Challenges in Molecular Structure Determination


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Introduction

Structure Determination

The close connection between experimental NMR, molecular modeling, and MD simulation has a long history. Molecular modeling approaches and simulations are necessary to interpret the data, whilst NMR experiments serve to act as a guide for the improvement of force fields. The study of long time-scale dynamics and unstructured proteins provides new and exciting challenges to both theoreticians and experimentalists. The authors have declared that no competing interests exist. National Center for Biotechnology Information , U.

Problems from Previous Years' Exams

PLoS Comput Biol. Published online Sep Phineus R.

Johanna McEntyre, Editor. Author information Copyright and License information Disclaimer. Copyright Markwick et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

This article has been cited by other articles in PMC. Abstract The function of bio-macromolecules is determined by both their 3D structure and conformational dynamics. Introduction The function of bio-macromolecules is determined by both their 3D structure and conformational dynamics. Open in a separate window. Figure 1. Illustration of structural data that can be obtained from NMR experiments, with the example of a backbone NH group. Increasing speed and reliability of NMR structure determination NMR structure determination still presents some considerable challenges: the method is limited to systems of relatively small molecular mass, data collection times are long, data analysis remains a lengthy procedure, and it is difficult to evaluate the quality of the final structures.

Towards objective NMR structures In order to calculate a 3D structure from data, it is necessary to use a model or a theory to calculate the data from the atomic coordinates. Probing Structural Dynamics by NMR The most severe approximation to structure determination is the general assumption that the experimental data can be represented by a single structure, neglecting the effects of internal dynamics.

Figure 2. Fast time-scale local motions Precise information about local dynamics on pico- to nano-second time-scales can be obtained by spin relaxation measurements. Going beyond the nano-second limit Many biologically important processes, such as enzyme catalysis, signal transduction, ligand binding, and allosteric regulation occur on the micro- to milli-second time-scale.

Conclusions and Outlook The fundamental challenge to NMR remains to combine and reconcile all the available information, both structural and dynamic, into a complete, and therefore intrinsically more accurate, representation of the conformational space sampled by biomolecular systems, with the aim of resolving the relationship between structure, dynamics, and function.

Footnotes The authors have declared that no competing interests exist. References 1. Wishart DS. NMR spectroscopy and protein structure determination: Applications to drug discovery and development. Curr Pharm Biotechnol. Recent developments in structural proteomics for protein structure determination. Automation of NMR structure determination of proteins. Curr Opin Struct Biol. Nuclear magnetic resonance spectroscopy of highmolecular-weight proteins. Annu Rev Biochem.

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Spectroscopy Problems

Simultaneous definition of high resolution protein structure and backbone conformational dynamics using NMR residual dipolar couplings. NMR of proteins and nucleic acids. New York: John Wiley; Iwahara J, Clore GM. Detecting transient intermediates in macromolecular binding by paramagnetic NMR. NMR evidence for slow collective motions in cyanometmyoglobin. Nature Struct Biol.

Structural Biology by NMR: Structure, Dynamics, and Interactions

Tjandra N, Bax A. Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium. Use of chemical shifts in macromolecular structure determination. Methods Enzymol. Protein structure determination from NMR chemical shifts. Consistent blind protein structure generation from NMR chemical shift data. Structure of a protein determined by solid-state magic-angle-spinning NMR spectroscopy. Solution NMR in structural genomics. Methods Mol Biol. Optimal isotope labelling for NMR protein structure determinations.

An integrated platform for automated analysis of protein NMR structures. Completely automated, highly error-tolerant macromolecular structure determination from multidimensional nuclear Overhauser enhancement spectra and chemical shift assignments.

J Am Chem Soc. J Mol Biol. A topology-constrained distance network algorithm for protein structure determination from NOESY data. Jung YS, Zweckstetter M. Mars—Robust automatic backbone assignment of proteins. J Biomol NMR. Automated protein structure determination from NMR spectra. Grishaev A, Llinas M. Direct use of unassigned resonances in NMR structure calculations with proxy residues. Determination of protein backbone structure using only residual dipolar couplings. Molecular fragment replacement approach to protein structure determination by chemical shift and dipolar homology database mining.

A polynomial-time algorithm for de novo protein backbone structure determination from nuclear magnetic resonance data. J Comput Biol. Meiler J, Baker D. Rapid protein fold determination using unassigned NMR data. Refinement of multidomain protein structures by combination of solution small-angle X-ray scattering and NMR data. Proton—proton Overhauser NMR spectroscopy with polypeptide chains in large structures. Sprangers R, Kay LE. Quantitative dynamics and binding studies of the 20S proteasome by NMR. J Biol Chem.

Visualization of transient encounter complexes in protein—protein association. Evaluating protein structures determined by structural genomics consortia. Quantitative evaluation of experimental NMR restraints. Inferential structure determination. Structure validation of the Josephin domain of ataxin Conclusive evidence for an open conformation.

Specialty Grand Challenge ARTICLE

Protein NMR recall, precision, and f-measure scores RPF scores : Structure quality assessment measures based on information retrieval statistics. Refinement of protein structures in explicit solvent. Jack A, Levitt M. Refinement of large structures by simultaneous minimization of energy and R factor. Acta Cryst.

Problems from Previous Years' Exams

Brunger AT, Nilges M. Computational challenges for macromolecular structure determination by X—ray crystallography and solution NMR spectroscopy. Quart Rev BioPhys. The precision of NMR structure ensembles revisited. Clustering algorithms for identifying core atom sets and for assessing the precision of protein structure ensembles. Traditional biomolecular structure determination by NMR spectroscopy allows for major errors.

Weighting of experimental evidence in macromolecular structure determination.

Challenges in Molecular Structure Determination Challenges in Molecular Structure Determination
Challenges in Molecular Structure Determination Challenges in Molecular Structure Determination
Challenges in Molecular Structure Determination Challenges in Molecular Structure Determination
Challenges in Molecular Structure Determination Challenges in Molecular Structure Determination
Challenges in Molecular Structure Determination Challenges in Molecular Structure Determination
Challenges in Molecular Structure Determination Challenges in Molecular Structure Determination
Challenges in Molecular Structure Determination Challenges in Molecular Structure Determination
Challenges in Molecular Structure Determination Challenges in Molecular Structure Determination
Challenges in Molecular Structure Determination

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