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. Several databases provide experimentally determined topologies of membrane proteins. They include Uniprot, TOPDB, OPM, and ExTopoDB. There is also a database of domains located conservatively on a certain side of membranes, TOPDOM. Several computational methods were developed, with a limited success, for predicting transmembrane alpha-helices and their topology. Pioneer methods utilized the fact that membrane-spanning regions contain more hydrophobic residues than other parts of the protein, however applying different hydrophobic scales altered the prediction results. Later, several statistical methods were developed to improve the topography prediction and a special alignment method was introduced. According to the positive-inside rule, cytosolic loops near the lipid bilayer contain more positively-charged amino acids. Applying this rule resulted in the first topology prediction methods. There is also a negative-outside rule in transmembrane alpha-helices from single-pass proteins, although negatively charged residues are rarer than positively charged residues in transmembrane segments of proteins. As more structures were determined, machine learning algorithms appeared. Supervised learning methods are trained on a set of experimentally determined structures, however, these methods highly depend on the training set. Unsupervised learning methods are based on the principle that topology depends on the maximum divergence of the amino acid distributions in different structural parts. It was also shown that locking a segment location based on prior knowledge about the structure improves the prediction accuracy. This feature has been added to some of the existing prediction methods. The most recent methods use consensus prediction (i.e. they use several algorithm to determine the final topology) and automatically incorporate previously determined experimental informations. HTP database provides a collection of topologies that are computationally predicted for human transmembrane proteins. Discrimination of signal peptides and transmembrane segments is an additional problem in topology prediction treated with a limited success by different methods. Both signal peptides and transmembrane segments contain hydrophobic regions which form α-helices. This causes the cross-prediction between them, which is a weakness of many transmembrane topology predictors. By predicting signal peptides and transmembrane helices simultaneously (Phobius), the errors caused by cross-prediction are reduced and the performance is substantially increased. Another feature used to increase the accuracy of the prediction is the homology (PolyPhobius).” It is also possible to predict beta-barrel membrane proteins' topology. (Wikipedia).
What Is Network Topology? | Types of Network Topology | BUS, RING, STAR, TREE, MESH | Simplilearn
In this video on Network Topology, we will understand What is Network topology, the role of using topology while designing a network, Different types of Topologies in a Network. Network topology provides us with a way to configure the most optimum network design according to our requiremen
From playlist Cyber Security Playlist [2023 Updated]🔥
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From playlist Network Security
Topology 1.3 : Basis for a Topology
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Topology (What is a Topology?)
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From playlist Topology
I define closed sets, an important notion in topology and analysis. It is defined in terms of limit points, and has a priori nothing to do with open sets. Yet I show the important result that a set is closed if and only if its complement is open. More topology videos can be found on my pla
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Topology 1.7 : More Examples of Topologies
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From playlist Topology
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How Proteins Get Where They’re Supposed to Go in Cells - T. Miller - 5/11/2016
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David Aasen - Topological Defect Networks for Fracton Models - IPAM at UCLA
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From playlist Graduate Summer School 2021: Mathematics of Topological Phases of Matter
Physics of Membranes and their interactions (Lecture - 2) by Ana-Suncana Smith
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Using topology to solve equations. - Music: Deep Relaxation Kevin MacLeod (incompetech.com) Licensed under Creative Commons: By Attribution 3.0 License http://creativecommons.org/licenses/by/3.0/
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Continuum "xy- model" on deformable surfaces: equilibrium... by Yashodhan Hatwalne
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A TQFT Perspective on Fracton Order
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WSU: Fundamental Lessons from String Theory with Cumrun Vafa
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Computer Networks. Part Four: LAN Topology
This is fourth in a series about computer networks. The word topology refers to the layout and wiring of a local area network. This video describes the main layouts including the bus, the star, the ring and the mesh, in terms of their advantages and disadvantages. It also describes the
From playlist Computer Networks