NMR and X-ray Crystallography Glossary

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  • Published: Jan 8, 2014
  • Channels: X-ray Spectrometry / NMR Knowledge Base

This glossary has been reproduced with the permission of
Cambridge Healthtech Institute

Suggestions? Comments? Questions? mchitty@healthtech.com
Related glossaries include: Protein StructuresStructural Genomics.

2D NMR: Includes COSY and NOESY. 

3D NMR: See multidimensional NMR. 

4D NMRSee multidimensional NMR. 


atomic resolution data:
 Until the mid-1990's there were few reports extant of proteins that diffracted to resolutions better than 1.3 Å. With improvements in techniques for protein purification and the availability of third-generation synchrotron beamlines, atomic-resolution data collection on macromolecules has become much more common. These experiments provide exciting new insights into the structure and dynamics of macromolecules because they enable visualization of details inaccessible at lower resolution. (Industrial Macromolecular Crystallography Association, "Scientific Accomplishments of IMCA-CAT in 1999") http://icarus.csrri.iit.edu/~ahoward/peb99/peb99science.html
  

beamline: Beamlines at these storage rings, or synchrotrons, are the facilities at which crystallographers and other researchers get access to the tunable and high-intense X-ray beams they need for their research. (Introduction to the Professions, Illinois Institute of Technology, Sept. 26, 2000)    http://icarus.csrri.iit.edu/itp/itpmacro.html 

Related terms: synchrotrons; Industrial Macromolecular Crystallography Association IMCA.


bicelle
: (Nico) Tjandra & (Ad) Bax recently developed a new nuclear magnetic resonance (NMR) technique that gently aligns protein molecules in a bath of liquid crystals, allowing researchers to determine how each bond between neighboring atoms is oriented with respect to the rest of the molecule. By compiling all such orientations between atoms, a precise map of the protein can be derived. In aqueous solution, just above room temperature, the lipids switch from a gel to a Liquid Crystal (LC) phase, where they form disc shaped particles, often referred to as bicelles. (Avanti Polar Lipids website) http://www.avantilipids.com/BicellePreparation.asp 


13
C: 
Carbon isotopes used in NMR labeling. 


COSY:
 Correlated Spectroscopy, 2D NMR


chemical shift: 
The frequency at which each nucleus resonates when a magnetic field is applied, provides information about the chemical environment of a nucleus.   (Aileen Constans "Taking It Higher: State-of-the-Art NMR technology offers answers for the solution and solid states" Scientist 14 (21): 26, Oct. 30, 2000)  http://www.the-scientist.com/yr2000/oct/profile1_001030.html 


chemical shift anisotropy CSA
: A "relaxation" property. (CHI Structural proteomics). 

IUPAC Provisional Recommendations: NMR Nomenclature: Nuclear Spin Properties and Conventions for Chemical Shifts, Physical and Biophysical Chemistry Division, Commission Molecular Structure and Spectroscopy Comments by Aug. 21, 2001 
http://www.iupac.org/reports/provisional/abstract01/harris_310801.html 


cryogenic probe
:
 One of the engineering challenges has been to cool the detection circuitry to these very low temperatures while maintaining the sample itself at ambient temperatures.  The first generation of these cryoprobes provides a factor of three improvement in signal-to-noise ratio, which means about a factor of nine or ten reduction in data collection time.

Soon we will be able to combine the cryoprobes with the NOESY data collection and residual dipolar coupling to determine complete high-quality protein structures much faster.  (CHI Structural proteomics)
Related terms cryoprobemicrocryoprobetriple resonance cryoprobes


cryoprobe
:
 Bruker has developed  high-performance cryogenic probes for high-resolution applications. These probes have improved signal/noise (S/N) ratios obtained by reducing the operating temperature of the coil and the pre-amplifier. The dramatic increase in the S/N ratio by a factor of  4, as compared to conventional probes, leads to a possible reduction in experiment time of 16  or a reduction in required sample concentration by a factor of 4.
(Bruker website) Related terms cryogenic probe, microcryoprobeshttp://www.bruker.de/analytic/nmr-dep/probes/cryoprobe.htm 


crystallography:
 The branch of science that deals with the geometric description of crystals and their internal arrangement. (OMD)  Narrower term X-ray crystallography


Dalton: 
(back to top) Unit of mass equal to the unified atomic mass (atomic mass  constant). (IUPAC Compendium) After John Dalton (1766-1844) British chemist and physicist. 


dephases:
 (Electricity.) To put out of phase, as two parts of a single alternating  current. (dictionary.com)  http://www.dictionary.com/cgi-bin/dict.pl?term=dephase 


deuterium-decoupled triple-resonance NMR:
 Gives an improvement in sensitivity.  If you randomly change some of the hydrogens in the sample to deuterium, then all of the other peaks in the spectrum can be made sharper, and the pulse sequence can be designed to erase, or decouple, the resonance-splitting effects of deuterium. (CHI Structural proteomics). 


