Krzysztof Kuczera

Krzysztof Kuczera
  • Professor
He/him/his

Contact Info

785-864-4670
5090 Malott

Biography —

My research area is computational modeling of biomolecular structure, dynamics and interactions. The main goal is to uncover relations of molecular conformations and motions with their biological function - folding, binding, enzymatic activity, cellular signaling. Besides providing a basic understanding of biologically important processes, the simulation results generate predictions on how to manipulate the properties for practical purposes, like design of new drugs and materials. The tools used in my group include molecular dynamics and free energy simulations, normal mode analysis, enhanced conformational sampling, virtual ligand screening and machine learning. In my M.Sc. work at Warsaw University, I studied microscopic solvation of nucleotide bases. My Ph.D. research at the Polish Academy of Sciences was devoted to modeling effects of nucleotide tautomerism on IR spectra. In my postdoctoral work at Harvard University, with 2013 Chemistry Nobel Prize winner Prof. Martin Karplus, I started on the path of molecular dynamics and free energy simulations of proteins.

I am currently a professor at the University of Kansas, with a joint appointment in Chemistry and Molecular Biosciences Departments.

Education —

Postdoctoral fellow and research associate, Harvard University, 1991
Ph.D., Institute of Physics, Polish Academy of Sciences, 1986, Warsaw, Poland
M.S., Department of Physics, Warsaw University, 1980, Warsaw, Poland

Research —

Since 1992 at the University of Kansas I have developed a program that applies computer simulations to explaining the observed behavior of peptides, proteins and membranes, including applications to drug design.  Computational modeling provides a wide range of information about molecular behavior, enabling the description of motions of individual atoms, biomolecules and cellular machinery. The practical applications of simulations are limited by the accuracy of the approximations and the computational cost and complexity of modeling processes at biochemically interesting scales of space and time.

My research focuses on developing approaches to overcome these limitations while solving interesting chemical and biological problems. Current projects include studies of effects of environment on peptide structure and dynamics, influence of point mutations on protein stability, and design of drugs that act by disrupting protein-protein interactions. My work involves extensive collaborations with several experimental and computational groups, located in the USA and in Poland.

Teaching —

  • BIOL 750 Advanced Biochemistry
  • BIOL 918 Modern Biochemical and Biophysical Methods
  • CHEM 510 Biological Physical Chemistry

My teaching is split between physical chemistry (in the Chemistry Department) and advanced graduate biochemistry (in Molecular Biosciences). In both departments I focus on biological applications of basic principles of chemistry and physics, including mathematics, programming, visualization and active learning in the teaching process. BIOL 750 and BIOL 918 are team-taught classes, with large contributions from experts working in modern biochemical and biophysical research.

An important part of my teaching is advising graduate and undergraduate researchers in applications of computational tools to answer chemical and biological questions.

Selected Publications —

See other papers by Krzysztof Kuczera on PubMed

  • Rydzewski, Jakub; Walczewska-Szewc, Katarzyna ; Czach, Sylwia; Caricato, Marco; Ren, Sijin; Stanton, Clara; Nowak, Wiesław; Kuczera, Krzysztof. Enhancing the Inhomogeneonus Photodynamics of Canonical Bacteriophytochrome. J.  Phys. Chem. B 2022, 126, 2647-2657.
  • Alex A Meier, Krzysztof Kuczera and Minae Mure. A 3D-predicted structure of the amine oxidase domain of lysyl oxidase-like 2. Int J Mol Sci 2022, 23, 13385.  doi.org/10.3390/ijms232113385
  • A. Wosztyl, K. Kuczera and R. Szoszkiewicz. Analytical approaches for deriving internal friction for selected alpha-helical peptides based entirely on molecular dynamics simulations. J. Phys Chem B, 2022, 126, 8901-8912. doi.org/10.1021/acs.jpcb.2c03076
  • K. Kuczera, R. Szoszkiewicz, C.L. Shaffer and G.S. Jas. GB1 hairpin dynamics: capturing the folding pathway with molecular dynamics, replica exchange and optimal dimensionality reduction. J Biomolec Struct Dyn, 41, 11671-11680, 2023. doi.org/10.1080/07391102.2022.2163427
  • Lou, Hao, Zhang, Yilue, Kuczera, Krzysztof, Hageman, Michael. and Schoneich, Christian. Molecular dynamics simulation of an iron(III) binding site on the Fc domain of IgG1 relevant for visible light-induced protein fragmentation. Molecular Pharmaceutics, 2024, 21, 501-512. 10.1021/acs.molpharmaceut.3c00612
  • K.H. Lee and K.Kuczera. Comparison of the Effect of Fluorinated Aliphatic and Aromatic Amino Acids on Stability at a Solvent-Exposed Position of a Globular Protein. Molecular Simulation, 2024, 50, 345-352. 10.1080/08927022.2024.2312141
  • Elinaz Farokhi, Ahmed Alaofi, Vivitri D. Prasasty, Filia Stephanie, Marlyn D. Laksitorini, Krzysztof Kuczera and Teruna J. Siahaan. Mechanism of the Blood-Brain Barrier Modulation by Cadherin Peptides, Exploration of Drug Science, 2024, 2:322-338. doi: 10.37349/eds.2024.00049.
  • Adam Świątek, Krzysztof Kuczera and Robert Szoszkiewicz. The effects of proline on internal friction in simulated folding dynamics of several alanine-based α-helical peptides. J Phys Chem B, 2024, 128, 3856-3869. doi:10.1021/acs.jpcb.4c00623