title: Methods for Efficiently and Accurately Computing Quantum Mechanical Free Energies for Enzyme Catalysis.
abstract: Enzyme activity is inherently linked to free energies of transition states, ligand binding, protonation/deprotonation, etc.; these free energies, and thus enzyme function, can be affected by residue mutations, allosterically induced conformational changes, and much more. Therefore, being able to predict free energies associated with enzymatic processes is critical to understanding and predicting their function. Free energy simulation (FES) has historically been a computational challenge as it requires both the accurate description of inter- and intramolecular interactions and adequate sampling of all relevant conformational degrees of freedom. The hybrid quantum mechanical molecular mechanical (QM/MM) framework is the current tool of choice when accurate computations of macromolecular systems are essential. Unfortunately, robust and efficient approaches that employ the high levels of computational theory needed to accurately describe many reactive processes (ie, ab initio, DFT), while also including explicit solvation effects and accounting for extensive conformational sampling are essentially nonexistent. In this chapter, we will give a brief overview of two recently developed methods that mitigate several major challenges associated with QM/MM FES: the QM non-Boltzmann Bennett's acceptance ratio method and the QM nonequilibrium work method. We will also describe usage of these methods to calculate free energies associated with (1) relative properties and (2) along reaction paths, using simple test cases with relevance to enzymes examples.
authors: University of South Florida, Tampa, FL, United States.
authors: F L
authors: FL
authors: Kearns
authors: University of South Florida, Tampa, FL, United States.
authors: P S
authors: PS
authors: Hudson
authors: Faculty of Chemistry, University of Vienna, Vienna, Austria. Electronic address: stefan@mdy.univie.ac.at.
authors: S
authors: S
authors: Boresch
authors: University of South Florida, Tampa, FL, United States. Electronic address: hlw@usf.edu.
authors: H L
authors: HL
authors: Woodcock
mesh_terms: D000818:Animals; D055162:Biocatalysis; D003198:Computer Simulation; D004798:Enzymes / Q000737:chemistry / Q000378:metabolism*; D006801:Humans; D008956:Models, Chemical; D011789:Quantum Theory; D013816:Thermodynamics
chemical_list: D004798:Enzymes
keywords: Bennett's acceptance ratio (BAR); Free energy; Potential of mean force; QM-Non-Boltzmann Bennett (QM-NBB); QM/MM; Reaction path; Reweighting