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Resolution (electron Density)
Resolution in the context of structural biology is the ability to distinguish the presence or absence of Atom, atoms or groups of atoms in a Biomolecule, biomolecular structure. Usually, the structure originates from methods such as X-ray crystallography, electron crystallography, or Cryogenic electron microscopy, cryo-electron microscopy. The resolution is measured of the "map" of the structure produced from experiment, where an atomic model would then be fit into. Due to their different natures and interactions with matter, in X-ray methods the map produced is of the electron density of the system (usually a Crystal structure, crystal), whereas in electron methods the map is of the electrostatic potential of the system. In both cases, atomic positions are assumed similarly. Qualitative measures In structural biology, Optical resolution, resolution can be broken down into 4 groups: (1) sub-atomic, when information about the electron density is obtained and quantum effects can be ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Backbone-dependent Rotamer Library
In biochemistry, a backbone-dependent rotamer library provides the frequencies, mean dihedral angles, and standard deviations of the discrete conformations (known as rotamers) of the amino acid Side_chain#Biochemistry, side chains in proteins as a function of the protein backbone, backbone dihedral angles φ and ψ of the Ramachandran plot, Ramachandran map. By contrast, backbone-independent rotamer libraries express the frequencies and mean dihedral angles for all side chains in proteins, regardless of the backbone conformation of each residue type. Backbone-dependent rotamer libraries have been shown to have significant advantages over backbone-independent rotamer libraries, principally when used as an energy term, by speeding up search times of side-chain packing algorithms used in protein structure prediction and protein design. History The first backbone-dependent rotamer library was developed in 1993 by Roland Dunbrack and Martin Karplus to assist the prediction of the Carte ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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GroEL Resolution Series
GroEL is a protein which belongs to the chaperonin family of molecular chaperones, and is found in many bacteria. It is required for the proper folding of many proteins. To function properly, GroEL requires the lid-like cochaperonin protein complex GroES. In eukaryotes the organellar proteins Hsp60 and Hsp10 are structurally and functionally nearly identical to GroEL and GroES, respectively, due to their endosymbiotic origin. HSP60 is implicated in mitochondrial protein import and macromolecular assembly. It may facilitate the correct folding of imported proteins, and may also prevent misfolding and promote the refolding and proper assembly of unfolded polypeptides generated under stress conditions in the mitochondrial matrix. HSP60 interacts with HRAS and with HBV protein X and HTLV-1 protein p40tax. HSP60 belongs to the chaperonin (HSP60) family. Note: This description may include information from UniProtKB. Alternate Names: 60 kDa chaperonin, Chaperonin 60, CPN60, Heat sh ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Alpha Helices
An alpha helix (or α-helix) is a sequence of amino acids in a protein that are twisted into a coil (a helix). The alpha helix is the most common structural arrangement in the secondary structure of proteins. It is also the most extreme type of local structure, and it is the local structure that is most easily predicted from a sequence of amino acids. The alpha helix has a right-handed helix conformation in which every backbone N−H group hydrogen bonds to the backbone C=O group of the amino acid that is four residues earlier in the protein sequence. Other names The alpha helix is also commonly called a: * Pauling–Corey–Branson α-helix (from the names of three scientists who described its structure) * 3.613-helix because there are 3.6 amino acids in one ring, with 13 atoms being involved in the ring formed by the hydrogen bond (starting with amidic hydrogen and ending with carbonyl oxygen) Discovery In the early 1930s, William Astbury showed that there were dras ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Structural Biology
Structural biology deals with structural analysis of living material (formed, composed of, and/or maintained and refined by living cells) at every level of organization. Early structural biologists throughout the 19th and early 20th centuries were primarily only able to study structures to the limit of the naked eye's visual acuity and through magnifying glasses and light microscopes. In the 20th century, a variety of experimental techniques were developed to examine the 3D structures of biological molecules. The most prominent techniques are X-ray crystallography, nuclear magnetic resonance, and Electron microscope, electron microscopy. Through the discovery of X-ray, X-rays and its applications to protein crystals, structural biology was revolutionized, as now scientists could obtain the three-dimensional structures of biological molecules in atomic detail. Likewise, Nuclear magnetic resonance spectroscopy, NMR spectroscopy allowed information about protein structure and dynamic ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Gold Standard (test)
In medicine and medical statistics, the gold standard, criterion standard, or reference standard is the diagnostic test or benchmark that is the best available under ''reasonable'' conditions. It is the test against which new tests are compared to gauge their validity, and it is used to evaluate the efficacy of treatments. The meaning of "gold standard" may differ between practical medicine and the statistical ideal. With some medical conditions, only an autopsy can guarantee diagnostic certainty. In these cases, the gold standard test is the best test that keeps the patient alive, and even gold standard tests can require follow-up to confirm or refute the diagnosis. History The term 'gold standard' in its current sense in medical research was coined by Rudd in 1979, in reference to the monetary gold standard. In medicine "Gold standard" can refer to popular clinical endpoints by which scientific evidence is evaluated. For example, in resuscitation research, the "gold standar ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Fourier Transform
