Abstract
Previously, we examined the application of a molecular dynamics-based simulated annealing cycling protocol to docking peptides to proteins using two implicit-solvent models: a distance-dependent dielectric model (ε(r) = 4r) and a version of the Generalized Born model termed GBMV. We found that rescoring structures obtained from one implicit-solvent model with the other could improve the identification of the correct docking pose. Here, we guide interested readers on how to perform a similar study, using the docking between a hexapeptide and the protein phosphatase YopH inYersinia pestis as an example.
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References
Kirkpatrick, S., Gelatt Jr., C. D., and Vecchi, M. P. (1983) Optimization by Simulated Annealing,Science 220, 671–680.
Huang, Z., Wong, C. F., and Wheeler, R. A. (2008) Flexible Protein-Flexible Ligand Docking with Disrupted Velocity Simulated Annealing,Proteins: Struct. Funct. Bioinform. 71, 440–454.
Huang, Z., and Wong, C. F. (2010) Incorporating Protein Flexibility in Molecular Docking by Molecular Dynamics: Applications to Protein Kinase and Phosphatase Systems InComputational Studeis of New Materials II (George, T. F., Jelski, D., Letfullin, R. R., and Zhang, G., Eds.), pp 219-249, World Scientific, Singapore.
Mitsutake, A., Sugita, Y., and Okamoto, Y. (2001) Generalized-Ensemble Algorithms for Molecular Simulations of Biopolymers,Biopolymers 60, 96–123.
Sugita, Y., and Okamoto, Y. (2002) Replica-Exchange Multicanonical Algorithm and Multicanonical Replica-exchange Method for Simulating Systems with Rough Energy Landscape,Chem. Phys. Lett. 329, 261–270.
Lee, M. S., et al. (2003) New Analytic Approximation to the Standard Molecular Volume Definition and Its Application to Generalized Born Calculations,J. Comput. Chem. 24, 1348–1356.
Lee, M. S., Salsbury Jr., F. R., and Brooks III, C. L. (2002) Novel Generalized Born Methods,J. Chem. Phys. 116, 10606–10614.
MacKerell Jr., A. D., et al. (1998) All-atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins,J. Phys. Chem. B 102, 3586–3616.
MacKerell Jr., A. D., Feig, M., and Brooks III, C. L. (2004) Extending the Treatment of Backbone Energetics in Protein Force Fields: Limitations of Gas-Phase Quantum Mechanics in Reproducing Protein Conformational Distributions in Molecular Dynamics Simulations,J. Comput. Chem. 25, 1400–1415.
Huang, Z., and Wong, C. F. (2009) Docking Flexible Peptide to Flexible Protein by Molecular Dynamics Using Two Implicit-Solvent Models: An Evaluation in Protein Kinase and Phosphatase Systems,J. Phys. Chem. B. 113, 14343–14354.
Phan, J., et al. (2003) High-resolution structure of theYersinia pestis protein tyrosine phosphatase YopH in complex with a phosphotyrosyl mimetic-containing hexapeptide,Biochemistry 42, 13113–13121.
Brooks, B. R., et al. (1983) CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations,J. Comput. Chem. 4, 187–217.
Brooks, B. R., et al. (2009) CHARMM: The biomolecular simulation program,J. Comput. Chem. 30, 1545–1614.
Feig, M., Karanicolas, J., and Brooks III, C. L. (2004) MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology,J. Mol. Graph. Model. 22, 377–395.
Case, D. A., et al. (2005) The Amber biomolecular simulation programs,J. Comput. Chem. 26, 1668–1688.
Huang, Z., and Wong, C. F. (2007) A Mining-minima Approach to Exploring the Docking Pathways of p-Nitrocatechol Sulfate to YopH,Biophys. J. 93, 4141–4150.
Chocholoušová, J., and Feig, M. (2006) Balancing an Accurate Representation of the Molecular Surface in Genelized Born Formalisms with Integrator Stability in Molecular Dynamics Simulations,J. Comput. Chem. 27, 719–729.
Li, H., Robertson, A. D., and Jensen, J. H. (2005) Very Fast Empirical Prediction and Rationalization of Protein pKa Values,Proteins Struct. Funct. Bioinform. 61, 704–721.
Dillet, V., Etten, R. L. V., and Bashford, D. (2000) Stabilization of charges and protonation states in the active site of the protein tyrosine phosphatases: A Computational study,J. Phys. Chem. B 104, 11321–11333.
Acknowledgments
This research was supported by a Research Award from the University of Missouri-Saint Louis, a Research Board Award from the University of Missouri System, the National Cancer Institute, and the National Institute of Allergy and Infectious Diseases. We also thank the University of Missouri Bioinformatics Consortium and the University of Missouri-Saint Louis Information Technology Services for providing computational resources.
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Huang, Z., Wong, C.F. (2012). A Case Study of Scoring and Rescoring in Peptide Docking. In: Baron, R. (eds) Computational Drug Discovery and Design. Methods in Molecular Biology, vol 819. Springer, New York, NY. https://doi.org/10.1007/978-1-61779-465-0_18
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DOI: https://doi.org/10.1007/978-1-61779-465-0_18
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