Naslov
Conformational Preference Functions for Predicting Helices in Membrane Proteins

Autori
Juretić, Davor ; Lee, Byungkook ; Trinajstić, Nenad ; Williams, Robert W.

Izvornik
Biopolymers (0006-3525) 33 (1993); 255-273

Vrsta, podvrsta i kategorija rada
Radovi u časopisima, članak, znanstveni

Ključne riječi
sequence-dependent preferences, membrane proteins, predicting, secondary structure, buried surface area

Sažetak
A suite of FORTRAN programs, PREF, is described for calculating preference functions from the data base of known protein structures and for comparing smoothed profiles of sequence-dependent preferences in proteins of unknown structure. Amino acid preferences for a secondary structure are considered as functions of a sequence environment. Sequence environment of amino acid residue in a protein is defined as an average over some physical, chemical, or statistical property of its primary structure neighbors. The frequency distribution of sequence environments in the data base of soluble protein structures is approximately normal for each amino acid type of known secondary conformation. An analytical expression for the dependence of preferences on sequence environment is obtained after each frequency distribution is replaced by corresponding Gaussian function. The preference for the alpha-helical conformation increases for each amino acid type with the increase of sequence environment of buried solvent-accessible surface areas. We show that a set of preference functions based on buried surface area is useful for predicting folding motifs in alpha-class proteins and in integral membrane proteins. The prediction accuracy for helical residues is 79% for 5 integral membrane proteins and 74% for 11 alpha-class soluble proteins. Most residues found in transmembrane segments of membrane proteins with known alpha-helical structure are predicted to be indeed in the helical conformation because of very high middle helix preferences. Both extramembrane and transmembrane helices in the photosynthetic reaction center M and L subunits are correctly predicted. We point out in the discussion that our method of conformational preference functions can identify what physical properties of the amino acids are important in the formation of particular secondary structure elements.

Izvorni jezik
Engleski

Znanstvena područja
Fizika, Kemija, Biologija

Napomena
Biopolymers journal is cited in the following
databases:
WILEY , 111 RIVER ST, HOBOKEN, USA, NJ, 07030-
5774
ISSN / eISSN:
0006-3525 / 1097-0282
Web of Science Core Collection:
Science Citation Index Expanded
Additional Web of Science Indexes:
Biological Abstracts | BIOSIS Previews | Current
Contents Life Sciences | Essential Science
Indicators

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