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Resolution (electron Density)
Resolution in terms of electron density is a measure of the resolvability in the electron density map of a molecule. In X-ray crystallography, resolution is the highest resolvable peak in the diffraction pattern, while resolution in cryo-electron microscopy is a frequency space comparison of two halves of the data, which strives to correlate with the X-ray definition.Frank, 2006, p250-251 Qualitative measures In structural biology, resolution can be broken down into 4 groups: (1) sub-atomic, individual elements are distinguishable and quantum effects can be studied, (2) atomic, individual atoms are visible and an accurate three-dimensional model can be constructed, (3) helical, secondary structure, such as alpha helices and beta sheets; RNA helices (in ribosomes), (4) domain, no secondary structure is resolvable. X-ray crystallography As the crystal's repeating unit, its unit cell, becomes larger and more complex, the atomic-level picture provided by X-ray crystallography bec ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 chains in proteins as a function of the backbone dihedral angles φ and ψ of the 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 Cartesian coordinates of a protein's side chains given the expe ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 shoc ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Crystal Structure
In crystallography, crystal structure is a description of the ordered arrangement of atoms, ions or molecules in a crystal, crystalline material. Ordered structures occur from the intrinsic nature of the constituent particles to form symmetric patterns that repeat along the principal directions of Three-dimensional space (mathematics), three-dimensional space in matter. The smallest group of particles in the 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 (geometry), translation of the unit cell along its principal axes. The translation vectors define the nodes of the Bravais lattice. The lengths of the principal axes, or edges, of the unit cell and the angles between them are the lattice constants, also called ''lattice parameters'' or ''cell parameters''. The symmetry properties of the crystal are described by the con ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Fourier Transform
A Fourier transform (FT) is a mathematical transform that decomposes functions into frequency components, which are represented by the output of the transform as a function of frequency. Most commonly functions of time or space are transformed, which will output a function depending on temporal frequency or spatial frequency respectively. That process is also called ''analysis''. An example application would be decomposing the waveform of a musical chord into terms of the intensity of its constituent pitches. The term ''Fourier transform'' refers to both the frequency domain representation and the mathematical operation that associates the frequency domain representation to a function of space or time. The Fourier transform of a function is a complex-valued function representing the complex sinusoids that comprise the original function. For each frequency, the magnitude (absolute value) of the complex value represents the amplitude of a constituent complex sinusoid with that ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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. The FSC originated in cryo-electron microscopy and gradually proliferated to other fields. To measure the FSC, two independently d ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Fourier Shell 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. The FSC originated in cryo-electron microscopy and gradually proliferated to other fields. To measure the FSC, two independently d ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Oxford University Press
Oxford University Press (OUP) is the university press of the University of Oxford. It is the largest university press in the world, and its printing history dates back to the 1480s. Having been officially granted the legal right to print books by decree in 1586, it is the second oldest university press after Cambridge University Press. It is a department of the University of Oxford and is governed by a group of 15 academics known as the Delegates of the Press, who are appointed by the vice-chancellor of the University of Oxford. The Delegates of the Press are led by the Secretary to the Delegates, who serves as OUP's chief executive and as its major representative on other university bodies. Oxford University Press has had a similar governance structure since the 17th century. The press is located on Walton Street, Oxford, opposite Somerville College, in the inner suburb of Jericho. For the last 500 years, OUP has primarily focused on the publication of pedagogical texts and ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
National Taiwan University
National Taiwan University (NTU; ) is a public research university in Taipei, Taiwan. The university was founded in 1928 during Japanese rule as the seventh of the Imperial Universities. It was named Taihoku Imperial University and served during the period of Japanese colonization. After World War II, the Nationalist Kuomintang (KMT) government assumed the administration of the university. The Ministry of Education reorganized and renamed the university to its current name on November 15, 1945, with its roots of liberal tradition from Peking University in Beijing by former NTU President Fu Ssu-nien. The university consists of 11 colleges, 56 departments, 133 graduate institutes, about 60 research centers, and a school of professional education and continuing studies. Notable alumni include Tsai Ing-Wen, current President of the Republic of China, former presidents Lee Teng-hui, Chen Shui-bian and Ma Ying-jeou, Turing Award laureate Andrew Yao, and Nobel Prize in Chemistry ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Virus
A virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea. 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,Dimmock p. 4 more than 9,000 virus species have been described in detail of the millions of types of viruses in the environment. Viruses are found in almost every ecosystem on Earth and are the most numerous type of biological entity. 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 particles, or ''virions'', consisting of (i) the genetic material, i. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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, 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 parallelogram or parallelepiped) that generates the whole tiling using only translations. There are two special cases of the unit cell: the primitive cell and the conventional cell. The primitive cell is a unit cell corresponding to a single lattice point, it is the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Electron Density
In quantum chemistry, electron density or electronic density is the measure of the probability of an electron being present at an infinitesimal element of space surrounding any given point. It is a scalar quantity depending upon three spatial variables and is typically denoted as either \rho(\textbf r) or n(\textbf r). The density is determined, through definition, by the normalised N-electron wavefunction which itself depends upon 4N variables (3N spatial and N spin coordinates). Conversely, the density determines the wave function modulo up to a phase factor, providing the formal foundation of density functional theory. According to quantum mechanics, due to the uncertainty principle on an atomic scale the exact location of an electron cannot be predicted, only the probability of its being at a given position; therefore electrons in atoms and molecules act as if they are "smeared out" in space. For one-electron systems, the electron density at any point is proportional to th ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Beta Sheets
The beta sheet, (β-sheet) (also β-pleated sheet) is a common motif of the regular protein secondary structure. Beta sheets consist of beta strands (β-strands) connected laterally by at least two or three backbone hydrogen bonds, forming a generally twisted, pleated sheet. A β-strand is a stretch of polypeptide chain typically 3 to 10 amino acids long with backbone in an extended conformation. The supramolecular association of β-sheets has been implicated in the formation of the fibrils and protein aggregates observed in amyloidosis, notably Alzheimer's disease. History The first β-sheet structure was proposed by William Astbury in the 1930s. He proposed the idea of hydrogen bonding between the peptide bonds of parallel or antiparallel extended β-strands. However, Astbury did not have the necessary data on the bond geometry of the amino acids in order to build accurate models, especially since he did not then know that the peptide bond was planar. A refined version was p ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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