Functional Evolution of Proteins.
CPASS
functional evolution
protein active-sites
proteins
Journal
Proteins
ISSN: 1097-0134
Titre abrégé: Proteins
Pays: United States
ID NLM: 8700181
Informations de publication
Date de publication:
06 2019
06 2019
Historique:
received:
16
05
2018
revised:
02
11
2018
accepted:
31
01
2019
pubmed:
5
2
2019
medline:
21
4
2020
entrez:
5
2
2019
Statut:
ppublish
Résumé
The functional evolution of proteins advances through gene duplication followed by functional drift, whereas molecular evolution occurs through random mutational events. Over time, protein active-site structures or functional epitopes remain highly conserved, which enables relationships to be inferred between distant orthologs or paralogs. In this study, we present the first functional clustering and evolutionary analysis of the RCSB Protein Data Bank (RCSB PDB) based on similarities between active-site structures. All of the ligand-bound proteins within the RCSB PDB were scored using our Comparison of Protein Active-site Structures (CPASS) software and database (http://cpass.unl.edu/). Principal component analysis was then used to identify 4431 representative structures to construct a phylogenetic tree based on the CPASS comparative scores (http://itol.embl.de/shared/jcatazaro). The resulting phylogenetic tree identified a sequential, step-wise evolution of protein active-sites and provides novel insights into the emergence of protein function or changes in substrate specificity based on subtle changes in geometry and amino acid composition.
Identifiants
pubmed: 30714210
doi: 10.1002/prot.25670
pmc: PMC6462239
mid: NIHMS1017877
doi:
Substances chimiques
Amino Acids
0
Proteins
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
492-501Subventions
Organisme : NIAID NIH HHS
ID : R21AI081154
Pays : United States
Organisme : NIGMS NIH HHS
ID : P20 GM113126
Pays : United States
Organisme : NCRR NIH HHS
ID : C06 RR015468
Pays : United States
Organisme : NIH HHS
ID : RR015468-01
Pays : United States
Organisme : NIAID NIH HHS
ID : R21 AI081154
Pays : United States
Organisme : NIGMS NIH HHS
ID : P30 GM103335
Pays : United States
Informations de copyright
© 2019 Wiley Periodicals, Inc.
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