To function properly, proteins must fold. Therefore, as a precondition to fully understanding a protein's function, one must acquire knowledge of a protein's structure and its biochemical properties, including meta-stable states.  To model these, we are developing an off-lattice coarse-grained (CG) protein model.   This model cheaply and efficiently samples a protein's conformational space and has several advantages over all-atom models.  The CG model is being used in conjunction with replica exchange Langevin dynamics, to simulate the kinetics and thermodynamics of two small, fast-folding proteins during the process of thermal denaturation.  Using protein G-related albumin binding (pdb: 1prb) and beta-1 immunoglobulin binding (pdb: 2qmt) domains, we validate our model's efficacy for both alpha-helix and beta-sheet systems.  Melting curves, in conjunction with a two-state folding model, were used to derive thermochemical properties melting point, folding enthalpy, and change in heat capacity.  For both proteins our computed results match closely with experiment.

Thermochemical analysis of two small fast-folding proteins using coarse-grained simulation

244th National Meeting (2012)

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