Folding and Unfolding Simulations of a Three-Stranded Beta-Sheet Protein

DOI: 10.4236/msce.2016.41003   PDF   HTML   XML   2,319 Downloads   2,683 Views   Citations

Abstract

Understanding the folding processes of a protein into its three-dimensional native structure only with its amino-acid sequence information is a long-standing challenge in modern science. Two- hundred independent folding simulations (starting from non-native conformations) and two- hundred independent unfolding simulations (starting from the folded native structure) are performed using the united-residue force field and Metropolis Monte Carlo algorithm for betanova (three-stranded antiparallel beta-sheet protein). From these extensive computer simulations, two representative folding pathways and two representative unfolding pathways are obtained in the reaction coordinates such as the fraction of native contacts, the radius of gyration, and the root- mean-square deviation. The folding pathways and the unfolding pathways are similar each other. The largest deviation between the folding pathways and the unfolding pathways results from the root-mean-square deviation near the folded native structure. In general, unfolding computer simulations could capture the essentials of folding simulations.

Share and Cite:

Kim, S. (2016) Folding and Unfolding Simulations of a Three-Stranded Beta-Sheet Protein. Journal of Materials Science and Chemical Engineering, 4, 13-17. doi: 10.4236/msce.2016.41003.

Conflicts of Interest

The authors declare no conflicts of interest.

References

[1] Creighton, W.E. (1993) Proteins: Structures and Molecular Properties. 2nd Edition, W.H. Freeman and Company, New York.
[2] Hughes, J., Smith, T.W., Kosterlitz, H.W., Fothergill, L.A., Morgan, B.A. and Morris, H.R. (1975) Identification of Two Related Pentapeptides from the Brain with Potent Opiate Agonist Activity. Nature, 258, 577-579. http://dx.doi.org/10.1038/258577a0
[3] Pauling, L., Corey, R.B. and Branson, H.R. (1951) The Structure of Proteins: Two Hydrogen-Bonded Configurations of the Polypeptide Chain. Proceedings of the National Academy of Sciences of the United States of America, 37, 205- 211. http://dx.doi.org/10.1073/pnas.37.4.205
[4] Pain, R.H. (2000) Mechanisms of Protein Folding. 2nd Edition, Oxford University Press, New York.
[5] Friesner, R.A. (2002) Computational Methods for Protein Folding. John Wiley & Sons, New York. http://dx.doi.org/10.1002/0471224421
[6] Kortemme, T., Ramirez-Alvarado, M. and Serrano, L. (1998) Design of a 20-Amino Acid, Three-Stranded Beta-Sheet Protein. Science, 281, 253-256. http://dx.doi.org/10.1126/science.281.5374.253
[7] Lee, J., Kim, S.-Y. and Lee, J. (2004) Design of a Protein Potential Energy Landscape by Parameter Optimization. Journal of Physical Chemistry B, 108, 4525-4534. http://dx.doi.org/10.1021/jp037076c
[8] Fishman, G.S. (1996) Monte Carlo: Concepts, Algorithms, and Applications. Springer-Verlag, New York. http://dx.doi.org/10.1007/978-1-4757-2553-7
[9] Kim, S.-Y., Lee, J. and Lee, J. (2005) Folding Simulations of Small Proteins. Biophysical Chemistry, 115, 195-200. http://dx.doi.org/10.1016/j.bpc.2004.12.040
[10] Kim, S.-Y., Lee, J. and Lee, J. (2004) Folding of Small Proteins Using a Single Continuous Potential. Journal of Chemical Physics, 120, 8271-8276. http://dx.doi.org/10.1063/1.1689643

  
comments powered by Disqus

Copyright © 2020 by authors and Scientific Research Publishing Inc.

Creative Commons License

This work and the related PDF file are licensed under a Creative Commons Attribution 4.0 International License.