SOSUI
SOSUI is a freely available online program that calculates a certain part of the secondary structure of proteins , the α-helix , from an amino acid sequence entered by the user . The main task of the program, however, is to use certain properties of the α-helices found to predict with a relatively high degree of certainty whether the given amino acid sequence is that of a soluble protein or that of a transmembrane protein .
history
The SOSUI algorithm was developed in 1996 at the University of Tokyo, the name means in Japanese u. a. "hydrophobic (to be)" and thus alludes to the "victims" of the program.
functionality
First, SOSUI looks for α-helices that can be relatively easily predicted taking into account the known " helix potentials " (see article α-helix) of the amino acids. This is followed by the much more demanding task of distinguishing between α-helices in soluble proteins and α-helices in transmembrane proteins. SOSUI bases its calculation on four properties of the amino acid sequence:
- Hydropathy : "hydropathy index" according to Kyte and Doolittle (1982)
- Weighted occurrence of amphiphilic amino acids and their localization: "amphiphilicity index"
- Amino Acid Charge (AA)
- Length of the sequence
A decisive advance compared to the sole consideration of hydropathy is the introduction of the so-called "amphiphilicity index" , which is calculated by assigning a certain value resulting from the molecular structure to each AA with an amphiphilic residue. To be amphiphilic for SOSUI, the hydrophilic polar residue must not be attached directly to the β-carbon atom; rather, at least one non-polar carbon atom must be interposed (it follows that lysine, arginine, histidine, glutamate, glutamine, tryptophan and tyrosine are relevant for the "amphiphilicity index" ). SOSUI succeeds in differentiating between transmembrane α-helices and the other, widespread α-helices by detecting the characteristic "accumulation" of amphiphilic AS at both ends of the transmembrane α-helices (which in vivo ensures that these α-helices, the transmembrane positioning with the ends at the lipid-water interfaces is particularly favorable in terms of energy). The charge of the AS is included in the calculation as is its length; SOSUI makes use of the fact that biological lipid membranes have a certain thickness (approx. 8 nm) and transmembrane domains must therefore have a similar length.
This procedure allowed a differentiation in 99% of the proteins examined in a study. However, this study was carried out by the SOSUI creators themselves; in practice, SOSUI does not achieve such a high hit rate. According to an independent study, in which the number of transmembrane α-helices of 122 known transmembrane proteins with α-helix was predicted by various programs, SOSUI was correct in almost 60% of the cases. Even if the number is often inaccurately predicted, the distinction between transmembrane proteins and soluble proteins is usually possible (since it is sufficient to find out whether a protein has a transmembrane α-helix at all). Of course, membrane proteins that are not anchored by a transmembrane α-helix cannot be identified in this way, e.g. B. Porins or proteins covalently bound to a lipid molecule .
Results
SOSUI displays some general information at the top of the results page, such as length and average hydrophobicity . If it is a transmembrane protein, the number of transmembrane domains and their location are given. Then follows a hydropathy -profile with highlighting the hydrophobic portions, including at transmembrane proteins, the helical wheel - ( " helical wheel " ) diagrams with colored marking of polar or charged AS side chains . Finally, a schematic overview of the entire AA sequence is provided in which the "primary" and "secondary" α-helices are designated separately (the authors describe an α-helix as primary, if it is strongly hydrophobic, as secondary , even if it also has hydrophilic parts and therefore cannot be classified as a transmembrane domain with certainty based on the degree of its hydrophobicity, but only when the other three properties are taken into account).
See also
- Harvester is a bioinformatics meta search engine that a. uses SOSUI
Web links
swell
- ↑ Hirokawa, Boon-Chieng, Mitaku: SOSUI: Classification and secondary structure prediction for membrane proteins , Bioinformatics Vol.14 pp. 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) ( Memento of the original from March 25, 2006 in the Internet Archive ) Info: Der Archive link was inserted automatically and has not yet been checked. Please check the original and archive link according to the instructions and then remove this notice.
