Journal
MOLECULAR PHYSICS
Volume 108, Issue 2, Pages 215-220Publisher
TAYLOR & FRANCIS LTD
DOI: 10.1080/00268971003623393
Keywords
haemoglobin; bromophenol blue; electrophoresis; molecular modelling
Funding
- Science Foundation for The Excellent Youth Scholars of Tongji University, China [2008kj0670]
- Science Foundation for Youths of Shanghai Health Bureau, China [2008Y020]
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It has been observed that bromophenol blue interacted specifically with chicken haemoglobin but not with carp haemoglobin during electrophoresis, but the mechanism of interaction is still not well understood. In this computational study, the binding of bromophenol blue to chicken haemoglobin has been investigated using sequence alignment, homology modelling, electrostatic potential distribution and flexible docking methods. Molecular modelling studies reveal that bromophenol blue-binding site, formed by residues Val1 alpha, Leu2 alpha, Ala131 alpha, Thr134 alpha, Ala138 alpha and Arg141 alpha, is located between two alpha chains of chicken haemoglobin, and the binding is dominated by hydrophobic interactions. Moreover, comparison of chicken and carp haemoglobin structural models provides a structural rationale for the recognition of bromophenol blue by chicken haemoglobin. These principles can in turn be used to study the molecular recognition mechanism and design a mimic of bromophenol blue for the development of new haemoglobin binders.
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