De novo determination of protein structure by NMR using orientational and long-range order restraints

Abstract

Orientational and novel long-range order restraints available from paramagnetic systems have been used to determine the backbone solution structure of the cytochrome c H 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 de®ne uniquely the fold and re®ne the tertiary structure of the protein (0.73 A Ê backbone rmsd for 82/129 amino acid residues) starting from random atomic Cartesian coordinates. The structure calculation protocol, developed using speci®c 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¯oat freely, and are thus simultaneously determined, and found to converge, during the structure calculation.

Structure determination and dynamics of protein–RNA complexes by NMR spectroscopy

“…In addition to assisting global protein fold determination [273,285], paramagnetic relaxation enhancement has been widely used for positioning components in macromolecular complexes relative to one another, especially when no or only a sparse number of intermolecular NOEs or RDC measurements were available or not sufficient [275,[286][287][288]. Clore and coworkers in particular made very interesting usage of PRE measurements for elucidating transient macromolecular interactions in protein-protein and protein-DNA complexes [272,289].…”

Nuclear Magnetic Resonance-Based Modeling and Refinement of Protein Three-Dimensional Structures and Their Complexes

“…the calculation process. They have been implemented in several computer programs, among which are CNS [11], Xplor-NIH [37], CYANA [38], SCULPTOR [39], the SANDER module of AMBER [40], and even GROMACS [41]. The most commonly used are CYANA and Xplor/CNS.…”

Quantitative Analysis of Biomolecular NMR Spectra: A Prerequisite for the Determination of the Structure and Dynamics of Biomolecules

“…A strategy for structure determination using RDCs along with long-range order restraints available from paramagnetic systems [144] has permitted the de novo determination of a cytochrome structure.…”