Myoglobin is a cytoplasmic hemoprotein expressed solely in cardiac myocytes and
April 5, 2017
Myoglobin is a cytoplasmic hemoprotein expressed solely in cardiac myocytes and oxidative skeletal muscle fibers that reversibly binds O2 by its heme residue. in with 27% similarity of template which is usually absent in PDB is used as subject for study (Accession: “type”:”entrez-protein” attrs :”text”:”AGG38019.1″ term_id :”456650379″ term_text :”AGG38019.1″AGG38019.1) Visualization and Model Validation: The three dimensional structure of myoglobin was generated by using PyMOL program (Physique 1). To verify the predicted structure validation was carried out with PROCHECK program. Ramachandran plot of non-glycine and non-proline residue in the structure showed that 94.5% of the total amino acids were presented in most favored regions and the other 5.5% of amino acids were presented in allowed regions including disallowed region with 0.0%. VERIFY_3D shows 99.32% of the residues had an averaged 3D-1D score greater than 0.2 indicates that the environment profile of the model is good. ERRAT2 shows 99.275% overall quality factors indicating good resolution structure. Moreover quality of the model can be compared to reference structure of high resolution obtained from X-Ray crystallography analysis through Z score and “0” is the average Z score for good model. The Z score of myoglobin is usually -7.8 showing the possibility to be a better model. Physique 1 3 structure of the predicted model by PyMOL. BTZ043 Prediction of Protein Structure: The secondary Rabbit polyclonal to PLS3. analysis indicates whether a given amino acid is located in helix strand or coil. The result obtained from SOPMA described that about 70.75% of amino acids presented in alpha helix 6.12% of amino acids in beta turn and 23.13% of amino acids in random coil. Prediction of Active Site: A total BTZ043 of 15 active sites were evaluated in the structure through CASTp software with ideal parameters. All 15 pockets were characterized to find out its residues around probe radius of 1 1.4? and among them largest active site has an area of 803.6 ? and volume of 905.3 ?. The green color (Physique 2) shows BTZ043 the largest active site position in the build protein which lies between amino acid 1 and 147. Physique 2 Active site in predicted model computed with CASTp. Green color represents active site with largest area BTZ043 and volume and other colors represent the remaining active site with different areas and volumes. Predicting of Antigenic Determinants: There are total 8 antigenic determinants in the sequence. These antigenic determinants are: PHE4-GLY12 ARG20-THR31 GLU35-ASP50 THR53-GLU70 GLY76-HIS89 HIS93-PHE100 LEU102-GLU109 and ALA124-THR134. Prediction of Heme Binding Sites: There are total 17 ligand binding sites present in the structure. These sites are THR36 LEU39 PHE40 PRO41 LYS42 HIS60 THR63 VAL64 LYS67 LEU85 SER88 HIS89 HIS93 ILE95 ASN99 PHE100 and ILE103 which can bind to one cluster of 25 ligands (heme). Accessible surface area (ASA) analysis of the predicted model showed the amino acids with low ASA value are buried inside the catalytic cleft and with high ASA values are on the surface of the cleft. Some of the residues were found to have high ASA values (GLU15 PRO41 LYS42 LYS83 LYS92 HIS93) and some others were found to have low ASA values (VAL7 VAL14 GLY22 LEU26 ILE51 VAL57 GLY61 LEU72 LEU82 ALA90 ALA108 LEU111 GLY121 LEU125 VAL128 TYR140). The active site amino acids which are hydrophobic are VAL7 VAL14 GLY22 LEU72 LEU82 LEU111 VAL128 with low ASA values. While those active site amino acids which is usually hydrophilic are LYS42 LYS92 HIS93 with high values. The protein has 22% amino acids are hydrophilic 50 are hydrophobic and 27% others. Molecular weight of the protein is usually 15806.42 g/mol isoelectric point is pH=7.51. The protein has poor water solubility. Conclusion In this study we proposed a valid and stable 3D model of Myoglobin in Channa striata whose structure is not present in PDB (Protein Data Lender). Further analysis provides information about its active sites ligand binding sites antigenic determinants and their ASA value analysis in the predicted model. On the basis of the findings it could be concluded that further characterization of Myoglobin in Channa striata will be important as the nitric oxide (NO) scavenger and myoglobinmediated oxidative phosphorylation. This study can be used in broad screening on inhibitors of the protein and can be effectively used to raise monoclonal.