Ligand and interfacial dynamics in a homodimeric hemoglobin | Zendy

Prashant Kumar Gupta | Zendy; Markus Meuwly | Zendy

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Ligand and interfacial dynamics in a homodimeric hemoglobin

Author(s) -

Prashant Kumar Gupta,

Markus Meuwly

Publication year - 2016

Publication title -

structural dynamics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 1.415

H-Index - 29

ISSN - 2329-7778

DOI - 10.1063/1.4940228

Subject(s) - ligand (biochemistry) , chemistry , molecular dynamics , crystallography , heme , side chain , salt bridge , stereochemistry , chemical physics , computational chemistry , receptor , polymer , biochemistry , organic chemistry , mutant , gene , enzyme

The structural dynamics of dimeric hemoglobin (HbI) from Scapharcainaequivalvis in different ligand-binding states is studied fromatomistic simulations on the μs time scale. Theintermediates are between the fully ligand-bound (R) and ligand-free (T) states.Tertiary structural changes, such as rotation of the side chain of Phe97,breaking of the Lys96–heme salt bridge, and the Fe–Fe separation,are characterized and the water dynamics along the R-T transition is analyzed.All these properties for the intermediates are bracketed by those determinedexperimentally for the fully ligand-bound and ligand-free proteins,respectively. The dynamics of the two monomers is asymmetric on the 100 nstimescale. Several spontaneous rotations of the Phe97 side chain are observedwhich suggest a typical time scale of 50–100 ns for this process.Ligand migration pathways include regions between the B/G and C/G helices and,if observed, take place in the 100 ns time scale

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