667:
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.
304:
experiment is only able to transfer magnetization between protons on adjacent atoms, whereas in the total correlation spectroscopy experiment the protons are able to relay the magnetization, so it is transferred among all the protons that are connected by adjacent atoms. Thus in a conventional correlation spectroscopy, an alpha proton transfers magnetization to the beta protons, the beta protons transfers to the alpha and gamma protons, if any are present, then the gamma proton transfers to the beta and the delta protons, and the process continues. In total correlation spectroscopy, the alpha and all the other protons are able to transfer magnetization to the beta, gamma, delta, epsilon if they are connected by a continuous chain of protons. The continuous chain of protons are the sidechain of the individual
312:’s sidechain. Which chemical shifts corresponds to which nuclei in the spin system is determined by the conventional correlation spectroscopy connectivities and the fact that different types of protons have characteristic chemical shifts. To connect the different spinsystems in a sequential order, the nuclear Overhauser effect spectroscopy experiment has to be used. Because this experiment transfers magnetization through space, it will show crosspeaks for all protons that are close in space regardless of whether they are in the same spin system or not. The neighbouring residues are inherently close in space, so the assignments can be made by the peaks in the NOESY with other spin systems.
796:). 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. So far, only the FLYA and the UNIO approach were proposed to perform the entire protein NMR structure determination process in an automated manner without any human intervention. Modules in the
110:. Data collection relies on placing the sample inside a powerful magnet, sending radio frequency signals through the sample, and measuring the absorption of those signals. Depending on the environment of atoms within the protein, the nuclei of individual atoms will absorb different frequencies of radio signals. Furthermore, the absorption signals of different nuclei may be perturbed by adjacent nuclei. This information can be used to determine the distance between nuclei. These distances in turn can be used to determine the overall structure of the protein.
742:-based experiments. 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 100 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
434:). Usually several of these experiments are required to resolve overlap in the carbon dimension. This procedure is usually less ambiguous than the NOESY-based method since it is based on through bond transfer. In the NOESY-based methods, additional peaks corresponding to atoms that are close in space but that do not belong to sequential residues will appear, confusing the assignment process. Following the initial sequential resonance assignment, it is usually possible to extend the assignment from the C
600:
242:, which has no amide-hydrogen due to the cyclic nature of its backbone. Additional 15N-HSQC signals are contributed by each residue with a nitrogen-hydrogen bond in its side chain (W, N, Q, R, H, K). The 15N-HSQC is often referred to as the fingerprint of a protein because each protein has a unique pattern of signal positions. Analysis of the 15N-HSQC allows researchers to evaluate whether the expected number of peaks is present and thus to identify possible problems due to multiple
539:
591:, 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.
219:. Pulse sequences allow the experimenter to investigate and select specific types of connections between nuclei. The array of nuclear magnetic resonance experiments used on proteins fall in two main categories — one where magnetization is transferred through the chemical bonds, and one where the transfer is through space, irrespective of the bonding structure. The first category is used to assign the different
755:
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.
144:
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103:(bonded atoms are typically a fraction of a nanometer apart), a factor of a million. This change of scale requires much higher sensitivity of detection and stability for long term measurement. In contrast to MRI, structural biology studies do not directly generate an image, but rely on complex computer calculations to generate three-dimensional molecular models.
271:
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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:
95:") of the atom. These properties depend on the local molecular environment, and their measurement provides a map of how the atoms are linked chemically, how close they are in space, and how rapidly they move with respect to each other. These properties are fundamentally the same as those used in the more familiar
524:. Another approach uses the chemical shifts to generate angle restraints. Both methods use the fact that the geometry around the alpha carbon affects the coupling constants and chemical shifts, so given the coupling constants or the chemical shifts, a qualified guess can be made about the torsion angles.
670:
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
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attempt to satisfy as many of the restraints as possible, in addition to general properties of proteins such as bond lengths and angles. 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
315:
One important problem using homonuclear nuclear magnetic resonance is overlap between peaks. This occurs when different protons have the same or very similar chemical shifts. This problem becomes greater as the protein becomes larger, so homonuclear nuclear magnetic resonance is usually restricted to
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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
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Depending on the concentration of the sample, the magnetic field of the spectrometer, and the type of experiment, a single multidimensional nuclear magnetic resonance experiment on a protein sample may take hours or even several days to obtain suitable signal-to-noise ratio through signal averaging,
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The ensemble of structures obtained is an "experimental model", i.e., a representation of certain kind of experimental data. To acknowledge this fact is important because it means that the model could be a good or bad representation of that experimental data. In general, the quality of a model will
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The most commonly performed 15N experiment is the H-N HSQC. The experiment is highly sensitive and therefore can be performed relatively quickly. It is often used to check the suitability of a protein for structure determination using NMR, as well as for the optimization of the sample conditions.
