Prediction and Validation of a Protein's Free Energy Surface Using Hydrogen Exchange and (Importantly) Its Denaturant Dependence.
Journal
Journal of chemical theory and computation
ISSN: 1549-9626
Titre abrégé: J Chem Theory Comput
Pays: United States
ID NLM: 101232704
Informations de publication
Date de publication:
11 Jan 2022
11 Jan 2022
Historique:
pubmed:
23
12
2021
medline:
7
4
2022
entrez:
22
12
2021
Statut:
ppublish
Résumé
The denaturant dependence of hydrogen-deuterium exchange (HDX) is a powerful measurement to identify the breaking of individual H-bonds and map the free energy surface (FES) of a protein including the very rare states. Molecular dynamics (MD) can identify each partial unfolding event with atomic-level resolution. Hence, their combination provides a great opportunity to test the accuracy of simulations and to verify the interpretation of HDX data. For this comparison, we use
Identifiants
pubmed: 34936354
doi: 10.1021/acs.jctc.1c00960
pmc: PMC8757463
doi:
Substances chimiques
Proteins
0
Hydrogen
7YNJ3PO35Z
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
550-561Subventions
Organisme : NIGMS NIH HHS
ID : R01 GM055694
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM130122
Pays : United States
Organisme : NIGMS NIH HHS
ID : R29 GM055694
Pays : United States
Références
Science. 1995 Jul 14;269(5221):192-7
pubmed: 7618079
Biochemistry. 2002 Oct 15;41(41):12308-12
pubmed: 12369818
Proc Natl Acad Sci U S A. 2016 Apr 26;113(17):4747-52
pubmed: 27078098
Proc Natl Acad Sci U S A. 1999 Nov 23;96(24):13674-8
pubmed: 10570131
PLoS Comput Biol. 2018 Dec 27;14(12):e1006342
pubmed: 30589846
Biochemistry. 1998 Jan 27;37(4):1067-75
pubmed: 9454598
Biochemistry. 2000 Sep 26;39(38):11696-701
pubmed: 10995237
Science. 2017 Jul 14;357(6347):168-175
pubmed: 28706065
J Mol Biol. 2000 Aug 11;301(2):247-56
pubmed: 10926507
Phys Rev Lett. 1986 Nov 24;57(21):2607-2609
pubmed: 10033814
J Mol Biol. 2010 Apr 2;397(3):777-88
pubmed: 20144618
Proc Natl Acad Sci U S A. 2018 May 22;115(21):E4758-E4766
pubmed: 29735687
Proc Natl Acad Sci U S A. 2013 May 7;110(19):7684-9
pubmed: 23603271
Proc Natl Acad Sci U S A. 2015 Aug 18;112(33):10383-8
pubmed: 26195754
Biophys Chem. 2012 Apr;163-164:21-34
pubmed: 22425325
J Am Soc Mass Spectrom. 2019 Jan;30(1):67-76
pubmed: 30338451
Protein Sci. 2007 Nov;16(11):2378-90
pubmed: 17962401
Protein Sci. 1995 Oct;4(10):2138-48
pubmed: 8535251
J Mol Biol. 1996 Oct 11;262(5):756-72
pubmed: 8876652
Nat Struct Biol. 1996 Sep;3(9):782-7
pubmed: 8784352
Structure. 2006 Jan;14(1):97-106
pubmed: 16407069
Anal Chem. 2014 Oct 21;86(20):10303-10
pubmed: 25207790
Proteins. 2004 Dec 1;57(4):702-10
pubmed: 15476259
Front Mol Biosci. 2017 Mar 10;4:13
pubmed: 28344973
Nat Struct Biol. 1999 Oct;6(10):910-2
pubmed: 10504722
Proc Natl Acad Sci U S A. 1998 Feb 17;95(4):1562-7
pubmed: 9465055
Methods Mol Biol. 2007;350:69-81
pubmed: 16957318
J Phys Chem B. 2018 Oct 11;122(40):9314-9323
pubmed: 30222348
Biochemistry. 2008 Jun 10;47(23):6178-88
pubmed: 18479148
PLoS Comput Biol. 2018 Dec 27;14(12):e1006578
pubmed: 30589834
Proc Natl Acad Sci U S A. 2007 Sep 25;104(39):15317-22
pubmed: 17878304
Proteins. 1999 Aug 1;36(2):175-91
pubmed: 10398365
Proteins. 1993 Sep;17(1):75-86
pubmed: 8234246
Science. 1993 Nov 5;262(5135):873-6
pubmed: 8235609
Proc Natl Acad Sci U S A. 2009 Feb 24;106(8):2595-600
pubmed: 19196963
J Am Soc Mass Spectrom. 2012 Jan;23(1):43-56
pubmed: 22012689
J Chem Theory Comput. 2014 Nov 11;10(11):5113-5124
pubmed: 25400522
Proc Natl Acad Sci U S A. 2014 Nov 11;111(45):15975-80
pubmed: 25349413
Biophys J. 2019 Jan 8;116(1):49-56
pubmed: 30558884
Biophys J. 2020 Apr 7;118(7):1649-1664
pubmed: 32105651
J Chem Phys. 2008 Sep 28;129(12):124105
pubmed: 19045004
Curr Opin Pharmacol. 2010 Dec;10(6):709-14
pubmed: 20951644
Methods Enzymol. 1995;259:344-56
pubmed: 8538461
J Am Chem Soc. 2003 Dec 24;125(51):15686-7
pubmed: 14677926
J Mol Biol. 2007 Jan 19;365(3):881-91
pubmed: 17097105
J Mol Biol. 2001 Jan 19;305(3):593-602
pubmed: 11152615
Protein Sci. 2012 Jul;21(7):987-95
pubmed: 22544567
J Am Chem Soc. 2011 Nov 2;133(43):17463-72
pubmed: 21913704