Role of Mutations in Differential Recognition of Viral RNA Molecules by Peptides.

HIV-1 / genetics Humans Mutation Peptides / chemistry RNA, Viral / metabolism Virus Replication rev Gene Products, Human Immunodeficiency Virus / genetics

Journal

Journal of chemical information and modeling
ISSN: 1549-960X
Titre abrégé: J Chem Inf Model
Pays: United States
ID NLM: 101230060

Informations de publication

Date de publication:
25 07 2022
Historique:
pubmed: 15 7 2022
medline: 27 7 2022
entrez: 14 7 2022
Statut: ppublish

Résumé

The conserved noncoding RNA elements in viral genomes interact with proteins to regulate various events during viral replication. We report studies on the recognition mechanisms of two helical peptides, namely, a native (Rev) peptide and a lab-evolved (RSG1.2) peptide, by a highly conserved viral RNA element from the human immunodeficiency virus 1 genome. Specifically, we investigated the physical interactions between the viral RNA molecule and helical peptides by computing free energy changes on mutating key amino acid residues involved in recognition of an internal loop in the viral RNA molecule.

Identifiants

DOI: 10.1021/acs.jcim.2c00376 PMID: 35833626 PMC: PMC10129845
pubmed: 35833626
doi: 10.1021/acs.jcim.2c00376
pmc: PMC10129845
mid: NIHMS1888922
doi:

Substances chimiques

Peptides 0
RNA, Viral 0
rev Gene Products, Human Immunodeficiency Virus 0

Types de publication

Journal Article Research Support, U.S. Gov't, Non-P.H.S. Research Support, N.I.H., Extramural

Langues

eng

Sous-ensembles de citation

IM

Pagination

3381-3390

Subventions

Organisme : NIGMS NIH HHS
ID : R35 GM138217
Pays : United States

Références

PLoS One. 2011;6(8):e23300
pubmed: 21853108
J Chem Theory Comput. 2013 Jul 9;9(7):3084-95
pubmed: 26583988
Curr Opin Struct Biol. 2008 Jun;18(3):290-8
pubmed: 18515081
Proc Natl Acad Sci U S A. 1997 Oct 28;94(22):11887-92
pubmed: 9342332
Proc Natl Acad Sci U S A. 1991 Feb 1;88(3):683-7
pubmed: 1992459
J Mol Biol. 2009 Sep 25;392(3):774-86
pubmed: 19631217
Cell. 1990 Feb 23;60(4):675-83
pubmed: 2406030
Biochemistry. 2001 Jul 10;40(27):7947-56
pubmed: 11434763
Biochemistry. 1994 Mar 15;33(10):2741-7
pubmed: 8130185
Phys Chem Chem Phys. 2021 Nov 10;23(43):24773-24779
pubmed: 34714308
Nucleic Acids Res. 1999 Nov 1;27(21):4128-34
pubmed: 10518602
Biochimie. 2007 Nov;89(11):1291-303
pubmed: 17825469
Virology. 2018 Jan 15;514:1-8
pubmed: 29128752
Nucleic Acids Res. 2018 Jul 27;46(13):6401-6415
pubmed: 29961805
Nat Commun. 2020 Jun 19;11(1):3137
pubmed: 32561731
Science. 1996 Sep 13;273(5281):1547-51
pubmed: 8703216
J Mol Graph. 1996 Feb;14(1):33-8, 27-8
pubmed: 8744570
Nat Struct Mol Biol. 2016 May;23(5):426-33
pubmed: 27065196
Nucleic Acids Res. 2001 Feb 15;29(4):943-54
pubmed: 11160927
Retrovirology. 2018 Dec 22;15(1):79
pubmed: 30577804
Mol Cell. 2020 Apr 2;78(1):9-29
pubmed: 32243832
Nucleic Acids Symp Ser. 1995;(33):46-8
pubmed: 8643394
Phys Chem Chem Phys. 2018 Mar 28;20(13):8432-8449
pubmed: 29547221
RNA Biol. 2013 Apr;10(4):540-52
pubmed: 23535706
J Mol Biol. 1996 Dec 20;264(5):863-77
pubmed: 9000617
Nat Struct Biol. 2001 Feb;8(2):146-50
pubmed: 11175904
J Chem Theory Comput. 2012 Aug 14;8(8):2606-16
pubmed: 26592106
J Chem Theory Comput. 2016 Jan 12;12(1):430-43
pubmed: 26632962
Annu Rev Microbiol. 2006;60:211-30
pubmed: 16712436
J Comput Chem. 2005 Dec;26(16):1781-802
pubmed: 16222654
Nature. 1985 Jul 11-17;316(6024):170-4
pubmed: 4010788
J Mol Biol. 1994 Aug 12;241(2):193-207
pubmed: 8057359
Cell. 1996 Oct 4;87(1):115-25
pubmed: 8858154
Virology. 1987 Apr;157(2):414-20
pubmed: 2881398
J Chem Phys. 2020 Jul 28;153(4):044130
pubmed: 32752662
Annu Rev Biophys Biomol Struct. 2005;34:379-98
pubmed: 15869395
Methods Enzymol. 2019;623:339-372
pubmed: 31239053
Nucleic Acids Res. 2019 Feb 20;47(3):1523-1531
pubmed: 30481318
Curr Opin Struct Biol. 2000 Jun;10(3):332-40
pubmed: 10851193
Int Rev Immunol. 2010 Dec;29(6):533-56
pubmed: 20923332
J Chem Theory Comput. 2007 Nov;3(6):2312-34
pubmed: 26636222
Nucleic Acids Res. 2000 Dec 15;28(24):4944-55
pubmed: 11121486
Science. 1990 Feb 16;247(4944):845-8
pubmed: 2406903
RNA. 2020 Aug;26(8):937-959
pubmed: 32398273
Mol Ther Nucleic Acids. 2020 Mar 6;19:627-642
pubmed: 31945726
J Biol Chem. 2020 Dec 4;295(49):16470-16486
pubmed: 33051202
J Chem Inf Model. 2019 Apr 22;59(4):1497-1507
pubmed: 30789733
PLoS Biol. 2005 Jan;3(1):e5
pubmed: 15630477
Nature. 2009 Aug 6;460(7256):711-6
pubmed: 19661910
Biophys J. 2021 Nov 16;120(22):5060-5073
pubmed: 34710377
J Comput Chem. 2013 Sep 30;34(25):2135-45
pubmed: 23832629
Proteins. 2005 Dec 1;61(4):704-21
pubmed: 16231289
Nature. 2005 Aug 18;436(7053):933-8
pubmed: 16107832

