Solid-state NMR methods can be applied to study the structure and dynamics of very large biomolecules such as membrane proteins or polymeric assemblies as found in amyloid fibers. A unique feature of the NMR Facility is that it houses, in one location, instrumentation for high resolution solution and solid-state NMR spectroscopy with magnets at several field strengths. There are a total of seven spectrometers dedicated to biological NMR. The MHz spectrometer is equipped with solids capabilities as well. All spectrometers are fully equipped with hardware for modern, state-of-the-art multinuclear experiments, including gradient probes and the capability for multi-channel pulsing with deuterium decoupling.
Cryoprobes have been installed at every field strength except MHz. Variable temperature control. Conventional high resolution probe s. Linux based PC control workstation. Ultra-low temperature Magic Angle Spinning equipped. Common techniques include addition of bacteriophages or bicelles to the sample, or preparation of the sample in a stretched polyacrylamide gel.
This creates a local environment that favours certain orientations of nonspherical molecules. Normally in solution NMR the dipolar couplings between nuclei are averaged out because of the fast tumbling of the molecule. The slight overpopulation of one orientation means that a residual dipolar coupling remains to be observed.
The dipolar coupling is commonly used in solid state NMR and provides information about the relative orientation of the bond vectors relative to a single global reference frame. Initially, residual dipolar couplings were used for refinement of previously determined structures, but attempts at de novo structure determination have also been made.
NMR spectroscopy is nucleus specific. Thus it can distinguish between hydrogen and deuterium. The amide protons in the protein exchange readily with the solvent, and, if the solvent contains a different isotope, typically deuterium , the reaction can be monitored by NMR spectroscopy. How rapidly a given amide exchanges reflects its solvent accessibility. Thus amide exchange rates can give information on which parts of the protein are buried, hydrogen bonded etc.
A common application is to compare the exchange of a free form versus a complex. The amides that become protected in the complex, are assumed to be in the interaction interface. The experimentially determined restraints can be used as input for the structure calculation process. The algorithms convert the restraints and the general protein properties into energy terms, and then try to minimize this energy. The process results in an ensemble of structures that, if the data were sufficient to dictate a certain fold, will converge. Is important to note that the ensemble of structures obtained is an "experimental model", i.
To acknowledge this fact is really important because it means that the model could be a good or bad representation of that experimental data.
Vorlesung "Biomolecular NMR Spectroscopy"
It is important to remember that every experiment has associated errors. Random errors will affect the reproducibility and precision of the resulting structures. If the errors are systematic, the accuracy of the model will be affected.
The precision indicates the degree of reproducibility of the measurement and is often expressed as the variance of the measured data set under the same conditions. The accuracy, however, indicates the degree to which a measurement approaches its "true" value. Ideally, a model of a protein will be more accurate the more fit the actual molecule that represents and will be more precise as there is less uncertainty about the positions of their atoms. In practice there is no "standard molecule" against which to compare models of proteins, so the accuracy of a model is given by the degree of agreement between the model and a set of experimental data.
Historically, the structures determined by NMR have been, in general, of lower quality than those determined by X-ray diffraction. This is due, in part, to the lower amount of information contained in data obtained by NMR. Because of this fact, it has become common practice to establish the quality of NMR ensembles, by comparing it against the unique conformation determined by X-ray diffraction, for the same protein. However, the X-ray diffraction structure may not exist, and, since the proteins in solution are flexible molecules, a protein represented by a single structure may lead to underestimate the intrinsic variation of the atomic positions of a protein.
A set of conformations, determined by NMR or X-ray crystallography may be a better representation of the experimental data of a protein than a unique conformation.
The utility of a model will be given, at least in part, by the degree of accuracy and precision of the model. An accurate model with relatively poor precision could be useful to study the evolutionary relationships between the structures of a set of proteins, whereas the rational drug design requires both precise and accurate models.
