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Titolo:
Molecular dynamics studies on the interaction of 4-acetylamino-5-hydroxynapthalene-2,7-disulfonic acid with catalytic domain of avian sarcoma virus integrase dimer
Autore:
Kothekar, V; Shankar, S;
Indirizzi:
All India Inst Med Sci, Dept Biophys, New Delhi 110029, India All India Inst Med Sci New Delhi India 110029 s, New Delhi 110029, India
Titolo Testata:
JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM
, volume: 540, anno: 2001,
pagine: 35 - 46
SICI:
0166-1280(20010504)540:<35:MDSOTI>2.0.ZU;2-U
Fonte:
ISI
Lingua:
ENG
Soggetto:
HUMAN-IMMUNODEFICIENCY-VIRUS; DNA-BINDING DOMAIN; CARBOXYL-TERMINAL DOMAINS; HIV-1 INTEGRASE; ACTIVE-SITE; IN-VITRO; RETROVIRAL INTEGRASE; ESCHERICHIA-COLI; DIVALENT-CATIONS; TYPE-1;
Keywords:
ASV-IN Y3 dimer; MD simulation 500 ps; potency Y3;
Tipo documento:
Article
Natura:
Periodico
Settore Disciplinare:
Physical, Chemical & Earth Sciences
Citazioni:
58
Recensione:
Indirizzi per estratti:
Indirizzo: Kothekar, V All India Inst Med Sci, Dept Biophys, New Delhi 110029, India All India Inst Med Sci New Delhi India 110029 110029, India
Citazione:
V. Kothekar e S. Shankar, "Molecular dynamics studies on the interaction of 4-acetylamino-5-hydroxynapthalene-2,7-disulfonic acid with catalytic domain of avian sarcoma virus integrase dimer", J MOL ST-TH, 540, 2001, pp. 35-46

Abstract

We report here 500 ps molecular dynamics (MD) simulation results on two molecules of 4-acetylamino-5-hydroxy naphthalene 2-7-disulfonic acid (Y-3) inthe catalytic domain (residues 54-199) of avian sarcoma virus integrase (ASV-IN) dimer. Starting model was obtained on the basis of PDB coordinates (PDB code 1A5X) of ASV-IN-Y3 monomer by Lubkowski et al. [Proc. Natl Acad. Sci. USA, 95 (1998) 4831-4836]. Two molecules of Y3 were docked in the active cavity of the dimer using IMF [Phys. Edu., 5 (1988) 169-176]. Energy minimization (EM) and MD simulation were carried out using Sander's module of AMBER 5.0 [AMBER 5.0: Assisted Model building with Energy Refinement: a computer simulation software developed by the University of California, USA, 1997] with all atom force field for Y3 and united atom force field for IN. Analysis of the ligand protein interaction and perturbative changes in the complex is presented in the paper. Salient features related to higher pharmacological activity of Y-3 compared to other analogs from acetyl-amino-naphthalene series are enumerated. (C) 2001 Elsevier Science B.V. All rights reserved.

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Documento generato il 26/10/20 alle ore 13:39:02