Structural analysis of viral infectivity factor of HIV type 1 and its interaction with A3G, EloC and EloB

PloS One
Kauê Santana da CostaJerônimo Lameira


The virion infectivity factor (Vif) is an accessory protein, which is essential for HIV replication in host cells. Vif neutralizes the antiviral host protein APOBEC3 through recruitment of the E3 ubiquitin ligase complex. Fifty thousand Vif models were generated using the ab initio relax protocol of the Rosetta algorithm from sets of three- and nine-residue fragments using the fragment Monte Carlo insertion-simulated annealing strategy, which favors protein-like features, followed by an all-atom refinement. In the protocol, a constraints archive was used to define the spatial relationship between the side chains from Cys/His residues and zinc ions that formed the zinc-finger motif that is essential for Vif function. We also performed centroids analysis and structural analysis with respect to the formation of the zinc-finger, and the residue disposal in the protein binding domains. Additionally, molecular docking was used to explore details of Vif-A3G and Vif-EloBC interactions. Furthermore, molecular dynamics simulation was used to evaluate the stability of the complexes Vif-EloBC-A3G and Vif-EloC. The zinc in the HCCH domain significantly alters the folding of Vif and changes the structural dynamics of the HCCH region. Ab init...Continue Reading


Jan 1, 1985·Journal of Molecular Evolution·M HasegawaT Yano
Apr 26, 1996·The Journal of Biological Chemistry·X YangDana Gabuzda
Dec 1, 1996·Journal of Biomolecular NMR·R A LaskowskiJ M Thornton
Sep 1, 1995·Molecular Medicine Today·A Sali
May 22, 1998·Journal of Molecular Biology·F Melo, E Feytmans
Oct 29, 1998·The Journal of Biological Chemistry·X Yang, Dana Gabuzda
Feb 8, 2002·Biometals : an International Journal on the Role of Metal Ions in Biology, Biochemistry, and Medicine·D S Auld
Jan 16, 2003·Nucleic Acids Research·S Sri KrishnaNick V Grishin
Jun 18, 2003·Cell·Reuben S HarrisMichael H Malim
Jul 16, 2003·Cell·Roberto MarianiNathaniel R Landau
Mar 20, 2004·Science·Priscilla TurelliDidier Trono
Apr 6, 2004·Methods in Enzymology·Carol A RohlDavid Baker
May 4, 2004·Nucleic Acids Research·Rodolphe SuspèneJean-Pierre Vartanian
Aug 7, 2004·Current Biology : CB·Kate N BishopMichael H Malim
Aug 19, 2004·The Biochemical Journal·Reynel CancioGiovanni Maga
Sep 18, 2004·Bioinformatics·Chin Lung Lu, Yen Pin Huang
Jan 13, 2005·Proteins·Zheng YuanRohan D Teasdale
Oct 4, 2005·Journal of Computational Chemistry·David A CaseRobert J Woods
Oct 21, 2005·Journal of Molecular Biology·S HenrietRoland Marquet
Nov 23, 2005·Bioinformatics·Konstantin ArnoldTorsten Schwede
Jan 13, 2006·Nucleic Acids Research·Hal P BogerdBryan R Cullen
Feb 24, 2006·Proceedings of the National Academy of Sciences of the United States of America·Keiko SakaiMichael J Lenardo
Apr 26, 2006·The Journal of Biological Chemistry·Andrew MehleDana Gabuzda
Nov 3, 2006·Gene·Amy E HulmeJohn V Moran
Nov 30, 2006·Proceedings of the National Academy of Sciences of the United States of America·Indrani PaulErnest L Maynard
Jan 24, 2007·Journal of Chemical Information and Modeling·Marwen NaïmEnrico O Purisima
May 8, 2007·Molecular Biology and Evolution·Ziheng Yang
Sep 15, 2007·Biochimica Et Biophysica Acta·Kirti PatelSusheel Durani
Sep 18, 2007·Journal of Molecular Biology·Zuoxiang XiaoXiao-Fang Yu
Mar 14, 2008·Current HIV Research·Pierre BarraudCarine Tisné
Apr 16, 2008·Annual Review of Biochemistry·Rhiju Das, David Baker
Jul 8, 2008·Microbes and Infection·Tomoki YamashitaMasako Nomaguchi
Jul 16, 2008·Journal of Molecular Biology·Zhiwen HeXiao-Fang Yu
Sep 16, 2008·Antiviral Research·Warner C GreeneTomas Cihlar
Feb 17, 2009·Protein Engineering, Design & Selection : PEDS·Tali H ReingewertzAssaf Friedler
Apr 21, 2009·Methods in Molecular Biology·Stéphane GuindonOlivier Gascuel
Apr 22, 2009·Biopolymers·Kalyan Giri, Ernest L Maynard
Jan 8, 2010·Protein Science : a Publication of the Protein Society·Chu WangDavid Baker
May 14, 2010·Journal of Virology·Leslie S WolfeYong Xiong
Nov 13, 2010·Proceedings of the National Academy of Sciences of the United States of America·Taisuke IzumiAkifumi Takaori-Kondo
Jul 19, 2011·Journal of Molecular Biology·Sean R MarcsisinJohn R Engen
Mar 16, 2012·Chemical Biology & Drug Design·Anderson H LimaCláudio Nahum Alves
Sep 4, 2012·Journal of Chemical Information and Modeling·Nelson Alberto N de AlencarVicent Moliner
Apr 13, 2013·BMC Infectious Diseases·Maria Clara BizinotoLuiz Mário Janini
Nov 15, 2013·Open Biology·Zhisheng LuMark R Sanderson
Oct 21, 2014·Metallomics : Integrated Biometal Science·A Gerard Daniel, Nicholas P Farrell


Apr 19, 2016·Database : the Journal of Biological Databases and Curation·Megan DruceTulio De Oliveira
Apr 27, 2017·AIDS Research and Human Retroviruses·Fabiola VillanovaÉlcio Leal
Sep 9, 2017·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Huan ChenYong-Tang Zheng
Jul 1, 2016·Microbiology and Molecular Biology Reviews : MMBR·Guangdi Li, Erik De Clercq

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