495:
in the
Integrative NMR platform perform this task automatically on manually pre-processed listings of peak positions and peak volumes, coupled to a structure calculation. Direct access to the raw NOESY data without the cumbersome need of iteratively refined peak lists is so far only granted by the
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Schematic of an HNCA and HNCOCA for four sequential residues. The nitrogen-15 dimension is perpendicular to the screen. Each window is focused on the nitrogen chemical shift of that amino acid. The sequential assignment is made by matching the alpha carbon chemical shifts. In the HNCA each residue
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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
246:
or sample heterogeneity. The relatively quick heteronuclear single quantum correlation experiment helps determine the feasibility of doing subsequent longer, more expensive, and more elaborate experiments. It is not possible to assign peaks to specific atoms from the heteronuclear single quantum
303:
spectroscopy (NOESY). A two-dimensional nuclear magnetic resonance experiment produces a two-dimensional spectrum. The units of both axes are chemical shifts. The COSY and TOCSY transfer magnetization through the chemical bonds between adjacent protons. The conventional correlation spectroscopy
210:
by which it can be recognized. However, in large molecules such as proteins the number of resonances can typically be several thousand and a one-dimensional spectrum inevitably has incidental overlaps. Therefore, multidimensional experiments that correlate the frequencies of distinct nuclei are
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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 considerable interest in automating the process to increase the throughput of structure determination and to make protein NMR
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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
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and provides information about the relative orientation of the bond vectors relative to a single global reference frame. Typically the orientation of the N-H vector is probed in an HSQC-like experiment. Initially, residual dipolar couplings were used for refinement of previously determined
85:, among others. Structure determination by NMR spectroscopy usually consists of several phases, each using a separate set of highly specialized techniques. The sample is prepared, measurements are made, interpretive approaches are applied, and a structure is calculated and validated.
121:). Frequently, the interacting pair of proteins may have been identified by studies of human genetics, indicating the interaction can be disrupted by unfavorable mutations, or they may play a key role in the normal biology of a "model" organism like the fruit fly, yeast, the worm
503:
To obtain as accurate assignments as possible, it is a great advantage to have access to carbon-13 and nitrogen-15 NOESY experiments, since they help to resolve overlap in the proton dimension. This leads to faster and more reliable assignments, and in turn to better structures.
563:. 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
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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. There are several methods to validate structures, some are statistical like
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performed. The additional dimensions decrease the chance of overlap and have a larger information content, since they correlate signals from nuclei within a specific part of the molecule. Magnetization is transferred into the sample using pulses of electromagnetic (
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It is of great importance to assign the NOESY peaks to the correct nuclei based on the chemical shifts. If this task is performed manually it is usually very labor-intensive, since proteins usually have thousands of NOESY peaks. Some computer programs such as
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Kuszewski J, Schwieters CD, Garrett DS, Byrd RA, Tjandra N, Clore GM (May 2004). "Completely automated, highly error-tolerant macromolecular structure determination from multidimensional nuclear overhauser enhancement spectra and chemical shift assignments".
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Nuclear magnetic resonance structure determination generates an ensemble of structures. The structures will converge only if the data is sufficient to dictate a specific fold. In these structures, it is the case for only a part of the structure. From
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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
808:) are integrated so that it offers full automation with visual verification capability in each step. Efforts have also been made to standardize the structure calculation protocol to make it quicker and more amenable to automation. Recently, the
467:. The intensity of a NOESY peak is proportional to the distance to the minus 6th power, so the distance is determined according to the intensity of the peak. The intensity-distance relationship is not exact, so usually a distance range is used.
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The blue arrows represent the orientation of the N – H bond of selected peptide bonds. By determining the orientation of a sufficient amount of bonds relative to the external magnetic field, the structure of the protein can be determined. From
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It is one of the standard suite of experiments used for the determination of the solution structure of protein. The HSQC can be further expanded into three- and four dimensional NMR experiments, such as N-TOCSY-HSQC and N-NOESY-HSQC.
205:
Protein NMR utilizes multidimensional nuclear magnetic resonance experiments to obtain information about the protein. Ideally, each distinct nucleus in the molecule experiences a distinct electronic environment and thus has a distinct
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and to allow for sufficient evolution of magnetization transfer through the various dimensions of the experiment. Other things being equal, higher-dimensional experiments will take longer than lower-dimensional experiments.
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Chandak MS, Nakamura T, Makabe K, Takenaka T, Mukaiyama A, Chaudhuri TK, et al. (July 2013). "The H/D-exchange kinetics of the
Escherichia coli co-chaperonin GroES studied by 2D NMR and DMSO-quenched exchange methods".
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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
450:
In order to make structure calculations, a number of experimentally determined restraints have to be generated. These fall into different categories; the most widely used are distance restraints and angle restraints.
1224:"Automated error-tolerant macromolecular structure determination from multidimensional nuclear Overhauser enhancement spectra and chemical shift assignments: improved robustness and performance of the PASD algorithm"
410:. These experiments allow each H-N peak to be linked to the preceding carbonyl carbon, and sequential assignment can then be undertaken by matching the shifts of each spin system's own and previous carbons. The
1139:
Bax A, Ikura M (May 1991). "An efficient 3D NMR technique for correlating the proton and 15N backbone amide resonances with the alpha-carbon of the preceding residue in uniformly 15N/13C enriched proteins".
