Structure Prediction of a Multi-domain EF-hand Ca2+ Binding Protein by PROPAINOR

Overview

Journal J Mol Model

Publisher Springer

Specialty Molecular Biology

Date 2005 Aug 12

PMID 16094534

Citations 4

Authors

Subramanian Jyothi

Sourajit M Mustafi

Kandala V R Chary

Rajani R Joshi

Affiliations

Soon will be listed here.

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.

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References

Stanfel L . A new approach to clustering the amino acids. J Theor Biol. 1996; 183(2):195-205. DOI: 10.1006/jtbi.1996.0213. View

Katchalski-Katzir E, Shariv I, Eisenstein M, Friesem A, Aflalo C, Vakser I . Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. Proc Natl Acad Sci U S A. 1992; 89(6):2195-9. PMC: 48623. DOI: 10.1073/pnas.89.6.2195. View

Atreya H, Sahu S, Bhattacharya A, Chary K, Govil G . NMR derived solution structure of an EF-hand calcium-binding protein from Entamoeba Histolytica. Biochemistry. 2001; 40(48):14392-403. DOI: 10.1021/bi0114978. View

Kolaskar A, Kulkarni-Kale U . Prediction of three-dimensional structure and mapping of conformational epitopes of envelope glycoprotein of Japanese encephalitis virus. Virology. 1999; 261(1):31-42. DOI: 10.1006/viro.1999.9859. View

Holm L, Sander C . Database algorithm for generating protein backbone and side-chain co-ordinates from a C alpha trace application to model building and detection of co-ordinate errors. J Mol Biol. 1991; 218(1):183-94. DOI: 10.1016/0022-2836(91)90883-8. View

Moorthy A, Gopal B, Satish P, Bhattacharya S, Bhattacharya A, Murthy M . Thermodynamics of target peptide recognition by calmodulin and a calmodulin analogue: implications for the role of the central linker. FEBS Lett. 1999; 461(1-2):19-24. DOI: 10.1016/s0014-5793(99)01380-0. View

Colovos C, Yeates T . Verification of protein structures: patterns of nonbonded atomic interactions. Protein Sci. 1993; 2(9):1511-9. PMC: 2142462. DOI: 10.1002/pro.5560020916. View

Jyothi S, Joshi R . Protein structure determination by non-parametric regression and knowledge-based constraints. Comput Chem. 2001; 25(3):283-99. DOI: 10.1016/s0097-8485(00)00104-2. View

Vakser I . Protein docking for low-resolution structures. Protein Eng. 1995; 8(4):371-7. DOI: 10.1093/protein/8.4.371. View

10.

Aszodi A, Gradwell M, Taylor W . Global fold determination from a small number of distance restraints. J Mol Biol. 1995; 251(2):308-26. DOI: 10.1006/jmbi.1995.0436. View

11.

Rodriguez R, Chinea G, Lopez N, Pons T, Vriend G . Homology modeling, model and software evaluation: three related resources. Bioinformatics. 1998; 14(6):523-8. DOI: 10.1093/bioinformatics/14.6.523. View

12.

Joshi R, Jyothi S . Ab-initio prediction and reliability of protein structural genomics by PROPAINOR algorithm. Comput Biol Chem. 2003; 27(3):241-52. DOI: 10.1016/s0097-8485(02)00074-8. View

13.

Guex N, Peitsch M . SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis. 1998; 18(15):2714-23. DOI: 10.1002/elps.1150181505. View

14.

Joshi R, Jyothi S . Ab initio structure of human seminal plasma prostatic inhibin gives significant insight into its biological functions. J Mol Model. 2002; 8(2):50-7. DOI: 10.1007/s00894-001-0063-8. View

15.

Chou P, Fasman G . Conformational parameters for amino acids in helical, beta-sheet, and random coil regions calculated from proteins. Biochemistry. 1974; 13(2):211-22. DOI: 10.1021/bi00699a001. View

16.

Maulet Y, Cox J . Structural changes in melittin and calmodulin upon complex formation and their modulation by calcium. Biochemistry. 1983; 22(24):5680-6. DOI: 10.1021/bi00293a035. View

17.

Sippl M . Knowledge-based potentials for proteins. Curr Opin Struct Biol. 1995; 5(2):229-35. DOI: 10.1016/0959-440x(95)80081-6. View

18.

Sippl M . Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. J Mol Biol. 1990; 213(4):859-83. DOI: 10.1016/s0022-2836(05)80269-4. View