EPR Electron Paramagnetic Resonance
: See ESR. 


ESR Electron Spin Resonance
: ESR, often called Electron Paramagnetic Resonance (EPR), is similar to Nuclear Magnetic Resonance (NMR), the fundamental difference being that ESR is concerned with the magnetically induced splitting of electronic spin states, while NMR describes the splitting of nuclear spin states. In both ESR and NMR, the sample material is immersed in a strong static magnetic field and exposed to an orthogonal low-amplitude high-frequency field. ESR usually requires microwave-frequency radiation (GHz), while NMR is observed at lower radio frequencies (MHz). With ESR, energy is absorbed by the sample when the frequency of the radiation is appropriate to the energy difference between two states of the electrons in the sample, but only if the transition satisfies the appropriate selection rules. Splitting can occur only when the electron is in a state with non-zero total angular momentum, i.e. electrons in atoms with closed atomic shells cannot show this behavior. The term ESR refers specifically to the case in which the spins of the electrons absorbing the radiation are only weakly interacting ("weakly coupled") with each other. In NMR the static magnetic field splits the quantum states of a nucleus which has non-zero nuclear spin. The observation of NMR requires that the total electronic spin be zero. (Senior Physics Lab, California Institute of Technology, US, Sept. 2000) http://www.pma.caltech.edu/~ph77/labs/exp6.html 


flexible linkages
: In proteins. 


four-D:
 See 4D


free induction decay (FID)
See spin; In-Depth FT-NMR. 


FT-NMR
: Fourier Transform NMR: Fourier-transform NMR spectrometers use a pulse of radiofrequency (RF) radiation to cause nuclei in a magnetic field to flip into the higher-energy alignment. Due to the Heisenberg uncertainty principle, the frequency width of the RF pulse (typically 1-10 µs) is wide enough to simultaneously excite nuclei in all local environments. All of the nuclei will re-emit RF radiation at their respective resonance frequencies, creating an interference pattern in the resulting RF emission versus time, known as a free induction decay (FID). The frequencies are extracted from the FID by a Fourier transform of the time-based data. (Juhyoun Kwak, Chemistry, KAIST, Korea Institute of Advanced Science & Technology) http://elchem.kaist.ac.kr/vt/chem-ed/spec/spin/ftnmr.htm 


1
H: 
Hydrogen isotope used in NMR labeling. 


HMQC Heteronuclear Multiple Quantum Correlation:
  (back to top)  Much of protein NMR spectroscopy relies on spectral editing techniques using 13C or 15N nuclei (heteronuclei). Spectral editing allows a subset of an entire spectrum to be observed. Normally, we observe a subset of 1H spectra that has been selected based upon which nucleus the protons are attached to. The same techniques involved in spectral editing allow the measurement of heteronuclear correlations (which, for example, allows you to know which 1H are attached to which 13C). (Arthur S. Edison, University of Florida, "Theory and Applications of NMR Spectroscopy, April 2000) http://ascaris.health.ufl.edu/classes/bch6746/new/html/note5.html 


hr-MAS High Resolution Magic Angle Spinning
:
 The sample is spun at a high speed at a well-defined angle to the main magnetic field. Orienting the sample in this manner is a technique that was developed originally for solid state NMR to minimize the spectral line broadening introduced by intermolecular dipolar coupling or sample inhomogeneity. The appeal of hr-MAS is that it allows the study of systems that were previously not accessible with NMR. Some particularly interesting recent applications of this technology include the study of biological tissues and combinatorial chemistry samples that have been isolated on polymer beads.  (Aileen Constans "Taking It Higher: State-of-the-Art NMR technology offers answers for the solution and solid states" Scientist 14 (21): 26, Oct. 30, 2000)  Broader term: MAS Magic Angle Spinning  http://www.the-scientist.com/yr2000/oct/profile1_001030.html 


