- About this Journal ·
- Abstracting and Indexing ·
- Aims and Scope ·
- Annual Issues ·
- Article Processing Charges ·
- Author Guidelines ·
- Bibliographic Information ·
- Citations to this Journal ·
- Contact Information ·
- Editorial Board ·
- Editorial Workflow ·
- Free eTOC Alerts ·
- Publication Ethics ·
- Recently Accepted Articles ·
- Reviewers Acknowledgment ·
- Submit a Manuscript ·
- Subscription Information ·
- Table of Contents
Journal of Biomedicine and Biotechnology
Volume 2012 (2012), Article ID 121034, 11 pages
Predicting Protein Interactions by Brownian Dynamics Simulations
1Department of Physiology and Biophysics, Virginia Commonwealth University, 1220 East Broad Street, P.O. Box 980551, Richmond, VA 23298, USA
2State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China
3Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, NY 10029, USA
Received 15 July 2011; Accepted 19 October 2011
Academic Editor: Sergio Pantano
Copyright © 2012 Xuan-Yu Meng et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
- S. Dutta and H. M. Berman, “Large macromolecular complexes in the protein data bank: a status report,” Structure, vol. 13, no. 3, pp. 381–388, 2005.
- H. M. Berman, T. Battistuz, T. N. Bhat et al., “The protein data bank,” Acta Crystallographica Section D, vol. 58, no. 6 I, pp. 899–907, 2002.
- D. W. Ritchie, “Recent progress and future directions in protein-protein docking,” Current Protein and Peptide Science, vol. 9, no. 1, pp. 1–15, 2008.
- R. Méndez, R. Leplae, M. F. Lensink, and S. J. Wodak, “Assessment of CAPRI predictions in Rounds 3-5 shows progress in docking procedures,” Proteins: Structure, Function and Genetics, vol. 60, no. 2, pp. 150–169, 2005.
- R. Chen, L. Li, and Z. Weng, “ZDOCK: an initial-stage protein-docking algorithm,” Proteins: Structure, Function and Genetics, vol. 52, no. 1, pp. 80–87, 2003.
- H. A. Gabb, R. M. Jackson, and M. J. E. Sternberg, “Modelling protein docking using shape complementarity, electrostatics and biochemical information,” Journal of Molecular Biology, vol. 272, no. 1, pp. 106–120, 1997.
- M. Eisenstein and E. Katchalski-Katzir, “On proteins, grids, correlations, and docking,” Comptes Rendus Biologies, vol. 327, no. 5, pp. 409–420, 2004.
- J. J. Gray, S. Moughon, C. Wang et al., “Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations,” Journal of Molecular Biology, vol. 331, no. 1, pp. 281–299, 2003.
- J. Fernández-Recio, M. Totrov, and R. Abagyan, “ICM-DISCO docking by global energy optimization with fully flexible side-chains,” Proteins: Structure, Function and Genetics, vol. 52, no. 1, pp. 113–117, 2003.
- S. Vajda and D. Kozakov, “Convergence and combination of methods in protein-protein docking,” Current Opinion in Structural Biology, vol. 19, no. 2, pp. 164–170, 2009.
- C. S. Pangali, M. Rao, and B. J. Berne, “MonteCarlo simulation of water,” Abstracts of Papers of the American Chemical Society, vol. 175, p. 1, 1978.
- C. S. Pangali, M. Rao, and B. J. Berne, “Determination of potential of mean force of 2 noble-gas atoms dissolved in water,” Abstracts of Papers of the American Chemical Society, vol. 175, p. 4, 1978.
- P. J. Rossky, J. D. Doll, and H. L. Friedman, “Brownian dynamics as smart Monte Carlo simulation,” The Journal of Chemical Physics, vol. 69, no. 10, pp. 4628–4633, 1978.
- I. V. Ouporov, H. R. Knull, and K. A. Thomasson, “Brownian dynamics simulations of interactions between aldolase and G- or F-actin,” Biophysical Journal, vol. 76, no. 1 I, pp. 17–27, 1999.
- D. C. Pearson and E. L. Gross, “Brownian dynamics study of the interaction between plastocyanin and cytochrome f,” Biophysical Journal, vol. 75, no. 6, pp. 2698–2711, 1998.
- S. L. Lowe, C. Adrian, I. V. Ouporov, V. F. Waingeh, and K. A. Thomasson, “Brownian dynamics simulations of glycolytic enzyme subsets with F-Actin,” Biopolymers, vol. 70, no. 4, pp. 456–470, 2003.
- D. Motiejunas, R. Gabdoulline, T. Wang et al., “Protein-protein docking by simulating the process of association subject to biochemical constraints,” Proteins: Structure, Function and Genetics, vol. 71, no. 4, pp. 1955–1969, 2008.
- I. V. Ouporov, H. R. Knull, A. Huber, and K. A. Thomasson, “Brownian dynamics simulations of aldolase binding glyceraldehyde 3-phosphate dehydrogenase and the possibility of substrate channeling,” Biophysical Journal, vol. 80, no. 6, pp. 2527–2535, 2001.
- A. H. Elcock, D. Sept, and J. A. McCammon, “Computer simulation of protein-protein interactions,” Journal of Physical Chemistry B, vol. 105, no. 8, pp. 1504–1508, 2001.
