Quantitative evaluation of experimental NMR restraints (original) (raw)
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Concepts and tools for NMR restraint analysis and validation
Concepts in Magnetic Resonance, 2004
The quality of NMR-derived biomolecular structure models can be assessed by validation on the level of structural characteristics as well as the NMR data used to derive the structure models. Here, an overview is given of the common methods to validate experimental NMR data. These methods provide measures of quality and goodness of fit of the structure to the data. A detailed discussion is given of newly developed methods to assess the information contained in experimental NMR restraints, which provide powerful tools for validation and error analysis in NMR structure determination.
Combining NMR and EPR Methods for Homodimer Protein Structure Determination
2010
There is a general need to develop more powerful and more robust methods for structural characterization of homodimers, homo-oligomers, and multiprotein complexes using solution-state NMR methods. In recent years, there has been increasing emphasis on integrating distinct and complementary methodologies for structure determination of multiprotein complexes. One approach not yet widely used is to obtain intermediate and long-range distance constraints from paramagnetic relaxation enhancements (PRE) and electron paramagnetic resonance (EPR)-based techniques such as double electron electron resonance (DEER), which, when used together, can provide supplemental distance constraints spanning to 10-70 Å. In this Communication, we describe integration of PRE and DEER data with conventional solution-state nuclear magnetic resonance (NMR) methods for structure determination of Dsy0195, a homodimer (62 amino acids per monomer) from Desulfitobacterium hafniense. Our results indicate that combination of conventional NMR restraints with only one or a few DEER distance constraints and a small number of PRE constraints is sufficient for the automatic NMR-based structure determination program CYANA to build a network of interchain nuclear Overhauser effect constraints that can be used to accurately define both the homodimer interface and the global homodimer structure. The use of DEER distances as a source of supplemental constraints as described here has virtually no upper molecular weight limit, and utilization of the PRE constraints is limited only by the ability to make accurate assignments of the protein amide proton and nitrogen chemical shifts.
Modern NMR spectroscopy of proteins and peptides in solution and its relevance to drug design
The knowledge of the three-dimensional (3D) structures and conformational dynamics of proteins and peptides is important for the understanding of biochemical and genetic data derived for these molecules. This understanding can ultimately be of help in drug design. We describe here the role of Nuclear Magnetic Resonance (NMR) spectroscopy in this process for three distinct situations: for small proteins, where relatively simple NMR methods can be used for fhll 3D structure determination; for larger proteins that require multinuclear multidimensional NMR but for which full 3D structures can still be obtained; and for small peptides that are studied in interaction with macromolecules (receptors) using specialized NMR techniques. A fourth situation, pertaining to large systems where only partial structural information can be obtained from NMR data, is briefly discussed. Molecules of interest to the biomedical field (C5a and stromelysin) are discussed as examples.
Extending the Applicability of Exact Nuclear Overhauser Enhancements to Large Proteins and RNA
Chembiochem : a European journal of chemical biology, 2018
Distance-dependent NOEs are one of the most popular and important experimental restraints for calculating NMR structures. Despite this, they are mostly employed as semi-quantitative upper distance bounds, which discards a wealth of information that is encoded in the cross-relaxation rate constant. Information that is lost includes exact distances between protons and dynamics that occur on the sub-millisecond time-scale. Our recently introduced exact measurement of the NOE (eNOE) requires little additional experimental effort relative to other NMR observables. So far, we have used eNOEs to calculate multi-state ensembles of proteins up to ~150 residues. Here, we briefly revisit the eNOE methodology and present two new directions for the use of eNOEs: Applications to large proteins and RNA.
Journal of Bioinformatics and Computational Biology, 2008
Nuclear Overhauser effects (NOE) distance constraints and torsion angle constraints are major conformational constraints for nuclear magnetic resonance (NMR) structure refinement. In particular, the number of NOE constraints has been considered as an important determinant for the quality of NMR structures. Of course, the availability of torsion angle constraints is also critical for the formation of correct local conformations. In our recent work, we have shown how a set of knowledge-based short-range distance constraints can also be utilized for NMR structure refinement, as a complementary set of conformational constraints to the NOE and torsion angle constraints. In this paper, we show the results from a series of structure refinement experiments by using different types of conformational constraints — NOE, torsion angle, or knowledge-based constraints — or their combinations, and make a quantitative assessment on how the experimentally acquired constraints contribute to the quali...
Trends in Food Science & Technology, 2019
The characterization of the original chemical structure and induced changes of micro-and macro-molecules using analytical techniques with concise and detailed outcomes is potentially one of the major challenges for food scientists. To this end, the non-invasive nuclear magnetic resonance (NMR) technique can play a significant role through employment of different NMR methods. The Nuclear Overhauser effect (NOE) and rotating-frame Overhauser effect (ROE) techniques are powerful NMR methods that have attracted great interest because they provide precise information about the three dimensional spatial structure of the molecules, as well as about possible chemical reactions and interactions. Scope and approach In this article, we reviewed the basic principles as well as applications of two NMR techniques: Nuclear Overhauser effect spectroscopy (NOESY) and rotating-frame Overhauser effect spectroscopy (ROESY). Hereby, we focused mainly on the applications and importance of these techniques in food science research. Both the structural (configuration and conformation) changes and the complexes formed by interacting compounds could be better studied using these techniques. Key findings and conclusions The inter-and intra-molecular interactions within food-based ingredient mixtures, as well as configurational and conformational analyses can be more efficiently studied with the aid of NOESY and ROESY. These methods as complementary analysis tools can be exploited for the straightforward elucidation of the spatial proximity of either novel, native or modified compounds. In the future, these techniques may be helpful to better understand the interaction between polymers, such as protein-polysaccharide interactions.
Model-independent refinement of interproton distances generated from 1H NMR overhauser intensities
Journal of Magnetic Resonance (1969), 1991
A recursive method to refine interproton distances compatible with two-dimensional nuclear Overhauser effect (NOESY) experiments has been tested. Convergence does not depend on the initial estimate of the parameters. Hence, no approximate initial structure of the molecule is required: the iterative process can be started from the experimentally measured NOESY cross-peak volumes, supplemented with arbitrary cross-peak and autopeak values to obtain an initial NOESY matrix. The relaxation matrix is calculated from the NOESY matrix, and its diagonal elements (p,) are adjusted at each iteration until the difference between theoretical and experimental cross peaks is a minimum. The improvement comes from using interproton distances calculated from the off-diagonal (uU) elements to generate p, values. The method was applied to alumichrome, a rigid cyclohexapeptide of virtually identical solution and crystallographic structures. The experimental data consisted of the integrated volumes of NOESY cross peaks at 500 MHz. Convergence was tested by resorting to different initial conditions, one of them being a NOESY matrix in which the experimentally unobserved off-diagonal elements were set equal to zero and the diagonal elements to 0.5. The iterations rapidly converge, in all cases, to a set of distances whose root-mean-squares deviation (rmsd) from the crystallographic distances is co.05 A. The acronym MIDGE (model-independent distance generation) for the procedure is proposed.