HSQC Heteronuclear single quantum correlation:
 When a molecule binds a protein, the chemical environment of the protein's binding site changes and results in the chemical shift perturbation of nuclei at that site. Two-dimensional 1H -15N heteronuclear single-quantum correlation  (HSQC)-NMR spectroscopy screens for ligand binding by detecting only the amide signals of 15N-labeled protein. (Jennifer B. Miller, "Why NMR is attracting drug designers"  Today's Chemist at Work 9 (1) : 44-49  Jan. 2000)   http://pubs.acs.org/hotartcl/tcaw/00/jan/miller.html 


high-field NMR
:
 The spectra of complex biomolecules contain a large number of peaks, many of which are close together or overlap. Higher field magnets, or higher frequency instruments, offer better peak resolution, enabling analysis of larger and larger molecules. Also, in NMR, sensitivity increases almost with the square of the magnetic field, so when magnetic field strength is doubled, sensitivity increases about fourfold. Data can thus be acquired faster, or alternatively, samples can be run at lower concentrations in the same experimental time. The latter advantage is particularly important to the study of large biomolecules, which are often difficult to express and purify in large quantities and can aggregate and precipitate out of solution at high concentrations. Finally, high-field NMR can lead to the development of new NMR experiments that exploit properties exhibited by molecules at high magnetic fields.  (Aileen Constans "Taking It Higher: State-of-the-Art NMR technology offers answers for the solution and solid states" Scientist 14 (21): 26, Oct. 30, 2000)  http://www.the-scientist.com/yr2000/oct/profile1_001030.html 


hyphenated techniques:
 NMR together with chromatography and/ or mass spectrometry. Includes LC-NMR


Industrial Macromolecular Crystallography Association IMCA
: Academic crystallographers generally determine unknown structures; industrial crystallographers spend the majority of their time examining structures of complexes between a protein of known structure and a small-molecule ligand. These structures can be studied by difference Fourier methods, and are therefore simpler to execute and faster to complete than de novo structure determinations. ... The result of these difficulties is that pharmaceutical crystallographers began, in the mid-1980's, to search for a venue of their own to pursue their goals. ... Keith Watenpaugh of Upjohn and Noel Jones of Eli Lilly & Co. recognized that a single corporation was unlikely to make the financial commitment necessary for building a dedicated industrial beamline at a major facility, whereas a consortium involving several corporations could make such a commitment. They discussed this concept with colleagues at other large pharmaceutical and chemical companies, and formed the Industrial Macromolecular Crystallography Association (IMCA) to pursue the goal of a pharmaceutical beamline at a storage ring. They chose the Advanced Photon Source at Argonne National Laboratory as the site for their facility, since the APS was then under construction and promised the highest brilliance and the best opportunity for developing specialized beamlines. In 1992 IMCA contracted with Illinois Institute of Technology to build and operate the IMCA beamlines at the APS. (Andrew. Howard "Participation of Pharmaceutical Companies in Synchrotron Radiation Research" Illinois Institute of Technology, June 1998) http://icarus.csrri.iit.edu/~ahoward/pharm_sr.html See also synchrotrons


J coupling: 
See spin-spin coupling. 


kD:
 kilo Dalton. Also abbreviated kDa. 


LC-NMR
: Liquid Chromatography-Nuclear Magnetic Resonance: 
For more than 25 years, high performance liquid chromatography has been a workhorse technology in laboratories doing pharmaceutical, life science, industrial chemical, food and beverage research and development. Used alone or in combination with other technologies, HPLC is necessary for efficiently separating constituents in a complex mixture in order for those constituents to be accurately quantified and further characterized by  NMR and mass spectrometry. One-dimensional and multi-dimensional NMR can provide very specific and accurate structural information from protein and other biomolecular drug targets to small molecule lead compounds generated by medicinal or combinatorial chemistry. NMR is a key enabling technology used in the pharmaceutical and biotech industries in drug discovery, development, metabolism studies, animal model research, etc. When NMR is coupled with liquid chromatography, the resulting hyphenated technique of HPLC/ NMR can provide highly specific information-rich structural information on complex mixtures, which complements the traditional HPLC/MS information(Bruker press release, March 13, 2000)  http://www.bruker.com/nmr/AboutUs/Pdf_files/Waters.pdf


labels:
 See spin labels. 


