Technologies
term index Related glossaries include Protein
Structures,
Protein informatics
Proteomics
2D NMR:
Includes COSY and NOESY
3D NMR: See multidimensional NMR
4D NMR: See multidimensional NMR
beamline:
In
particle
physics, a beamline is the line along which a beam of particles
travels through, or when projected from, a particle
accelerator. It may refer to the line of travel within an actual
accelerator, and to the equipment that maintains that beam in a storage ring
or accelerates it in a linear
accelerator. It may also refer to a beam of X-rays
projected to stations for doing crystallography
Beamline, Wikipedia, accessed Oct. 3, 2005 Related
terms: synchrotrons, Industrial Macromolecular Crystallography Association IMCA
bicelles:
in certain regimes so-called bilayered mixed
micelles or “bicelles” are formed. In the simplest case, they can be described
as microscopic disks where a bilayer patch is encircled by a “rim” of detergent
molecules. Bicelles represent a new instance of lipid morphology and are
extensively applicable to structural studies of lipid membranes and protein
structure.1
Dürr UHN, Gildenberg M, Ramamoorthy A. The Magic of Bicelles Lights Up Membrane
Protein Structure. Chemical Reviews. 2012;112(11):6054-6074.
doi:10.1021/cr300061w.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3497859/
13C :
Carbon isotopes used in NMR labeling.
COSY:
Correlated Spectroscopy, 2D NMR.
chemical shift:
The variation of the resonance frequency of a nucleus in nuclear magnetic resonance (NMR) spectroscopy in consequence of its magnetic
environment. The chemical shift of a nucleus, is expressed in ppm by its frequency, cpd, relative to a standard, ref, and defined as = 106(cpd - ref)/o
where o is the operating frequency of the spectrometer. For 1H and 13C NMR the reference signal is usually that of tetramethylsilane (SiMe4).
Other references are used in the older literature and in other solvents, such as D2O.
If a resonance signal occurs at lower frequency or higher applied field than an arbitrarily selected reference signal, it is said to be upfield, and if
resonance occurs at higher frequency or lower applied field, the signal is downfield. Resonance lines upfield from SiMe4 have positive, and
resonance lines downfield from SiMe4 have negative -values. IUPAC
Physical Organic Chemistry chemical shift anisotropy CSA:
A “relaxation” property.
comparative spectral analysis CoSA: SEE under Quantitative
13C
NMR Spectrometric Data- Activity Relationships Modeling QSDAR
comparative structural connectivity spectra analysis CoSCSA: SEE under
Quantitative 13C NMR Spectrometric
Data- Activity Relationships Modeling QSDAR
comparative structurally assigned spectral analysis CoSASA: SEE under
Quantitative 13C NMR Spectrometric
Data- Activity Relationships Modeling QSDAR
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. Related
terms: cryoprobe, microcryoprobes, triple resonance cryoprobes.
crystallography:
the experimental science of determining the arrangement of atoms in
crystalline solids (see crystal
structure). The word "crystallography" derives from the Greek words crystallon "cold
drop, frozen drop", with its meaning extending to all solids with some degree of
transparency, and graphein "to write". .. X-ray
crystallography is used to determine the structure of large biomolecules such
as proteins. Wikipedia
accessed 2018 Oct 18
https://en.wikipedia.org/wiki/Crystallography
Narrower terms: protein crystallography, X-ray crystallography, synchrotron-
based x-ray crystallography --
or are these equivalent? Related term: Industrial Macromolecular
Crystallography Association Dalton:
Unit of mass equal to the unified atomic mass (atomic
mass constant). [IUPAC Compendium] After John Dalton (1766-1844)
British chemist and physicist. more Chemistry
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.
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. Technische Universität Braunschweig
http://www.pci.tu-bs.de/aggericke/PC4/Kap_I/ftnmr.htm
flexible linkages:
In proteins.
free induction decay FID: See spin, FT-NMR
1H:
Hydrogen isotope used in NMR labeling.
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
high-field NMR:
A type of spectroscopy where the energy states of spin-active nuclei placed in a
static (>300 MHz) magnetic field are interrogated by inducing transitions
between the states via radio frequency irradiation. Each experiment consists of
a sequence of radio frequency pulses with delay periods in between them. Royal
Society of Chemistry
http://www.rsc.org/publishing/journals/prospect/ontology.asp?id=CMO:0000723&MSID=b920545b
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
high pressure NMR:
Advanced high-resolution NMR spectroscopy, including
two-dimensional NMR techniques, combined with high pressure capability,
represents a powerful new tool in the study of proteins.