234:(HSQC) spectrum, where "heteronuclear" refers to nuclei other than 1H. In theory, the heteronuclear single quantum correlation has one peak for each H bound to a heteronucleus. Thus, in the 15N-HSQC, with a
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Brünger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, et al. (September 1998). "Crystallography & NMR system: A new software suite for macromolecular structure determination".
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The analyte molecules in a sample can be partially ordered with respect to the external magnetic field of the spectrometer by manipulating the sample conditions. Common techniques include addition of
308:. Thus these two experiments are used to build so called spin systems, that is build a list of resonances of the chemical shift of the peptide proton, the alpha protons and all the protons from each
1906:"Attenuated T2 relaxation by mutual cancellation of dipole-dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution"
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A typical study might involve how two proteins interact with each other, possibly with a view to developing small molecules that can be used to probe the normal biology of the interaction ("
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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 T
1963:
Markus MA, Dayie KT, Matsudaira P, Wagner G (October 1994). "Effect of deuteration on the amide proton relaxation rates in proteins. Heteronuclear NMR experiments on villin 14T".
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experiment signifies spatial proximity between the two nuclei in question. Thus each peak can be converted into a maximum distance between the nuclei, usually between 1.8 and 6
17:
223:
to a specific nucleus, and the second is primarily used to generate the distance restraints used in the structure calculation, and in the assignment with unlabelled protein.
500:, the ATNOS/CANDID approach implemented in the UNIO software package, and the PONDEROSA-C/S and thus indeed guarantees objective and efficient NOESY spectral analysis.
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that transfer magnetisation over the peptide bond, and thus connect different spin systems through bonds. This is usually done using some of the following experiments,
1007:
Clore GM, Gronenborn AM (1989). "Determination of three-dimensional structures of proteins and nucleic acids in solution by nuclear magnetic resonance spectroscopy".
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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.
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99:, but the molecular applications use a somewhat different approach, appropriate to the change of scale from millimeters (of interest to radiologists) to
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to the rest of the sidechain using experiments such as HCCH-TOCSY, which is basically a TOCSY experiment resolved in an additional carbon dimension.
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of the measured data set under the same conditions. The accuracy, however, indicates the degree to which a measurement approaches its "true" value.
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The experimentally determined restraints can be used as input for the structure calculation process. Researchers, using computer programs such as
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In order to analyze the nuclear magnetic resonance data, it is important to get a resonance assignment for the protein, that is to find out which
1085:
Clore GM, Gronenborn AM (1991). "Applications of three- and four-dimensional heteronuclear NMR spectroscopy to protein structure determination".
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Clore GM, Gronenborn AM (June 1991). "Structures of larger proteins in solution: three- and four-dimensional heteronuclear NMR spectroscopy".
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With unlabelled protein the usual procedure is to record a set of two-dimensional homonuclear nuclear magnetic resonance experiments through
135:
of the molecule, which is desirable because the isotopes behave differently and provide methods for identifying overlapping NMR signals.
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of the model will be affected. The precision indicates the degree of reproducibility of the measurement and is often expressed as the
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to determine order parameters, correlation times, and chemical exchange rates. NMR relaxation is a consequence of local fluctuating
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relaxation measurements may not be representative of the whole protein. Therefore, techniques utilising relaxation measurements of
282:. The TOCSY shows off diagonal crosspeaks between all protons in the spectrum, but the COSY only has crosspeaks between neighbours.
231:
263:
using information derived from several different types of NMR experiment. The exact procedure depends on whether the protein is
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Spronk CA, Nabuurs SB, Krieger E, Vriend G, Vuister GW (2004). "Validation of protein structures derived by NMR spectroscopy".
688:
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depend on both the quantity and quality of experimental data used to generate it and the correct interpretation of such data.
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NOESY-Based
Strategy for Assignments of Backbone and Side Chain Resonances of Large Proteins without Deuteration (a protocol)
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protein. Usually, the sample consists of between 300 and 600 microlitres with a protein concentration in the range 0.1 – 3
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sees the alpha carbon of itself and the preceding residue. The HNCOCA only sees the alpha carbon of the preceding residue.
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suite, the successor of programs mentioned above, has been released to provide modern GUI tools and AI/ML features.
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394:. All six experiments consist of a H-N plane (similar to a HSQC spectrum) expanded with a carbon dimension. In the
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plane contains the peaks from the carbonyl carbon from its residue as well the preceding one in the sequence. The
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488:
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contains the carbonyl carbon chemical shift from only the preceding residue, but is much more sensitive than
74:
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2660:
1323:
Schwieters CD, Kuszewski JJ, Clore GM (2006). "Using Xplor-NIH for NMR molecular structure determination".
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Web service for the recognition of errors in experimentally or theoretically determined protein structures
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of proteins. By using these techniques it has been possible to study proteins in complex with the 900 kDa
512:
In addition to distance restraints, restraints on the torsion angles of the chemical bonds, typically the
2006:
Fiaux J, Bertelsen EB, Horwich AL, Wüthrich K (July 2002). "NMR analysis of a 900K GroEL GroES complex".
