Welcome to the research page of Bhattacharyay Lab

We explore the interplay of protein dynamics and catalysis in complex chemical systems using theory and molecular modeling. One of the chemical systems being studied is a quione reductase enzyme, which involves a substrate shuttling during hydride transfer reactions. We are also working with aminoacyl-tRNA synthetases, which employ coupled domain dynamics in enzyme catalysis.

Project 1. Redox chemistry and its role in ping-pong enzyme kinetics

Project 2. Enzyme catalysis and its link to protein dynamics and allostery

Extended collabrative group with Dr. Hati

 

People

PI: Sudeep Bhattacharyay

 

Current students

 

Clorice R.

Reinhardt

 

Clorice is studying flavin-substrate non-covalent interactions. This type of interactions occur in many enzymes including quinone oxidoreductases. She is trying to understand how these interactions are shaping the kinetics and thermodynamics of reactions either in the aqueous state or within an enzyme active site. Using quantum mechanical/molecular mechanical simulations, she is studying the role of enzyme matrix on thermodynamics and kinetics of the catalytic reactions.

She has co-authored a recent article (Effect of Stacking Interactions on the Thermodynamics and Kinetics of Lumiflavin: A Study with Improved Density Functionals and Density Functional Tight-Binding Protocol J. Phys. Chem. A 2015, 119, 172–182.) 

Matthew P.

Mocol

 Matt is studying the binding and release of substrate in prolyl tRNA synthetase. He is using extended molecular dynamics simulations and adaptive biasing force technique to simulate the binding/release of the substrate from the active site pocket.

Tiffany T.

Huynh

 Tiffany is interested in modeling enzyme catalysis. Tiffany has been working on simulating the prolyl adenylation reaction in the active site of the prolyl-tRNA synthetase. In particular, she is studying the activation barrier of the reaction for cognate and non-cognate amino acids using quantum mechanical/molecular mechanical simulations. The overall goal is to identify local and global dynamics that favors the selection and binding of cognate amino acids.

Tanner C.

Jaglinski

Tanner is involved in the study of the hydride transfer reaction of quinones by flavin. Using density functional theory, he is exploring the effect of substituents on the thermodynamics and kinetics of the redox reactions.

 

Ryan J.

Andrews

 

Ryan is interested in protein dynamics, he is involved in extracting coupled motions of various protein segments that are related to its function. These functional motions are slow and are believed to be instrumental for a number of protein's function such as substrate binding, catalysis, allosteric control etc.

Former students