High-Resolution,
High-Pressure NMR Studies of Proteins
J. Jonas,* L. Ballard,#
and D. Nash# Biophysical Journal Volume 75 July 1998 445–452
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1299717/pdf/9649405.pdf
high-resolution diffusion-ordered spectroscopy
HR-DOSY:
Philip
Hodge and Gareth Morris and their colleagues at the University of Manchester
[are] using NMR to help them pick out the best host molecules from an array of
hopefuls for use in analytical sensor applications. ... A multi- dimensional
version of NMR, which disperses signals for the members of the library according
to an additional criterion: their diffusion coefficients. Normally all the
members will diffuse relatively rapidly. However, when a soluble polymer, with
an added side-group of interest, is added to the combinatorial array, each
member of the array that binds to the functionality on the polymer diffuses more
slowly than before. The magnitude of the shift indicates the strength of the
interaction. The spectrum of the most tightly bound molecule can then be
plotted. [Elemental Discoveries Mar. 2001, Issue 39] http://www.sciencebase.com/mar01iss.html
hyphenated techniques:
NMR together with chromatography and/ or
mass spectrometry. Includes LC- NMR.
Industrial Macromolecular Crystallography
Association IMCA: IMCA-CAT
is a synchrotron-based structural biology research facility for
industrial macromolecular crystallography aimed at accelerating
pharmaceutical drug discovery programs.
https://www.linkedin.com/company/imca-cat/
IMCA-CAT is dedicated to high-throughput macromolecular
crystallography for the pharmaceutical industry. The beamlines are
equipped with robotics and automated for sample screening, ranking,
data acquisition, and data processing.
https://www.mitegen.com/learn/beamline-guides/aps-17-id-imca-cat/
Related terms: beamline,
synchrotrons infrared spectromicroscopy: Microscopy
isotope:
A form of a chemical element that contains the same number of
protons but a different number of neutrons than other forms of the element.
Isotopes are often used to trace atoms or molecules in a metabolic
pathway. In NMR, only one isotope of each element contains the correct magnetic
properties to be useful. NIGMS, US Structures of Life glossary
https://publications.nigms.nih.gov/structlife/glossary.html
J coupling: See spin-spin coupling.
kD:
kilo Dalton. Also abbreviated
kDa.
macromolecular crystallography:
a technique used to study biological molecules such as
proteins, viruses and nucleic acids (RNA and DNA) to a resolution higher than
~5Å. This high resolution helps elucidate the detailed mechanism by which these
macromolecules carry out their functions in living cells and organisms. Protein
molecules can crystallize under regulated conditions; the crystals
are made up of multiple copies of the molecule arranged in a regular
3-dimensional lattice. The x-rays deflected ("scattered") by the atoms in
equivalent positions in the crystal lattice concentrate into sharp intense spots
(crystal diffraction
pattern). The macromolecular structure can be determined by analysis of the
intensities and positions of the diffraction spots. Stanford Synchrotron
Radiaiton Lightsource SLAC National Accelerator Laboratory
http://smb.slac.stanford.edu/
MAD Multiwavelength Anomalous
Diffraction : An approach to solving the phase
problem in protein structure
determination by comparing structure factors collected at different
wavelengths, including the absorption edge of a heavy-atom scatterer. Also known
as multiple-wavelength anomalous diffraction or multiwavelength anomalous
dispersion.
http://reference.iucr.org/dictionary/Multiwavelength_anomalous_diffraction_(MAD))
A technique used in X-ray
crystallography that accelerates the determination of protein structures. It
uses X-rays of different wavelengths, relieving crystallographers from having to
make several different metal- containing crystals. NIGMS, US Structures
of Life glossary
https://publications.nigms.nih.gov/structlife/glossary.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
Narrower term: hrMAS
mmCIF dictionary Macromolecular Crystallographic Information File
glossary, Protein Data Bank MMCIF
http://mmcif.wwpdb.org/docs/tutorials/glossary/pdbx-mmcif-glossary.html
multidimensional (three- and four-dimensional) NMR:
This technology has the advantage of resolving the
severe overlap in 2D spectra and represents a very important breakthrough. Related terms: 3D NMR, 4D NMR
15N:
Nitrogen isotope label for NMR.