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labelled protein, one signal is expected for each nitrogen atom in the back bone, with the exception of
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235:
78:
1578:"PONDEROSA-C/S: client-server based software package for automated protein 3D structure determination"
127:, or mice. To prepare a sample, methods of molecular biology are typically used to make quantities by
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and adjusted to the desired solvent conditions. The NMR sample is prepared in a thin-walled glass
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2136:"NMR data collection and analysis protocol for high-throughput protein structure determination"
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128:
123:
2195:"POKY: a software suite for multidimensional NMR and 3D structure calculation of biomolecules"
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de Alba E, Tjandra N (2004). "Residual dipolar couplings in protein structure determination".
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Lee W, Cornilescu G, Dashti H, Eghbalnia HR, Tonelli M, Westler WM, et al. (April 2016).
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Every experiment has associated errors. Random errors will affect the reproducibility and
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of structures that, if the data were sufficient to dictate a certain fold, will converge.
8:
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1529:"The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data"
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Typically, the first experiment to be measured with an isotope-labelled protein is a 2D
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or not, since a lot of the assignment experiments depend on carbon-13 and nitrogen-15.
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When the protein is labelled with carbon-13 and nitrogen-15 it is possible to record
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proteins are usually easier to produce in sufficient quantity, and this method makes
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Rieping W, Habeck M, Bardiaux B, Bernard A, Malliavin TE, Nilges M (February 2007).
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Liu G, Shen Y, Atreya HS, Parish D, Shao Y, Sukumaran DK, et al. (July 2005).
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2015:
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1830:"What can we learn by computing 13Calpha chemical shifts for X-ray protein models?"
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1444:"ARIA2: automated NOE assignment and data integration in NMR structure calculation"
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215:) energy and between nuclei using delays; the process is described with so-called
58:
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1355:
Herrmann T (2010). "Protein structure calculation and automated NOE restraints".
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structures, but attempts at de novo structure determination have also been made.
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190:
176:
168:
107:
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1717:"Integrative Protein Modeling in RosettaNMR from Sparse Paramagnetic Restraints"
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Proceedings of the
National Academy of Sciences of the United States of America
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Proceedings of the
National Academy of Sciences of the United States of America
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295:(COSY), of which several types include conventional correlation spectroscopy,
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such as APES (two-letter-code: ae), I-PINE/PINE-SPARKY (two-letter-code: ep;
599:
552:
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Protein nuclear magnetic resonance is performed on aqueous samples of highly
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2019:
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Fundamentals of
Protein NMR Spectroscopy (Focus on Structural Biology)
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Rance M, Cavanagh J, Fairbrother WJ, Hunt III AW, Skelton NJ (2007).
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Wüthrich K (November 2001). "The way to NMR structures of proteins".
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588:
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472:
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2087:"NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy"
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Güntert P (2004). "Automated NMR structure calculation with CYANA".
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Kuszewski JJ, Thottungal RA, Clore GM, Schwieters CD (August 2008).
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Bax A, Grzesiek S (1993). "Methodological advances in protein NMR".
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163:. The source of the protein can be either natural or produced in a
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is used to obtain information about the structure and dynamics of
1527:
Lee W, Petit CM, Cornilescu G, Stark JL, Markley JL (June 2016).
1276:
Schwieters CD, Kuszewski JJ, Tjandra N, Clore GM (January 2003).
968:"Protein structure determination in solution by NMR spectroscopy"
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710:
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remains to be observed. The dipolar coupling is commonly used in
274:
Comparison of a COSY and TOCSY 2D spectra for an amino acid like
239:
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91:
involves the quantum-mechanical properties of the central core ("
46:
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1678:. Methods in Molecular Biology. Vol. 278. pp. 89–106.
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Currently most samples are examined in a solution in water, but
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Kuenze, G; Bonneau, R; Leman, JK; Meiler, J (5 November 2019).
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of the resulting structures. If the errors are systematic, the
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can yield information on the dynamics of various parts of the
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Protein structure determination from sparse experimental data
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2005:
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1278:"The Xplor-NIH NMR molecular structure determination package"
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713:. This usually involves measuring relaxation times such as T
270:
1962:
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Arnautova YA, Vila JA, Martin OA, Scheraga HA (July 2009).
1827:
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to the sample, or preparation of the sample in a stretched
108:
methods are being developed to also work with solid samples
1904:
Pervushin K, Riek R, Wider G, Wüthrich K (November 1997).
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corresponds to which atom. This is typically achieved by
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88:
62:
1714:
1322:
837:
Nuclear magnetic resonance spectroscopy of nucleic acids
832:
Nuclear magnetic resonance spectroscopy of carbohydrates
738:
relaxation times can be measured using various types of
350:
Triple-resonance nuclear magnetic resonance spectroscopy
117:") or to provide possible leads for pharmaceutical use (
1526:
1482:
1009:
Critical
Reviews in Biochemistry and Molecular Biology
1767:
Laskowski RA (2003). "Structural quality assurance".
