title: Protein-protein docking on molecular models of Aspergillus niger RNase and human actin: novel target for anticancer therapeutics.
abstract: The 3D models of human actin protein and A.niger RNase were designed using the templates ACTBIND (PDB ID: 3D3Z) and crystalline profilin-beta-actin (PDB ID: 2BTF), respectively in Modeller9v5. These models are testified using several validation methods including PROCHECK, ERRAT, WHAT-IF, PROSA2003 and VERIFY-3D. The stereo-chemical quality of the models was judged by Ramachandran plot with PROCHECK. The total quality G-factor -0.2, shows a good quality model. The ERRAT score for the human actin and A.niger RNase models are 86.104 and 84.615, respectively, fit well within the range of a high quality model. The ERRAT score for the templates 2BTF and 3D3Z are 91.111 and 97.391, respectively. The WHAT-IF evaluation justifies a reasonable homology model structure as none of the scores for each residue in the homology model is lower than -5.0. The energy-minimized model of human actin with PROSA reveals the Z-score value -10.52 between native conformations of the crystal structures. The VERIFY 3D average score is 0.36. All evidence suggests that the geometric quality of the backbone conformation, the residue interaction, the residue contact and the energy profile of the structures were well within the limits of reliable structures. The interaction energy of docking was calculated using the HEX server. The Etotal, lowest docked energy, and calculated RMSD values were -1.608 kcal mol(-1), -8.369 kcal mol(-1) and 0.617 Å, respectively. The study presented in the current project may be useful to design molecules that may have anticancer activity.
authors.affiliation: School of Biochemical Engineering, Institute of Technology, Banaras Hindu University, Varanasi 221005, India. ravi_33102000@yahoo.com
authors.forename: Ravi Kumar
authors.initials: RK
authors.lastname: Gundampati
authors.forename: Rajasekhar
authors.initials: R
authors.lastname: Chikati
authors.forename: Moni
authors.initials: M
authors.lastname: Kumari
authors.forename: Anurag
authors.initials: A
authors.lastname: Sharma
authors.forename: Daliparthy Devi
authors.initials: DD
authors.lastname: Pratyush
authors.forename: Medicherla V
authors.initials: MV
authors.lastname: Jagannadham
authors.forename: Chitta Suresh
authors.initials: CS
authors.lastname: Kumar
authors.forename: Mira
authors.initials: M
authors.lastname: Debnath Das
mesh_terms: D000199:Actins / Q000737:chemistry*; D000595:Amino Acid Sequence; D000970:Antineoplastic Agents / Q000737:chemistry; D001234:Aspergillus niger / Q000201:enzymology*; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D015203:Reproducibility of Results; D012260:Ribonucleases / Q000737:chemistry*; D016415:Sequence Alignment
chemical_list: D000199:Actins; D000970:Antineoplastic Agents; D012260:Ribonucleases