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Beta Bulge
A beta bulge can be described as a localized disruption of the regular hydrogen bonding of beta sheet by inserting extra residues into one or both hydrogen bonded β-strands. Types β-bulges can be grouped according to their length of the disruption, the number of residues inserted into each strand, whether the disrupted β-strands are parallel or antiparallel and by their dihedral angles (which controls the placement of their side chains). Two types occur commonly. One, the ''classic beta bulge'', occurs within, or at the edge of, antiparallel beta-sheet; the first residue at the outwards bulge typically has the αR, rather than the normal β, conformation. The other type is the G1 ''beta bulge'', of which there are two common sorts, both mainly occurring in association with antiparallel sheet; one residue has the αL conformation and is usually a glycine. In one sort, the beta bulge loop, one of the hydrogen bonds of the beta-bulge also forms a beta turn or alpha turn, such that t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Beta Bulge Loop
Beta bulge loops are commonly occurring motifs in proteins and polypeptides consisting of five to six amino acids. There are two types: type 1, which is a pentapeptide; and type 2, with six amino acids. They are regarded as a type of beta bulge, and have the alternative name of type G1 beta bulge. Compared to other beta bulges, beta bulge loops give rise to chain reversal such that they often occur at the loop ends of beta hairpins; hairpins of this sort can be described as 3:5 (for a type 1 β bulge loop) or 4:6 (for type 2). Two websites are available for finding and examining β bulge loops in proteins, Motivated Proteins and PDBeMotif Type I beta bulge loops have two characteristic inter-main-chain hydrogen bonds. One is between the CO of residue i and the NH of residue i+3 (a β-turn); the other is between the CO of residue i+4 and the NH of residue i. Type 2 beta bulge loops have two characteristic inter-main-chain hydrogen bonds. One is between the CO of residue i and the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Hydrogen Bond
In chemistry, a hydrogen bond (or H-bond) is a primarily electrostatic force of attraction between a hydrogen (H) atom which is covalently bound to a more electronegative "donor" atom or group (Dn), and another electronegative atom bearing a lone pair of electrons—the hydrogen bond acceptor (Ac). Such an interacting system is generally denoted , where the solid line denotes a polar covalent bond, and the dotted or dashed line indicates the hydrogen bond. The most frequent donor and acceptor atoms are the second-row elements nitrogen (N), oxygen (O), and fluorine (F). Hydrogen bonds can be intermolecular (occurring between separate molecules) or intramolecular (occurring among parts of the same molecule). The energy of a hydrogen bond depends on the geometry, the environment, and the nature of the specific donor and acceptor atoms and can vary between 1 and 40 kcal/mol. This makes them somewhat stronger than a van der Waals interaction, and weaker than fully covalent o ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Beta Sheet
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 w ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Dihedral Angle
A dihedral angle is the angle between two intersecting planes or half-planes. In chemistry, it is the clockwise angle between half-planes through two sets of three atoms, having two atoms in common. In solid geometry, it is defined as the union of a line and two half-planes that have this line as a common edge. In higher dimensions, a dihedral angle represents the angle between two hyperplanes. The planes of a flying machine are said to be at positive dihedral angle when both starboard and port main planes (commonly called wings) are upwardly inclined to the lateral axis. When downwardly inclined they are said to be at a negative dihedral angle. Mathematical background When the two intersecting planes are described in terms of Cartesian coordinates by the two equations : a_1 x + b_1 y + c_1 z + d_1 = 0 :a_2 x + b_2 y + c_2 z + d_2 = 0 the dihedral angle, \varphi between them is given by: :\cos \varphi = \frac and satisfies 0\le \varphi \le \pi/2. Alternatively, if and ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Beta-sheet
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 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Beta Turn
β turns (also β-bends, tight turns, reverse turns, Venkatachalam turns) are the most common form of turns—a type of non-regular secondary structure in proteins that cause a change in direction of the polypeptide chain. They are very common motifs in proteins and polypeptides. Each consists of four amino acid residues (labelled ''i'', ''i+1'', ''i+2'' and ''i+3''). They can be defined in two ways: # By the possession of an intra-main-chain hydrogen bond between the CO of residue ''i'' and the NH of residue ''i+3''; # By having a distance of less than 7Å between the Cα atoms of residues ''i'' and ''i+3''. The hydrogen bond criterion is the one most appropriate for everyday use, partly because it gives rise to four distinct categories; the distance criterion gives rise to the same four categories but yields additional turn types. Definition Hydrogen bond criterion The hydrogen bond criterion for beta turns, applied to polypeptides whose amino acids are linked by t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Beta Hairpin
