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A three-dimensional model of a figure-eight knot.The figure-eight knot is a prime knot and has an Alexander–Briggs notation of 4 1.. Topology (from the Greek words τόπος, 'place, location', and λόγος, 'study') is the branch of mathematics concerned with the properties of a geometric object that are preserved under continuous deformations, such as stretching, twisting, crumpling ...
Topology of a transmembrane protein refers to locations of N- and C-termini of membrane-spanning polypeptide chain with respect to the inner or outer sides of the biological membrane occupied by the protein. [1] Group I and II transmembrane proteins have opposite final topologies.
In biology literature, the term topology is also used to refer to mutual orientation of regular secondary structures, such as alpha-helices and beta strands in protein structure [3]. For example, two adjacent interacting alpha-helices or beta-strands can go in the same or in opposite directions.
The topology equation shows that there is a one-to-one relationship between changes in Tw and Wr. For example, if a secondary "Watson–Crick" twist is removed, then a right-handed supertwist must have been removed simultaneously (or, if the chromosome is relaxed, with no supertwists, then a left-handed supertwist must be added).
A topologically associating domain (TAD) is a self-interacting genomic region, meaning that DNA sequences within a TAD physically interact with each other more frequently than with sequences outside the TAD. [1] The average size of a topologically associating domain (TAD) is 1000 kb in humans, 880 kb in mouse cells, and 140 kb in fruit flies.
All beta-barrel transmembrane proteins have simplest up-and-down topology, which may reflect their common evolutionary origin and similar folding mechanism. [7] In addition to the protein domains, there are unusual transmembrane elements formed by peptides. A typical example is gramicidin A, a peptide that forms a dimeric transmembrane β-helix ...
The topology of the CW complex is the topology of the quotient space defined by these gluing maps. In general, an n-dimensional CW complex is constructed by taking the disjoint union of a k -dimensional CW complex (for some k < n {\displaystyle k<n} ) with one or more copies of the n -dimensional ball .
Topology Analysis analyzes the topology of a network to identify relevant participates and substructures that may be of biological significance. The term encompasses an entire class of techniques such as network motif search, centrality analysis, topological clustering, and shortest paths. These are but a few examples, each of these techniques ...