Structure prediction of a multi-domain EF-hand Ca2+ binding protein by PROPAINOR |
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Authors: | Subramanian Jyothi Sourajit M Mustafi Kandala V R Chary Rajani R Joshi |
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Institution: | (1) Department Mathematics, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India;(2) Statistics Division, Nicholas-Piramal (India) Ltd., Mumbai, India;(3) Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, 400005, India |
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Abstract: | 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.
Figure The predicted 3D Structure of EhCaBP with bound Ca2+ ions (CaBP-0). In the structure, α-helices are shown in pink and the β-strands in yellow. Ca2+ ions are depicted as fluorescent green balls. Some of the residues in the calcium-binding loops are depicted in space-fill
representation.
![MediaObjects/894_2005_256_Figa_HTML.jpg](/content/mr32000037jh5126/MediaObjects/894_2005_256_Figa_HTML.jpg) |
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Keywords: | Computational protein structure prediction Distance geometry NMR Nonparametric statistics |
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