Multiscale Modeling of Enzymatic Reactions and Bioimaging Probes

Multiscale Modeling of Enzymatic Reactions and Bioimaging Probes Abstract This project addresses a critical technology/software gap — the accessibility of ab initio quantum mechan- ical molecular mechanical (QM/MM) multiscale modeling tools in the enzymology and bioimaging fields — by developing machine-learning-based and physics-based electronic structure and molecular simulation methods. In our R01 funding period, we made several methodological advances, especially (a) the first !-learning poten- tial for simulating the enzyme reaction free energy (as demonstrated with the modeling of chorismate mutase catalysis), (b) an advance to the multiple time-step free energy simulation methodology, and (c) an analysis tool for interpreting/predicting the substitution effect on chromophore emission wavelength based on chromophore- substituent orbital interactions. Building on these method developments, we will further develop robust active-learning protocols for training !-learning potentials for ground and excited electronic states for systems in the macromolecular or solvent en- vironments. These !-learning potentials, when validated against advanced physics-based models, will enable routine (a) enzyme reaction simulations and (b) optoacoustic and other bioimaging probe modeling in our lab and the larger community. CRISPR-Cas proteins will be used as our primary test enzyme systems. We will employ the !-learning potentials in molecular dynamics simulations and seek an atomistic understanding of (a) the effect of SpyCas9 conformational changes on HNH- and RuvC-domain catalyzed DNA cleavage activity, and (b) the mechanism of AsCas12a and FnCas12a RuvC-domain catalyzed non-target strand DNA cleavage. For bioimaging probes, we will seek general guiding principles for designing optoacoustic imaging probes. It will be achieved by performing ab initio-QM/MM-quality multiscale modeling to explore the impact of struc- tural modifications (especially the attachment of halogen atoms and flexible alkane chains) on the molecular absorbance and nonradiative decay rate, both key factors in the optoacoustic signal generation.