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SOSUI is a free online tool that predicts a part of the
secondary structure Protein secondary structure is the three dimensional form of ''local segments'' of proteins. The two most common secondary structural elements are alpha helices and beta sheets, though beta turns and omega loops occur as well. Secondary struct ...
of
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, respon ...
s from a given
amino acid sequence Protein primary structure is the linear sequence of amino acids in a peptide or protein. By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end. Protein biosynthesi ...
(AAS). The main objective is to determine whether the protein in question is a soluble or a
transmembrane protein A transmembrane protein (TP) is a type of integral membrane protein that spans the entirety of the cell membrane. Many transmembrane proteins function as gateways to permit the transport of specific substances across the membrane. They frequentl ...
.


History

SOSUI's
algorithm In mathematics and computer science, an algorithm () is a finite sequence of rigorous instructions, typically used to solve a class of specific problems or to perform a computation. Algorithms are used as specifications for performing ...
was developed in 1996 at Tokyo University. The name means as much as "
hydrophobic In chemistry, hydrophobicity is the physical property of a molecule that is seemingly repelled from a mass of water (known as a hydrophobe). In contrast, hydrophiles are attracted to water. Hydrophobic molecules tend to be nonpolar and, ...
", an allusion to its molecular "clients".


How SOSUI works

First of all, SOSUI looks for
α helices 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 earli ...
that are relatively easy to predict, taking into account the known
helical potential Helical may refer to: * Helix, the mathematical concept for the shape * Helical engine, a proposed spacecraft propulsion drive * Helical spring, a coilspring * Helical plc, a British property company, once a maker of steel bar stock * Helicoil ...
s of the given amino acid sequence(AAS). The much more difficult task is to differentiate between the α helices in soluble proteins and the ones in transmembrane proteins, the α helix being a very common secondary structure pattern in proteins. SOSUI uses 4 characteristics of the AAS in its prediction: # "
hydropathy index Hydrophobicity scales are values that define the relative hydrophobicity or hydrophilicity of amino acid residues. The more positive the value, the more hydrophobic are the amino acids located in that region of the protein. These scales are commonly ...
" (Kyte und Doolittle 1982) # weighted presence of
amphiphilic An amphiphile (from the Greek αμφις amphis, both, and φιλíα philia, love, friendship), or amphipath, is a chemical compound possessing both hydrophilic (''water-loving'', polar) and lipophilic (''fat-loving'') properties. Such a compoun ...
amino acids (AA) and their localization: "amphiphilicity index" # the AA's charge # the length of the AAS An important improvement compared to Kyte und Doolittle's "hydropathy index", which relies entirely on one characteristic, is the introduction of the so-called "amphiphilicity index". It is calculated by giving every AA with an amphiphilic residue a certain value which is derived from the AA's molecular structure. To meet SOSUI's criteria for amphiphilicity, the
polar Polar may refer to: Geography Polar may refer to: * Geographical pole, either of two fixed points on the surface of a rotating body or planet, at 90 degrees from the equator, based on the axis around which a body rotates *Polar climate, the cli ...
, hydrophilic residue may not be linked directly to the beta-carbon; there must be at least one
apolar In chemistry, polarity is a separation of electric charge leading to a molecule or its chemical groups having an electric dipole moment, with a negatively charged end and a positively charged end. Polar molecules must contain one or more pola ...
carbon interposed (therefore only lysine, arginine, histidine, glutamic acid, glutamine, tryptophan and tyrosine are relevant). SOSUI then looks for accumulations of amphiphilic AAs at the ends of α helices, which seems to be typical for transmembrane α helices (it makes the transmembrane position the energetically best one for these α helices by placing amphiphilic AAs at the lipid-water boundary and is thus co-responsible for the protein's correct localization). The AA's charge is also taken into consideration; the length is important because biological
lipid membrane The lipid bilayer (or phospholipid bilayer) is a thin polar membrane made of two layers of lipid molecules. These membranes are flat sheets that form a continuous barrier around all cells. The cell membranes of almost all organisms and many ...
s have a certain thickness determining the length of membrane-spanning proteins. According to a study published by SOSUI's developers it successfully differentiated 99% of a chosen group of proteins with known structure . However, another study that had several prediction tools perform on the AAS's of 122 known proteins claimed that SOSUI was correct about the number of α helices in only about 60% of the cases . But even if the number of transmembrane domains is not always exact, the differentiation between soluble and transmembrane proteins often works, as it is only necessary to find out if a protein has such a domain at all. Of course, membrane proteins which don't have transmembrane α helices (e.g.
porins Porins are beta barrel proteins that cross a cellular membrane and act as a pore, through which molecules can diffuse. Unlike other membrane transport proteins, porins are large enough to allow passive diffusion, i.e., they act as channels that ...
) or which are fixed with a covalent bond cannot be found by SOSUI.


Results

The result page first shows general information (length, average hydrophobicity). If the protein in question is a transmembrane protein, the number of transmembrane domains and their localization is noted. A "hydropathy-profile" with colored accents of hydrophobic parts; the helical wheel diagrams of potential transmembrane domains are shown as well. The last image shows a schematic overview of the transmembrane protein's location.


Sources

# Hirokawa, Boon-Chieng, Mitaku, ''SOSUI: Classification and secondary structure prediction for membrane proteins'', Bioinformatics Vol.14 S.378-379 (1998

# Masami Ikeda, Masafumi Arai, Toshio Shimizu, ''Evaluation of transmembrane topology prediction methods by using an experimentally characterized topology dataset'', Genome Informatics 11: 426–427 (2000

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External links


SOSUI-homepage
Bioinformatics software