Auteurs

Amit Kumar (A)

Department of Chemical Engineering, University of New Hampshire, Durham 03824, New Hampshire, United States.

Harish Vashisth (H)

Department of Chemical Engineering, University of New Hampshire, Durham 03824, New Hampshire, United States.
ORCID: 0000-0002-2087-2880

Articles similaires

[Redispensing of expensive oral anticancer medicines: a practical application].

Lisanne N van Merendonk, Kübra Akgöl, Bastiaan Nuijen
1.00
Humans Antineoplastic Agents Administration, Oral Drug Costs Counterfeit Drugs

Smoking Cessation and Incident Cardiovascular Disease.

Jun Hwan Cho, Seung Yong Shin, Hoseob Kim et al.
1.00
Humans Male Smoking Cessation Cardiovascular Diseases Female

Evaluation of Low-Value Services Across Major Medicare Advantage Insurers and Traditional Medicare.

Ciara Duggan, Adam L Beckman, Ishani Ganguli et al.
1.00
Humans United States Aged Cross-Sectional Studies Medicare Part C

Effectiveness of Virtual Yoga for Chronic Low Back Pain: A Randomized Clinical Trial.

Hallie Tankha, Devyn Gaskins, Amanda Shallcross et al.
1.00
Humans Yoga Low Back Pain Female Male

Classifications MeSH

questionsmedicales.fr › Virus › Virus à ARN › Retroviridae › Lentivirus › Lentivirus des primates › VIH (Virus de l'Immunodéficience Humaine) › VIH-1 (Virus de l'Immunodéficience Humaine de type 1) › Role of Mutations in Differential Recognition...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › Role of Mutations in Differential Recognition...
questionsmedicales.fr › Phénomènes génétiques › Variation génétique › Mutation › Role of Mutations in Differential Recognition...
questionsmedicales.fr › Acides aminés, peptides et protéines › Peptides › Role of Mutations in Differential Recognition...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ARN › ARN viral › Role of Mutations in Differential Recognition...
questionsmedicales.fr › Phénomènes microbiologiques › Phénomènes physiologiques viraux › Réplication virale › Role of Mutations in Differential Recognition...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Protéines virales › Protéines virales régulatrices ou accessoires › Transactivateurs › Produits du gène rev › Produits du gène rev du virus de l'immunodéficience humaine › Role of Mutations in Differential Recognition...