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:

Depressive symptoms in caregivers of patients with dementia: demographic variables and burden

De Fazio P, Ciambrone P, Cerminara G, Barbuto E, Bruni A, Gentile P, Talarico A, Lacava R, Gareri P, Segura-Garcia C

Clinical Interventions in Aging 2015, 10:1085-1090

Published Date: 1 July 2015

Enzalutamide for the treatment of metastatic castration-resistant prostate cancer

Rodriguez-Vida A, Galazi M, Rudman S, Chowdhury S, Sternberg CN

Drug Design, Development and Therapy 2015, 9:3325-3339

Published Date: 29 June 2015

Bladder cancer in the elderly patient: challenges and solutions

Guancial EA, Roussel B, Bergsma DP, Bylund KC, Sahasrabudhe D, Messing E, Mohile SG, Fung C

Clinical Interventions in Aging 2015, 10:939-949

Published Date: 10 June 2015

Impact of potential inappropriate NSAIDs use in chronic pain

Ussai S, Miceli L, Pisa FE, Bednarova R, Giordano A, Della Rocca G, Petelin R

Drug Design, Development and Therapy 2015, 9:2073-2077

Published Date: 9 April 2015

Neuroprotective therapies for glaucoma

Song W, Huang P, Zhang C

Drug Design, Development and Therapy 2015, 9:1469-1479

Published Date: 11 March 2015

Noncoding RNAs as potential biomarkers to predict the outcome in pancreatic cancer

Jin K, Luo G, Xiao Z, Liu Z, Liu C, Ji S, Xu J, Liu L, Long J, Ni Q, Yu X

Drug Design, Development and Therapy 2015, 9:1247-1255

Published Date: 26 February 2015

Design and in vivo evaluation of oxycodone once-a-day controlled-release tablets

Kim JY, Lee SH, Park CW, Rhee YS, Kim DW, Park J, Lee M, Seo JW, Park ES

Drug Design, Development and Therapy 2015, 9:695-706

Published Date: 30 January 2015