neutron
crystallography:
Neutron crystallography has had an important, but relatively small role
in structural biology over the years. In this review of recently
determined neutron structures, a theme emerges of a field currently
expanding beyond its traditional boundaries, to address larger and more
complex problems, with smaller samples and shorter data collection
times, and employing more sophisticated structure determination and
refinement methods. The origin of this transformation can be found in a
number of advances including first, the development of neutron
image-plates and quasi-Laue methods at nuclear reactor neutron sources
and the development of time-of-flight Laue methods and electronic
detectors at spallation neutron sources; second, new facilities and
methods for sample perdeuteration and crystallization; third, new
approaches and computational tools for structure determination. Neutron
crystallography: opportunities, challenges, and limitations. Matthew P
Blakeley,1 Paul Langan,2,3 Nobuo Niimura,4 and Alberto Podjarny5 Curr
Opin Struct Biol. 2008 Oct;18(5):593-600. Epub 2008 Aug 7.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2586829/
neutron scattering:
Because of the neutron's particular
properties, it is possible to obtain information on biomolecular
structures, dynamics and interactions that is not accessible to other
methodologies and neutron-scattering experiments should play an
essential role if we hope to achieve a reasonable understanding of
biology at the molecular level. The special advantages of neutrons
combined with the progress in biochemistry and molecular biology are
powerful reasons to stimulate a rebirth of neutron-scattering
experiments in biology in the post genome sequencing era. Neutrons in
biology in the post genome sequencing era
G. Zaccai
Applied Physics A: Materials Science &
Processing
Volume 74, Supplement 1,
s6-s10, DOI: 10.1007/s003390101253
http://www.springerlink.com/content/rb5f4htntlvk5e83/
Wikipedia
http://en.wikipedia.org/wiki/Neutron_scattering
NMR Nuclear Magnetic Resonance:
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. Narrower terms:
2D NMR, 3D NMR, 4D NMR, COSY, deuterium decoupled
triple resonance 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, TROSY, FT-NMR
Fourier Transform NMR triple resonance NMR. Related term: ESR Electron
Spin Resonance
NMR active atom:
An atom that has the correct magnetic
properties to be useful for NMR. For some atoms, the NMR-active form
is a rare isotope, such as 13C or 15N. NIGMS, US Structures of Life
glossary,
https://publications.nigms.nih.gov/structlife/glossary.html NMR Nuclear Magnetic Resonance - 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, 1998
NMR spin relaxation spectroscopy:
A powerful approach for characterizing intramolecular and overall rotational
motions in proteins. This review describes experimental methods for measuring
laboratory frame spin relaxation rate constants by high- resolution solution-
state NMR spectroscopy, together with theoretical approaches for interpreting
spin relaxation data in order to quantify protein conformational dynamics on
picosecond- nanosecond time scales. AG Palmer 3rd NMR
probes of molecular dynamics: overview and comparison with other techniques.
Annual Rev Biophys Biomol Struct.30:129- 155, 2001
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]
Wikipedia http://en.wikipedia.org/wiki/Nuclear_Overhauser_effect
Related term: NOESY
NOESY Nuclear Overhauser Effect (NOE)
SpectroscopY: An NMR
technique used to help determine protein structures. It reveals how close
different protons (hydrogen nuclei) are to each other in space. NIGMS, US
Structures of Life glossary
https://publications.nigms.nih.gov/structlife/glossary.html
NOESY, ROESY and
TROESY: what is the difference? FAQ 98-08.1 NMR FAQ, Chemistry Dept. Univ. of Alberta,
Canada http://nmr.chem.ualberta.ca/nmr_news/98-08.htm
NOESY spectra:
Allow the space interactions between atoms to
be measured and generate a 3D structure of the protein.
phasing techniques:
Include
Multiple Anonymous Dispersion MAD phasing, Multiple Isomorphous Replacement MIR
Bernhard Rupp, Protein Crystallography Tutorial Site, 2005 http://ruppweb.dyndns.org/Xray/101index.html
protein
crystallography: Crystallography is a widely recognized tool that supports
protein science. For Membrane Proteins, this tool is elevated into an important
science that aids in the efforts to reveal structures and functions. This course
describes how crystallography works, including highlights of Membrane Proteins
and automation. For stable protein-protein and protein–nucleic acid complexes, mechanistic
understanding comes most readily with the highest levels of structural detail
(general shape). Thus, atomic resolution generally is the ultimate goal in
analysis of any biological structure. Crystallography and some imaging
techniques offer this potential but have very specialized sample requirements
and limitations, are not high throughput, and provide only a static picture of
the complex. DOE, Genomics GTL Roadmap: Molecular
Machines 2005 http://genomicscience.energy.gov/roadmap/pdf/GTL05_05MolMachines.pdf
Is there any kind of protein
crystallography that isn't x-ray crystallography?
pulse sequence:
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.
