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Single Wavelength Anomalous Dispersion
Single-wavelength anomalous diffraction (SAD) is a technique used in X-ray crystallography that facilitates the determination of the structure of proteins or other biological macromolecules by allowing the solution of the phase problem. In contrast to multi-wavelength anomalous diffraction, SAD uses a single dataset at a single appropriate wavelength. One advantage of the technique is the minimization of time spent in the beam by the crystal, thus reducing potential radiation damage to the molecule while collecting data. SAD is sometimes called "single-wavelength anomalous dispersion", but no dispersive differences are used in this technique since the data are collected at a single wavelength. Today, selenium-SAD is commonly used for experimental phasing due to the development of methods for selenomethionine incorporation into recombinant proteins. See also * Multi-wavelength anomalous dispersion (MAD) * Multiple isomorphous replacement (MIR) *Anomalous scattering *Anomalous X-ra ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
X-ray Crystallography
X-ray crystallography is the experimental science determining the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to diffract into many specific directions. By measuring the angles and intensities of these diffracted beams, a crystallographer can produce a three-dimensional picture of the density of electrons within the crystal. From this electron density, the mean positions of the atoms in the crystal can be determined, as well as their chemical bonds, their crystallographic disorder, and various other information. Since many materials can form crystals—such as salts, metals, minerals, semiconductors, as well as various inorganic, organic, and biological molecules—X-ray crystallography has been fundamental in the development of many scientific fields. In its first decades of use, this method determined the size of atoms, the lengths and types of chemical bonds, and the atomic-scale differences among variou ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Proteins
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, providing structure to cells and organisms, and transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific 3D structure that determines its activity. A linear chain of amino acid residues is called a polypeptide. A protein contains at least one long polypeptide. Short polypeptides, containing less than 20–30 residues, are rarely considered to be proteins and are commonly called peptides. The individual amino acid residues are bonded together by peptide bonds and adjacent amino acid residues. The sequence of amino acid residu ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Phase Problem
In physics, the phase problem is the problem of loss of information concerning the phase that can occur when making a physical measurement. The name comes from the field of X-ray crystallography, where the phase problem has to be solved for the determination of a structure from diffraction data. The phase problem is also met in the fields of imaging and signal processing. Various approaches of phase retrieval have been developed over the years. Overview Light detectors, such as photographic plates or CCDs, measure only the intensity of the light that hits them. This measurement is incomplete (even when neglecting other degrees of freedom such as polarization and angle of incidence) because a light wave has not only an amplitude (related to the intensity), but also a phase (related to the direction), and polarization which are systematically lost in a measurement. In diffraction or microscopy experiments, the phase part of the wave often contains valuable information on the st ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Multi-wavelength Anomalous Diffraction
Multi-wavelength anomalous diffraction (sometimes Multi-wavelength anomalous dispersion; abbreviated MAD) is a technique used in X-ray crystallography that facilitates the determination of the three-dimensional structure of biological macromolecules (e.g. DNA, drug receptors) via solution of the phase problem. MAD was developed by Wayne Hendrickson while working as a postdoctoral researcher under Jerome Karle at the United States Naval Research Laboratory. The mathematics upon which MAD (and progenitor Single wavelength anomalous dispersion) were based were developed by Jerome Karle, work for which he was awarded the 1985 Nobel Prize in Chemistry (along with Herbert Hauptman). See also * Single wavelength anomalous dispersion (SAD) * Multiple isomorphous replacement (MIR) *Anomalous scattering *Anomalous X-ray scattering Anomalous X-ray scattering (AXRS or XRAS) is a non-destructive determination technique within X-ray diffraction that makes use of the anomalous dispersion that o ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Dispersion (optics)
In optics, and by analogy other branches of physics dealing with wave propagation, dispersion is the phenomenon in which the phase velocity of a wave depends on its frequency; sometimes the term chromatic dispersion is used for specificity to optics in particular. A medium having this common property may be termed a dispersive medium (plural ''dispersive media''). Although the term is used in the field of optics to describe light and other electromagnetic waves, dispersion in the same sense can apply to any sort of wave motion such as acoustic dispersion in the case of sound and seismic waves, and in gravity waves (ocean waves). Within optics, dispersion is a property of telecommunication signals along transmission lines (such as microwaves in coaxial cable) or the pulses of light in optical fiber. Physically, dispersion translates in a loss of kinetic energy through absorption. In optics, one important and familiar consequence of dispersion is the change in the angle of ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Selenomethionine
Selenomethionine (SeMet) is a naturally occurring amino acid. The L-selenomethionine enantiomer is the main form of selenium found in Brazil nuts, cereal grains, soybeans, and grassland legumes, while ''Se''-methylselenocysteine, or its γ-glutamyl derivative, is the major form of selenium found in ''Astragalus'', ''Allium'', and ''Brassica'' species. ''In vivo'', selenomethionine is randomly incorporated instead of methionine. Selenomethionine is readily oxidized. Selenomethionine's antioxidant activity arises from its ability to deplete reactive oxygen species. Selenium and methionine also play separate roles in the formation and recycling of glutathione, a key endogenous antioxidant in many organisms, including humans. Substitution chemistry issues Selenium and sulfur are chalcogens that share many chemical properties so the substitution of methionine with selenomethionine may have only a limited effect on protein structure and function. However, the incorporation of seleno ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Multi-wavelength Anomalous Dispersion