A model that is not accurate, regardless of the degree of precision with which it was obtained will not be very useful. Since protein structures are experimental models that can contain errors, it is very important to be able to detect these errors. The process aimed at the detection of errors is known as validation. In addition to structures, nuclear magnetic resonance can yield information on the dynamics of various parts of the protein.
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This usually involves measuring relaxation times such as T 1 and T 2 to determine order parameters, correlation times, and chemical exchange rates. NMR relaxation is a consequence of local fluctuating magnetic fields within a molecule. Local fluctuating magnetic fields are generated by molecular motions. In this way, measurements of relaxation times can provide information of motions within a molecule on the atomic level. In NMR studies of protein dynamics the nitrogen isotope is the preferred nucleus to study because its relaxation times are relatively simple to relate to molecular motions This, however, requires isotope labeling of the protein.
The types of motions that can be detected are motions that occur on a time-scale ranging from about 10 picoseconds to about 10 nanoseconds. In addition slower motions, which take place on a time-scale ranging from about 10 microseconds to milliseconds, can also be studied. However, since nitrogen atoms are found mainly in the backbone of a protein, the results mainly reflect the motions of the backbone, which is the most rigid part of a protein molecule.
Thus, the results obtained from nitrogen relaxation measurements may not be representative for the whole protein.
Journal of Biomolecular NMR
Therefore, techniques utilising relaxation measurements of carbon and deuterium have recently been developed, which enables systematic studies of motions of the amino acid side-chains in proteins. A challenging and special case of study regarding dynamics and flexibility of peptides and full-length proteins is represented by disordered structures. Nowadays, it is an accepted concept that proteins can exhibit a more flexible behaviour known as disorder or lack of structure; however, it is possible to describe an ensemble of structures instead of a static picture representing a fully functional state of the protein.
Many advances are represented in this field in particular in terms of new pulse sequences, technological improvement, and rigorous training of researchers in the field. Traditionally, nuclear magnetic resonance spectroscopy has been limited to relatively small proteins or protein domains. This is in part caused by problems resolving overlapping peaks in larger proteins, but this has been alleviated by the introduction of isotope labelling and multidimensional experiments.
Another more serious problem is the fact that in large proteins the magnetization relaxes faster, which means there is less time to detect the signal. This in turn causes the peaks to become broader and weaker, and eventually disappear. Two techniques have been introduced to attenuate the relaxation: transverse relaxation optimized spectroscopy TROSY  and deuteration  of proteins. Structure determination by NMR has traditionally been a time consuming process, requiring interactive analysis of the data by a highly trained scientist.
There has been a considerable interest in automating the process to increase the throughput of structure determination and to make protein NMR accessible to non-experts See structural genomics. The two most time consuming processes involved are the sequence-specific resonance assignment backbone and side-chain assignment and the NOE assignment tasks. Several different computer programs have been published that target individual parts of the overall NMR structure determination process in an automated fashion. Most progress has been achieved for the task of automated NOE assignment.
From Wikipedia, the free encyclopedia. Main article: Heteronuclear single quantum coherence spectroscopy.
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Main article: Triple-resonance nuclear magnetic resonance spectroscopy. Main article: Residual dipolar coupling. Main article: Hydrogen—deuterium exchange. See also: Protein dynamics. Marius Encyclopedia of Magnetic Resonance. Progress in Nuclear Magnetic Resonance Spectroscopy. Accounts of Chemical Research. Journal of the American Chemical Society. Journal of Biomolecular NMR.
Biological 1H NMR spectroscopy. - Abstract - Europe PMC
Bibcode : JMagR. Protein structure calculation and automated NOE restraints. Methods Mol. Acta Crystallographica Section D. Residual dipolar couplings in protein structure determination. Structural quality assurance. Methods of Biochemical Analysis. Bibcode : PNAS Heteronuclear NMR experiments on villin 14T". J Magn Reson B.
HT 3: Protein structure determination by NMR
Bibcode : JMRB.. July Bibcode : PNAS.. Protein structural analysis. Hydrogen-deuterium exchange Site-directed mutagenesis Chemical modification. Equilibrium unfolding.
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