Nucleic Acids Research, 2003, Vol. 31, No. 15 4625-4631
© 2003 Oxford University Press
Structural details (kinks and non-
conformations) in transmembrane helices are intrahelically determined and can be predicted by sequence pattern descriptors
Bioinformatics and Pattern Discovery Research Group, IBM Thomas J. Watson Research Center, PO Box 218, Yorktown Heights, NY 10598, USA, 1 Victor Chang Cardiac Research Institute, St Vincent’s Hospital, 384 Victoria Street, Darlinghurst 2010, New South Wales, Australia and 2 School of Biochemistry and Molecular Genetics, University of New South Wales, Kensington 2052, New South Wales, Australia
*To whom correspondence should be addressed. Tel: +1 914 945 1384; Fax: +1 914 945 4104; Email: rigoutso{at}us.ibm.com
One of the promising methods of protein structure prediction involves the use of amino acid sequence-derived patterns. Here we report on the creation of non-degenerate motif descriptors derived through data mining of training sets of residues taken from the transmembrane-spanning segments of polytopic proteins. These residues correspond to short regions in which there is a deviation from the regular 
-helical character (i.e. 
-helices, 310-helices and kinks). A ‘search engine’ derived from these motif descriptors correctly identifies, and discriminates amongst instances of the above ‘non-canonical’ helical motifs contained in the SwissProt/TrEMBL database of protein primary structures. Our results suggest that deviations from -helicity are encoded locally in sequence patterns only about 7–9 residues long and can be determined in silico directly from the amino acid sequence. Delineation of such variations in helical habit is critical to understanding the complex structure–function relationships of polytopic proteins and for drug discovery. The success of our current methodology foretells development of similar prediction tools capable of identifying other structural motifs from sequence alone. The method described here has been implemented and is available on the World Wide Web at http://cbcsrv.watson.ibm.com/Ttkw.html.
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