Instytut Podstawowych Problemów Techniki
Polskiej Akademii Nauk


John Hermansen

Central University of the Caribbean (US)

Ostatnie publikacje
1.  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.

Słowa kluczowe:
molecular dynamics simulations, fluorescence anisotropy, peptides, orientational motion

Afiliacje autorów:
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. - inna afiliacja

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