Metalloproteins
ANAMBS
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.
The tool can be used for studying the metal group binding modes with relevance to protein structure, function, prediction, modeling and design. The information obtained can be used to generate structural templates from metal binding sites of known enzymes, and to develop constraints for computational modeling of metalloproteins. This tool can be used to validate the side chain placement in metal binding sites built by computational techniques like homology modelling.
MEDB
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.
AAPP
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).
Publication:
- https://www.ncbi.nlm.nih.gov/pubmed/20205657