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Event Entry
What and Who
Self-consistent Assignment of Asparagine and Glutamine Side-Chain Amide Rotamers
Christian Weichenberger
Universität Salzburg
AG3 Talk
AG 1, AG 2, AG 3, AG 4, AG 5, SWS
Public Audience
English
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Date, Time and Location
Thursday, 22 February 2007
14:00
-- Not specified --
E1 4
023
Saarbrücken
Abstract
We address the rotamer assignment problem of asparagine (Asn) and
glutamine (Gln) side-chain amides encountered in protein structures
solved by X-ray crystallography. The amide groups in the side-chains of
Asn and Gln are specific examples of functional groups which act
simultaneously as hydrogen bond donors and acceptors. These amide groups
frequently participate in hydrogen bond networks, ligand binding,
protein protein interactions, and catalysis. The electron density near
the nitrogen and oxygen atoms of Asn and Gln amide groups is compatible
with two rotamers which are related by a two-fold symmetry axis.
Therefore, electron density maps obtained from X-ray diffraction
experiments of protein crystals yield the positions of the oxygen and
nitrogen atoms with high precision but not their identity resulting in
the perpetual assignment of wrong rotamers in the order of 20 to 25%.
However, incorrect rotamers in general result in unfavorable
interactions and should be clearly detectable by proper energy calculations.
Here we present an automated method to assign the correct rotamer with
high accuracy. We derive a mean force heavy atom potential from the
complete crystal environment of a set of 833 protein structures
determined at high resolution where any two protein chains have less
than 20% sequence identity. We compare our assignments with an expert
annotated set of 100 protein structures and find sensitivity and
selectivity values higher than 90%. A web service is available at
http://flipper.services.came.sbg.ac.at.
glutamine (Gln) side-chain amides encountered in protein structures
solved by X-ray crystallography. The amide groups in the side-chains of
Asn and Gln are specific examples of functional groups which act
simultaneously as hydrogen bond donors and acceptors. These amide groups
frequently participate in hydrogen bond networks, ligand binding,
protein protein interactions, and catalysis. The electron density near
the nitrogen and oxygen atoms of Asn and Gln amide groups is compatible
with two rotamers which are related by a two-fold symmetry axis.
Therefore, electron density maps obtained from X-ray diffraction
experiments of protein crystals yield the positions of the oxygen and
nitrogen atoms with high precision but not their identity resulting in
the perpetual assignment of wrong rotamers in the order of 20 to 25%.
However, incorrect rotamers in general result in unfavorable
interactions and should be clearly detectable by proper energy calculations.
Here we present an automated method to assign the correct rotamer with
high accuracy. We derive a mean force heavy atom potential from the
complete crystal environment of a set of 833 protein structures
determined at high resolution where any two protein chains have less
than 20% sequence identity. We compare our assignments with an expert
annotated set of 100 protein structures and find sensitivity and
selectivity values higher than 90%. A web service is available at
http://flipper.services.came.sbg.ac.at.
Contact
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Ruth Schneppen-Christmann, 01/24/2007 11:03
Ruth Schneppen-Christmann, 01/24/2007 09:48 -- Created document.
Ruth Schneppen-Christmann, 01/24/2007 09:48 -- Created document.