atsugi, Kanagawa, Japan

Paper No. DETC2012-70591, pp. 55-64; 10 pages
doi:10.1115/DETC2012-70591
From:
  • ASME 2012 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference
  • Volume 4: 36th Mechanisms and Robotics Conference, Parts A and B
  • Chicago, Illinois, USA, August 12–15, 2012
  • Conference Sponsors: Design Engineering Division, Computers and Information in Engineering Division
  • ISBN: 978-0-7918-4503-5
  • Copyright © 2012 by ASME

abstract

An analogous relationship exists between the kinematic structures of proteins and robotic mechanisms. Hence, using this analogy, we attempt to understand the internal motions of proteins from the perspective of robot kinematics. In this study, we propose a method called group forced response (GFR) method for predicting the internal motion of proteins on the basis of their three-dimensional structural data (PDB data). In this method, we apply forces in static equilibrium to groups of atoms (e.g., secondary structures, domains, and subunits) and not to specific atoms. Furthermore, we predict the internal motion of proteins by analyzing the relative motion caused among groups by the applied forces. First, we show a method for approximately modeling protein structures as a robotic mechanism and the basic kinematic equations of the model. Next, the GFR method is formulated (e.g., Jacobian matrix for group motions, magnitude of forces applied to groups, and decomposition of motions into modes according to structural compliances). Finally, we present example applications of the proposed method in real protein structures. Despite the approximations in the model, low computational cost, and use of simple calculation parameters, the results almost agree with measured internal motions.

Copyright © 2012 by ASME

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