Back to Browse Journals » Drug Design, Development and Therapy » Volume 3

Analysis of HSP90-related folds with MED-SuMo classification approach

Authors Olivia Doppelt-Azeroual, Fabrice Moriaud, François Delfaud, Alexandre G de Brevern

Published Date February 2009 Volume 2009:3 Pages 59—72

DOI http://dx.doi.org/10.2147/DDDT.S4706

Published 26 February 2009

Olivia Doppelt-Azeroual1,2, Fabrice Moriaud1, François Delfaud1, Alexandre G de Brevern2

1MEDIT SA, Palaiseau, France; 2INSERM UMR-S 726, Equipe de Bioinformatique Génomique and Moléculaire, (EBGM), DSIMB, Institut National de Transfusion Sanguine (INTS), Université Paris Diderot, Paris, France

Abstract: Three-dimensional structural information is critical for understanding functional protein properties and the precise mechanisms of protein functions implicated in physiological and pathological processes. Comparison and detection of protein binding sites are key steps for annotating structures with functional predictions and are extremely valuable steps in a drug design process. In this research area, MED-SuMo is a powerful technology to detect and characterize similar local regions on protein surfaces. Each amino acid residue’s potential chemical interactions are represented by specific surface chemical features (SCFs). The MED-SuMo heuristic is based on the representation of binding sites by a graph structure suitable for exploration by an efficient comparison algorithm. We use this approach to analyze one particular SCOP superfamily which includes HSP90 chaperone, MutL/DNA topoisomerase, histidine kinases, and α-ketoacid dehydrogenase kinase C (BCK). They share a common fold and a common region for ATP-binding. To analyze both similar and differing features of this fold, we use a novel classification method, the MED-SuMo multi approach (MED-SMA). We highlight common and distinct features of these proteins. The different clusters created by MED-SMA yield interesting observations. For instance, one cluster gathers three types of proteins (HSP90, topoisomerase VI, and BCK) which all bind the drug radicicol.

Keywords: functional classification, surface similarity, protein surface chemical feature, radicicol binding

Download Article [PDF] 

Creative Commons License This work is published by Dove Medical Press Limited, and licensed under Creative Commons Attribution - Non Commercial (unported, v3.0) License. The full terms of the License are available at http://creativecommons.org/licenses/by-nc/3.0/. Non-commercial uses of the work are permitted without any further permission from Dove Medical Press Limited, provided the work is properly attributed. Permissions beyond the scope of the License are administered by Dove Medical Press Limited. Information on how to request permission may be found at: http://www.dovepress.com/permissions.php

Readers of this article also read:

Diabetes reversal via gene transfer: building on successes in animal models

Gerace D, Martiniello-Wilks R, Simpson AM

Research and Reports in Endocrine Disorders 2015, 5:15-29

Published Date: 29 January 2015

Corneal laceration caused by river crab

Vinuthinee N, Azreen-Redzal A, Juanarita J, Zunaina E

Clinical Ophthalmology 2015, 9:203-206

Published Date: 29 January 2015

Ocular surface disease in posttrabeculectomy/mitomycin C patients

Lam J, Wong TT, Tong L

Clinical Ophthalmology 2015, 9:187-191

Published Date: 29 January 2015

Pharmacokinetics and pharmacodynamics of acetylsalicylic acid after intravenous and oral administration to healthy volunteers

Nagelschmitz J, Blunck M, Kraetzschmar J, Ludwig M, Wensing G, Hohlfeld T

Clinical Pharmacology: Advances and Applications 2014, 6:51-59

Published Date: 19 March 2014

Population pharmacokinetics of olprinone in healthy male volunteers

Kunisawa T, Kasai H, Suda M, Yoshimura M, Sugawara A, Izumi Y, Iida T, Kurosawa A, Iwasaki H

Clinical Pharmacology: Advances and Applications 2014, 6:43-50

Published Date: 4 March 2014

Detemir as a once-daily basal insulin in type 2 diabetes

Nelson SE

Clinical Pharmacology: Advances and Applications 2011, 3:27-37

Published Date: 18 August 2011