Multi-wavelength anomalous diffraction (sometimes Multi-wavelength anomalous dispersion; abbreviated MAD) is a technique used in X-ray crystallography that facilitates the determination of the three-dimensional structure of biological macromolecules (e.g. DNA, drug receptors) via solution of the phase problem. MAD was developed by Wayne Hendrickson while working as a postdoctoral researcher under Jerome Karle at the United States Naval Research Laboratory. The mathematics upon which MAD (and progenitor Single wavelength anomalous dispersion) were based were developed by Jerome Karle, work for which he was awarded the 1985 Nobel Prize in Chemistry (along with Herbert Hauptman). See also * Single wavelength anomalous dispersion Single-wavelength anomalous diffraction (SAD) is a technique used in X-ray crystallography that facilitates the determination of the structure of proteins or other biological macromolecules by allowing the solution of the phase problem. In contrast ... (S ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Multiple Isomorphous Replacement
Multiple isomorphous replacement (MIR) is historically the most common approach to solving the phase problem in X-ray crystallography studies of proteins. For protein crystals this method is conducted by soaking the crystal of a sample to be analyzed with a heavy atom solution or co-crystallization with the heavy atom. The addition of the heavy atom (or ion) to the structure should not affect the crystal formation or unit cell dimensions in comparison to its native form, hence, they should be isomorphic. Data sets from the native and heavy-atom derivative of the sample are first collected. Then the interpretation of the Patterson difference map reveals the heavy atom's location in the unit cell. This allows both the amplitude and the phase of the heavy-atom contribution to be determined. Since the structure factor of the heavy atom derivative (Fph) of the crystal is the vector sum of the lone heavy atom (Fh) and the native crystal (Fp) then the phase of the native Fp and Fph vect ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Anomalous Scattering
Anomalous X-ray scattering (AXRS or XRAS) is a non-destructive determination technique within X-ray diffraction that makes use of the anomalous dispersion that occurs when a wavelength is selected that is in the vicinity of an absorption edge of one of the constituent elements of the sample. It is used in materials research to study nanometer sized differences in structure. Atomic scattering factors In X-ray diffraction the scattering factor ''f'' for an atom is roughly proportional to the number of electrons that it possesses. However, for wavelengths that approximate those for which the atom strongly absorbs radiation the scattering factor undergoes a change due to anomalous dispersion. The dispersion not only affects the magnitude of the factor but also imparts a phase shift in the elastic collision of the photon. The scattering factor can therefore best be described as a complex number : f= fo + Δf' + i.Δf" Contrast variation The anomalous aspects of X-ray scattering have b ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Anomalous X-ray Scattering
Anomalous X-ray scattering (AXRS or XRAS) is a non-destructive determination technique within X-ray diffraction that makes use of the anomalous dispersion that occurs when a wavelength is selected that is in the vicinity of an absorption edge of one of the constituent elements of the sample. It is used in materials research to study nanometer sized differences in structure. Atomic scattering factors In X-ray diffraction the scattering factor ''f'' for an atom is roughly proportional to the number of electrons that it possesses. However, for wavelengths that approximate those for which the atom strongly absorbs radiation the scattering factor undergoes a change due to anomalous dispersion. The dispersion not only affects the magnitude of the factor but also imparts a phase shift in the elastic collision of the photon. The scattering factor can therefore best be described as a complex number : f= fo + Δf' + i.Δf" Contrast variation The anomalous aspects of X-ray scattering have b ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Patterson Map
The Patterson function is used to solve the phase problem in X-ray crystallography. It was introduced in 1935 by Arthur Lindo Patterson while he was a visiting researcher in the laboratory of Bertram Eugene Warren at MIT. The Patterson function is defined as :P(u,v,w) = \sum\limits_ \left, F_\^2 \;e^. It is essentially the Fourier transform of the intensities rather than the structure factors. The Patterson function is also equivalent to the electron density convolved with its inverse: :P\left(\vec\right) = \rho\left(\vec\right) * \rho\left(-\vec\right). Furthermore, a Patterson map of ''N'' points will have peaks, excluding the central (origin) peak and any overlap. The peaks' positions in the Patterson function are the interatomic distance vectors and the peak heights are proportional to the product of the number of electrons in the atoms concerned. Because for each vector between atoms ''i'' and ''j'' there is an oppositely oriented vector of the same length (between ato ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Keith Hodgson
Keith O. Hodgson (born 1947 in Virginia) is a Professor of Chemistry at Stanford University and formerly director of the Stanford Synchrotron Radiation Lightsource. Education He received his B.S. in 1969 from the University of Virginia and his Ph.D. in 1972 from University of California at Berkeley. Research He joined Stanford's Chemistry department in 1973 and then he became a full-time chemistry professor in 1984. His principal research interests include Inorganic chemistry, inorganic, Bioinorganic chemistry, bioinorganic, structural and Biophysical chemistry, biophysical chemistry. His research group focuses on questions relating to how structure at different organizational levels relates to function. His research is done using a number of different x-ray spectroscopic and scattering techniques such as x-ray absorption spectroscopy (XAS). One of his main area of focus is the active site of the enzyme nitrogenase, which is responsible for conversion of atmospheric dinitr ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
