Protein structure determination from NMR chemical shifts

Abstract

NMR spectroscopy plays a major role in the determination of the structures and dynamics of proteins and other biological macromolecules. Chemical shifts are the most readily and accurately measurable NMR parameters, and they reflect with great specificity the conformations of native and nonnative states of proteins. We show, using 11 examples of proteins representative of the major structural classes and containing up to 123 residues, that it is possible to use chemical shifts as structural restraints in combination with a conventional molecular mechanics force field to determine the conformations of proteins at a resolution of 2 Å or better. This strategy should be widely applicable and, subject to further development, will enable quantitative structural analysis to be carried out to address a range of complex biological problems not accessible to current structural techniques.NMR spectroscopy ͉ structural biology

Quantitative approaches to defining normal and aberrant protein homeostasis

“…1 Comparison between protein structures determined by X-ray crystallography (pink) and by the technique that we have recently introduced that uses only NMR chemical shift information (blue). 37 Despite being only at the initial stages of development of the method, we are already able to generate structures of globular proteins of up to 120 residues in length that agree with the those determined by conventional methods with RMSD values of 1.2-1.8 A for the backbone atoms and 2.1-2.6 A for the side-chain atoms.…”

“…[35][36][37][38] (2) New ideas about protein aggregation, 10,28 including the finding that the ability to assemble into stable and highly organised structures (e.g. amyloid fibrils) is not an unusual feature exhibited by a small group of peptides and proteins with special sequence or structural properties, but rather a property shared by most, if not all, proteins; (3) The discovery that specific aspects of protein behaviour, including their aggregation propensities 21,23,39,40 and the cellular toxicity associated with the aggregation process, 24,41 can be predicted with a remarkable degree of accuracy from the knowledge of their amino acid sequences; (4) The realisation that a wide variety of techniques originally devised for applications in nanotechnology can be used to probe the nature of protein aggregation and assembly and of the structures that emerge; 30,[42][43][44] and (5) The development of powerful approaches using model organisms for probing the origins and progression of misfolding diseases by linking concepts and principles emerging from in vitro studies to in vivo phenomena such as neurodegeneration.…”

Cross-Validation of the Structure of a Transiently Formed and Low Populated FF Domain Folding Intermediate Determined by Relaxation Dispersion NMR and CS-Rosetta

“…as RDCs can be incorporated to improve structure quality [48][49][50][51]. Typically a protocol is used whereby small fragments are selected from a database of structures based on agreement with experimental data, with models derived subsequently from fragment assembly.…”

NMR reveals novel mechanisms of protein activity regulation

“…40,53,82,83,87 Incorporation of chemical shifts in NMR structure refinement and the development of new NMR experiments that can report on internuclear vector orientations in excited conformational states provide valuable structural constraints that may enable direct structural characterization of higher energy protein conformations. [88][89][90] Kay and coworkers recently reported the structure of an ''invisible'' protein folding intermediate, a remarkable achievement convincingly showing that structure determination of weakly populated conformational states are within reach. 91 Under favorable conditions, NMRdetected paramagnetic relaxation enhancement (PRE) can be used to determine the structure of weakly populated conformational states.…”