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Pi Helix
A pi helix (or π-helix) is a type of secondary structure found in proteins. Discovered by crystallographer Barbara Low in 1952 and once thought to be rare, short π-helices are found in 15% of known protein structures and are believed to be an evolutionary adaptation derived by the insertion of a single amino acid into an α-helix. Because such insertions are highly destabilizing, the formation of π-helices would tend to be selected against unless it provided some functional advantage to the protein. π-helices therefore are typically found near functional sites of proteins. Standard structure The amino acids in a standard π-helix are arranged in a right-handed helical structure. Each amino acid corresponds to an 87° turn in the helix (i.e., the helix has 4.1 residues per turn), and a translation of along the helical axis. Most importantly, the N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid ''five'' residues earlier; this repeated ' ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Pi Helix Neg55 Neg70 Sideview
The number (; spelled out as "pi") is a mathematical constant that is the ratio of a circle's circumference to its diameter, approximately equal to 3.14159. The number appears in many formulas across mathematics and physics. It is an irrational number, meaning that it cannot be expressed exactly as a ratio of two integers, although fractions such as \tfrac are commonly used to approximate it. Consequently, its decimal representation never ends, nor enters a permanently repeating pattern. It is a transcendental number, meaning that it cannot be a solution of an equation involving only sums, products, powers, and integers. The transcendence of implies that it is impossible to solve the ancient challenge of squaring the circle with a compass and straightedge. The decimal digits of appear to be randomly distributed, but no proof of this conjecture has been found. For thousands of years, mathematicians have attempted to extend their understanding of , sometimes by computing ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Chirality (chemistry)
In chemistry, a molecule or ion is called chiral () if it cannot be superposed on its mirror image by any combination of rotations, translations, and some conformational changes. This geometric property is called chirality (). The terms are derived from Ancient Greek χείρ (''cheir'') 'hand'; which is the canonical example of an object with this property. A chiral molecule or ion exists in two stereoisomers that are mirror images of each other, called enantiomers; they are often distinguished as either "right-handed" or "left-handed" by their absolute configuration or some other criterion. The two enantiomers have the same chemical properties, except when reacting with other chiral compounds. They also have the same physical properties, except that they often have opposite optical activities. A homogeneous mixture of the two enantiomers in equal parts is said to be racemic, and it usually differs chemically and physically from the pure enantiomers. Chiral molecules ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
3 10 Helix
A 310 helix is a type of secondary structure found in proteins and polypeptides. Of the numerous protein secondary structures present, the 310-helix is the fourth most common type observed; following α-helices, β-sheets and reverse turns. 310-helices constitute nearly 10–15% of all helices in protein secondary structures, and are typically observed as extensions of α-helices found at either their N- or C- termini. Because of the α-helices tendency to consistently fold and unfold, it has been proposed that the 310-helix serves as an intermediary conformation of sorts, and provides insight into the initiation of α-helix folding. Discovery Max Perutz, the head of the Medical Research Council Laboratory of Molecular Biology at the University of Cambridge, wrote the first paper documenting the elusive 310-helix. Together with Lawrence Bragg and John Kendrew, Perutz published an exploration of polypeptide chain configurations in 1950, based on cues from noncrystalline dif ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Alpha Helix
The alpha helix (α-helix) is a common motif in the secondary structure of proteins and is a right hand- helix conformation in which every backbone N−H group hydrogen bonds to the backbone C=O group of the amino acid located four residues earlier along the protein sequence. The alpha helix is also called a classic Pauling–Corey–Branson α-helix. The name 3.613-helix is also used for this type of helix, denoting the average number of residues per helical turn, with 13 atoms being involved in the ring formed by the hydrogen bond. Among types of local structure in proteins, the α-helix is the most extreme and the most predictable from sequence, as well as the most prevalent. Discovery In the early 1930s, William Astbury showed that there were drastic changes in the X-ray fiber diffraction of moist wool or hair fibers upon significant stretching. The data suggested that the unstretched fibers had a coiled molecular structure with a characteristic repeat of ≈. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Data Bank
The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The data, typically obtained by X-ray crystallography, NMR spectroscopy, or, increasingly, cryo-electron microscopy, and submitted by biologists and biochemists from around the world, are freely accessible on the Internet via the websites of its member organisations (PDBe, PDBj, RCSB, and BMRB). The PDB is overseen by an organization called the Worldwide Protein Data Bank, wwPDB. The PDB is a key in areas of structural biology, such as structural genomics. Most major scientific journals and some funding agencies now require scientists to submit their structure data to the PDB. Many other databases use protein structures deposited in the PDB. For example, SCOP and CATH classify protein structures, while PDBsum provides a graphic overview of PDB entries using information from other sources, such as Gene ontology. History Two ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Methane Monooxygenase
Methane monooxygenase (MMO) is an enzyme capable of oxidizing the C-H bond in methane as well as other alkanes. Methane monooxygenase belongs to the class of oxidoreductase enzymes (). There are two forms of MMO: the well-studied soluble form (sMMO) and the particulate form (pMMO). The active site in sMMO contains a di-iron center bridged by an oxygen atom (Fe-O-Fe), whereas the active site in pMMO utilizes copper. Structures of both proteins have been determined by X-ray crystallography; however, the location and mechanism of the active site in pMMO is still poorly understood and is an area of active research. The particulate methane monooxygenase and related ammonia monooxygenase are integral membrane proteins, occurring in methanotrophs and ammonia oxidisers, respectively, which are thought to be related. These enzymes have a relatively wide substrate specificity and can catalyse the oxidation of a range of substrates including ammonia, methane, halogenated hydrocarbons, and ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ribonucleotide Reductase
