Talk abstracts
Talk on Tuesday 10:00-10:15am submitted by Paige Bowling
Fragmented Proteins Don’t Live in a Vacuum
Paige E. Bowling (Biophysics), Dustin R. Boderick (Chemistry & Biochemistry), John M. Herbert (Chemistry & Biochemistry)
Abstract:
Quantum-chemical models of enzymatic active sites require hundreds of atoms to obtain converged reaction energies, severely limiting the levels of theory that can be used. We use fragment-based methods to compute converged thermochemical properties for several large active site models, avoiding the steep nonlinear scaling associated with conventional quantum chemistry by running smaller byte-sized fragment calculations in parallel, and we have developed a protocol for such calculations as applied to enzymatic reactions. In the presence of charged amino acid residues, the conventional low-order many-body expansion fails to converge under vacuum boundary conditions, although it converges at three-body terms when low-dielectric (ε = 4) boundary conditions are used instead. This suggests that benchmark studies of the many-body expansion that aim to reproduce gas-phase supersystem results for proteins are fundamentally misguided. For calculations with continuum boundary conditions, sub-kcal/mol accuracy is obtained using our fragmentation protocol, at lower (in total CPU time) as compared to brute-force supersystem calculations.
References:
Preprint: https://chemrxiv.org/engage/chemrxiv/article-details/63f8083c897b18336f06f598
Keywords: quantum chemistry, computational modeling, enzymatic thermochemistry