1395:. Methods Mol. Biol. Vol. 278. pp. 353–78.
917:
758:
687:, or a mixture of statistical and physics principles
430:
contains both the alpha carbon and the beta carbon (C
344:
Carbon-13 and nitrogen-15 nuclear magnetic resonance
2349:
Nuclear magnetic resonance spectroscopy of proteins
2133:
1879:
Progress in
Nuclear Magnetic Resonance Spectroscopy
1325:
Progress in Nuclear Magnetic Resonance Spectroscopy
1087:
Progress in Nuclear Magnetic Resonance Spectroscopy
326:
Heteronuclear single quantum coherence spectroscopy
31:
Nuclear magnetic resonance spectroscopy of proteins
2314:
147:The NMR sample is prepared in a thin-walled glass
53:, and their complexes. The field was pioneered by
2296:Protein NMR spectroscopy: principles and practice
2084:
683:while others are based on physical principles as
2694:
2192:
2438:
1575:
1084:
1041:
1006:
516:, can be generated. One approach is to use the
418:works similarly, just with the alpha carbons (C
189:The purified protein is usually dissolved in a
18:Protein nuclear magnetic resonance spectroscopy
2269:Structural biology: practical NMR applications
1673:
575:
2424:
2193:Lee W, Rahimi M, Lee Y, Chiu A (March 2021).
1576:Lee W, Stark JL, Markley JL (November 2014).
2245:
1520:
1271:
1269:
1267:
786:
766:transverse relaxation optimized spectroscopy
2085:Lee W, Tonelli M, Markley JL (April 2015).
1627:"Integrative NMR for biomolecular research"
1111:
918:Clore GM, Wasylishen RL, Harris RK (2011).
868:
2431:
2417:
1132:
804:) and PONDEROSA (two-letter-code: c3, up;
2380:Software for the analysis of NMR dynamics
2218:
2169:
2159:
2110:
1939:
1929:
1853:
1766:
1740:
1650:
1601:
1552:
1459:
1400:
1264:
1247:
983:
527:
2312:
2298:(2nd ed.). Boston: Academic Press.
1386:
1384:
1354:
1217:
1215:
1186:Journal of the American Chemical Society
1138:
965:
874:
598:
594:
537:
333:
269:
232:heteronuclear single quantum correlation
142:
2718:Nuclear magnetic resonance spectroscopy
1965:Journal of Magnetic Resonance, Series B
1390:
1350:
1348:
1346:
636:
445:
250:
14:
2695:
925:. In Harris RK, Wasylishen RL (eds.).
454:
320:Nitrogen-15 nuclear magnetic resonance
287:Homonuclear nuclear magnetic resonance
2412:
1381:
1212:
422:) rather than the carbonyls, and the
138:
2266:
1343:
1176:
911:
520:, to generate angle restraints from
972:The Journal of Biological Chemistry
507:
24:
2238:
1771:. Vol. 44. pp. 273–303.
1357:Encyclopedia of Magnetic Resonance
927:Encyclopedia of Magnetic Resonance
759:NMR spectroscopy on large proteins
200:
25:
2729:
2337:
2317:NMR of proteins and nucleic acids
131:. This also permits changing the
2526:Dual-polarization interferometry
1365:10.1002/9780470034590.emrstm1151
920:"Adventures in Biomolecular NMR"
97:magnetic resonance imaging (MRI)
2186:
2127:
2078:
2042:
1999:
1956:
1897:
1870:
1821:
1708:
1667:
1618:
1569:
1476:
1435:
1316:
792:accessible to non-experts (See
2557:Analytical ultracentrifugation
2399:- an introductory presentation
2211:10.1093/bioinformatics/btab180
1105:
1078:
1035:
1000:
959:
496:PASD algorithm implemented in
13:
1:
2562:Size exclusion chromatography
2454:Cryogenic electron microscopy
2246:Hitchens TK, Rule GS (2005).
2103:10.1093/bioinformatics/btu830
1461:10.1093/bioinformatics/btl589
1302:10.1016/S1090-7807(02)00014-9
1282:Journal of Magnetic Resonance
1114:Accounts of Chemical Research
985:10.1016/S0021-9258(18)45665-7
862:
2661:Protein structure prediction
2363:Resources in other libraries
2052:Journal of Molecular Biology
1099:10.1016/0079-6565(91)80002-J
966:Wüthrich K (December 1990).
356:triple resonance experiments
316:small proteins or peptides.