MAD Multiple Anomalous Dispersion methods: 
 (back to top)  Multiple and single anomalous dispersion measurements are becoming increasingly popular as a method to solve protein structures. The possibility of obtaining completely unbiased phases at any resolution makes these methods intrinsically more reliable and robust than any other phasing technique used currently. (Ana Gonzalez, Staff Scientist, EMBL Research Station, Hamburg, Germany) http://www-db.embl-heidelberg.de:4321/emblGroups/g_81.html 


MAS Magic Angle Spinning
:
 NMR strategy in which the tube is rotated at very high speed and at a  specific angle which cancels out the line broadening effects of inhomogeneities in the sample. This yields high resolution and high sensitivity which are very useful in trace analysis or in looking at solid phase synthesis resins. (IUPAC Combinatorial Chemistry). 

Has since long been proven powerful in the studies of heterogeneous samples such as powdered solids, compartmentalized liquid samples, or heterogeneous solid-liquid mixtures. Recently it has been shown that higher resolution could be achieved if high-resolution  magnetic-susceptibility-matching probe (Nano.nmr probe) technology was used in conjunction to MAS High resolution liquid NMR and magic angle spinning. (M. Delepierre ,"High Resolution Liquid NMR and Magic Angle Spinning" J. Chim. Phys., Vol. 95 (2) February 1998)  http://www.edpsciences.org/articles/jcp/abs/1998/02/dele/dele.html 

Narrower term: hrMAS 


MicroCryo Probes
Bruker offers these for 3 mm sample tubes. Traditionally, NMR samples are placed in 5 mm tubes, with a high solvent-to-sample ratio. With the increased sensitivity offered by accessories such as the CryoProbes, researchers have noticed more solvent impurities in their spectra. The 3 mm tubes and MicroCryoProbes allow spectroscopists to study mass-limited samples, such as natural products and metabolites, in less solvent.  (Aileen Constans "Taking It Higher: State-of-the-Art NMR technology offers answers for the solution and solid states" Scientist 14 (21): 26, Oct. 30, 2000) See also cryogenic probes, cryoprobe.  http://www.the-scientist.com/yr2000/oct/profile1_001030.html 

Based on cryogenically cooled receiver coils and electronics ... can make routine measurements in the nanogram range (Bruker website) http://www.bruker.com/nmr/AboutUs/Pdf_files/microcryoprobe.pdf


mmCIF dictionary Macromolecular Crystallographic Information File
: IUCF's (International Union of Crystallography) preferred archive file format for macromolecular data and structural reports. http://www.iucr.ac.uk/iucr-top/cif/mmcif/ndb/background/index.html


mmCIF Dictionary website
, Rutgers Univ. US http://ndbserver.rutgers.edu/mmcif/dictionary/


multidimensional (three- and four-dimensional) NMR
:
 Introduced about 12-15 years ago. This technology has the advantage of resolving the severe overlap in 2D spectra and represents a very important breakthrough. (CHI Structural proteomics) Related terms 3D NMR, 4D NMR 


15
N: 
Nitrogen isotope label for NMR.


NMR Nuclear Magnetic Resonance
:  (back to top)   NMR spectroscopy makes it possible to discriminate nuclei, typically protons, in different chemical environments. The electron distribution gives rise to a chemical shift of the resonance frequency. The chemical shift, , of a nucleus is expressed in parts per million (ppm) by its frequency, n, relative to a standard, ref, and defined as = 106 (n - ref)/o, where o is the operating frequency of the spectrometer. It is an indication of the chemical state of the group containing the nucleus. More information is derived from the spin-spin couplings between nuclei, which give rise to multiplet patterns. Greater detail may be derived from two- or three-dimensional techniques. These use pulses of radiation at different nuclear frequencies, after which the response of the spin system is recorded as a free induction decay (FID). Multi-dimensional techniques, such as COSY and NOESY, make it possible to deduce the structure of a relatively complex molecule such as a small protein (molecular weight up to 25 000). In proteins containing paramagnetic centres, nuclear hyperfine interactions can give rise to relatively large shifts of resonant frequencies known as contact and pseudo-contact (dipolar) shifts, and considerable increases in the nuclear spin relaxation rates. From this type of measurement, structural information can be obtained about the paramagnetic site. (IUPAC Bioinorganic). 