- E. J. Haddadian and E. L. Gross, “Brownian dynamics study of cytochrome f interactions with cytochrome c 6 and plastocyanin in Chlamydomonas reinhardtii plastocyanin, and cytochrome c6 mutants,” Biophysical Journal, vol. 88, no. 3, pp. 2323–2339, 2005.
- M. Cui, J. Shen, J. M. Briggs et al., “Brownian dynamics simulations of interaction between scorpion toxin Lq2 and potassium ion channel,” Biophysical Journal, vol. 80, no. 4, pp. 1659–1669, 2001.
- M. Cui, J. Shen, J. M. Briggs et al., “Brownian dynamics simulations of the recognition of the scorpion toxin P05 with the small-conductance calcium-activated potassium channels,” Journal of Molecular Biology, vol. 318, no. 2, pp. 417–428, 2002.
- L. Yu, C. Sun, D. Song et al., “Nuclear magnetic resonance structural studies of a potassium channel-charybdotoxin complex,” Biochemistry, vol. 44, no. 48, pp. 15834–15841, 2005.
- S. H. Northrup, T. Laughner, and G. Stevenson, “Macrodox macromolecular simulation program,” 1999.
- L. Wesson and D. Eisenberg, “Atomic solvation parameters applied to molecular dynamics of proteins in solution,” Protein Science, vol. 1, no. 2, pp. 227–235, 1992.
- M. Cui, M. Mezei, and R. Osman, “Prediction of protein loop structures using a local move Monte Carlo approach and a grid-based force field,” Protein Engineering, Design and Selection, vol. 21, no. 12, pp. 729–735, 2008.
- J. Fernández-Recio, M. Totrov, and R. Abagyan, “Soft protein-protein docking in internal coordinates,” Protein Science, vol. 11, no. 2, pp. 280–291, 2002.
- S. H. Northrup, J. O. Boles, and J. C. L. Reynolds, “Electrostatic effects in the Brownian Dynamics of association and orientation of heme proteins,” Journal of Physical Chemistry, vol. 91, no. 23, pp. 5991–5998, 1987.
- S. H. Northrup, K. A. Thomasson, C. M. Miller et al., “Effects of charged amino acid mutations on the bimolecular kinetics of reduction of yeast iso-1-ferricytochrome c by bovine ferrocytochrome b5,” Biochemistry, vol. 32, no. 26, pp. 6613–6623, 1993.
- M. Cui, M. Mezei, and R. Osman, “Modeling dimerizations of transmembrane proteins using Brownian dynamics simulations,” Journal of Computer-Aided Molecular Design, vol. 22, no. 8, pp. 553–561, 2008.
- G. M. Morris, D. S. Goodsell, R. S. Halliday et al., “Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function,” Journal of Computational Chemistry, vol. 19, no. 14, pp. 1639–1662, 1998.
- E. L. Mehler and T. Solmajer, “Electrostatic effects in proteins: comparison of dielectric and charge models,” Protein Engineering, vol. 4, no. 8, pp. 903–910, 1991.
- V. Tsui and D. A. Case, “Theory and applications of the Generalized Born solvation model in macromolecular simulations,” Biopolymers, vol. 56, no. 4, pp. 275–291, 2000.
- R. Huey, G. M. Morris, A. J. Olson, and D. S. Goodsell, “Software news and update a semiempirical free energy force field with charge-based desolvation,” Journal of Computational Chemistry, vol. 28, no. 6, pp. 1145–1152, 2007.
- J. A. Nelder and R. Mead, “A simplex-method for function minimization,” Computer Journal, vol. 7, no. 4, pp. 308–313, 1965.
- W. Im, M. S. Lee, and C. L. Brooks, “Generalized born Model with a simple smoothing function,” Journal of Computational Chemistry, vol. 24, no. 14, pp. 1691–1702, 2003.
- W. Fu, M. Cui, J. M. Briggs et al., “Brownian dynamics simulations of the recognition of the scorpion toxin maurotoxin with the voltage-gated potassium ion channels,” Biophysical Journal, vol. 83, no. 5, pp. 2370–2385, 2002.
- X. Huang, H. Liu, M. Cui et al., “Simulating the interactions of toxins with K+ channels,” Current Pharmaceutical Design, vol. 10, no. 9, pp. 1057–1067, 2004.
- H. Pelletier and J. Kraut, “Crystal structure of a complex between electron transfer partners, cytochrome c peroxidase and cytochrome c,” Science, vol. 258, no. 5089, pp. 1748–1755, 1992.
- R. Norel, D. Petrey, H. J. Wolfson, and R. Nussinov, “Examination of shape complementarity in docking of unbound proteins,” Proteins: Structure, Function and Genetics, vol. 36, no. 3, pp. 307–317, 1999.
- P. N. Palma, L. Krippahl, J. E. Wampler, and J. J. G. Moura, “Bigger: a new (soft) docking algorithm for predicting protein interactions,” Proteins: Structure, Function and Genetics, vol. 39, no. 4, pp. 372–384, 2000.
- N. Guex and M. C. Peitsch, “SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling,” Electrophoresis, vol. 18, no. 15, pp. 2714–2723, 1997.