Protofold: A Successive Kinetostatic Compliance Method for Protein Conformation Prediction

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

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), 712-717 (Aug 05, 2004) (6 pages) doi:10.1115/1.1867502 History: Received February 16, 2004; Revised August 05, 2004

This paper presents an efficient and novel computational protein prediction methodology called kineto-static compliance method. Successive kineto-static fold compliance is a methodology for predicting a protein molecule’s motion under the effect of an inter-atomic force field without the need for molecular-dynamic simulation. Instead, the chain complies under the kineto-static effect of the force field in such a manner that each rotatable joint changes by an amount proportional to the effective torque on that joint. This process successively iterates until all of the joint torques have converged to a minimum. This configuration is equivalent to a stable, globally optimized potential energy state of the system or, in other words, the final conformation of the protein. This methodology is implemented in a computer software package named PROTOFOLD . In this paper, we have used PROTOFOLD to predict the final conformation of a small peptide chain segment, an alpha helix, and the Triponin protein chains from a denatured configuration. The results show that torques in each joint are minimized to values very close to zero, which demonstrates the method’s effectiveness for protein conformation prediction.

Copyright © 2005 by American Society of Mechanical Engineers
Topics: Force , Atoms , Chain , Proteins , Torque
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Figure 1

A current conformation of a protein chain

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Figure 2

Resultant forces Fp and Fq are shown on atoms (points) p and q on two rigid bodies of the kinematic chain

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Figure 3

Equivalent force–torque couples at the base

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Figure 4

Convergence of small peptide unit DRGD. The graph shows torque versus computer cycle

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Figure 5

DRGD peptide unit final conformation

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Figure 6

Convergence of alpha helix to its final conformation. These graphs illustrate the torque versus computation cycle. (a) First set of joints, (b) second set of joints, (c) third set of joints, (d) fourth set of joints.

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Figure 7

Alpha helix final conformation

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Figure 8

Convergence of some typical joint torques in Triponin

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Figure 9

Triponin final conformation predicted by PROTOFOLD



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