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ResiCon: a method for the identification of dynamic domains, hinges and interfacial regions in proteins

Maciej Dziubiński¹, Paweł Daniluk², Bogdan Lesyng²

¹Department of Biophysics and CoE BioExploratorium, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland and.

Bioinformatics (Oxford, England)

|September 6, 2015

Abstract

Motivation:

Structure of most proteins is flexible. Identification and analysis of intramolecular motions is a complex problem. Breaking a structure into relatively rigid parts, the so-called dynamic domains, may help comprehend the complexity of protein's mobility. We propose a new approach called ResiCon (Residue Contacts analysis), which performs this task by applying a data-mining analysis of an ensemble of protein configurations and recognizes dynamic domains, hinges and interfacial regions, by considering contacts between residues.

Results:

Dynamic domains found by ResiCon are more compact than those identified by two other popular methods: PiSQRD and GeoStaS. The current analysis was carried out using a known reference set of 30 NMR protein structures, as well as molecular dynamics simulation data of flap opening events in HIV-1 protease. The more detailed analysis of HIV-1 protease dataset shows that ResiCon identified dynamic domains involved in structural changes of functional importance.

Availability And Implementation:

The ResiCon server is available at URL: http://dworkowa.imdik.pan.pl/EP/ResiCon.

Contact:

pawel@bioexploratorium.pl

Supplementary Information:

Supplementary data are available at Bioinformatics online.

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