1567 Irving Hill Rd
Lawrence, KS 66045
- Computer Simulations of Biomolecular Structure
Physical and theoretical chemistry: molecular dynamics simulations, statistical mechanics, quantum chemistry, biological molecules and solutions.
Studies of fundamental properties of complex biological and organic molecules have profound implications for many areas of science, as well as practical applications in curing disease, protecting the environment, improving industrial processes and designing new materials. Although experimental investigations remain the main source of information on large molecular systems, their theoretical and computational studies are gaining importance in recent years. This is due to great increases in computer power and development of efficient computational algorithms, and to the growing understanding that simulations provide unprecedented detail of information which can be fruitfully employed to uncover the microscopic mechanisms of observable, macroscopic properties of molecular systems.
Professor Kuczera's research focuses on the use of methods of modern computational chemistry to study structure, dynamics and thermodynamics of complex molecular systems. The methods used involve mainly molecular dynamics simulations and quantum chemistry. The overall goal is to relate the detailed microscopic information provided by the simulations to observable, macroscopic physical, chemical and biological properties. Besides providing a basic understanding of important classes of molecules, the simulation results provide predictions on how to manipulate the properties for practical purposes. The work involves using existing simulation programs, development of new methods and algorithms for molecular modeling, and collaborations with experimental groups on specific systems.
Recent projects include modeling of properties of the protein calmodulin in its normal and oxidatively damaged states, related to understanding the processes of aging and/or development of neurodegenerative diseases; simulations of the structure and dynamics of the membrane protein phospholamban, aimed at explaining the mechanism by which it regulates transmembrane calcium pumping; normal mode and molecular dynamics studies of domain motions in the enzyme S-Adenosylhomocysteine hydrolase, explaining microscopic details of its activity and guiding design of effective inhibitors; modeling the water-membrane transfer and helix-coil equilibria in model peptides, providing microscopic insights into the detailed effects of temperature and environment on peptide structure; simulations the structure and molecular motions in carbon-dioxide expanded organic liquids, helping explain how the physical properties of these novel environmentally beneficial media can be modulated by adjusting operating pressure.
Selected Publications —
Meier, A.A., et al., Oligomeric States and Hydrodynamic Properties of Lysyl Oxidase-Like 2. Biomolecules, 2021. 11(12): p. 13.
Lee, K.H. and K. Kuczera, Free energy simulations to understand the effect of Met -> Ala mutations at positions 205, 206 and 213 on stability of human prion protein. Biophysical Chemistry, 2021. 275: p. 9.
Kuczera, K., et al., Length Dependent Folding Kinetics of Alanine-Based Helical Peptides from Optimal Dimensionality Reduction. Life-Basel, 2021. 11(5): p. 16.
Jas, G.S., et al., Dissecting Multiple Pathways in the Relaxation Dynamics of Helix <= =>Coil Transitions with Optimum Dimensionality Reduction. Biomolecules, 2021. 11(9): p. 15.
Jas, G.S., et al., Probing the Internal Dynamics and Shape of Simple Peptides in Urea, Guanidinium Hydrochloride, and Proline Solutions with Time-Resolved Fluorescence Anisotropy and Atomistic Cosolvent Simulations. Journal of Physical Chemistry B, 2021. 125(39): p. 10972-10984.
Jas, G.S., E.W. Childs, and K. Kuczera, Probing coupled motions of peptides in solution with fluorescence anisotropy and molecular dynamics simulation. Chemical Physics, 2021. 541: p. 14.
Kuczera, K., et al., Reorientation motions of N-acetyl-tryptophan-amide (NATA dipeptide) in aqueous solution and with co-solvents: Molecular dynamics vs hydrodynamic model. Physics of Fluids, 2020. 32(12): p. 14.
Jas, G.S., et al., Dynamic elements and kinetics: Most favorable conformations of peptides in solution with measurements and simulations. Journal of Chemical Physics, 2019. 151(22): p. 16.
Lee, B.L., et al., Unassisted N-acetyl-phenylalanine-amide transport across membrane with varying lipid size and composition: kinetic measurements and atomistic molecular dynamics simulation. Journal of Biomolecular Structure & Dynamics: p. 16.
Jas, G.S., et al., Observing reorientation dynamics with Time-Resolved fluorescence and molecular dynamics in varying periodic boundary conditions. Journal of Biomolecular Structure & Dynamics: p. 15.