Modeling pH-Dependent NMR Chemical Shift Perturbations in Peptides.
Journal
Biophysical journal
ISSN: 1542-0086
Titre abrégé: Biophys J
Pays: United States
ID NLM: 0370626
Informations de publication
Date de publication:
23 07 2019
23 07 2019
Historique:
received:
20
12
2018
revised:
20
04
2019
accepted:
03
06
2019
pubmed:
1
7
2019
medline:
12
9
2020
entrez:
1
7
2019
Statut:
ppublish
Résumé
Modeling the pH dependence of protein and peptide chemical shifts outside the range of physiological values (6.5-7) is key to understanding structure-function relationships of these systems. These capabilities are largely not available in current chemical shift prediction software. In this study, we utilize a combination of molecular dynamics and quantum mechanics to investigate the through-space and through-bond contributions of protonation-dependent chemical shift perturbations (CSPs) in model tripeptides. By altering the protonation state of the titratable group in the tripeptides, we observe a notable difference in the conformational ensembles and attendantly compute significant CSPs for all nuclei near the site of protonation. We thus demonstrate the ability to recapitulate experimental pH-dependent CSPs with good agreement (R = 0.85, 0.99, and 0.98 for
Identifiants
pubmed: 31255294
pii: S0006-3495(19)30449-7
doi: 10.1016/j.bpj.2019.06.003
pmc: PMC6700603
pii:
doi:
Substances chimiques
Nitrogen Isotopes
0
Nitrogen-15
0
Peptides
0
Protons
0
Types de publication
Journal Article
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
258-268Informations de copyright
Copyright © 2019 Biophysical Society. Published by Elsevier Inc. All rights reserved.
Références
J Biomol NMR. 2000 Sep;18(1):43-8
pubmed: 11061227
J Biomol NMR. 2001 Dec;21(4):321-33
pubmed: 11824752
Biopolymers. 2002 Dec 15;65(6):408-23
pubmed: 12434429
J Am Chem Soc. 2002 Nov 27;124(47):14075-84
pubmed: 12440906
J Am Chem Soc. 2003 Aug 13;125(32):9556-7
pubmed: 12903999
J Comput Chem. 2003 Nov 15;24(14):1691-702
pubmed: 12964188
J Am Chem Soc. 2004 Apr 14;126(14):4726-34
pubmed: 15070392
J Mol Graph Model. 2004 May;22(5):377-95
pubmed: 15099834
J Magn Reson. 2005 Apr;173(2):193-207
pubmed: 15780912
Biophys J. 2006 Feb 15;90(4):L36-8
pubmed: 16361340
Proc Natl Acad Sci U S A. 2007 Jun 5;104(23):9615-20
pubmed: 17535901
Proteins. 2008 Jul;72(1):333-43
pubmed: 18214953
J Biomol NMR. 2008 Mar;40(3):153-5
pubmed: 18288446
Proc Natl Acad Sci U S A. 2008 Aug 26;105(34):12259-64
pubmed: 18713857
Proc Natl Acad Sci U S A. 2008 Sep 23;105(38):14389-94
pubmed: 18787110
J Mol Biol. 1991 Nov 20;222(2):311-33
pubmed: 1960729
J Am Chem Soc. 2009 Oct 7;131(39):13894-5
pubmed: 19739624
Proc Natl Acad Sci U S A. 2009 Oct 6;106(40):16972-7
pubmed: 19805131
Proteins. 2010 Mar;78(4):843-57
pubmed: 19899070
Chem Soc Rev. 2010 Feb;39(2):578-90
pubmed: 20111782
J Biomol NMR. 2010 Sep;48(1):13-22
pubmed: 20628786
Prog Nucl Magn Reson Spectrosc. 2011 Feb;58(1-2):62-87
pubmed: 21241884
J Biomol NMR. 2011 May;50(1):43-57
pubmed: 21448735
J Biomol NMR. 2013 Feb;55(2):201-9
pubmed: 23297019
J Chem Theory Comput. 2012 Sep 11;8(9):3257-3273
pubmed: 23341755
J Comput Chem. 2013 Sep 30;34(25):2135-45
pubmed: 23832629
J Biomol NMR. 2014 Nov;60(2-3):109-29
pubmed: 25239571
J Phys Chem B. 2014 Oct 23;118(42):12168-75
pubmed: 25255209
Annu Rev Biophys. 2015;44:53-75
pubmed: 25747592
J Chem Theory Comput. 2014 Jan 14;10(1):122-33
pubmed: 26579896
J Chem Theory Comput. 2013 Apr 9;9(4):2104-14
pubmed: 26583557
J Chem Theory Comput. 2012 Apr 10;8(4):1480-92
pubmed: 26596758
J Chem Theory Comput. 2012 Nov 13;8(11):4818-27
pubmed: 26605634
PeerJ. 2015 Oct 20;3:e1344
pubmed: 26623185
Protein Eng Des Sel. 2016 Jul;29(7):271-80
pubmed: 27284086
Biochemistry. 1986 Nov 18;25(23):7751-9
pubmed: 3542033
Biopolymers. 1968;6(9):1255-62
pubmed: 5669465
Biochemistry. 1993 Jan 19;32(2):412-20
pubmed: 8422350
Science. 1993 Jun 4;260(5113):1491-6
pubmed: 8502992