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Journal of Molecular Modeling

, 25:361 | Cite as

Cooperativity of hydrogen bonding network in microsolvated biotin, the ligand of avidin class proteins

  • Aneta Jezierska
  • Jarosław Jan PanekEmail author
Original Paper
Part of the following topical collections:
  1. Zdzislaw Latajka 70th Birthday Festschrift

Abstract

Biotin is well known to be bound with exceptional strength by the avidin class of proteins. This ability comes from a match between the biotin-binding pocket of the protein and the structural elements of biotin, including its ureido and thiolane rings. Here we investigate the solvation shell of biotin in water as revealed by classical force field molecular dynamics with GAFF force field. Snapshots from the classical molecular dynamics were then used to generate microsolvated structures. Details of hydrogen bonding patterns present in these microsolvated structures were studied by symmetry-adapted perturbation theory (SAPT). Interaction energy values for small models of biotin hydrated by 5 or 6 water molecules show that the cooperativity constitutes 15–22% of the total interaction energy and corresponds roughly to formation of one additional hydrogen bond to biotin. The SAPT analysis shows the differences underlying hydrogen bonds of similar strength (with oxygen or sulfur atoms as the hydrogen bond acceptors, and with nitrogen atom playing a dual role of the donor and acceptor).

Keywords

Biotin Avidin ligand Microsolvation Hydrogen bonding cooperativity Interaction energy Symmetry-adapted perturbation theory 

Notes

Acknowledgments

The use of computational resources of Wrocław Center for Networking and Supercomputing (WCSS) and Interdisciplinary Center of Modeling (ICM Warsaw) is gratefully acknowledged.

Funding information

The authors received financial support from the National Science Centre (NCN Poland) under the grant no. UMO-2013/09/B/ST4/00279.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

894_2019_4253_MOESM1_ESM.pdf (509 kb)
ESM 1 (PDF 509 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Faculty of ChemistryUniversity of WrocławWrocławPoland

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