Understanding protein structural changes for oncogenic missense variants.
Oncogenic missense variants
Protein structure prediction
Structural classification
Journal
Heliyon
ISSN: 2405-8440
Titre abrégé: Heliyon
Pays: England
ID NLM: 101672560
Informations de publication
Date de publication:
Jan 2021
Jan 2021
Historique:
received:
14
06
2020
revised:
20
08
2020
accepted:
15
01
2021
entrez:
8
2
2021
pubmed:
9
2
2021
medline:
9
2
2021
Statut:
epublish
Résumé
Understanding and predicting the changes of protein structure and function upon mutation and their relationship to human health is a critical element to translate the genomic revolution into actionable interventions. Therefore, it is pertinent to explore how mutations result in structural changes leading to pathogenic proteins, but due to the protein structural knowledge gap, experimental approaches are lacking. Protein structure prediction methods, such as I-TASSER, have made it possible to predict the structure of a given amino acid sequence, thus opening a new way to explore protein structure changes upon mutations when experimental information is not available. Using known mutations from the Catalogue of Somatic Mutation in Cancer (COSMIC) and ClinVar databases, we compare predicted structure-derived properties from wild type (WT) and mutated proteins and find differences between the local and global 3D protein structures of the WT and the mutants. The studies in this relatively small sample reveal that the structural changes are quite diverse.
Identifiants
pubmed: 33553733
doi: 10.1016/j.heliyon.2021.e06013
pii: S2405-8440(21)00118-3
pmc: PMC7846930
doi:
Types de publication
Journal Article
Langues
eng
Pagination
e06013Subventions
Organisme : NLM NIH HHS
ID : T15 LM007124
Pays : United States
Organisme : NCATS NIH HHS
ID : UL1 TR002538
Pays : United States
Informations de copyright
© 2021 The Authors.
Références
Bioinformatics. 2016 Oct 1;32(19):2936-46
pubmed: 27318206
Database (Oxford). 2010 Aug 05;2010:baq020
pubmed: 20689021
J Comput Chem. 2004 Oct;25(13):1605-12
pubmed: 15264254
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W382-8
pubmed: 15980494
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D187-91
pubmed: 16381842
Br J Cancer. 2004 Jul 19;91(2):355-8
pubmed: 15188009
BMC Bioinformatics. 2014;15 Suppl 7:S11
pubmed: 25080018
Pigment Cell Melanoma Res. 2019 Sep;32(5):734-738
pubmed: 31001908
Bioinformatics. 2018 Feb 1;34(3):511-513
pubmed: 28968714
Proteins. 2008 Aug;72(2):793-803
pubmed: 18260109
Nucleic Acids Res. 2014 Jan;42(Database issue):D980-5
pubmed: 24234437
J Natl Cancer Inst. 2018 Dec 1;110(12):1380-1385
pubmed: 29659923
Nat Protoc. 2010 Apr;5(4):725-38
pubmed: 20360767
Nucleic Acids Res. 2000 Jan 1;28(1):235-42
pubmed: 10592235
Nat Methods. 2015 Jan;12(1):7-8
pubmed: 25549265
BMC Bioinformatics. 2008 Jan 23;9:40
pubmed: 18215316
Sci Rep. 2020 Sep 21;10(1):15387
pubmed: 32958805
Am J Hum Genet. 2007 Nov;81(5):1006-24
pubmed: 17924342
Nucleic Acids Res. 2019 Jan 8;47(D1):D506-D515
pubmed: 30395287
PLoS One. 2010 Oct 27;5(10):e15386
pubmed: 21060880
Protein Sci. 2008 Jul;17(7):1212-9
pubmed: 18469178
Nucleic Acids Res. 2011 Sep 1;39(17):e118
pubmed: 21727090
Nat Genet. 2014 Mar;46(3):310-5
pubmed: 24487276
Biopolymers. 1983 Dec;22(12):2577-637
pubmed: 6667333
PLoS Genet. 2017 Apr 19;13(4):e1006739
pubmed: 28422960
Nucleic Acids Res. 2005 Apr 22;33(7):2302-9
pubmed: 15849316
Proteins. 2012 Jul;80(7):1780-90
pubmed: 22434500
Hum Mutat. 2011 Oct;32(10):1161-70
pubmed: 21853506
Proteins. 2019 Dec;87(12):1011-1020
pubmed: 31589781