Developing similarity matrices for antibody-protein binding interactions.
Journal
PloS one
ISSN: 1932-6203
Titre abrégé: PLoS One
Pays: United States
ID NLM: 101285081
Informations de publication
Date de publication:
2023
2023
Historique:
received:
16
05
2023
accepted:
17
10
2023
medline:
30
10
2023
pubmed:
26
10
2023
entrez:
26
10
2023
Statut:
epublish
Résumé
The inventions of AlphaFold and RoseTTAFold are revolutionizing computational protein science due to their abilities to reliably predict protein structures. Their unprecedented successes are due to the parallel consideration of several types of information, one of which is protein sequence similarity information. Sequence homology has been studied for many decades and depends on similarity matrices to define how similar or different protein sequences are to one another. A natural extension of predicting protein structures is predicting the interactions between proteins, but similarity matrices for protein-protein interactions do not exist. This study conducted a mutational analysis of 384 non-redundant antibody-protein antigen complexes to calculate antibody-protein interaction similarity matrices. Every important residue in each antibody and each antigen was mutated to each of the other 19 commonly occurring amino acids and the percentage changes in interaction energies were calculated using three force fields: CHARMM, Amber, and Rosetta. The data were used to construct six interaction similarity matrices, one for antibodies and another for antigens using each force field. The matrices exhibited both commonalities, such as mutations of aromatic and charged residues being the most detrimental, and differences, such as Rosetta predicting mutations of serines to be better tolerated than either Amber or CHARMM. A comparison to nine previously published similarity matrices for protein sequences revealed that the new interaction matrices are more similar to one another than they are to any of the previous matrices. The created similarity matrices can be used in force field specific applications to help guide decisions regarding mutations in protein-protein binding interfaces.
Identifiants
pubmed: 37883504
doi: 10.1371/journal.pone.0293606
pii: PONE-D-23-14979
pmc: PMC10602319
doi:
Substances chimiques
Amber
0
Proteins
0
Amino Acids
0
Antigen-Antibody Complex
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
e0293606Subventions
Organisme : NIGMS NIH HHS
ID : R35 GM138220
Pays : United States
Informations de copyright
Copyright: © 2023 Islam, Pantazes. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist.
Références
Protein Sci. 2000 Aug;9(8):1576-88
pubmed: 10975579
Science. 2021 Aug 20;373(6557):871-876
pubmed: 34282049
Protein Sci. 2022 Jun;31(6):e4353
pubmed: 35634782
J Mol Biol. 2014 Nov 11;426(22):3729-3743
pubmed: 25174334
Proteins. 2003 Nov 1;53(2):201-19
pubmed: 14517972
Crit Care. 2002 Feb;6(1):66-71
pubmed: 11940268
PLoS One. 2023 Mar 16;18(3):e0282689
pubmed: 36928239
J Mol Biol. 1997 Apr 25;268(1):209-25
pubmed: 9149153
Proteins. 2013 Nov;81(11):1980-7
pubmed: 23843247
Proc Natl Acad Sci U S A. 1992 Nov 15;89(22):10915-9
pubmed: 1438297
Bioinformatics. 2016 Aug 15;32(16):2451-6
pubmed: 27153634
Biochemistry. 1990 Aug 7;29(31):7133-55
pubmed: 2207096
Proteins. 2001 May 1;43(2):89-102
pubmed: 11276079
Protein Sci. 2011 Apr;20(4):753-7
pubmed: 21432939
Methods. 2016 Nov 1;110:73-80
pubmed: 27346249
J Comput Chem. 2008 Apr 15;29(5):701-15
pubmed: 17918282
Biochim Biophys Acta. 2012 Mar;1824(3):520-32
pubmed: 22246133
Protein Sci. 1997 Aug;6(8):1661-81
pubmed: 9260279
Bioinformatics. 2019 Feb 1;35(3):462-469
pubmed: 30020414
Protein Eng Des Sel. 2011 Sep;24(9):635-48
pubmed: 21676899
Curr Opin Chem Biol. 2004 Feb;8(1):91-7
pubmed: 15036162
Science. 2009 Apr 10;324(5924):203-7
pubmed: 19359577
Mol Biol Evol. 2002 Jan;19(1):8-13
pubmed: 11752185
Annu Int Conf IEEE Eng Med Biol Soc. 2008;2008:1347-50
pubmed: 19162917
J Chem Theory Comput. 2015 Aug 11;11(8):3696-713
pubmed: 26574453
J Chem Theory Comput. 2014 Apr 8;10(4):1770-1780
pubmed: 24803870
Bioinformatics. 2017 Oct 01;33(19):2971-2976
pubmed: 28633399
J Mol Biol. 1999 Feb 5;285(5):2177-98
pubmed: 9925793
BMC Bioinformatics. 2006 May 05;7:246
pubmed: 16677385
Protein Eng. 1993 Apr;6(3):267-78
pubmed: 8506261
Nucleic Acids Res. 2013 Jul;41(Web Server issue):W333-9
pubmed: 23723246
Curr Med Chem. 2009;16(8):953-64
pubmed: 19275605
Curr Opin Struct Biol. 2004 Jun;14(3):313-24
pubmed: 15193311
Proteins. 2005 Aug 15;60(3):353-66
pubmed: 15906321
Proteins. 2002 Sep 1;48(4):605-10
pubmed: 12211027
Nature. 2021 Aug;596(7873):583-589
pubmed: 34265844
J Chem Inf Model. 2017 Jan 23;57(1):60-72
pubmed: 27936711
J Comput Chem. 2009 Jul 30;30(10):1545-614
pubmed: 19444816
Bioinformatics. 2014 Feb 01;30(3):317-25
pubmed: 24281694
BMC Bioinformatics. 2009 Dec 02;10:396
pubmed: 19954534
Methods Mol Biol. 2016;1415:211-23
pubmed: 27115635
Proteins. 2021 Jun;89(6):671-682
pubmed: 33469973
Bioinformatics. 2022 Mar 28;38(7):1881-1887
pubmed: 35099504
IEEE/ACM Trans Comput Biol Bioinform. 2015 May-Jun;12(3):686-94
pubmed: 26357279
J Chem Theory Comput. 2017 Jun 13;13(6):3031-3048
pubmed: 28430426
J Mol Biol. 2007 Jun 22;369(5):1318-32
pubmed: 17482644
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W239-42
pubmed: 16845001
PLoS One. 2014 Sep 22;9(9):e107353
pubmed: 25243403
Proteins. 2007 Sep 1;68(4):803-12
pubmed: 17546660
EMBO J. 2003 Jul 15;22(14):3486-92
pubmed: 12853464
FEBS J. 2014 Jan;281(1):306-19
pubmed: 24279419
Curr Opin Struct Biol. 2002 Jun;12(3):368-73
pubmed: 12127457
Bioinformatics. 2004 Apr 12;20(6):847-53
pubmed: 14764567
Protein J. 2008 Jan;27(1):59-70
pubmed: 17851740
Bioinformatics. 2014 Feb 01;30(3):335-42
pubmed: 24281696
J Mol Biol. 1990 Oct 5;215(3):403-10
pubmed: 2231712
Prog Biophys Mol Biol. 2017 Sep;128:3-13
pubmed: 27913149
Bioinformatics. 2012 Oct 15;28(20):2600-7
pubmed: 22859501
Biol Chem. 2000 Sep-Oct;381(9-10):955-9
pubmed: 11076027