7:
2619:Hydrogen–deuterium exchange
2440:Protein structural analysis
1891:10.1016/j.pnmrs.2004.08.003
1631:Journal of Biomolecular NMR
1582:Journal of Biomolecular NMR
1533:Journal of Biomolecular NMR
1337:10.1016/j.pnmrs.2005.10.001
1228:Journal of Biomolecular NMR
1142:Journal of Biomolecular NMR
815:
705:In addition to structures,
694:
582:Hydrogen–deuterium exchange
576:Hydrogen–deuterium exchange
73:, Angela Gronenborn at the
27:Field of structural biology
10:
2734:
827:Nuclear magnetic resonance
707:nuclear magnetic resonance
698:
640:
579:
531:
347:
323:
2674:
2653:
2637:
2624:Site-directed mutagenesis
2611:
2580:
2549:
2508:
2482:
2446:
2358:Resources in your library
2064:10.1016/j.jmb.2013.04.008
1846:10.1107/S0907444909012086
1769:Structural Bioinformatics
1733:10.1016/j.str.2019.08.012
1684:10.1385/1-59259-809-9:089
1643:10.1007/s10858-016-0029-x
1594:10.1007/s10858-014-9855-x
1545:10.1007/s10858-016-0036-y
1498:10.1107/s0907444998003254
1411:10.1385/1-59259-809-9:353
1240:10.1007/s10858-008-9255-1
1021:10.3109/10409238909086962
929:. John Wiley & Sons.
877:Nature Structural Biology
787:Automation of the process
565:residual dipolar coupling
534:Residual dipolar coupling
301:nuclear Overhauser effect
299:spectroscopy (TOCSY) and
2469:Electron crystallography
1931:10.1073/pnas.94.23.12366
293:correlation spectroscopy
2588:Fluorescence anisotropy
2550:Translational diffusion
2541:Fluorescence anisotropy
2405:Protein NMR experiments
2161:10.1073/pnas.0504338102
1777:10.1002/0471721204.ch14
1056:10.1126/science.2047852
842:Protein crystallization
1985:10.1006/jmrb.1994.1122
1676:Protein NMR Techniques
1393:Protein NMR Techniques
613:
548:
528:Orientation restraints
340:
283:
152:
129:bacterial fermentation
2683:Quaternary structure→
2645:Equilibrium unfolding
2629:Chemical modification
2598:Dielectric relaxation
2459:X-ray crystallography
935:10.1002/9780470034590
857:X-ray crystallography
602:
595:Structure calculation
541:
337:
273:
265:isotopically labelled
146:
33:(usually abbreviated
2581:Rotational diffusion
2271:. Berlin: Springer.
2252:. Berlin: Springer.
1727:(11): 1721–1734.e5.
806:PONDEROSA web server
643:Structure validation
637:Structure validation
446:Restraint generation
251:Resonance assignment
133:isotopic composition
2678:←Tertiary structure
2321:. New York: Wiley.
2313:Wüthrich K (1986).
2277:2005stbi.book.....T
2152:2005PNAS..10210487L
2146:(30): 10487–10492.
2020:10.1038/nature00860
1977:1994JMRB..105..192M
1922:1997PNAS...9412366P
1916:(23): 12366–12371.
1294:2003JMagR.160...65S
1126:10.1021/ar00028a001
1050:(5011): 1390–1399.
978:(36): 22059–22062.
889:10.1038/nsb1101-923
794:structural genomics
455:Distance restraints
247:correlation alone.
173:genetic engineering
171:techniques through
2593:Flow birefringence
2521:Circular dichroism
2389:2011-05-11 at the
1154:10.1007/BF01874573
614:
561:polyacrylamide gel
549:
522:coupling constants
514:psi and phi angles
341:
284:
261:sequential walking
153:
139:Sample preparation
83:Harvard University
39:structural biology
2713:Protein structure
2690:
2689:
2666:Molecular docking
2495:Mass spectrometry
2490:Fiber diffraction
2483:Medium resolution
2344:Library resources
2328:978-0-471-82893-8
2305:978-0-12-164491-8
2286:978-0-387-24367-2
2259:978-1-4020-3499-2
2205:(18): 3041–3042.
2014:(6894): 207–211.
1840:(Pt 7): 697–703.
1693:978-1-59259-809-0
1492:(Pt 5): 905–921.
1420:978-1-59259-809-0
1198:10.1021/ja049786h
1192:(20): 6258–6273.
802:I-PINE web server
459:A crosspeak in a
297:total correlation
165:production system
16:(Redirected from
2725:
2567:Light scattering
2433:
2426:
2419:
2410:
2409:
2332:
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2233:
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2222:
2190:
2184:
2183:
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2125:
2124:
2114:
2097:(8): 1325–1327.
2082:
2076:
2075:
2046:
2040:
2039:
2003:
1997:
1996:
1960:
1954:
1953:
1943:
1933:
1901:
1895:
1894:
1885:(3–4): 315–337.