A technology for protein structure determination. NMR generally gives a lower-resolution structure than X-ray crystallography does, but it does not require crystallization. NMR is currently applicable only to smaller proteins. (CHI Structural proteomics). 

In the last few years the role of Nuclear Magnetic Resonance (NMR) in both pharmaceutical and academic research has evolved dramatically. NMR has long been a powerful tool for characterizing protein structures. However, recent breakthroughs in NMR pulse methods and molecular alignment techniques have extended the size of systems to be studied and the accuracy with which structures can be determined. In pharmaceutical research, NMR screening of libraries and rational design of high-affinity ligands are now a main focus of numerous preclinical discovery efforts. NMR methods and instrumentation are being developed rapidly as groups seek high-throughput, low-cost approaches to accelerating the drug discovery process. Such approaches will be necessary as scientists attempt to characterize the large number of proteins currently being generated by structural genomics initiatives. NMR: Drug Discovery and Design ? Post-Genomic Analysis Oct. 24-26, 2000. 

Narrower terms include: 2D NMR, LC-NMR, 4D NMR, COSY, deuterium decoupled triple resonance NMR, FT-NMR, high-field NMR, LC-NMR, multidimensional NMR, NMR-biomolecular, NOESY, ROESY, reduced dimensionality triple resonance NMR, SAR by NMR, STD-NMR, solid state NMR, solution state NMR, TOCSY, triple resonance NMR, TROSY. Related term ESR Electron Spin Resonance 


NMR Link
spectroscopyNOW, NMR Knowledge Base
http://www.spectroscopynow.com/Spy/nmr/
NMR-related Feature Articles, News, Directory of Links, Employment Section, and more.


NMR-biomolecular
: NMR spectroscopy on small- to medium-size biological macromolecules. This is often used for structural investigation of proteins and nucleic acids, and often involves more than one isotope. (MeSH).


NOE Nuclear Overhauser Effect
: The interaction between the dipole moments of two nuclei in spatial proximity, provides information about the distance between nuclei and is one of the parameters studied in multidimensional NMR. (Aileen Constans "Taking It Higher: State-of-the-Art NMR technology offers answers for the solution and solid states" Scientist 14 (21): 26, Oct. 30, 2000) Related term NOESY 
http://www.the-scientist.com/yr2000/oct/profile1_001030.html

The Nuclear Overhauser Effect is a tremendously powerful tool for examining spatial relationships in molecular systems. The effect is characterized by a transfer of polarization (spins) from one nucleus to another through space (not through bonds). The distance dependence of the NOE is r6 so only short range interactions are ever seen. (Ted Bartlett, Joel Gohdes, Fourier Transform NMR Lab Manual, Chem 454, Ft. Lewis College, US, Fall 2000) http://faculty.fortlewis.edu/gohdes_J/c454f00lm.html


NOESY
: Nuclear Overhauser Effect (NOE) SpectroscopY. 

FAQ 98-08.1 NOESY, ROESY and TROESY: what is the difference? 
http://nmr.chem.ualberta.ca/AOWWW/nmr_news/98-08.htm#FAQ 98-08.1 (NMR FAQ). 


NOESY spectra
: Allow the space interactions between atoms to be measured and generate a 3D structure of the protein. (CHI Structural proteomics). 


pulse sequence
(back to top)   The application of a set of radio frequencies to a sample to produce a specific form of an NMR signal. Many different types of pulse sequences have been designed for modulating the NMR signal; pulse sequences allow the optimization of the NMR signal for the study of different types of samples. The result is a sharpening of all the peaks and a significant improvement their signal-to-noise ratios and their value for structural analysis. (CHI Structural proteomics).


pulsed field gradients PFG
: indicating that a probe is capable of doing gradient-enhanced spectroscopy. (Glossary, AO-VNMR, Univ. of Alberta, Canada) http://nmr.chem.ualberta.ca/AOWWW/glossary.htm 

Introduced into NMR imaging more than 20 years ago. A number of technical problems had to be overcome before gradients could be successfully incorporated into high-resolution NMR studies. ... Experiments enhanced with pulsed-field gradients have fewer artifacts, suffer far less from problems of solvents suppression and have reduced phase cycling requirements relative to the non-gradient experiments. (North Carolina State Univ. NMR Facility News, 1998) http://www2.ncsu.edu/ncsu/chemistry/NMRfeature.html 


ROESY
: Rotating frame Overhauser Enhancement SpectroscopY.


reduced dimensionality triple resonance NMR
: Being pioneered by people like Professor Thomas Szyperski at the State University of New York in Buffalo to exploit the higher sensitivity of cryogenic probes. (CHI Structural proteomics) Related term In-depth triple-resonance NMR relaxation: Passage of an excited or otherwise perturbed system towards or into thermal equilibrium with its environment. (IUPAC Photochemistry). 

