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Knotted Protein
Knotted proteins are proteins whose backbones entangle themselves in a knot. One can imagine pulling a protein chain from both termini, as though pulling a string from both ends. When a knotted protein is “pulled” from both termini, it does not get disentangled. Knotted proteins are very rare, making up only about one percent of the proteins in the Protein Data Bank, and their folding mechanisms and function are not well understood. Although there are experimental and theoretical studies that hint to some answers, systematic answers to these questions have not yet been found. Although number of computational methods have been developed to detect protein knots, there are still no completely automatic methods to detect protein knots without necessary manual intervention due to the missing residues or chain breaks in the X-ray structures or the nonstandard PDB formats. Most of the knots discovered in proteins are deep trefoil (31) knots. Figure eight knots (41), three-twist kno ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Smoothed Knot
In statistics and image processing, to smooth a data set is to create an approximating function that attempts to capture important patterns in the data, while leaving out noise or other fine-scale structures/rapid phenomena. In smoothing, the data points of a signal are modified so individual points higher than the adjacent points (presumably because of noise) are reduced, and points that are lower than the adjacent points are increased leading to a smoother signal. Smoothing may be used in two important ways that can aid in data analysis (1) by being able to extract more information from the data as long as the assumption of smoothing is reasonable and (2) by being able to provide analyses that are both flexible and robust. Many different algorithms are used in smoothing. Smoothing may be distinguished from the related and partially overlapping concept of curve fitting in the following ways: * curve fitting often involves the use of an explicit function form for the result, wher ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Complex Lasso Proteins
Complex lasso proteins (also called pierced lasso bundles or tadpoles) are proteins in which a covalent loop (portion of the backbone closed with a covalent bridge) is pierced by another piece of the backbone. Subclass of complex lasso proteins are Lasso peptides in which the loop is formed by post-translational amide bridge. Classification of complex lassos Complex lassos can be divided according to the number of piercings through the minimal surface spanned on the covalent loop. In particular, four classes of complex lasso proteins exist: * the Ln class (simple lasso), where one tail pierces the surface n times; * the LSn class (the supercoiling lasso), where one tail pierces the surface n times, winding around the loop; * the LLi,j class (double lasso), where both tails pierce the surface i and j times respectively; * the LSLi,j class, where one tail pierces the surface i times in the supercoiling manner, and the second pierces the surface in the simple manner. Another clas ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Web Servers
A web server is computer software and underlying hardware that accepts requests via HTTP (the network protocol created to distribute web content) or its secure variant HTTPS. A user agent, commonly a web browser or web crawler, initiates communication by making a request for a web page or other resource using HTTP, and the server responds with the content of that resource or an error message. A web server can also accept and store resources sent from the user agent if configured to do so. The hardware used to run a web server can vary according to the volume of requests that it needs to handle. At the low end of the range are embedded systems, such as a router that runs a small web server as its configuration interface. A high-traffic Internet website might handle requests with hundreds of servers that run on racks of high-speed computers. A resource sent from a web server can be a preexisting file (static content) available to the web server, or it can be generated a ... [...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 force ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cystine Knot
A cystine knot is a protein structural motif containing three disulfide bridges (formed from pairs of cysteine residues). The sections of polypeptide that occur between two of them form a loop through which a third disulfide bond passes, forming a rotaxane substructure. The cystine knot motif stabilizes protein structure and is conserved in proteins across various species. There are three types of cystine knot, which differ in the topology of the disulfide bonds: * The growth factor cystine knot (GFCK) * inhibitor cystine knot (ICK) common in spider and snail toxins * Cyclic Cystine Knot, or cyclotide The growth factor cystine knot was first observed in the structure of nerve growth factor (NGF), solved by X-ray crystallography and published in 1991 by Tom Blundell in Nature.; The GFCK is present in four superfamilies. These include nerve growth factor, transforming growth factor beta (TGF-β), platelet-derived growth factor, and glycoprotein hormones including human chorioni ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Solomon's Knot