1874:
1868:
1867:
1857:
1825:
1819:
1818:
1812:
1808:
1806:
1798:
1764:
1755:
1754:
1744:
1712:
1706:
1705:
1671:
1665:
1664:
1654:
1622:
1616:
1615:
1605:
1573:
1567:
1566:
1556:
1524:
1518:
1517:
1480:
1474:
1473:
1463:
1439:
1433:
1432:
1404:
1388:
1379:
1378:
1352:
1341:
1340:
1320:
1314:
1313:
1273:
1262:
1261:
1251:
1219:
1210:
1209:
1180:
1174:
1173:
1136:
1130:
1129:
1109:
1103:
1102:
1082:
1076:
1075:
1039:
1033:
1032:
1004:
998:
997:
987:
963:
957:
956:
924:
915:
909:
908:
872:
852:Relaxation (NMR)
847:Protein dynamics
822:NMR spectroscopy
701:Protein dynamics
518:Karplus equation
508:Angle restraints
429:
425:
417:
413:
409:
405:
397:
393:
387:
381:
375:
369:
363:
175:. Recombinantly
119:drug development
115:chemical biology
55:Richard R. Ernst
43:NMR spectroscopy
37:) is a field of
21:
2733:
2732:
2728:
2727:
2726:
2724:
2723:
2722:
2703:Protein methods
2693:
2692:
2691:
2686:
2685:
2680:
2670:
2649:
2633:
2607:
2576:
2545:
2504:
2478:
2447:High resolution
2442:
2437:
2391:Wayback Machine
2369:
2368:
2367:
2352:
2351:
2347:
2340:
2335:
2329:
2306:
2287:
2267:Teng Q (2005).
2260:
2241:
2239:Further reading
2236:
2191:
2187:
2132:
2128:
2083:
2079:
2058:(14): 2541–60.
2047:
2043:
2004:
2000:
1961:
1957:
1902:
1898:
1875:
1871:
1826:
1822:
1810:
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1765:
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1481:
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1436:
1421:
1402:10.1.1.332.4843
1389:
1382:
1375:
1353:
1344:
1321:
1317:
1274:
1265:
1220:
1213:
1181:
1177:
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1106:
1083:
1079:
1040:
1036:
1005:
1001:
964:
960:
953:
922:
916:
912:
883:(11): 923–925.
873:
869:
865:
818:
789:
761:
737:
733:
723:magnetic fields
720:
716:
703:
697:
645:
639:
597:
584:
578:
569:solid state NMR
536:
530:
510:
457:
448:
441:
437:
433:
427:
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403:
401:
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371:
365:
359:
352:
346:
328:
322:
289:
253:
221:chemical shifts
217:pulse sequences
203:
201:Data collection
191:buffer solution
169:recombinant DNA
141:
28:
23:
22:
15:
12:
11:
5:
2731:
2721:
2720:
2715:
2710:
2705:
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2338:External links
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2199:Bioinformatics
2185:
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2091:Bioinformatics
2077:
2041:
1998:
1971:(2): 192–195.
1955:
1896:
1869:
1820:
1811:|journal=
1785:
1756:
1707:
1692:
1666:
1637:(4): 307–332.
1617:
1588:(2–3): 73–75.
1568:
1519:
1475:
1454:(3): 381–382.
1448:Bioinformatics
1434:
1419:
1380:
1374:978-0470034590
1373:
1342:
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1263:
1234:(4): 221–239.
1211:
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1120:(4): 131–138.
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1015:(5): 479–564.
999:
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641:Main article:
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580:Main article:
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553:bacteriophages
532:Main article:
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348:Main article:
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324:Main article:
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257:chemical shift
252:
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213:radiofrequency
208:chemical shift
202:
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79:Gerhard Wagner
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2654:Computational
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2100:
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2017:
2013:
2009:
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1994:
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1786:9780471202004
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1148:(1): 99–104.
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952:9780470034590
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803:
799:
798:NMRFAM-SPARKY
795:
784:
782:
778:
775:
771:
767:
756:
753:
749:
745:
741:
729:
724:
712:
708:
702:
692:
690:
686:
682:
678:
672:
668:
664:
662:
658:
654:
649:
644:
634:
631:
627:
623:
619:
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592:
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583:
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558:
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546:
540:
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499:
494:
493:PONDEROSA-C/S
491:, and AUDANA/
490:
486:
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478:
474:
468:
466:
462:
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443:
392:
386:
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368:
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244:conformations
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98:
94:
90:
86:
84:
80:
76:
72:
68:
64:
60:
59:Kurt Wüthrich
56:
52:
51:nucleic acids
48:
44:
40:
36:
32:
19:
2602:
2571:
2536:Fluorescence
2515:
2463:
2348:
2316:
2295:
2268:
2248:
2202:
2198:
2188:
2143:
2139:
2129:
2094:
2090:
2080:
2055:
2051:
2044:
2011:
2007:
2001:
1968:
1964:
1958:
1913:
1909:
1899:
1882:
1878:
1872:
1837:
1833:
1823:
1768:
1724:
1720:
1710:
1675:
1669:
1634:
1630:
1620:
1585:
1581:
1571:
1539:(2): 51–57.
1536:
1532:
1522:
1489:
1485:
1478:
1451:
1447:
1437:
1392:
1356:
1331:(1): 47–62.
1328:
1324:
1318:
1288:(1): 65–73.
1285:
1281:
1231:
1227:
1189:
1185:
1178:
1145:
1141:
1134:
1117:
1113:
1107:
1093:(1): 43–92.
