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Ligand and interfacial dynamics in a homodimeric hemoglobin

Gupta, Prashant Kumar and Meuwly, Markus. (2016) Ligand and interfacial dynamics in a homodimeric hemoglobin. Structural Dynamics, 3 (1). 012003.

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Abstract

The structural dynamics of dimeric hemoglobin (HbI) from Scapharca inaequivalvis in different ligand-binding states is studied from atomistic simulations on the μs time scale. The intermediates 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 determined experimentally for the fully ligand-bound and ligand-free proteins, respectively. The dynamics of the two monomers is asymmetric on the 100 ns timescale. Several spontaneous rotations of the Phe97 side chain are observed which 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.
Faculties and Departments:05 Faculty of Science > Departement Chemie > Chemie > Physikalische Chemie (Meuwly)
UniBasel Contributors:Meuwly, Markus
Item Type:Article, refereed
Publisher:AIP Publishing
e-ISSN:2329-7778
Note:Publication type according to Uni Basel Research Database: Journal article
Language:English
Identification Number:
Last Modified:24 Apr 2017 09:49
Deposited On:25 Jan 2017 12:33

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