Ribonucleotide reductase (RNR), also known as ribonucleoside diphosphate reductase (rNDP), is an enzyme that catalyzes the formation of deoxyribonucleotides from ribonucleotides. It catalyzes this formation by removing the 2'-hydroxyl group of the ribose ring of nucleoside diphosphates. This reduction produces deoxyribonucleotides. Deoxyribonucleotides in turn are used in the synthesis of DNA. The reaction catalyzed by RNR is strictly conserved in all living organisms. Furthermore, RNR plays a critical role in regulating the total rate of DNA synthesis so that DNA to cell mass is maintained at a constant ratio during cell division and DNA repair. A somewhat unusual feature of the RNR enzyme is that it catalyzes a reaction that proceeds via a free radical mechanism of action. The substrates for RNR are ADP, GDP, CDP and UDP. dTDP (deoxythymidine diphosphate) is synthesized by another enzyme ( thymidylate kinase) from dTMP (deoxythymidine monophosphate). Structure Ribonucleo ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Rubrerythrin
Rubrerythrin (RBR) is a non-heme iron-containing metalloprotein involved in oxidative stress tolerance within anaerobic bacteria. It contains a di-iron active site, where peroxide is reduced into two water molecules, and a mono-iron rubredoxin-like domain thought to be involved in electron transfer. A majority of known RBR families are utilized as peroxide "scavengers" to defend organisms against oxidative stress. Function As a member of the Ferritin-like superfamily, RBRs primary function is iron storage and detoxification. Rubrerythrins utilize their di-iron centers to bind with reactive oxygen species such as Hydrogen Peroxide, further reducing them into water. RBR reduction is theorized as a particularly important adaptation that occurred in response to the Great Oxygenation event, increasing defensive fitness of all cells exposed to relatively high levels of oxygen and similar byproducts. Although primarily studied within anaerobic bacteria, RBRs have been discovered in mu ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bacterioferritin
Bacterioferritin (Bfr) is an oligomeric protein containing both a binuclear iron centre and haem b. The tertiary and quaternary structure of Bfr is very similar to that of ferritin. The physiological functions of BFR, which may be other than just iron uptake, are not clear. Bfr forms a roughly spherical, hollow shell from 24 identical subunits, incorporating 12 haem groups. Iron is stored as a hydrated ferric oxide mineral in its central cavity (about 80 Å diameter). The overall complex has cubic (432) symmetry. Each subunit includes a binuclear metalbinding site (the diiron site) linking together the four major helices of the subunit, which has been identified as the ferroxidase active site. Bfr from ''Pseudomonas aeruginosa'' (''Pa''Bfr), unlike other Bfrs, is found to contain two subunit types, which differ considerably in their amino acid sequences. A similar hetero-assembly is seen in the ferritins of higher eukaryotes. Bfr from ''Escherichia coli'' (''Ec''Bfr) which nat ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ferritin
Ferritin is a universal intracellular protein that stores iron and releases it in a controlled fashion. The protein is produced by almost all living organisms, including archaea, bacteria, algae, higher plants, and animals. It is the primary ''intracellular iron-storage protein'' in both prokaryotes and eukaryotes, keeping iron in a soluble and non-toxic form. In humans, it acts as a buffer against iron deficiency and iron overload. Ferritin is found in most tissues as a cytosolic protein, but small amounts are secreted into the serum where it functions as an iron carrier. Plasma ferritin is also an indirect marker of the total amount of iron stored in the body; hence, serum ferritin is used as a diagnostic test for iron-deficiency anemia. Aggregated ferritin transforms into a toxic form of iron called hemosiderin. Ferritin is a globular protein complex consisting of 24 protein subunits forming a hollow nanocage with multiple metal–protein interactions. Ferritin th ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
DSSP (algorithm)
The DSSP algorithm is the standard method for assigning secondary structure to the amino acids of a protein, given the atomic-resolution coordinates of the protein. The abbreviation is only mentioned once in the 1983 paper describing this algorithm, where it is the name of the Pascal program that implements the algorithm ''Define Secondary Structure of Proteins''. Algorithm DSSP begins by identifying the intra-backbone hydrogen bonds of the protein using a purely electrostatic definition, assuming partial charges of -0.42 ''e'' and +0.20 ''e'' to the carbonyl oxygen and amide hydrogen respectively, their opposites assigned to the carbonyl carbon and amide nitrogen. A hydrogen bond is identified if ''E'' in the following equation is less than -0.5 kcal/mol: : E = 0.084 \left\ \cdot 332 \, \mathrm where the r_ terms indicate the distance between atoms A and B, taken from the carbon (C) and oxygen (O) atoms of the C=O group and the nitrogen (N) and hydrogen (H) atoms of the N-H ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Pi-helix Within An Alpha-helix
A pi helix (or π-helix) is a type of secondary structure found in proteins. Discovered by crystallographer Barbara Low in 1952 and once thought to be rare, short π-helices are found in 15% of known protein structures and are believed to be an evolutionary adaptation derived by the insertion of a single amino acid into an α-helix. Because such insertions are highly destabilizing, the formation of π-helices would tend to be selected against unless it provided some functional advantage to the protein. π-helices therefore are typically found near functional sites of proteins. Standard structure The amino acids in a standard π-helix are arranged in a right-handed helical structure. Each amino acid corresponds to an 87° turn in the helix (i.e., the helix has 4.1 residues per turn), and a translation of along the helical axis. Most importantly, the N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid ''five'' residues earlier; this repeat ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
