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Proceedings Paper

Molecular dynamics simulation of ferredoxin in different electronic states
Author(s): Nikolay K. Balabaev; A. S. Lemak
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Paper Abstract

Molecular dynamics simulation of bacterial ferredoxin (Peptococcus aerogenes) at constant temperature have been performed. There are two iron-sulfur Fe4S4 clusters in the protein molecule of ferredoxin, which can be in various charge states. After the protein was changed instantaneously from oxidized state in reduced one, the unexpected behavior of the distance between clusters had been observed. Strong coupling of negative charged clusters to the protein matrix provides the clusters come closer together by approximately 0.5 angstroms when the charge on one of them have been increased, even though this charge change leads to an increase in the intercluster repulsion. The molecular dynamics trajectory have been used to specify a quasi-harmonical model to describe a low frequency motions of the protein. In the model each of amino acids and each of iron-sulfur clusters appears as an elementary unit.

Paper Details

Date Published: 17 June 1993
PDF: 11 pages
Proc. SPIE 1921, Laser Spectroscopy of Biomolecules, (17 June 1993); doi: 10.1117/12.146144
Show Author Affiliations
Nikolay K. Balabaev, Institute of Mathematical Problems of Biology (Russia)
A. S. Lemak, Institute of Mathematical Problems of Biology (Russia)


Published in SPIE Proceedings Vol. 1921:
Laser Spectroscopy of Biomolecules

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