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Journal of Chemical Physics / Volume 133 / Issue 8 / ARTICLES / Biological Molecules, Biopolymers, and Biological Systems

J. Chem. Phys. 133, 085102 (2010); http://dx.doi.org/10.1063/1.3481485 (8 pages)

The role of stochasticity on compactness of the native state of protein peptide backbone

P. H. Figueirêdo1, M. A. Moret2, S. Coutinho3, and E. Nogueira, Jr.4

1Departamento de Física, Universidade Federal Rural de Pernambuco, Recife, Pernambuco, CEP 52171-900, Brazil
2Departamento de Física, Universidade Estadual de Feira de Santana, Feira de Santana, Bahia, CEP 44031-460, Brazil
3Departamento de Física, Universidade Federal de Pernambuco, Recife, Pernambuco CEP 50670-901, Brazil
4Departamento de Física, Universidade Federal da Paraíba, João Pessoa, Paraíba, CEP 58059-900, Brazil

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(Received 23 July 2009; accepted 2 August 2010; published online 30 August 2010)

A restricted angular random-walk model to build up polypeptide structures, which encompasses properties of the dihedral-angle Ramachandran map of folded proteins, is proposed to study the role of stochasticity on the compactness of the native state of proteins. Sample structures will be built with lengths ranging from 125 up to 400 amino acids for the different fractions of secondary structure motifs, from which dihedral angles were randomly chosen according to narrow Gaussian probability distributions. Physical properties of these polypeptide protein backbones such as the radius of gyration, the compactness parameter, the number of contacts, and the associated energy were computed and analyzed from an ensemble of thousands of realizations of protein peptide chains built with different rates of α-helix or β-strand motifs. Such geometric and physical parameters are compared to data from several globular proteins extracted from the Protein Data Bank indicating that a certain (small fraction) randomness is an essential ingredient for achieving the folded state of proteins, suggesting that they are neither driven by deterministic nor random-walk processes.

© 2010 American Institute of Physics

Article Outline

  1. INTRODUCTION
  2. THE ANGULAR RANDOM-WALK MODEL
  3. RESULTS AND DISCUSSION
    1. The radius of gyration
    2. The compactness parameter
    3. The contour length scaling
    4. The average contact number and potential energy
  4. SUMMARY AND CONCLUSIONS

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KEYWORDS and PACS

Keywords

Gaussian distribution, molecular biophysics, proteins

PACS

ARTICLE DATA

Digital Object Identifier
http://dx.doi.org/10.1063/1.3481485

PUBLICATION DATA

ISSN

0021-9606 (print)  
1089-7690 (online)

Publisher

$abstract.society.value is a Member of CrossRef American Institute of Physics

For access to fully linked references, you need to log in.
    R. H. A. D. Shaw and J. A. Tuszynski, Phys. Rev. E 67, 031102 (2003).

    M. B. Enright and D. M. Leitner, Phys. Rev. E 71, 011912 (2005).

    J. Liang and K. Dill, Biophys. J. 81, 751 (2001)JCPSA6000118000013006102000001.

    M. A. Moret, J. G. V. Miranda, E. Nogueira, Jr., M. C. Santana, and G. F. Zebende, Phys. Rev. E 71, 012901 (2005).

    F. Valle, M. Favre, P. De Los Rios, A. Rosa, and G. Dietler, Phys. Rev. Lett. 95, 158105 (2005).

    E. Ercolini, F. Valle, J. Adamcik, G. Witz, R. Metzler, P. De Los Rios, J. Roca, and G. Dietler, Phys. Rev. Lett. 98, 058102 (2007).

    J. Zhang, R. Chen, C. Tang, and J. Liang, J. Chem. Phys. 118, 6102 (2003)JCPSA6000118000013006102000001.


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