Development & Application of Constant pH Molecular Dynamics (CPHMD ) for Investigating pH-mediated Transient Conformational States and Their Effects on Nucleic Acid & Protein Activity.

Transient States;Constant pH Molecular Dynamics;Electrostatics;pH;Molecular Modeling;Chemistry;Physics;Science (General);Science;Chemistry

Goh, Garrett B.Carlson, Heather A. ;

University of Michigan

关键词: Transient States;    Constant pH Molecular Dynamics;    Electrostatics;    pH;    Molecular Modeling;    Chemistry;    Physics;    Science (General);    Science;    Chemistry;   

Others  :  https://deepblue.lib.umich.edu/bitstream/handle/2027.42/113562/gbgoh_1.pdf?sequence=1&isAllowed=y

瑞士|英语

来源: The Illinois Digital Environment for Access to Learning and Scholarship

【 摘 要 】

pH is a ubiquitous regulator of biological activity, with widespread impact ranging from its role in catalysis to carcinogenesis. Traditionally, a combination of biophysical and computational methods are used to measure pH-dependent activity profiles, and protonation equilibria (i.e. pKa values) of specific residues, and these data are used in conjunction with structural data to provide mechanistic understanding of pH-mediated biological function. More recent developments have also demonstrated the role of transient conformational states in a wide range of biological activities, which naturally leads to the question of how pH affects such transient states, and in turn, their resulting functional activity. In the study of biomolecular transient states, the detection limit is the key limitation of most experimental techniques. To bridge the gap in detection limit, we have developed an appropriate molecular dynamics based computational method, where protonation states are dynamically adjusted as a function of an external pH bath and the local environment surrounding the titrating site. Also known as the explicit solvent constant pH molecular dynamics (CPHMD^MSλD) framework, we use CPHMD^MSλD simulations and enhanced sampling methods to demonstrate the role of pH-regulated transient states in both nucleic acid and protein activity. First, we demonstrate the utility of CPHMD^MSλD simulations in conjunction with NMR experiments to characterize transiently populated Hoogsteen GC+ base pairs in DNA duplexes. The role of pH-dependent transient states is then generalized to RNA activity, including that of the catalytic mechanism of the hairpin ribozyme, where the existence of pH-dependent transient states can be used to reconcile a collection of seemingly inconsistent experimental observations in the literature. In addition, our CPHMD^MSλD simulations of proteins have elucidated the role of pH-dependent transient states in residues that are buried or occluded from solvent, including that of the pH-dependent optical properties of a cyan fluorescent protein mutant, where the existence of pH-dependent transient states can be used to explain its non-monotonic spectroscopic behavior.