If a system is disturbed from its state of equilibrium it relaxes to that state, and the process is referred to as relaxation. The branch of kinetics concerned with such processes is known as relaxation kinetics. Relaxation techniques include temperature jump and pressure jump. (See also chemical relaxation, IUPAC Compendium).


residual dipolar coupling
: A relatively new way to measure relative orientations of bonds with respect to one another. In NMR structure determination, distances are measured between atoms and interatomic distances are converted into 3D structures. Now relative orientations of bonds can also be measured to give many more constraints, allowing structures to be determined more precisely, or being able to deal with larger proteins. (CHI Structural proteomics).


resonance assignments
: An early step in the process of NMR-based structure determination can be done rapidly for proteins up to approximately 30 kDa. Although resonance assignments do not provide the complete structure of a protein, they often provide important structural information about a protein?s binding site, which can then be used to determine function. (CHI Structural proteomics). 


SAR by NMR Structure Activity Relationship by Nuclear Magnetic Resonance
(back to top)   Developed by Stephen Fesik of Abbott Laboratories. Allows the rapid screening and evaluation of thousands of compounds against a target protein. This screening technology detects whether a compound interacts by binding to the target protein, and it may also identify the binding epitope on the target. Different compounds may bind to adjacent, but different, sites. The next step in the SAR by NMR approach is to create structure-based-designed chemical libraries that link fragments of the original hits to yield high-potency leads. This method, however, requires a complete sequence-specific resonance assignment of the NMR-spectrum, which is still a time-consuming effort. (CHI Structural proteomics).


STD-NMR Saturation Transfer Difference NMR
: The difference of a saturation transfer and a normal NMR spectrum provides a new and fast method (STD NMR) to screen compound libraries for binding activity to proteins. STD NMR of mixtures of potential ligands with as little as 1 nmol of protein yields 1D and 2D NMR spectra that exclusively show signals from molecules with binding affinity. In addition, the ligand?s binding epitope is easily identified because ligand residues in direct contact to the protein show much stronger signals, e.g. the binding specificity of Lewisb-hexasaccharide to Aleuria aurantia agglutinin (AAA) can be mapped to the two fucosyl residues. (Characterization of Ligand Binding by Saturation Transfer Difference NMR Spectra, M. Mayer, B. Meyer, Angew. Chem. Int. Ed., 1999, 35, 1784-1788) http://sgi1.chemie.uni-hamburg.de/cgi-bin/abstracts.cgi?filename=pub29.html


single cell NMR imaging
: Spatial and temporal molecular species maps of intact single cells will be needed by biologists in the future. The development of single cell NMR imaging is thus particularly important for characterization of non-protein signaling elements within the cell. (National Center for Research Resources "Integrated Genomics Technologies Workshop Report" Jan 1999) http://www.ncrr.nih.gov/newspub/genomic.pdf


site-directed NMR analysis
: Understanding how ligands bind to a protein target is an essential part of drug development. Binding characteristics help determine how well the drug works - how effective and selective it is, and whether it can be administered in reasonable quantities. Traditionally, protein-ligand binding has been studied using X-ray crystallography (co-crystallography). But this approach can be time-consuming and does not allow researchers to see how the drug works in solution. Now it is becoming more common to use NMR for studies of ligand-binding conformations (i.e., a small molecule bound to a protein target). (CHI Structural proteomics). 


site-directed NMR
: See site-specific screening.


