Modeling of protein structure, dynamics and interactions.
Computer simulations provide a wide range of information about molecular behavior, enabling the description of motions of individual atoms, but the practical application of simulations is limited by the accuracy of the approximations, the difficulty in relating simulations to observable properties, and the insufficient length of feasible simulations relative to biochemically interesting time scales.
My research focuses on developing approaches to overcome these limitations while solving interesting chemical and biological problems. The simulations uncover relations between structure, flexibility, interactions of peptides and proteins with their biological function - folding, enzymatic activity, signaling. Besides providing a basic understanding of biologically important molecules, the simulation results provide predictions on how to manipulate the properties for practical purposes. The work involves both using existing simulation programs and development of new methods and algorithms for molecular modeling.
- G.S. Jas, W. Hegefeld, P. Majek, K. Kuczera and R. Elber. Experiments and comprehensive simulations of the formation of a helical turn. J. Phys. Chem. B 116:6598-6610 (2012).
- G.S. Jas and K. Kuczera. Computer simulations of helix folding in homo- and hetero-peptides. Molecular Simulation, 38:682-694 (2012). Invited article for special issue “New Developments in Molecular Simulation”.
- K. Kuczera and P. Kursula. Interaction of calmodulin with death-associated protein kinase peptides: experimental and modeling studies. J. Biomol. Struct. Dyn., 30:45-61 (2012).
- K.Y. DeLeon, A. P. Patel, K.Kuczera, C.K. Johnson and G.S. Jas. Structure and Reorientational Dynamics of Angiotensin I and II: A Microscopic Physical Insight. J. Biomol. Struct. Dyn., 29:671-690 (2012).
- A. Cardenas, G.S. Jas, K. Kuczera and R. Elber. Unassisted transport of N-acetyl-L-Tryptophanamide through DOPC membrane: Experiment and simulation. J. Phys. Chem. B., 116:2739-2750 (2012).
- S. Parthasarathy, A. Altuve, S. Terzyan, X. Zhang, K. Kuczera, M. Rivera and D.R. Benson. Accomodating a non-conservative internal mutation by water-mediated hydrogen bonding between beta-sheet strands: A comparison of human and rat type B (mitochondrial) cytochrome b5. Biochemistry, 50:5544-5554 (2011).
- W. Hegefeld, K. Kuczera and G.S. Jas. Structural dynamics of neuropeptide hPYY. Biopolymers, 95:487-502 (2011). PMID: 2136052
- W. Hegefeld, S.-E. Chen, K. DeLeon, K. Kuczera and G.S. Jas. Helix formation in a pentapeptide: Experiment and force-field dependent dynamics. J. Phys. Chem. B, 114:12391-12402 (2010).
- K. Kuczera, J. Unruh, C.K. Johnson and G.S. Jas, “Reorientations of Aromatic Acids and Their Side Chains Models: Anisotropy Measurements and Molecular Dynamics Simulations”, J.Phys.Chem. A, 114:133-142 (2010).
- J. Unruh, K. Kuczera and C.K. Johnson, “Conformational Heterogeneity of a Leucine Enkephalin Analog in Aqueous Solution and SDS Micelles: Comparison of Time-Resolved FRET and Molecular Dynamics Simulations”, J.Phys.Chem. B, 113:14381-14392 (2009).