Heal, J. W., Wells, Stephen A., Jiménez Roldán, J. E. (José Emilio), Freedman, R. B. and Roemer, Rudolf A.. (2011) Rigidity analysis of HIV-1 protease. Journal of Physics: Conference Series, Vol.286 (No.1). article no. 012006. ISSN 1742-6596

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Abstract

We present a rigidity analysis on a large number of X-ray crystal structures of the enzyme HIV-1 protease using the 'pebble game' algorithm of the software first. We find that although the rigidity profile remains similar across a comprehensive set of high resolution structures, the profile changes significantly in the presence of an inhibitor. Our study shows that the action of the inhibitors is to restrict the exibility of the beta-hairpin flaps which allow access to the active site. The results are discussed in the context of full molecular dynamics simulations as well as data from NMR experiments.

Item Type:	Journal Article
Subjects:	Q Science > QP Physiology Q Science > QR Microbiology > QR355 Virology
Divisions:	Faculty of Science > Life Sciences (2010- ) Faculty of Science > Molecular Organisation and Assembly in Cells (MOAC) Faculty of Science > Physics Faculty of Science > Centre for Scientific Computing
Library of Congress Subject Headings (LCSH):	HIV (Viruses) -- Enzymes -- Research, Protease inhibitors -- Research
Journal or Publication Title:	Journal of Physics: Conference Series
Publisher:	Institute of Physics Publishing Ltd.
ISSN:	1742-6596
Date:	2011
Volume:	Vol.286
Number:	No.1
Page Range:	article no. 012006
Identification Number:	10.1088/1742-6596/286/1/012006
Status:	Peer Reviewed
Publication Status:	Published
Access rights to Published version:	Restricted or Subscription Access
Version or Related Resource:	Heal, J. W., et al. (2010). Rigidity analysis of HIV-1 protease. Conference on Condensed Matter and Materials Physics (CMMP10), University of Warwick, Coventry, Dec 14-16, 2010
References:	[1] Jacobs D J and Thorpe M F 1995 Physical Review Letters 75 4051 [2] Wells S, Jimenez-Roldan J and Roemer R 2009 Physical Biology 6 [3] Collins J R, Burt S K and Erickson J W 1995 Nat Struct Mol Biol 2 334{338 [4] Freedberg D I, Ishima R, Jacob J, Wang Y, Kustanovich I, Louis J M and Torchia D A 2009 Protein Science 11 221{232 ISSN 09618368 [5] Rodriguez E J, Debouck C, Deckman I C, Abu-Soud H, Raushel F M and Meek T D 1993 Biochemistry 32 3557{3563 ISSN 0006-2960 PMID: 8466899 [6] Erickson J W 1995 Nat Struct Mol Biol 2 523{529 [7] Flexner C 1998 The New England Journal of Medecine 338 1281{1293 [8] Henzler-Wildman K and Kern D 2007 Nature 450 [9] Hornak V, Okur A, Rizzo R C and Simmerling C 2006 Proceedings of the National Academy of Sciences of the United States of America 103 915 {920 [10] Jacobs D, Rader A, Kuhn L and Thorpe M 2001 Proteins: Structure, Function and Genetics 44 150{165 [11] Thorpe M, Jacobs D, Chubynsky N and Rader A 1999 Rigidity theory and applications (Kluwer Academic, New York) [12] Ishima R, Freedberg D I, Wang Y, Louis J M and Torchia D A 1999 Structure 7 1047{1055, S1{S12 ISSN 0969-2126
URI:	http://wrap.warwick.ac.uk/id/eprint/38140

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