site-specific screening
: Researchers at the new Pharmacia spin-off, Biovitrum, also use NMR for structure-based, site-specific screening. Conceived of by Mats Wikstrom, head of macromolecular structures at Biovitrum, this method uses site-specific isotopic labeling of two amino acid residues, a technique described by Masatune Kainosho (Tokyo Metropolitan University) ... In this approach, two amino acid types are labeled with 13C and 15N. If this pair of amino acids occurs only once in the sequence, there will be only one peak in a one-dimensional/ two-dimensional HNCO-type NMR spectrum. This technique allows researchers to screen for only those binders that interact with a specific site of the receptor. (CHI Structural proteomics) Also referred to as site-directed NMR


solid state NMR
: Requires wider-bore (63 or even 89 mm diameter) magnets (than solution state NMR). The higher stored energy of these wide bore magnets means that they are significantly more difficult to build, and as a result high-field solid state NMR lags behind liquid state in terms of available field strength. The highest field currently available for a wide bore magnet is 800 MHz . (Aileen Constans "Taking It Higher: State-of-the-Art NMR technology offers answers for the solution and solid states" Scientist 14 (21): 26, Oct. 30, 2000) http://www.the-scientist.com/yr2000/oct/profile1_001030.html 

Can be used to study proteins that cannot be crystallized or are too large for solution state NMR methods. 


solution state NMR
: NMR in liquids.


spin
: The nuclei of certain atoms, for example, 1H, 13C, and 15N, exhibit a physical property known as spin. These nuclei can be viewed as tiny magnets that, when placed in an external magnetic field, can orient themselves in two possible ways, with spin vectors aligned in the direction of, or directly against, the field. For nuclei with a nuclear quantum spin number of 1/2, such as those listed above, these two orientations correspond, respectively, to a low energy state and a high-energy state. Transitions between the two states occur spontaneously, but infrequently. However, if the sample is irradiated with energy equivalent to the energy difference between the two states - in the radio frequency, or RF, range - transitions will occur more frequently. These induced transitions form the basis of NMR spectroscopy. When the magnetization vectors associated with the transitions are rotated perpendicular to the applied field, they precess about the direction of the field and induce a current in the receiver coil, which is recorded and plotted as a function of time. The resulting sine wave decays with time due to spin dephasing, and the signal is recorded as a free induction decay (FID), which is then converted into a frequency domain spectrum. (Aileen Constans "Taking It Higher: State-of-the-Art NMR technology offers answers for the solution and solid states" Scientist 14 (21): 26, Oct. 30, 2000) http://www.the-scientist.com/yr2000/oct/profile1_001030.html Related terms spin labelsspin probesspin propertiesspin-spin couplingspin-spin relaxation


spin labels
: A stable paramagnetic group that is attached to a part of another molecular entity whose microscopic environment is of interest and may be revealed by the electron paramagnetic resonance spectrum of the spin label. When a simple paramagnetic molecular entity is used in this way without covalent attachment to the molecular entity of interest it is frequently referred to as a "spin probe". (IUPAC Bioinorganic) See also 1H13C15N


spin probe
: See under spin labels. 


spin properties
: IUPAC Provisional Recommendations: NMR Nomenclature: Nuclear Spin Properties and Conventions for Chemical Shifts, Physical and Biophysical Chemistry Division, Commission Molecular Structure and Spectroscopy Comments by Aug. 21, 2001 http://www.iupac.org/reports/provisional/abstract01/harris_310801.html 


spin-spin coupling
: The interaction between the spin magnetic moments of different electrons and/or nuclei. In NMR spectroscopy it gives rise to multiplet patterns, and cross-peaks in two-dimensional NMR spectra. Between electron and nuclear spins this is termed the nuclear hyperfine interaction. Between electron spins it gives rise to relaxation effects and splitting of the EPR spectrum. (IUPAC Bioinorganic). 

Is this the same as J coupling? 


spin-spin relaxation
: A solid-state physics process involving raising temperatures using weak magnetic fields. 


storage rings
: See under beamline, synchrotrons.


synchrotrons
: Devices for accelerating protons or electrons in closed orbits where the accelerating voltage and magnetic field strength varies (the accelerating voltage is held constant for electrons) in order to keep the orbit radius constant. (MeSH). 

A key development in the high throughput crystallographic solving of protein structures, shortening X-ray diffraction data collection time from days to hours and reducing the size of crystals needed to produce useful data. (Terry Gaasterland "Structural genomics: Bioinformatics in the driver?s seat" Nature Biotechnology 16:625-627 July 1998). 

Related terms beamline; (nanoscience Miniaturization glossary). 


Synchrotron links
  
(back to top) 
Synchrotron X-ray sources in the world, ESRF European Synchrotron Radiation Facility, Grenoble, France. http://www.esrf.fr/navigate/synchrotrons.html 

See also beamline; Industrial Macromolecular Crystallography Association IMCA


TOCSY
: TOtal Correlation SpectroscopY. 


