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Sequence Analysis of Membrane Proteins with the Web Server SPLIT

Davor Juretić ; Physics Dept., Faculty of Natural Sciences, Mathematics and Education, University of Split, N. Tesle 12, HR–21000, Split, Croatia
Ana Jerončić ; Physics Dept., Faculty of Natural Sciences, Mathematics and Education, University of Split, N. Tesle 12, HR–21000, Split, Croatia
Damir Zucić ; Faculty of Electrical Engineering, University of Osijek, Istarska 3, HR–31000 Osijek, Croatia

Sažetak

In this work, recently solved crystal structures of membrane proteins are examined with respect to the performance of the Web server SPLIT in predicting sequence location, conformation and orientation of membrane associated polypeptide segments. The SPLIT predictor is based on the preference functions method. Preference functions serve to transform the input choice of amino acid attributes into sequence dependent conformational preferences. Transmembrane helical segments are accurately predicted with a good selection of preference functions extracted from the compiled database of non-homologous integral membrane proteins. Unlike other algorithms with similar high accuracy, the SPLIT predictor requires no homology information. With preference functions extracted from soluble proteins, the sequence location of shorter non-transmembrane helices can be also found in membrane proteins. In particular, Richardson's preference functions are even better than hydrophobic moments in finding interface helices at the water/lipid phase boundary. The Internet access for the SPLIT system is at the address: http://pref.etfos.hr/split.

Ključne riječi

sequence analysis; membrane proteins; prediction; secondary structure; preference functions; transmembrane helix; interface helix; hydrophobic moments; antibacterial peptides

Hrčak ID:

132316

URI

https://hrcak.srce.hr/132316

Datum izdavanja:

1.12.1999.

Posjeta: 1.103 *