Tests of the Structure-Based Models of Proteins

• Authors: M. Cieplak , J. Sułkowska
• Languages of publication: EN

Abstracts

EN

The structure-based models of proteins are defined through the condition that their ground state coincides with the native structure of the proteins. There are many variants of such models and they yield different properties. Optimal variants can be selected by making comparisons to experimental data on single-molecule stretching. Here, we discuss the 15 best performing variants and focus on fine tuning the selection process by adjusting the velocity of stretching to match the experimental conditions. The very best variant is found to correspond to the 10-12 potential in the native contacts with the energies modulated by the Miyazawa-Jernigan statistical potential and variable length parameters. The second best model incorporates the Lennard-Jones potential with uniform amplitudes. We then make a detailed comparison of the two models in which theoretical surveys of stretching properties of 7510 proteins were made previously.

Keywords

EN

87.80.Nj; 87.15.ap; 87.14.E-

Discipline

• 87.80.Nj: Single-molecule techniques(see also 82.37.Rs Single molecule manipulation of proteins and other biological molecules in physical chemistry)
• 87.14.E-: Proteins
• 87.15.ap: Molecular dynamics simulation

• Publisher: Institute of Physics, Polish Academy of Sciences
• Journal: Acta Physica Polonica A
• Year: 2009
• Volume: 115
• Issue: 2
• Pages: 441-445

Dates

published

2009-02

Contributors

author

M. Cieplak

• Institute of Physics, Polish Academy of Sciences, al. Lotników 32/46, 02-668 Warsaw, Poland

author

J. Sułkowska

• Institute of Physics, Polish Academy of Sciences, al. Lotników 32/46, 02-668 Warsaw, Poland
• CTBP, University of California, San Diego Gilman Dr. 9500, La Jolla 92037, USA

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Identifiers

DOI

10.12693/APhysPolA.115.441