Simultaneous single-structure and bundle representation of protein NMR structures in torsion angle space.

Journal of Biomolecular NMR
Daniel GottsteinPeter Güntert

Abstract

A method is introduced to represent an ensemble of conformers of a protein by a single structure in torsion angle space that lies closest to the averaged Cartesian coordinates while maintaining perfect covalent geometry and on average equal steric quality and an equally good fit to the experimental (e.g. NMR) data as the individual conformers of the ensemble. The single representative 'regmean structure' is obtained by simulated annealing in torsion angle space with the program CYANA using as input data the experimental restraints, restraints for the atom positions relative to the average Cartesian coordinates, and restraints for the torsion angles relative to the corresponding principal cluster average values of the ensemble. The method was applied to 11 proteins for which NMR structure ensembles are available, and compared to alternative, commonly used simple approaches for selecting a single representative structure, e.g. the structure from the ensemble that best fulfills the experimental and steric restraints, or the structure from the ensemble that has the lowest RMSD value to the average Cartesian coordinates. In all cases our method found a structure in torsion angle space that is significantly closer to the mean coordin...Continue Reading

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Citations

Aug 21, 2012·The Journal of Biological Chemistry·Nina A ChristJens Wöhnert
Mar 10, 2016·Progress in Nuclear Magnetic Resonance Spectroscopy·Azzurra CarlonClaudio Luchinat
Mar 25, 2015·Journal of Biomolecular NMR·Peter Güntert, Lena Buchner
Apr 5, 2014·Acta Crystallographica. Section D, Biological Crystallography·Mauro RinaldelliClaudio Luchinat
Oct 16, 2015·The Journal of Biological Chemistry·Carolin HackerJens Wöhnert
Apr 7, 2021·Chemistry : a European Journal·Johannes ZehnderThomas Wiegand
Jul 21, 2021·The Journal of Biological Chemistry·Lara RheinemannWesley I Sundquist
Aug 3, 2021·Journal of Biomolecular NMR·Stefano CucuzzaOliver Zerbe

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