Protein Engineering, Vol 11, 279-283, Copyright © 1998 by Oxford University Press
GV Nikiforovich
We have developed a novel, non-statistical procedure for predicting
possible breaks in transmembrane helices based on energy calculations. The
procedure consists of stepwise elongation of the 'core' helical fragment
determined by consensus results of several available prediction procedures.
At each step, we calculate the conformational energies corresponding to the
regular 'frozen' helical conformer of the 'core' fragment elongated by two
flanking residues, E(alpha), as well as those to several options for the
fragment to enter or exit the helix by changing conformations of the
flanking residues, Ei. The minimal values out of Ei - E(alpha), delta(k),
can be viewed as a profile of relative energies, where each minimum of
delta(k) is a signal to start or to stop transmembrane helix. We suggest
that boundaries of the transmembrane helix would be determined by the
signals closest to the 'core' sequence in the delta(k) profiles. Our
procedure was applied to prediction of the N- and C-termini for 45
transmembrane helices from the photosynthetic reaction center from
Rhodopseudomonas viridis, bacteriorhodopsin and the cytochrome c oxidase
from Paracoccus denitrificans. The results clearly showed that it is
significantly more probable that a prediction accuracy within an error of
+/- 2 residues will be obtained by our procedure than by three different
statistical approaches.
ARTICLES
A novel, non-statistical method for predicting breaks in transmembrane helices
Center for Molecular Design, Institute for Biomedical Computing, Washington University, St Louis, MO 63110, USA.
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