Nano-Kinematics for Analysis Of Protein Molecules

[+] Author and Article Information
Kazem Kazerounian, Khalid Latif, Kimberly Rodriguez

Mechanical Engineering Department,  University of Connecticut, Storrs, CT 06269-3139

Carlos Alvarado

 Polytechnic University of Puerto Rico, Hato Rey, PR 00918

J. Mech. Des 127(4), 699-711 (Aug 05, 2004) (13 pages) doi:10.1115/1.1867956 History: Received February 16, 2004; Revised August 05, 2004

Proteins are evolution’s mechanisms of choice. The study of nano-mechanical systems must encompass an understanding of the geometry and conformation of protein molecules. Proteins are open or closed loop kinematic chains of miniature rigid bodies connected by revolute joints. The Kinematics community is in a unique position to extend the boundaries of knowledge in nano biomechanical systems. In this work, we have presented a comprehensive methodology for kinematics notation and direct kinematics for protein molecules. These methods utilize the zero-position analysis method and draws upon other recent advances in robot manipulation theories. The procedures involved in finding the coordinates of every atom in the protein chain as a function of the dihedral and Rotamer angles are computationally the most efficient formulation developed to date. The notation and the methodologies of this paper are incorporated in the computer software package PROTOFOLD and will be made available to individuals interested in using it. PROTOFOLD is a software package that implements novel and comprehensive methodologies for ab initio prediction of the final three-dimensional conformation of a protein, given only its linear structure. In addition to the new kinematics methodologies mentioned above, we have also included all the basic kinematic parameter values that are needed in any kinematic analysis involving proteins. While these values are based on a body of knowledge recorded in the protein data bank, they are presented in a form conducive to kinematics.

Copyright © 2005 by American Society of Mechanical Engineers
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Figure 1

The ith residue in a long peptide chain

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Figure 2

A string of three amino acids

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Figure 3

An open loop chain that has n+1 solid links and n revolute joints

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Figure 4

(a) illustrates a protein in zero-position; (b) illustrates a protein in non-zero-position. Note that in (b) the second side chain has rotated about the second alpha carbon

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Figure 5

Body vector defining the location of the carbon atom C1 with respect to Cα1

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Figure 6

Body vectors from alpha carbons to mass centers in first even and first odd peptide planes

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Figure 7

Side chain body vectors for Leucine



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