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/index.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. Related term: triple resonance NMR
relaxation:
Passage of an excited or otherwise perturbed system
towards or into thermal equilibrium with its environment. [IUPAC
Photochemistry] Narrower term: chemical relaxation
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.
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.
SAR by NMR Structure Activity Relationship by Nuclear Magnetic Resonance:
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.
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). Related term 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. 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]
Can be used to study proteins that cannot be crystallized or are too large
for solution state
NMR methods.
solution-based
techniques:
such as cryoEM, NMR, and X-ray and neutron diffraction offer information that is
lower resolution but can be related more directly to the molecule’s structure
in a more natural environment. Multiple tools obviously will be needed to obtain
a more complete view of the structure of protein complexes, including shape,
relationship of interaction faces, and stoichiometry. DOE, Genomics GTL Roadmap:
Molecular Machines 2005 http://genomicscience.energy.gov/roadmap/pdf/GTL05_05MolMachines.pdf
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 Related terms spin labels, spin probes, spin properties, spin- spin coupling,
spin- 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 Narrower terms: 1H, 13C, 15N.
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
https://www.iupac.org/publications/pac/2001/pdf/7311x1795.pdf
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.
Superconducting QUantum Interference Devices
SQUIDs:
The most sensitive magnetic field detector ever devised ... SQUIDs have been
used in NMR measurements since the 1980s, but mostly for solid samples at
extremely low temperatures... SQUIDs can detect magnetic flux directly, sensing
the magnetic field generated by even a slowly precessing nucleus. The resulting
signal is weak but extremely sharp: the lower the magnetic field, the narrower
the NMR line, yielding a signal- to- noise ratio far superior to that of high-
field NMR. Paul Preuss "Measuring molecules with minute magnetic fields"
Lawrence Berkeley Lab, US, 2002
http://www.lbl.gov/Science-Articles/Archive/MSD-microtesla-Clarke.html
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, 1993
A large machine that accelerates electrically charged particles to nearly
the speed of light and maintains them in circular orbits. Originally designed
for use by high- energy physicists, synchrotrons are now heavily used by
structural biologists as a source of very intense X- rays. NIGMS, US
Structures of Life glossary,
https://publications.nigms.nih.gov/structlife/glossary.html 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,
Industrial Macromolecular Crystallography Association
IMCA; Synchrotron X-ray sources in the world, ESRF European
Synchrotron Radiation Facility http://www.esrf.eu/UsersAndScience/Links/Synchrotrons/
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.
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.
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.
X-ray
crystallography is an experimental technique that exploits the fact that X-rays
are diffracted by crystals. It is not an imaging technique. Bernard Rupp,
Crystallography 101 http://ruppweb.dyndns.org/Xray/101index.html
Related terms: beamlines,
protein crystallography, 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
NMR & Crystallography resources
Clark, Jim,
Understanding Chemistry, Nuclear Magnetic Resonance menu http://www.chemguide.co.uk/analysis/nmrmenu.html#top
Hornak, JP, Basics of NMR:
Glossary, Rochester Institute of Technology,
US 1997-1999 http://www.cis.rit.edu/htbooks/nmr/inside.htm
IUCR International Union of
Crystallography, Statistical descriptors in Crystallography, Glossary of statistical
terms, 1996 http://www.iucr.org/iucr-top/comm/cnom/statdes/index.html#gloss
IUPAC Recommendations: NMR Nomenclature: Nuclear Spin Properties
and Conventions for Chemical Shifts, Robin K. Harris et. al, Physical and Biophysical Chemistry
Division, Commission Molecular Structure and Spectroscopy, 2001
http://www.iupac.org/publications/pac/2001/7311/7311x1795.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/iupac.pdf
Joint Center for
Structural Genomics, Important Definitions, 40+ terms http://www.jcsg.org/help/robohelp/Definitions/Intro_to_Definitions.htm
Otter, Albin, AO-VNMR
Glossary, Chemistry Dept. Univ. of Alberta, Canada,
2001. http://nmr.chem.ualberta.ca/AOWWW/
About 50 terms. Click on Glossary
Rupp, Bernhard,
Crystallography 101, http://ruppweb.dyndns.org/Xray/101index.html
SLAC Glossary, Stanford Linear Accelerator Center,
Stanford Univ. US, 2002, 300 definitions. http://www.slac.
stanford.edu/history/
slacspeak/
How
to look for other unfamiliar terms
IUPAC definitions are reprinted with the
permission of the International Union of Pure and Applied Chemistry.
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