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South African Journal of Chemistry

On-line version ISSN 1996-840X
Print version ISSN 0379-4350

S.Afr.j.chem. (Online) vol.65  Durban  2012

 

RESEARCH ARTICLE

 

A molecular dynamics study of lunasin

 

 

Parvesh Singh; Krishna Bisetty*

Department of Chemistry, Durban University of Technology, Steve Biko campus, P. O. Box 1334, Durban, 4000, South Africa

 

 


ABSTRACT

Lunasin, a 43 amino acid peptide, suppresses chemically induced transformations in mammalian cells and skin carcinogenesis in mice. This peptide has also been reported to exhibit very good bioavailability after its oral administration. However, despite its biological and medicinal significance, the exact three-dimensional (3D) structure of lunasinis thus far not yet fully characterized. Thus this work is aimed at exploring the conformational profile of lunasin,using classical molecular dynamics (MD) simulations at the time scale of 300 ns. The results obtained from the MD trajectory reveal that lunasin has a strong propensity to exhibit three characteristic a helical bundles in its structure supported by residues His5-Cys10, Cys22-Ile30 and Asp35-Asp41. The reported cell adhesion motif (Arg-Gly-Asp) of lunasin responsible for its binding to cell chromatin, on other hand, did not exhibit any characteristic secondary feature. The structural information obtained from the current study could be useful to better understand the bioactive conformation of lunasin.

Keywords: Lunasin, molecular dynamics, amber, CLASICO, α-helix, β-turn, PTRAJ, RGD, RMSD


 

 

Full text available only in PDF format.

 

Acknowledgements

Dr. P. Singh gratefully acknowledges financial support from the Durban University of Technology and the National Research Foundation for the position of a Research Associate. K.B. gratefully acknowledges the experiences and insights gained from the Spanish collaborators (Professor Juan J Perez and co-workers) - through the SA-Spain bilateral agreement. The authors would like to express their acknowledgement to the Centre for High Performance Computing, an initiative supported by the Department of Science and Technology of South Africa.

 

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Received 18 November 2011
Revised 13 March 2012
Accepted 8 May 2012

 

 

Submitted by invitation to celebrate 2011 the 'International Year of Chemistry'.
* To whom correspondence should be addressed. E-mail: bisettyk@dut.ac.za

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