Title: Protein structure modeling using backbone chemical shifts
Abstract: Alexis Marius Wanko University of Liege Email: [email protected] Contact 1. Lisa R. Structure of the bamc two-domain protein obtained by rosetta with a limited nmr data set. 2011. 2. James M. Thompsona, Nikolaos G. Sgourakisa, Gaohua Liub, Paolo Rossib, Yuefeng Tangb, Jeffrey L. Millsc, Thomas Szyperskic, Gaetano T. Montelioneb, and David Bakera. Accurate protein structure modeling using sparse NMR data and homologous structure information. PNAS 2012 3. David S. Wishart, David Arndt, Mark Berjanskii, Peter Tang, Jianjun Zhou1 and Guohui Lin1 CS23D: a web server for rapid protein structure generation using NMR chemical shifts and sequence data. Nucleic Acids Research, 30 May 2008, Vol. 36. 4. Berjanskii,M.V., Neal,S. and Wishart,D.S. (2006) PREDITOR:a web server for predicting protein torsion angle restraints. Nucleic Acids Res. 5. Chris A.E.M. Spronka, Sander B. Nabuursa, Elmar Kriegera, Gert Vrienda, Geerten W. Vuisterb. Validation of protein structures derived by NMR spectroscopy. Nuclear Magnetic Resonance Spectroscopy 45 (2004) 315–337. 6. Mark Berjanskii, Peter Tang, Jack Liang, Joseph A. Cruz, Jianjun Zhou,Edward Bassett, Cam MacDonell, Paul Lu, Guohui Lin, and David S. Wishart. GeNMR: a web server for rapid NMR-based protein structure determination. Nucleic Acids Res, 2009. 7. Benjamin Bardiaux. Structure calculation of proteins from solution and solid-state NMR data : Application to monomers and symmetric aggregates. PhD thesis. January, 2009 8. Geerten W. Vuister , Rasmus H. Fogh, Pieter M. S. Hendrickx, Jurgen F. Doreleijers and Aleksandras Gutmanas. An overview of tools for the validation of protein NMR structures. J Biomol NMR (2014) 58:259–285 9. G. Fuentes, A.D.J. van Dijk, and A.M.J.J. Bonvin Nuclear Magnetic Resonance-Based Modeling and Refinement of Protein Three-Dimensional Structures and Their Complexes. Methods in Molecular Biology, vol. 443, Molecular Modelling of Proteins References The knowledge of the tridimensional structure of a protein is essential to study its interactions and understand its mode of action. In order to determine the three-dimensional structure of proteins, several NMR data can be used (Backbone chemical shifts (CS), NOE distances, residual dipolar coupling, ...). Among these parameters, backbone chemical shifts data are NMR parameters that can be rapidly, easily and accurately measured. This parameter is very sensitive to the conformation of amino acids and is used to deduct the secondary structure (TALOS, RCI,...). Therefore, the backbone chemical shifts can be used as constraints on dihedral angles to quickly and easily determine protein structure. Several « de novo » methods like CS-Rosetta, CS23D and CHESHIRE have been recently developed in this purpose. Introduction
Publication Year: 2015
Publication Date: 2015-12-01
Language: en
Type: article
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