Solomon's knot () is a traditional decorative motif used since ancient times, and found in many cultures. Despite the name, it is classified as a link, and is not a true knot according to the definitions of mathematical knot theory. Structure The Solomon's knot consists of two closed loops, which are doubly interlinked in an interlaced manner. If laid flat, the Solomon's knot is seen to have four crossings where the two loops interweave under and over each other. This contrasts with two crossings in the simpler Hopf link. In most artistic representations, the parts of the loops that alternately cross over and under each other become the sides of a central square, while four loopings extend outward in four directions. The four extending loopings may have oval, square, or triangular endings, or may terminate with free-form shapes such as leaves, lobes, blades, wings etc. Occurrences The Solomon's knot often occurs in ancient Roman mosaics, usually represented as two int ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Hopf Link
In mathematical knot theory, the Hopf link is the simplest nontrivial link with more than one component. It consists of two circles linked together exactly once, and is named after Heinz Hopf. Geometric realization A concrete model consists of two unit circles in perpendicular planes, each passing through the center of the other.. See in particulap. 77 This model minimizes the ropelength of the link and until 2002 the Hopf link was the only link whose ropelength was known. The convex hull of these two circles forms a shape called an oloid. Properties Depending on the relative orientations of the two components the linking number of the Hopf link is ±1. The Hopf link is a (2,2)-torus link with the braid word :\sigma_1^2.\, The knot complement of the Hopf link is R × ''S''1 × ''S''1, the cylinder over a torus. This space has a locally Euclidean geometry, so the Hopf link is not a hyperbolic link. The knot group of the Hopf link (the fund ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Slipknot Protein
The slip knot is a stopper knot which is easily undone by pulling the tail (working end). The slip knot is related to the running knot, which will release when the standing end is pulled. Both knots are identical and are composed of a slipped overhand knot, where a bight allows the knot to be released by pulling on an end; the working end for a slip knot, and the standing end for a running knot. The slip knot is used as a starting point for crochet and knitting. Standard creation The slip knot is formed by first creating a loop in the shape of a "p". Place a hand or hook through the loophole and grab a bight on the working end. Draw this bight through the first loop. Seat the knot and pull the bight until a small loop is created. See also * Knot * List of knots This list of knots includes many alternative names for common knots and lashings. Knot names have evolved over time, and there are many conflicting or confusing naming issues. The overhand knot, for example, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
TRNA (cytidine34-2'-O)-methyltransferase
tRNA (cytidine34-2'-O)-methyltransferase (, ''yibK (gene)'', ''methyltransferase yibK'', ''TrmL'', ''tRNA methyltransferase L'', ''tRNA (cytidine34/5-carboxymethylaminomethyluridine34-2'-O)-methyltransferase'') is an enzyme with systematic name ''S-adenosyl-L-methionine:tRNA (cytidine34/5-carboxymethylaminomethyluridine34-2'-O)-methyltransferase''. This enzyme catalyses the following chemical reaction : (1) S-adenosyl-L-methionine + cytidine34 in tRNA \rightleftharpoons S-adenosyl-L-homocysteine + 2'-O-methylcytidine34 in tRNA : (2) S-adenosyl-L-methionine + 5-carboxymethylaminomethyluridine34 in tRNALeu \rightleftharpoons S-adenosyl-L-homocysteine + 5-carboxymethylaminomethyl-2'-O-methyluridine34 in tRNALeu The enzyme from ''Escherichia coli'' catalyses the 2'-O-methylation of cytidine or 5-carboxymethylaminomethyluridine at the wobble position at nucleotide Nucleotides are organic molecules consisting of a nucleoside and a phosphate. They serve as monomeric units of t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein
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 residue ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Trefoil Knot
In knot theory, a branch of mathematics, the trefoil knot is the simplest example of a nontrivial knot. The trefoil can be obtained by joining together the two loose ends of a common overhand knot, resulting in a knotted loop. As the simplest knot, the trefoil is fundamental to the study of mathematical knot theory. The trefoil knot is named after the three-leaf clover (or trefoil) plant. Descriptions The trefoil knot can be defined as the curve obtained from the following parametric equations: :\begin x &= \sin t + 2 \sin 2t \\ y &= \cos t - 2 \cos 2t \\ z &= -\sin 3t \end The (2,3)-torus knot is also a trefoil knot. The following parametric equations give a (2,3)-torus knot lying on torus (r-2)^2+z^2 = 1: :\begin x &= (2+\cos 3t) \cos 2t \\ y &= (2+\cos 3t )\sin 2t \\ z &= \sin 3t \end Any continuous deformation of the curve above is also considered a trefoil knot. Specifically, any curve isotopic to a trefoil knot is also considered to be a trefoil. In addition, the mi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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