Research Papers

Hydrogen Bonds and Kinematic Mobility of Protein Molecules

[+] Author and Article Information
Zahra Shahbazi

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

Horea T. Ilieş

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

Kazem Kazerounian1

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

A native conformation, or native structure of functional proteins is a conformation corresponding to either a global minimum potential energy state or a stable, local minimum energy state that is observed in the nature as is related to specific function.

The limitations of the Grubler–Kutzbach criterion to the mobility analysis of multiloop mechanisms are discussed in Ref. 58. Note that one can easily employ in our procedure any other mobility criterion for multiloop spatial mechanisms.

This is required to make at least one hydrogen bond between residue numbers 1–5 and to transform the open loop linkage a rigid closed loop.


Corresponding author.

J. Mechanisms Robotics 2(2), 021009 (Apr 20, 2010) (9 pages) doi:10.1115/1.4001088 History: Received June 24, 2009; Revised October 30, 2009; Published April 20, 2010; Online April 20, 2010

Modeling protein molecules as kinematic chains provides the foundation for developing powerful approaches to the design, manipulation, and fabrication of peptide based molecules and devices. Nevertheless, these models possess a high number of degrees of freedom (DOFs) with considerable computational implications. On the other hand, real protein molecules appear to exhibit a much lower mobility during the folding process than what is suggested by existing kinematic models. The key contributor to the lower mobility of real proteins is the formation of hydrogen bonds during the folding process. In this paper, we explore the pivotal role of hydrogen bonds in determining the structure and function of the proteins from the point of view of mechanical mobility. The existing geometric criteria on the formation of hydrogen bonds are reviewed and a new set of geometric criteria is proposed. We show that the new criteria better correlate the number of predicted hydrogen bonds with those established by biological principles than other existing criteria. Furthermore, we employ established tools in kinematics mobility analysis to evaluate the internal mobility of protein molecules and to identify the rigid and flexible segments of the proteins. Our results show that the developed procedure significantly reduces the DOF of the protein models, with an average reduction of 94%. Such a dramatic reduction in the number of DOF can have enormous computational implications in protein folding simulations.

Copyright © 2010 by American Society of Mechanical Engineers
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Figure 1

Geometric parameters

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Figure 2

Hydrogen bonds identified by PROTOFOLD

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Figure 3

Open loop of connected amino acids in the sample protein

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Figure 4

Connectivity matrix for the sample protein shown in Fig. 3

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Figure 5

Reduced open loop and predicted hydrogen bonds

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Figure 6

New links created by hydrogen bonds

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Figure 7

Reduced connectivity matrix

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Figure 8

Graph representation of the connectivity matrix

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Figure 9

Three of identified loops

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Figure 10

Three search steps for the sample protein shown in Fig. 3. Our analysis points out that the original protein is in fact a rigid body

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Figure 11

1U7M protein whose mobility analysis was completed




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