1090:
1086:
1080:
1047:
1043:
1037:
1012:
1008:
1002:
975:
971:
961:
926:
913:
880:
876:
870:
790:
768:(TROSY) and
762:
704:
673:
669:
665:
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615:
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550:
511:
502:
469:
458:
449:
353:
329:
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296:
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254:
229:
225:
204:
188:
154:
122:
112:
105:
87:
71:Marius Clore
34:
30:
29:
2403:Protein NMR
943:11693/53364
770:deuteration
744:nitrogen-15
728:nitrogen-15
547:record 1KBH
306:amino acids
49:, and also
35:protein NMR
2708:Biophysics
2697:Categories
2531:Absorbance
863:References
699:See also:
630:RosettaNMR
428:CBCA(CO)NH
391:CBCA(CO)NH
280:methionine
186:possible.
161:millimolar
124:C. elegans
101:nanometers
2384:ProSA-web
1813:ignored (
1803:cite book
1721:Structure
1397:CiteSeerX
774:chaperone
752:deuterium
748:carbon-13
653:precision
618:XPLOR-NIH
589:deuterium
498:XPLOR-NIH
473:XPLOR-NIH
465:angstroms
276:glutamate
177:expressed
65:, and by
41:in which
2612:Chemical
2387:Archived
2229:33715003
2180:16027363
2121:25505092
2072:23583779
2028:12110894
1864:19564690
1795:12647391
1751:31522945
1702:15317993
1661:27023095
1612:25190042
1563:27169728
1514:33910776
1470:17121777
1429:15318003
1310:12565051
1258:18668206
1206:15149223
1170:20037190
905:26153265
897:11685234
816:See also
695:Dynamics
685:CheShift
677:PROCHECK
661:variance
657:accuracy
557:bicelles
426:and the
416:HN(CO)CA
408:HN(CA)CO
398:, each H
396:HN(CA)CO
379:HN(CO)CA
367:HN(CA)CO
184:labeling
181:isotopic
157:purified
47:proteins
2273:Bibcode
2220:8479676
2171:1180791
2148:Bibcode
2112:4393527
2036:2451574
1993:7952934
1973:Bibcode
1950:9356455
1918:Bibcode
1855:2703576
1742:6834914
1652:4861749
1603:4207954
1554:4921114
1506:9757107
1290:Bibcode
1249:2575051
1162:1668719
1072:2047852
1044:Science
1029:2676353
994:2266107
711:protein
681:WHAT IF
310:residue
240:proline
93:nucleus
61:at the
2346:about
2325:
2302:
2283:
2256:
2227:
2217:
2178:
2168:
2119:
2109:
2070:
2034:
2026:
2008:Nature
1991:
1948:
1938:
1862:
1852:
1793:
1783:
1749:
1739:
1700:
1690:
1659:
1649:
1610:
1600:
1561:
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1512:
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1468:
1427:
1417:
1399:
1371:
1308:
1256:
1246:
1204:
1168:
1160:
1070:
1062:
1027:
992:
949:
903:
895:
608:entry
424:HNCACB
385:HNCACB
167:using
77:, and
67:Ad Bax
2378:relax
2032:S2CID
1941:24947
1510:S2CID
1166:S2CID
1064:83376
923:(PDF)
901:S2CID
781:GroEL
777:GroES
734:and T
717:and T
628:, or
626:GeNMR
622:CYANA
481:CYANA
471:PASD/
461:NOESY
438:and C
2500:SAXS
2323:ISBN
2300:ISBN
2281:ISBN
2254:ISBN
2225:PMID
2176:PMID
2117:PMID
2068:PMID
2024:PMID
1989:PMID
1946:PMID
1860:PMID
1815:help
1791:PMID
1781:ISBN
1747:PMID
1698:PMID
1688:ISBN
1657:PMID
1608:PMID
1559:PMID
1502:PMID
1466:PMID
1425:PMID
1415:ISBN
1369:ISBN
1306:PMID
1254:PMID
1202:PMID
1158:PMID
1068:PMID
1060:OSTI
1025:PMID
990:PMID
947:ISBN
893:PMID
810:POKY
750:and
740:HSQC
689:PSVS
679:and
610:1SSU
485:ARIA
477:UNIO
414:and
412:HNCA
404:HNCO
388:and
373:HNCA
361:HNCO
195:tube
149:tube
57:and
2603:NMR
2572:NMR
2516:NMR
2474:EPR
2464:NMR
2215:PMC
2207:doi
2166:PMC
2156:doi
2144:102
2107:PMC
2099:doi
2060:doi
2056:425
2016:doi
2012:418
1981:doi
1969:105
1936:PMC
1926:doi
1887:doi
1850:PMC
1842:doi
1773:doi
1737:PMC
1729:doi
1680:doi
1647:PMC
1639:doi
1598:PMC
1590:doi
1549:PMC
1541:doi
1494:doi
1456:doi
1407:doi
1361:doi
1333:doi
1298:doi
1286:160
1244:PMC
1236:doi
1194:doi
1190:126
1150:doi
1122:doi
1095:doi
1052:doi
1048:252
1017:doi
980:doi
976:265
939:hdl
931:doi
885:doi
620:,
606:PDB
555:or
545:PDB
489:CNS
370:},
278:or
89:NMR
81:at
75:NIH
63:ETH
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