De novo determination of protein structure by NMR using orientational and long-range order restraints.
Orientational and novel long-range order restraints available from paramagnetic systems have been used to determine the backbone solution structure of the cytochrome c' protein to atomic resolution in the complete absence of restraints derived from the nuclear Overhauser effect. By exploiting the complementary geometric dependence of paramagnetic pseudocontact shifts and the recently proposed Curie-dipolar cross correlated relaxation effect, in combination with orientational constraints derived from residual dipolar coupling, autorelaxation rate ratios and secondary structure constraints, it is possible to define uniquely the fold and refine the tertiary structure of the protein (0.73 A backbone rmsd for 82/129 amino acid residues) starting from random atomic Cartesian coordinates. The structure calculation protocol, developed using specific models to describe the novel constraint interactions, is robust, requiring no precise a priori estimation of the various interaction strengths, and provides unambiguous convergence based only on the value of the target function. Tensor eigenvalues and their component orientations are allowed to float freely, and are thus simultaneously determined, and found to converge, during the structure calculation.
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Jean-Pierre Ebel C.N.R.S. C.E.A., Institut de Biologie Structurale, 41, rue Jules Horowitz, Grenoble Cedex, 38027, France.
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Blackledge
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D000465:Algorithms; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D003574:Cytochrome c Group / Q000737:chemistry* / Q000378:metabolism; D004583:Electrons; D008280:Magnetics; D008674:Metals, Rare Earth / Q000378:metabolism; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D010084:Oxidation-Reduction; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D015203:Reproducibility of Results; D016354:Rhodobacter capsulatus / Q000201:enzymology*; D013113:Spin Labels; D013816:Thermodynamics
D003574:Cytochrome c Group; D008674:Metals, Rare Earth; D013113:Spin Labels