XLIII Annual Meeting of SBBq
th
th
Foz do Iguaçu, PR, Brazil, May 17 to 20 , 2014
Effects of the Presence of Substrates, Products and Catalytic Water in HIV-1
Protease Flexibility by NMA.
De Conto, V.1; Braz, A.S.K.1 ; Scott, L.P.B.2; Perahia, D.3;Coutinho-Neto, M.D.1 ;
Homem-de-Mello, P.1
1
Centro de Ciências Naturais e Humanas-CCNH/UFABC, SP; 2 Centro de
Matemática, computação e Cognição-CMCC/UFABC, SP, Brazil; 3 Laboratoire de
Biologie et Pharmacologie Appliquée,Ecole Normale Supérieure de CachanENSC, Cachan, France.
INTRODUCTION:HIV-1 Protease (PR) is a homodimeric enzyme composed of
two polypeptide chains, each containing 99 residues. The active site, located at
the homodimer interface, cleaves ten non homologous sites along the gag and pol
viral polyproteins. Two catalytic Asp25 residues mediate a proton transfer from the
attacking catalytic water molecule to the leaving nitrogen atom of the substrate.
HIV-1 PR display significant flexibility in the flap region, with a significant role for
catalytic activity. OBJECTIVE: In this work, we studied the role of the presence of
substrates, products and catalytic water in HIV-1 PR flexibility. MATERIAL AND
METHODS: We used pdb structures of PR in semi-open conformation (2PC0),
closed conformation (1G6L), with substrates (1KJF, 1KJG, 1KJH and 3BXR) and
with products (4F73, 4F74, 4F75, 4F76 and 3BXS). The coordinates of catalytic
water were obtained from structural alignment with 1G6L pdb. Any mutation
present in pdbs was reverted by mutation and rotamers were adjusted by pymol
software. The inputs for Normal Mode Analysis were created through CHARMMGUI. NMA and structural analyses were performed using CHARMM and Bio3d
package, respectively. The structural images were generated using VMD and
pymol. RESULTS AND DISCUSSION: The semi-open conformation was more
flexible in flap region and less flexible than closed empty conformation in elbow
and active site regions. The flexibility of structures with substrates are more similar
to closed structure in elbow and flap regions, but was more similar to semi-open
structure flexibility in cantilever and active site. In structures with products we can
observe the greatest flexibility in elbow and fulcrum region. In structures with
substrates and catalytic water we can observe a significant reduction of flexibility
in elbow and fulcrum region when compare to structures with substrates.
CONCLUSION: These results show different patterns of flexibility according to the
ligand indicating that movements in certain regions can contribute to the
accommodation of the substrate and product release.
Key words: HIV-1 protease, molecular modelling, protein flexibility, normal mode
analysis.
Funding Agency: FAPESP.