Our Research

The Kamerlin Lab have broad research interests, that focus on applying the tools of computational (bio)chemistry to understanding the chemical basis for complex biological problems. This spans a range of scientific questions, from understanding fundamental chemical reactivity through to understanding the physicochemical parameters that allow for the evolution of new enzyme functions. Current projects in the research group include: (1) Studying the role of ligand-gated conformational changes in enzyme catalysis, with a particular focus on triosephosphate isomerase and glycerol-3-phosphate dehydrogenase. (2) Protein-DNA recognition, with a focus on transcription factors such as LacI, and other related proteins. (3) Enzyme evolution, with a particular focus on TIM-barrel proteins as well as enzymes that catalyze phosphoryl transfer reaction. (4) GTPase regulation, mechanism and evolution, examining a wide range of GTPases. (5) The dynamical behavior of disordered peptides, in particular the amyloid beta peptide and alpha synuclein. (6) The development of new approaches for computational enzymology, combined with force field parameterization and as dictated by the needs of individual projects, including approaches for enzyme design (CADEE), a recent update of the Q simulation package, and new models for describing metal ions in biomolecular simulations. Finally, although we primarily work with biological macromolecules, we are also interested in answering fundamental questions in physical organic chemistry, focusing on the study of small molecules (with a particular interest in phosphoryl and related group transfer reactions). 

• The Kasson lab is focused on understanding dynamic and conformational ensembles of flexible proteins as well as the pathways of enveloped virus entry.  Research in the lab focuses on using experimental data to refine structural models of flexible proteins to understand molecular recognition and conformational change.  We also perform single-virus microscopy experiments and use both molecular dynamics simulations and kinetic modeling to understand the mechanisms and individual molecular contributions behind these complex properties.  To support these computational modeling projects and make modeling of complex systems accessible to a greater range of scientists, we also do computational infrastructure development.  Research thus spans a range from experimental virology and biophysics to simulations of viral entry complexes, protein-membrane interactions, and spectroscopic and structural data on individual proteins and their conformational modulation.