TROESY
: Transverse Rotating Frame Overhauser Effect Spectroscopy. 


TROSY
 Transverse Relaxation Optimized Spectroscopy: Invented about 1997. First described by Professor Kurt Wuthrich. Useful for analyzing larger protein systems. TROSY is a method for getting sharper peaks on large proteins. 

TROSY is best at higher fields. If the aim is to study a large complex or a chemical shift perturbation when a protein binds to a receptor using NMR, it?s better to use a 900 MHz machine than a more standard lower-field machine. (CHI Structural proteomics).

three-D: See 3D

triple-resonance cryoprobes: By using a triple-resonance cryoprobe, we can collect in six hours the same data which required over two weeks of data-collection time with a conventional probe. (CHI Structural proteomics).


triple-resonance NMR
: Introduced in 1989, involves isotope labeling with 15N and 13C. (N = nitrogen; C = carbon.). Methods and software for automated analysis of now becoming available. (CHI Structural proteomics).

two-D: See 2D


X-ray crystallography
: The most widely used (and most accurate) method of obtaining structures, X-ray crystallography involves expressing highly purified protein samples, crystallizing these, and then performing X-ray diffraction of the protein to elucidate crystal structure. Computational software is then used (combined with extensive - but increasingly less - human judgment) to convert X-ray diffraction data into high-resolution structures. Note that many proteins cannot be crystallized at present. (CHI Structural proteomics) See also synchrotrons


X-ray diffraction
: <investigation> Basis of powerful technique for determining the three dimensional structure of molecules, including complex biological macromolecules such as proteins and nucleic acids, that form crystals or regular fibres. Low angle X-ray diffraction is also used to investigate higher levels of ordered structure, as found in muscle fibres (OMD 18 Nov 1997).


Bibliography
  (back to top) 

AO-VNMR Glossary, Albin Otter, Chemistry Dept. Univ. of Alberta, Canada, 2001. http://nmr.chem.ualberta.ca/AOWWW/ About 50 terms. 

Basics of NMR: Glossary, J.P. Hornak, Rochester Institute of Technology, US 1997-1999 http://www.cis.rit.edu/htbooks/nmr/inside.htm 

CCMC Crystallography Made Crystal Clear, Gale Rhodes, Chemistry Dept., Univ. of Southern Maine, US http://www.usm.maine.edu/~rhodes/CMCC/index.html Web resource for print Crystallography Made Crystal Clear (2nd ed.) 

(CHI Structural Proteomics) Structural Proteomics: High-Throughput Approaches Fuel Drug Discovery and Development, Cambridge Healthtech Institute report, Malorye Branca, Allan Haberman, Deidre Lockwood, 2001

Elves Manual Glossary of X-ray Terms, James Holton, Univ. of California Berkeley, US http://ucxray.berkeley.edu/~jamesh/elves/manual/basics.html 

IUPAC Recommendations for the Presentation of NMR Structures of Proteins and Nucleic Acids, John L Markley et. al. July 28, 1998 http://www.bmrb.wisc.edu/home/iupac.pdf 

IUPAC Provisional Recommendations: NMR Nomenclature: Nuclear Spin Properties and Conventions for Chemical Shifts, Physical and Biophysical Chemistry Division, Commission Molecular Structure and Spectroscopy Comments by Aug. 21, 2001 http://www.iupac.org/reports/provisional/abstract01/harris_310801.html 

Judging the Quality of Macromolecular models Glossary of Terms from Crystallography, NMR and Homology Modeling :Gale Rhodes, Chemistry Dept. Univ. of Southern Maine, US, 2000 http://www.usm.maine.edu/~rhodes/ModQual/index.html 

Statistical descriptors in Crystallography, Glossary of statistical terms, International Union of Crystallography, 1996 http://www.iucr.org/iucr-top/comm/cnom/statdes/index.html#gloss 

Virtual Library: Crystallography, International Union of Crystallography http://www.ch.iucr.org/cww-top/int.w3vlc.html 

Alpha Glossary Index  (back to top) 

 

This glossary has been reproduced with the permission of
Cambridge Healthtech Institute

Suggestions? Comments? Questions? mchitty@healthtech.com
Related glossaries include: Protein StructuresStructural Genomics.

IUPAC definitions are reprinted with the permission of the 
International Union of Pure and Applied Chemistry.

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