Institute of Fundamental Technological Research
Polish Academy of Sciences


Krzysztof Kuczera

Recent publications
1.  Kuczera K., Jas G.S., Ekiel-Jeżewska M.L., Melikhov Y., Reorientation motions of N-acetyl-tryptophan-amide (NATA dipeptide) in aqueous solution and with co-solvents: molecular dynamics vs hydrodynamic model, PHYSICS OF FLUIDS, ISSN: 1070-6631, DOI: 10.1063/5.0031554, Vol.32, pp.127111-1-14, 2020

We present a study of peptide reorientational dynamics in solution analyzed from the perspective of fluorescence anisotropy decay (FAD) experiments, and atomistic molecular dynamics (MD) and continuum hydrodynamics modeling. Earlier, FAD measurements and MD simulations of the model dipeptide N-acetyltryptophanamide (NATA) in explicit water and in aqueous solutions of urea, guanidinium chloride, and proline co-solvents identified excellent agreement of MD results with experimental data, indicating the presence of significant effects of peptide–solvent interactions, and the overall tumbling of the peptide could be well described by contributions from individual conformers, represented by dihedral-restrained MD. Here, we extend these studies by analyzing dynamic inhomogeneity in the solutions and by developing a hydrodynamic model (HM) of the conformer dynamics. The MD simulation data indicate the presence of markedly different dynamic microenvironments for the four studied solutions, with the average water reorientations being different in all systems, partly reflecting the bulk viscosities. Additionally, the water dynamics also exhibited a marked slowdown in the vicinity of the co-solvents, especially chloride and proline. To gain further insight, we applied the HM to predict rotational correlation times of tryptophan for the individual NATA conformers identified in MD. The hydrodynamic results were in very good agreement with MD simulations for the individual structures, showing that the HM model provides a realistic description of rotational diffusion for rigid peptide structures. Overall, our study generated new microscopic insights into the complex nature of the structure and dynamics of peptide solvation shells for systems containing water and denaturing and stabilizing co-solvents.

Kuczera K. - other affiliation
Jas G.S. - University of Kansas (US)
Ekiel-Jeżewska M.L. - IPPT PAN
Melikhov Y. - IPPT PAN
2.  Jas G.S., Rentchler E.C., Słowicka A.M., Hermansen J.R., Johnson C.K., Middaugh C.R., Kuczera K., Reorientation Motion and Preferential Interactions of a Peptide in Denaturants and Osmolyte, JOURNAL OF PHYSICAL CHEMISTRY B, ISSN: 1520-6106, DOI: 10.1021/acs.jpcb.6b00028, Vol.120, pp.3089-3099, 2016

Fluorescence anisotropy decay measurements and all atom molecular dynamics simulations are used to characterize the orientational motion and preferential interaction of a peptide, N-acetyl-tryptophan-amide (NATA) containing two peptide bonds, in aqueous, urea, guanidinium chloride (GdmCl), and proline solution. Anisotropy decay measurements as a function of temperature and concentration showed moderate slowing of reorientations in urea and GdmCl and very strong slowing in proline solution, relative to water. These effects deviate significantly from simple proportionality of peptide tumbling time to solvent viscosity, leading to the investigation of microscopic preferential interaction behavior through molecular dynamics simulations. Examination of the interactions of denaturants and osmolyte with the peptide backbone uncovers the presence of strongest interaction with urea, intermediate with proline, and weakest with GdmCl. In contrast, the strongest preferential solvation of the peptide side chain is by the nonpolar part of the proline zwitterion, followed by urea, and GdmCl. Interestingly, the local density of urea around the side chain is higher, but the GdmCl distribution is more organized. Thus, the computed preferential solvation of the side chain by the denaturants and osmolyte can account for the trend in reorientation rates. Analysis of water structure and its dynamics uncovered underlying differences between urea, GdmCl, and proline. Urea exerted the smallest perturbation of water behavior. GdmCl had a larger effect on water, slowing kinetics and stabilizing interactions. Proline had the largest overall interactions, exhibiting a strong stabilizing effect on both water–water and water–peptide hydrogen bonds. The results for this elementary peptide system demonstrate significant differences in microscopic behavior of the examined solvent environments. For the commonly used denaturants, urea tends to form disorganized local aggregates around the peptide groups and has little influence on water, while GdmCl only forms specific interactions with the side chain and tends to destabilize water structure. The protective osmolyte proline has the strongest and most specific interactions with the tryptophan side chain, and also stabilizes both water–water and water–peptide hydrogen bonds. Our results strongly suggest protein or peptide denaturation triggered by urea occurs by direct interaction, whereas GdmCl interacts favorably with side chains and destabilizes peptide–water hydrogen bonds. The stabilization of biopolymers by an osmolyte such as proline is governed by favorable preferential interaction with the side chains and stabilization of water.

molecular dynamics simulations, fluorescence anisotropy, peptides, orientational motion

Jas G.S. - University of Kansas (US)
Rentchler E.C. - University of Kansas (US)
Słowicka A.M. - IPPT PAN
Hermansen J.R. - Central University of the Caribbean (US)
Johnson C.K. - University of Kansas (US)
Middaugh C.R. - University of Kansas (US)
Kuczera K. - other affiliation

Conference abstracts
1.  Melikhov Y., Ekiel-Jeżewska M.L., Jas G.S., Kuczera K., Hydrodynamic approach to compute reorientation times of NATA protein in different solutions: comparison with Molecular Dynamics and experiment, APS/DFD 2019, 72nd Annual Meeting of the APS Division of Fluid Dynamics, 2019-11-23/11-26, Seattle (US), pp.1, 2019

Category A Plus


logo ippt            Pawińskiego 5B, 02-106 Warsaw
  +48 22 826 12 81 (central)
  +48 22 826 98 15

Find Us

© Institute of Fundamental Technological Research Polish Academy of Sciences 2021