Residue Level Inverse Kinematics of Peptide Chains in the Presence of Observation Inaccuracies and Bond Length Changes

[+] Author and Article Information
Raghavendran Subramanian

Department of Mechanical Engineering,  University of Connecticut, Storrs, CT 06269raghavendran@engr.uconn.edu

Kazem Kazerounian

Department of Mechanical Engineering,  University of Connecticut, Storrs, CT 06269kazem@engr.uconn.edu

J. Mech. Des 129(3), 312-319 (Mar 13, 2006) (8 pages) doi:10.1115/1.2406102 History: Received May 10, 2005; Revised March 13, 2006

The process of calculating the dihedral angles of a peptide chain from atom coordinates in the chain is called residue level inverse kinematics. The uncertainties and experimental observation inaccuracies in the atoms’ coordinates handicap this otherwise simple and straightforward process. In this paper, we present and analyze three new efficient methodologies to find all the dihedral angles of a peptide chain for a given conformation. Comparison of these results with the dihedral angle values reported in the protein data bank (PDB) indicates significant improvements. While these improvements benefit most modeling methods in protein analysis, it is in particular, very significant in homology modeling where the dihedral angles are the generalized coordinates (structural variables). The first method presented here fits a best plane through five atoms of each peptide unit. The angle between the successive planes is defined as the dihedral angle. The second method is based on the zero-position analysis method. Successive links in this method rotate by the dihedral angles so as to minimize the structural error between respective atoms in the model conformation with given atoms’ coordinates. Dihedral angle final values correspond to the minimum structural error configuration. In this method, singular value decomposition technique is used to best fit the atoms in the two conformations. The third method is a variant of the second method. In this instead of rotating all the links successively only three links are matched each time to extract the dihedral angle of the middle link. By doing so, the error accumulation on the successive links is reduced. This paper focuses on the Euclidean norm as the measure of merit (structural error) to compare different methods with the PDB. This Euclidean norm is further, minimized by optimizing the geometrical features of the peptide plane.

Copyright © 2007 by American Society of Mechanical Engineers
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Figure 1

Molecular model of a peptide plane with standard dimensions reported by Pauling and Corey

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Figure 2

Peptide chain-peptide planes sharing common Cα atoms

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Figure 3

(a) definition of dihedral angle ϕ: angle included between the successive planes; and (b) definition of dihedral angle φ: angle included between the successive planes

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Figure 4

Peptide plane as a combination of two links with a revolute joint along N‐Cα axis

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Figure 5

Dihedral angles: ϕ and φ with a planar peptide chain (peptide bond angle=180deg)

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Figure 6

(a) A protein in zero-positioz; and (b) a protein in nonzero position. Note that in (b) the second side chain has rotated about the second alpha carbon.

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Figure 7

A flowchart showing the steps involved in the method of successive best rotations




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