Structure prediction of a multi-domain EF-hand Ca2+ binding protein by PROPAINOR.
PROPAINOR is a new algorithm developed for ab initio prediction of the 3D structures of proteins using knowledge-based nonparametric multivariate statistical methods. This algorithm is found to be most efficient in terms of computational simplicity and prediction accuracy for single-domain proteins as compared to other ab initio methods. In this paper, we have used the algorithm for the atomic structure prediction of a multi-domain (two-domain) calcium-binding protein, whose solution structure has been deposited in the PDB recently (PDB ID: 1JFK). We have studied the sensitivity of the predicted structure to NMR distance restraints with their incorporation as an additional input. Further, we have compared the predicted structures in both these cases with the NMR derived solution structure reported earlier. We have also validated the refined structure for proper stereochemistry and favorable packing environment with good results and elucidated the role of the central linker.
Jyothi
Subramanian
S
Department Mathematics, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
Mustafi
Sourajit M
SM
Chary
Kandala V R
KV
Joshi
Rajani R
RR
D000818:Animals; D002118:Calcium / Q000737:chemistry* / Q000378:metabolism*; D002135:Calcium-Binding Proteins / Q000737:chemistry* / Q000378:metabolism*; D002413:Cations, Divalent / Q000737:chemistry; D019295:Computational Biology; D030562:Databases, Protein; D020832:EF Hand Motifs; D004748:Entamoeba histolytica / Q000737:chemistry / Q000378:metabolism; D020407:Internet; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D017434:Protein Structure, Tertiary
D002135:Calcium-Binding Proteins; D002413:Cations, Divalent; D002118:Calcium