Journal of Integrative Natural Science (통합자연과학논문집)

The Basic Science Institute Chosun University (조선대학교 기초과학연구원)
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Temperature Dependency on Conformational Sampling of 12-Crown-4 by Simulated Annealing

  • Gadhe, Changdev G. (Department of Biochemistry, Centre for Bioinformatics, University of Madras, Guindy campus) ;
  • Cho, Seung Joo (Department of Bio-New Drug Development and Department of Cellular.Molecular Medicine and Research Center for Resistant Cells, College of Medicine, Chosun University)
  • Received : 2013.02.18
  • Accepted : 2013.03.25
  • Published : 2013.03.30
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Abstract

In this manuscript, we report a protocol to determine most of the lowest energy conformations from the ensemble of conformations. 12-crown-4 was taken as study compound to get the most of energy minima conformations. Molecular dynamic (MD) simulation for 1 nanosecond (ns) was performed at 300, 500, 700, 900 and 1100 K temperature. At particular interval conformations were sampled. Then Gaussian program was used to minimize compounds using PM6 energy levels. Duplicates were removed by checking energy as well as mirror image conformations, and only unique conformations were retained for the next $6-31+G^*$ level minimization. It was observed that upto certain increment in temperature the number of unique conformations were increased, but afterword it decreased.

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References

  1. R. Elber and M. Karplus, "Enhanced sampling in molecular dynamics: use of the time-dependent Hartree approximation for a simulation of carbon monoxide diffusion through myoglobin", J. Am. Chem. Soc., Vol. 112, pp. 1961-1975, 1990.
  2. A. E. Garcia and K.Y. Sanbonmatsu, "Exploring the energy landscape of a beta hairpin in explicit solvent", Proteins, Vol. 42, pp. 345-354, 2001. https://doi.org/10.1002/1097-0134(20010215)42:3<345::AID-PROT50>3.0.CO;2-H
  3. K. Tai, "Conformational sampling for the impatient", Biophys. Chem., Vol. 107, pp. 213-220, 2004. https://doi.org/10.1016/j.bpc.2003.09.010
  4. R. E. Bruccoleri and M. Karplus, "Prediction of the folding of short polypeptide segments by uniform conformational sampling", Biopolymers, Vol. 26, pp. 137-168, 1987. https://doi.org/10.1002/bip.360260114
  5. M. Saunders, "Stochastic exploration of molecular mechanics energy surface: hunting for the global minimum", J. Am. Chem. Soc., Vol. 109, pp. 3150-3152, 1987. https://doi.org/10.1021/ja00244a051
  6. D. M. Ferguson and D. J. Raber, "A new approach to probing conformational space with molecular mechanics: random incremental pulse search", J. Am. Chem. Soc., Vol. 111, pp. 4371-4378, 1989. https://doi.org/10.1021/ja00194a034
  7. Z. Q. Li and H. A. Scheraga, "Monte-carlo-minimi-zation approach to the multiple-minima problem in protein folding", Proc. Natl. Acad. Sci. U. S. A. Vol. 84, pp. 6611-6615, 1987. https://doi.org/10.1073/pnas.84.19.6611
  8. S. H. R. SYBYL8.1; Tripos Inc., St. Louis, MO 63144 USA (2008).
  9. D. A. Case, T. A. Darden, T. E. Cheatham, III, C. L. Simmerling, J. Wang, R. E. Duke, R. Luo, R. C. Walker, W. Zhang, K. M. Merz, B. Roberts, S. Hayik, A. Roitberg, G. Seabra, J. Swails, A. W. Goetz, I. Kolossvary, K. F. Wong, F. Paesani, J. Vanicek, R. M. Wolf, J. Liu, X. Wu, S. R. Brozell, T. Steinbrecher, H. Gohlke, Q. Cai, X. Ye, J. Wang, M.-J. Hsieh, G. Cui, D. R. Roe, D. H. Mathews, M. G. Seetin, R. Salomon-Ferrer, C. Sagui, V. Babin, T. Luchko, S. Gusarov, A. Kovalenko, and P. A. Kollman, AMBER 12, University of California, San Francisco (2012).
  10. A. Jakalian, B. L. Bush, B. D. Jack, and C. I. Bayly, "Fast, efficient generation of high-quality atomic charges. AM1-BCC Model: I. Method", J. Comp. Chem., Vol. 21, pp. 132-146, 2000. https://doi.org/10.1002/(SICI)1096-987X(20000130)21:2<132::AID-JCC5>3.0.CO;2-P
  11. J. Wang, R. M. Wolf, J. W. Caldwell, P. A. Kollman, and D. A. Case, "Development and testing of a general amber force field", J. Comp. Chem., Vol. 25, pp. 1157-1173, 2004. https://doi.org/10.1002/jcc.20035
  12. S. J. Cho, "Meaning and definition of partial charge", J. Chosun Natural Sci., Vol. 3, pp. 231-236, 2010.
  13. S. J. Cho, "Calculation and application of partial charge". J. Chosun Natural Sci., Vol. 3, pp. 226-230, 2010.