ANALYSIS OF METAL BINDING SITES IN PROTEINS
ANAMBS is a GUI tool developed for analysis of the microenvironment of metal heteroatom in proteins.This standalone tool can be used to derive metal neighborhood information. The metal binding site composition, orientation of various amino acids and atoms along with the Hydropathy index within the metal binding site region can be measured.
The tool facilitates simple and easy way to analyze metal groups
and their neighbors in a given PDB file. It follows very fast two-step
procedure to identify and visualize metal binding site residues for every query
structure.Other features include extracting FASTA sequence from PDB,query
string search in the FASTA , Hydrophobicity prediction ,Hetroatom listing, Hydropathy
plot ,Angle matrix generation.
METAL ENVIRONMENT DATABASE
An interactive database to query metalloproteins on the basis of PDB ID , Name or Class.MEDB was built using the tool ANAMBS. It presents quantitative information on metal-binding sites in protein structures. It can be used for identification of trends or patterns in the metal-binding sites.
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AMINO ACID PHILICITY PROFILE
The philicity profile or likeness profile of the amino acids for various biologically important metals was studied. The amino acids that occur most frequently at a specific metal binding site are shown in the figure below :
This result was obtained after studying a large metalloprotein dataset generated by inhouse programs on the metallprotein structures obtained from the Protein Data Bank. The order in the table are as per most philicity or likeness (e.g, ZN will prefer mostly HIS in it's nearest vicidity followed by CYS, ASP and GLU consequtively. THR or ASN means that both THR and ASN were found to have the most probable occurence frequency in that order).
Kuntal Kumar Bhusan
Prof. P. Reddanna
Eicosanoids,Inflammation and Cancer Research Group
Dept. of Animal Science
University of HyderabadIndia
Publication Link : click here
Pubmed ID : 20205657
Development of Tools and Database for Analysis of Metal Binding Sites in Protein pp.765-773 (9)
Kuntal BK, Aparoy P, Reddanna P.
Protein Pept Lett. 2010;17(6):765-73.