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Title

 

 

 

 

 

Predicted metal binding sites for phytoremediation

Authors

 

Ashok Sharma*, Sudeep Roy, Kumar Parijat Tripathi, Pratibha Roy, Manoj Mishra, Feroz Khan, Abha Meena

 

Affiliation

 

Bioiformatics and In-Silico Biology, Central Institute of Medicinal and Aromatic Plants (Council of Scientific and Industrial Research), P.O Lucknow (226015), India

 

Email

 

ashoksharma@cimap.res.in

Article Type

 

Hypothesis

Date

 

Received March 05, 2009; Revised April 15, 2009; Accepted July 18, 2009; Published September 05, 2009

Abstract

Metal ion binding domains are found in proteins that mediate transport, buffering or detoxification of metal ions. The objective of the study is to design and analyze metal binding motifs against the genes involved in phytoremediation. This is being done on the basis of certain pre-requisite amino-acid residues known to bind metal ions/metal complexes in medicinal and aromatic plants (MAPís). Earlier work on MAPís have shown that heavy metals accumulated by aromatic and medicinal plants do not appear in the essential oil  and that some of these species are able to grow in metal contaminated sites.  A pattern search against the UniProtKB/Swiss-Prot and UniProtKB/TrEMBL databases yielded true positives in each case showing the high specificity of the motifs designed for the ions of  nickel, lead, molybdenum, manganese, cadmium, zinc, iron, cobalt and xenobiotic compounds. Motifs were also studied against PDB structures. Results of the study suggested the presence of binding sites on the surface of protein molecules involved. PDB structures of proteins were finally predicted for the binding sites functionality in their respective phytoremediation usage. This was further validated through CASTp server to study its physico-chemical properties. Bioinformatics implications would help in designing strategy for developing transgenic plants with increased metal binding capacity. These metal binding factors can be used to restrict metal update by plants. This helps in reducing the possibility of metal movement into the food chain.

 

Keywords

 

Phytoremediation; medicinal and aromatic plants (MAPs); putative metal binding sites

 

Citation

 

Sharma et al., Bioinformation 4(2): 66-70 (2009)

Edited by

 

P. Kangueane

 

ISSN

 

0973-2063

 

Publisher

 

Biomedical Informatics

 

License

 

 

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.