The beta hairpin (sometimes also called beta-ribbon or beta-beta unit) is a simple protein structural motif involving two beta strands that look like a hairpin. The motif consists of two strands that are adjacent in primary structure, oriented in an antiparallel direction (the N-terminus of one sheet is adjacent to the C-terminus of the next), and linked by a short loop of two to five amino acids. Beta hairpins can occur in isolation or as part of a series of hydrogen bonded strands that collectively comprise a beta sheet. Researchers such as Francisco Blanco ''et al.'' have used protein NMR to show that beta-hairpins can be formed from isolated short peptides in aqueous solution, suggesting that hairpins could form nucleation sites for protein folding. Classification Beta hairpins were originally categorized solely by the number of amino acid residues in their loop sequences, such that they were named one-residue, two-residue, etc. This system, however, is somewhat ambiguous ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Beta Link
Beta (, ; uppercase , lowercase , or cursive ; grc, βῆτα, bē̂ta or ell, βήτα, víta) is the second letter of the Greek alphabet. In the system of Greek numerals, it has a value of 2. In Modern Greek, it represents the voiced labiodental fricative while in borrowed words is instead commonly transcribed as μπ. Letters that arose from beta include the Roman letter and the Cyrillic letters and . Name Like the names of most other Greek letters, the name of beta was adopted from the acrophonic name of the corresponding letter in Phoenician, which was the common Semitic word ''*bait'' ('house'). In Greek, the name was ''bêta'', pronounced in Ancient Greek. It is spelled βήτα in modern monotonic orthography and pronounced . History The letter beta was derived from the Phoenician letter beth . Uses Algebraic numerals In the system of Greek numerals, beta has a value of 2. Such use is denoted by a number mark: Β′. Computing Finance Beta is used in ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Aneurysm
An aneurysm is an outward bulging, likened to a bubble or balloon, caused by a localized, abnormal, weak spot on a blood vessel wall. Aneurysms may be a result of a hereditary condition or an acquired disease. Aneurysms can also be a nidus (starting point) for clot formation ( thrombosis) and embolization. As an aneurysm increases in size, the risk of rupture, which leads to uncontrolled bleeding, increases. Although they may occur in any blood vessel, particularly lethal examples include aneurysms of the Circle of Willis in the brain, aortic aneurysms affecting the thoracic aorta, and abdominal aortic aneurysms. Aneurysms can arise in the heart itself following a heart attack, including both ventricular and atrial septal aneurysms. There are congenital atrial septal aneurysms, a rare heart defect. Etymology The word is from Greek: ἀνεύρυσμα, aneurysma, "dilation", from ἀνευρύνειν, aneurynein, "to dilate". Classification Aneurysms are classified b ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ribonuclease A
Pancreatic ribonuclease family (, ''RNase'', ''RNase I'', ''RNase A'', ''pancreatic RNase'', ''ribonuclease I'', ''endoribonuclease I'', ''ribonucleic phosphatase'', ''alkaline ribonuclease'', ''ribonuclease'', ''gene S glycoproteins'', ''Ceratitis capitata alkaline ribonuclease'', ''SLSG glycoproteins'', ''gene S locus-specific glycoproteins'', ''S-genotype-assocd. glycoproteins'', ''ribonucleate 3'-pyrimidino-oligonucleotidohydrolase'') is a superfamily of pyrimidine-specific endonucleases found in high quantity in the pancreas of certain mammals and of some reptiles. Specifically, the enzymes are involved in endonucleolytic cleavage of 3'-phosphomono nucleotides and 3'-phosphooligonucleotides ending in C-P or U-P with 2',3'-cyclic phosphate intermediates. Ribonuclease can unwind the RNA helix by complexing with single-stranded RNA; the complex arises by an extended multi-site cation-anion interaction between lysine and arginine residues of the enzyme and phosphate groups of th ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Azurin
Azurin is a small, periplasmic, bacterial blue copper protein found in ''Pseudomonas'', ''Bordetella'', or ''Alcaligenes'' bacteria. Azurin moderates single-electron transfer between enzymes associated with the cytochrome chain by undergoing oxidation-reduction between Cu(I) and Cu(II). Each monomer of an azurin tetramer has a molecular weight of approximately 14kDa, contains a single copper atom, is intensively blue, and has a fluorescence emission band centered at 308 nm. Azurins and pseudoazurins participate in the denitrification processes in bacteria., including the gram-negative bacteria ''Pseudomonas aeruginosa,'' by interacting with cytochrome c551. Azurin from ''P aeruginosa'' is a type I blue copper protein (cupredoxin), while cytochrome c551 (9 kDa) is a haem-containing cytochrome. Azurin possesses a relatively large hydrophobic patch close to the active site, and two residues in this hydrophobic patch, Met-44 and Met-64, are believed to be involved in its interact ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
