Shao Q, Hall CK. A Discontinuous Potential Model for Protein-Protein Interactions.
FOUNDATIONS OF MOLECULAR MODELING AND SIMULATION : SELECT PAPERS FROM FOMMS 2015. INTERNATIONAL CONFERENCE ON FOUNDATIONS OF MOLECULAR MODELING AND SIMULATION (6TH : 2015 : MOUNT HOOD, OR.) 2016;
2016:1-20. [PMID:
28580454 PMCID:
PMC5453719 DOI:
10.1007/978-981-10-1128-3_1]
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Abstract
Protein-protein interactions play an important role in many biologic and industrial processes. In this work, we develop a two-bead-per-residue model that enables us to account for protein-protein interactions in a multi-protein system using discontinuous molecular dynamics simulations. This model deploys discontinuous potentials to describe the non-bonded interactions and virtual bonds to keep proteins in their native state. The geometric and energetic parameters are derived from the potentials of mean force between sidechain-sidechain, sidechain-backbone, and backbone-backbone pairs. The energetic parameters are scaled with the aim of matching the second virial coefficient of lysozyme reported in experiment. We also investigate the performance of several bond-building strategies.
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