In mathematics, the Fourier transform (FT) is an integral transform that takes a function as input then outputs another function that describes the extent to which various frequencies are present in the original function. The output of the transform is a complex-valued function of frequency. The term ''Fourier transform'' refers to both this complex-valued function and the mathematical operation. When a distinction needs to be made, the output of the operation is sometimes called the frequency domain representation of the original function. The Fourier transform is analogous to decomposing the sound of a musical chord into the intensities of its constituent pitches. Functions that are localized in the time domain have Fourier transforms that are spread out across the frequency domain and vice versa, a phenomenon known as the uncertainty principle. The critical case for this principle is the Gaussian function, of substantial importance in probability theory and statist ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Fourier Ring Correlation
In structural biology, as well as in virtually all sciences that produce three-dimensional data, the Fourier shell correlation (FSC) measures the normalised cross-correlation coefficient between two 3-dimensional volumes over corresponding shells in Fourier space (i.e., as a function of spatial frequencyHarauz & van Heel, 1986). The FSC is the three-dimensional extension of the two-dimensional Fourier ring correlation (FRC);van Heel, 1982 also known as: spatial frequency correlation function.Saxton & Baumeister, 1982 Calculation : FSC(r) = \frac where F_1 is the complex structure Factor for volume 1, F_2^ is the complex conjugate of the structure Factor for volume 2, and r_i is the individual voxel element at radius r.van Heel & Schatz, 2005 In this form, the FSC takes two three-dimensional data sets and converts them into a one-dimensional array. Applications The FSC originated in cryo-electron microscopy and gradually proliferated to other fields. To measure the FSC, t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Cryo-electron Microscopy
Cryogenic electron microscopy (cryo-EM) is a transmission electron microscopy technique applied to samples cooled to cryogenic temperatures. For biological specimens, the structure is preserved by embedding in an environment of vitreous ice. An aqueous sample solution is applied to a grid-mesh and plunge-frozen in liquid ethane or a mixture of liquid ethane and propane. While development of the technique began in the 1970s, recent advances in detector technology and software algorithms have allowed for the determination of biomolecular structures at near-atomic resolution. This has attracted wide attention to the approach as an alternative to X-ray crystallography or NMR spectroscopy in the structural biology field. In 2017, the Nobel Prize in Chemistry was awarded to Jacques Dubochet, Joachim Frank, and Richard Henderson "for developing cryo-electron microscopy for the high-resolution structure determination of biomolecules in solution." '' Nature Methods'' also named cryo- ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Virus
A virus is a submicroscopic infectious agent that replicates only inside the living Cell (biology), cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea. Viruses are found in almost every ecosystem on Earth and are the most numerous type of biological entity. Since Dmitri Ivanovsky's 1892 article describing a non-bacterial pathogen infecting tobacco plants and the discovery of the tobacco mosaic virus by Martinus Beijerinck in 1898, more than 16,000 of the millions of List of virus species, virus species have been described in detail. The study of viruses is known as virology, a subspeciality of microbiology. When infected, a host cell is often forced to rapidly produce thousands of copies of the original virus. When not inside an infected cell or in the process of infecting a cell, viruses exist in the form of independent viral particles, or ''virions'', consisting of (i) genetic material, i.e., long ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Crystal Structure
In crystallography, crystal structure is a description of ordered arrangement of atoms, ions, or molecules in a crystalline material. Ordered structures occur from intrinsic nature of constituent particles to form symmetric patterns that repeat along the principal directions of three-dimensional space in matter. The smallest group of particles in a material that constitutes this repeating pattern is the unit cell of the structure. The unit cell completely reflects the symmetry and structure of the entire crystal, which is built up by repetitive translation of the unit cell along its principal axes. The translation vectors define the nodes of the Bravais lattice. The lengths of principal axes/edges, of the unit cell and angles between them are lattice constants, also called ''lattice parameters'' or ''cell parameters''. The symmetry properties of a crystal are described by the concept of space groups. All possible symmetric arrangements of particles in three-dimensional space ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Unit Cell
In geometry, biology, mineralogy and solid state physics, a unit cell is a repeating unit formed by the vectors spanning the points of a lattice. Despite its suggestive name, the unit cell (unlike a unit vector In mathematics, a unit vector in a normed vector space is a Vector (mathematics and physics), vector (often a vector (geometry), spatial vector) of Norm (mathematics), length 1. A unit vector is often denoted by a lowercase letter with a circumfle ..., for example) does not necessarily have unit size, or even a particular size at all. Rather, the primitive cell is the closest analogy to a unit vector, since it has a determined size for a given lattice and is the basic building block from which larger cells are constructed. The concept is used particularly in describing crystal structure in two and three dimensions, though it makes sense in all dimensions. A lattice can be characterized by the geometry of its unit cell, which is a section of the tiling (a parallelogra ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |