Dynamozones are the most obvious sign of the evolution of conformational dynamics in HIV-1 protease.
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
30 08 2023
30 08 2023
Historique:
received:
21
02
2023
accepted:
17
08
2023
medline:
1
9
2023
pubmed:
31
8
2023
entrez:
30
8
2023
Statut:
epublish
Résumé
Proteins are not static but are flexible molecules that can adopt many different conformations. The HIV-1 protease is an important target for the development of therapies to treat AIDS, due to its critical role in the viral life cycle. We investigated several dynamics studies on the HIV-1 protease families to illustrate the significance of examining the dynamic behaviors and molecular motions for an entire understanding of their dynamics-structure-function relationships. Using computer simulations and principal component analysis approaches, the dynamics data obtained revealed that: (i) The flap regions are the most obvious sign of the evolution of conformational dynamics in HIV-1 protease; (ii) There are dynamic structural regions in some proteins that contribute to the biological function and allostery of proteins via appropriate flexibility. These regions are a clear sign of the evolution of conformational dynamics of proteins, which we call dynamozones. The flap regions are one of the most important dynamozones members that are critical for HIV-1 protease function. Due to the existence of other members of dynamozones in different proteins, we propose to consider dynamozones as a footprint of the evolution of the conformational dynamics of proteins.
Identifiants
pubmed: 37648682
doi: 10.1038/s41598-023-40818-x
pii: 10.1038/s41598-023-40818-x
pmc: PMC10469195
doi:
Substances chimiques
p16 protease, Human immunodeficiency virus 1
EC 3.4.23.-
HIV Protease
EC 3.4.23.-
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
14179Informations de copyright
© 2023. Springer Nature Limited.
Références
J Phys Chem B. 2012 Feb 16;116(6):1884-900
pubmed: 22239286
Methods Mol Biol. 2015;1215:253-87
pubmed: 25330967
Biophys J. 2010 Mar 3;98(5):861-71
pubmed: 20197040
J Chem Theory Comput. 2011 Aug 9;7(8):2348-52
pubmed: 26606609
Nature. 1989 Feb 16;337(6208):615-20
pubmed: 2645523
Biochemistry. 2014 Feb 25;53(7):1134-45
pubmed: 24498949
PLoS Comput Biol. 2011 May;7(5):e1002056
pubmed: 21637798
Nucleic Acids Res. 2008 Oct;36(17):5645-51
pubmed: 18765473
Adv Immunol. 1990;48:1-40
pubmed: 2190448
J Biomol Struct Dyn. 2016 May;34(5):1008-19
pubmed: 26208540
Biophys J. 2006 Aug 1;91(3):948-56
pubmed: 16698773
J Am Chem Soc. 2013 Jul 3;135(26):9648-51
pubmed: 23782151
Nat Struct Biol. 1997 Jan;4(1):10-9
pubmed: 8989315
Annu Rev Biophys Biomol Struct. 1998;27:249-84
pubmed: 9646869
Biochem Biophys Rep. 2015 Dec 04;5:180-190
pubmed: 28955822
J Am Chem Soc. 2008 Jun 11;130(23):7184-5
pubmed: 18479129
Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 2000 Dec;62(6 Pt B):8438-48
pubmed: 11138145
Science. 2009 Apr 10;324(5924):203-7
pubmed: 19359577
Biochemistry. 2013 Jul 9;52(27):4605-19
pubmed: 23758161
Biophys J. 1993 Jan;64(1):9-15
pubmed: 8431552
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W522-5
pubmed: 17488841
Proc Natl Acad Sci U S A. 1990 Nov;87(22):8864-8
pubmed: 2247458
J Mol Biol. 2000 Sep 8;302(1):205-17
pubmed: 10964570
Biochemistry. 2009 Jun 2;48(21):4548-56
pubmed: 19348462
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W299-302
pubmed: 15980475
Nucleic Acids Res. 2000 Jan 1;28(1):235-42
pubmed: 10592235
J Am Chem Soc. 2007 Feb 7;129(5):1312-20
pubmed: 17263415
Science. 1990 Sep 21;249(4975):1425-8
pubmed: 2402636
Mol Biosyst. 2015 Apr;11(4):1061-6
pubmed: 25630418
Proteins. 1993 Dec;17(4):412-25
pubmed: 8108382
J Biol Chem. 2005 Jan 21;280(3):2324-30
pubmed: 15520005
Mol Biosyst. 2014 Apr;10(4):891-900
pubmed: 24503740
Sci Rep. 2018 Jan 17;8(1):903
pubmed: 29343701
Biochem Biophys Res Commun. 2007 May 18;356(4):1011-6
pubmed: 17408595
J Mol Biol. 1993 Nov 20;234(2):357-72
pubmed: 8230220
Bioinformatics. 2006 Nov 1;22(21):2695-6
pubmed: 16940322
EMBO J. 1986 Apr;5(4):823-6
pubmed: 3709526
PLoS One. 2012;7(7):e40786
pubmed: 22815819
Curr Opin Struct Biol. 1994 Dec;4(6):893-901
pubmed: 7712293
Phys Chem Chem Phys. 2010 Mar 28;12(12):2850-9
pubmed: 20449375
Protein Sci. 2010 Nov;19(11):2122-30
pubmed: 20812327
J Mol Biol. 2001 Jun 15;309(4):937-47
pubmed: 11399070
Phys Chem Chem Phys. 2013 Jan 28;15(4):1241-51
pubmed: 23229122
Cell Mol Life Sci. 2005 Nov;62(22):2531-9
pubmed: 16261257
J Mol Biol. 2002 Jan 11;315(2):131-40
pubmed: 11779234
Biochim Biophys Acta. 2000 Mar 7;1477(1-2):189-214
pubmed: 10708858
Curr Opin Chem Biol. 2006 Oct;10(5):498-508
pubmed: 16939713
Nat Struct Biol. 2002 Sep;9(9):646-52
pubmed: 12198485
J Biol Chem. 2013 Dec 13;288(50):35961-8
pubmed: 24158440
Curr Opin Struct Biol. 2010 Apr;20(2):142-7
pubmed: 20060708
Protein Sci. 2002 Feb;11(2):221-32
pubmed: 11790832
J Comput Biol. 2011 Aug;18(8):997-1005
pubmed: 21702691
J Chem Theory Comput. 2013 Nov 12;9(11):5127-5147
pubmed: 24250278
Bioessays. 2014 Feb;36(2):209-18
pubmed: 24272815
Cell. 2002 May 3;109(3):275-82
pubmed: 12015977
Proc Natl Acad Sci U S A. 2012 Dec 11;109(50):20449-54
pubmed: 23184967
Chem Rev. 2011 Dec 14;111(12):7595-624
pubmed: 21923192
J Chem Inf Model. 2014 Jul 28;54(7):2033-41
pubmed: 24954406
J Mol Biol. 1980 Jan 25;136(3):225-70
pubmed: 7373651
Biochemistry. 2003 Apr 8;42(13):3674-87
pubmed: 12667057
Biomacromolecules. 2008 Nov;9(11):3057-64
pubmed: 18828631
J Biomol Struct Dyn. 2021 Apr;39(7):2607-2616
pubmed: 32238094
J Mol Model. 2015 Sep;21(9):228
pubmed: 26267297
Annu Rev Med. 2002;53:595-614
pubmed: 11818491
PLoS Comput Biol. 2014 Oct 09;10(10):e1003863
pubmed: 25299346
Proteins. 2006 Nov 15;65(3):712-25
pubmed: 16981200
Proteins. 2010 May 15;78(7):1691-704
pubmed: 20143318
Proteins. 1991;11(3):205-17
pubmed: 1749773
J Mol Graph Model. 2006 May;24(6):465-74
pubmed: 16188477
Mol Cell. 2009 Jun 26;34(6):674-85
pubmed: 19560420
J Mol Biol. 2009 Jan 9;385(1):312-29
pubmed: 18952103
Trends Biochem Sci. 2003 Jul;28(7):361-8
pubmed: 12878003
EMBO J. 2000 Mar 1;19(5):979-88
pubmed: 10698939
Methods Mol Biol. 2008;443:89-106
pubmed: 18446283
Proc Natl Acad Sci U S A. 2009 Jan 6;106(1):139-44
pubmed: 19109437
Proc Natl Acad Sci U S A. 2005 May 10;102(19):6679-85
pubmed: 15870208
Proc Natl Acad Sci U S A. 2006 Jan 24;103(4):915-20
pubmed: 16418268
J Mol Biol. 1994 Feb 11;236(1):300-9
pubmed: 8107111
Cell. 2001 Apr 6;105(1):115-26
pubmed: 11301007
Annu Rev Biophys. 2020 May 6;49:267-288
pubmed: 32075411
Biochemistry. 2006 May 30;45(21):6606-14
pubmed: 16716071
J Chem Phys. 2007 Jan 7;126(1):014101
pubmed: 17212484
Phys Rev Lett. 2021 Aug 27;127(9):098103
pubmed: 34506164
Proc Natl Acad Sci U S A. 1974 Jul;71(7):2848-52
pubmed: 4527913
Protein Pept Lett. 2002 Oct;9(5):367-77
pubmed: 12370024
Proteins. 2005 Dec 1;61(4):704-21
pubmed: 16231289
Biophys J. 2008 Jul;95(1):296-311
pubmed: 18375510
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W320-4
pubmed: 24753421
Nat Struct Biol. 1995 Apr;2(4):274-80
pubmed: 7796263
Adv Pharmacol. 2007;55:261-98
pubmed: 17586318
Protein Sci. 2004 Apr;13(4):1108-23
pubmed: 15044738
Biochemistry. 2013 Feb 5;52(5):912-25
pubmed: 23298222