Literature DB >> 32178519

Reconciling NMR Structures of the HIV-1 Nucleocapsid Protein NCp7 Using Extensive Polarizable Force Field Free-Energy Simulations.

Léa El Khoury1,2, Frédéric Célerse1,3, Louis Lagardère4,5, Luc-Henri Jolly4, Etienne Derat3, Zeina Hobaika2, Richard G Maroun2, Pengyu Ren6, Serge Bouaziz7, Nohad Gresh1, Jean-Philip Piquemal1,6,8.   

Abstract

Using polarizable (AMOEBA) and nonpolarizable (CHARMM) force fields, we compare the relative free energy stability of two extreme conformations of the HIV-1 nucleocapsid protein NCp7 that had been previously experimentally advocated to prevail in solution. Using accelerated sampling techniques, we show that they differ in stability by no more than 0.75-1.9 kcal/mol depending on the reference protein sequence. While the extended form appears to be the most probable structure, both forms should thus coexist in water explaining the differing NMR findings.

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Year:  2020        PMID： 32178519      PMCID： PMC7375347          DOI： 10.1021/acs.jctc.9b01204

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN： 1549-9618            Impact factor:   6.006


  50 in total

1.  Time-reversible always stable predictor-corrector method for molecular dynamics of polarizable molecules.

Authors:  Jirí Kolafa
Journal:  J Comput Chem       Date:  2004-02       Impact factor: 3.376

2.  Synthesis and biological properties of novel pyridinioalkanoyl thiolesters (PATE) as anti-HIV-1 agents that target the viral nucleocapsid protein zinc fingers.

Authors:  J A Turpin; Y Song; J K Inman; M Huang; A Wallqvist; A Maynard; D G Covell; W G Rice; E Appella
Journal:  J Med Chem       Date:  1999-01-14       Impact factor: 7.446

3.  The zinc fingers of HIV nucleocapsid protein NCp7 direct interactions with the viral regulatory protein Vpr.

Authors:  H de Rocquigny; P Petitjean; V Tanchou; D Decimo; L Drouot; T Delaunay; J L Darlix; B P Roques
Journal:  J Biol Chem       Date:  1997-12-05       Impact factor: 5.157

4.  Tinker 8: Software Tools for Molecular Design.

Authors:  Joshua A Rackers; Zhi Wang; Chao Lu; Marie L Laury; Louis Lagardère; Michael J Schnieders; Jean-Philip Piquemal; Pengyu Ren; Jay W Ponder
Journal:  J Chem Theory Comput       Date:  2018-09-19       Impact factor: 6.006

5.  Adherence to nonnucleoside reverse transcriptase inhibitor-based HIV therapy and virologic outcomes.

Authors:  Jean B Nachega; Michael Hislop; David W Dowdy; Richard E Chaisson; Leon Regensberg; Gary Maartens
Journal:  Ann Intern Med       Date:  2007-04-17       Impact factor: 25.391

6.  Dynamical behavior of the HIV-1 nucleocapsid protein.

Authors:  B M Lee; R N De Guzman; B G Turner; N Tjandra; M F Summers
Journal:  J Mol Biol       Date:  1998-06-12       Impact factor: 5.469

7.  1H NMR structure and biological studies of the His23-->Cys mutant nucleocapsid protein of HIV-1 indicate that the conformation of the first zinc finger is critical for virus infectivity.

Authors:  H Déméné; C Z Dong; M Ottmann; M C Rouyez; N Jullian; N Morellet; Y Mely; J L Darlix; M C Fournié-Zaluski; S Saragosti
Journal:  Biochemistry       Date:  1994-10-04       Impact factor: 3.162

8.  How the HIV-1 nucleocapsid protein binds and destabilises the (-)primer binding site during reverse transcription.

Authors:  Sarah Bourbigot; Nick Ramalanjaona; Christian Boudier; Gilmar F J Salgado; Bernard P Roques; Yves Mély; Serge Bouaziz; Nelly Morellet
Journal:  J Mol Biol       Date:  2008-08-26       Impact factor: 5.469

9.  All-atom empirical potential for molecular modeling and dynamics studies of proteins.

Authors:  A D MacKerell; D Bashford; M Bellott; R L Dunbrack; J D Evanseck; M J Field; S Fischer; J Gao; H Guo; S Ha; D Joseph-McCarthy; L Kuchnir; K Kuczera; F T Lau; C Mattos; S Michnick; T Ngo; D T Nguyen; B Prodhom; W E Reiher; B Roux; M Schlenkrich; J C Smith; R Stote; J Straub; M Watanabe; J Wiórkiewicz-Kuczera; D Yin; M Karplus
Journal:  J Phys Chem B       Date:  1998-04-30       Impact factor: 2.991

10.  Small finger protein of avian and murine retroviruses has nucleic acid annealing activity and positions the replication primer tRNA onto genomic RNA.

Authors:  A C Prats; L Sarih; C Gabus; S Litvak; G Keith; J L Darlix
Journal:  EMBO J       Date:  1988-06       Impact factor: 11.598
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  2 in total

1.  High-resolution mining of the SARS-CoV-2 main protease conformational space: supercomputer-driven unsupervised adaptive sampling.

Authors:  Théo Jaffrelot Inizan; Frédéric Célerse; Olivier Adjoua; Dina El Ahdab; Luc-Henri Jolly; Chengwen Liu; Pengyu Ren; Matthieu Montes; Nathalie Lagarde; Louis Lagardère; Pierre Monmarché; Jean-Philip Piquemal
Journal:  Chem Sci       Date:  2021-02-02       Impact factor: 9.825

Review 2.  Overview of the Nucleic-Acid Binding Properties of the HIV-1 Nucleocapsid Protein in Its Different Maturation States.

Authors:  Assia Mouhand; Marco Pasi; Marjorie Catala; Loussiné Zargarian; Anissa Belfetmi; Pierre Barraud; Olivier Mauffret; Carine Tisné
Journal:  Viruses       Date:  2020-09-29       Impact factor: 5.048
  2 in total

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