Τομέας Βιολογίας Κυττάρου Και Βιοφυσικής
Library of the School of Science

2012-01-09

2010

Πουρνάρας Ευθύμιος

Καθηγητής Σ. Χαμόδρακας (επιβλέπων), Επικ. Καθηγητής Π. Μπάγκος, Λέκτωρ Β. Οικονομίδου

Υπολογισμός της Μέσης Πυκνότητας Πακεταρίσματος των 20 βασικών αμινοξικών καταλοίπων σε σετ διαμεμβρανικών πρωτεϊνών με ομολογία <30%

Greek

Our work has been focused on the calculations of “Mean Packing Density” for
each of the 20 common amino acid residues for a 30% non-redundant set of
transmembrane proteins. The aim was to compare the results with those acquired
from a 25% non-redundant set of globular water-soluble proteins in order to
find similarities or identify unknown differences, which may be used in
prediction methods beyond amyloidogenic propensity (which is predicted from the
2nd set).
The protein set was obtained from PDB-TM (update of May 2009) and the 30%
non-redundancy was achieved using the NON-RED on-line tool. It consists of 143
transmembrane protein chains (107 alpha-helical proteins and 36 beta-barrels).
The algorithm assumes that two residues are considered as “close” neighbors
when any pair of their heavy atoms is at a distance of <= 8.0 Angstroms
(excluding the ±1 covalently bonded residues). The Mean Packing Density per
residue was calculated from the 3D structures as the sum of observed close
neighbors of all residues (of the same type) divided by their total number in
the set.
The results may also work in the future as a tool for the identification of
alpha-helices or beta-strands in transmembrane proteins.

Amyloids, Packing, Density, Transmembrane, Protein

Yes

iv-vi

Yes

17

VII, 174

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https://pergamos.lib.uoa.gr/uoa/dl/object/1320561