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Insights into the substrate binding mechanism of SULT1A1 through molecular dynamics with excited normal modes simulations
- Source :
- Scientific Reports, Scientific Reports, Vol 11, Iss 1, Pp 1-13 (2021)
- Publication Year :
- 2021
-
Abstract
- Sulfotransferases (SULTs) are phase II drug-metabolizing enzymes catalyzing the sulfoconjugation from the co-factor 3′-phosphoadenosine 5′-phosphosulfate (PAPS) to a substrate. It has been previously suggested that a considerable shift of SULT structure caused by PAPS binding could control the capability of SULT to bind large substrates. We employed molecular dynamics (MD) simulations and the recently developed approach of MD with excited normal modes (MDeNM) to elucidate molecular mechanisms guiding the recognition of diverse substrates and inhibitors by SULT1A1. MDeNM allowed exploring an extended conformational space of PAPS-bound SULT1A1, which has not been achieved up to now by using classical MD. The generated ensembles combined with docking of 132 SULT1A1 ligands shed new light on substrate and inhibitor binding mechanisms. Unexpectedly, our simulations and analyses on binding of the substrates estradiol and fulvestrant demonstrated that large conformational changes of the PAPS-bound SULT1A1 could occur independently of the co-factor movements that could be sufficient to accommodate large substrates as fulvestrant. Such structural displacements detected by the MDeNM simulations in the presence of the co-factor suggest that a wider range of drugs could be recognized by PAPS-bound SULT1A1 and highlight the utility of including MDeNM in protein–ligand interactions studies where major rearrangements are expected.
- Subjects :
- 0301 basic medicine
Science
Phosphoadenosine Phosphosulfate
Chemical biology
Molecular Dynamics Simulation
Protein function predictions
Virtual drug screening
Article
Substrate Specificity
03 medical and health sciences
Molecular dynamics
Normal mode
Humans
chemistry.chemical_classification
Multidisciplinary
Binding Sites
030102 biochemistry & molecular biology
Mechanism (biology)
Cheminformatics
Substrate (chemistry)
Arylsulfotransferase
Computational biology and bioinformatics
030104 developmental biology
Enzyme
chemistry
Docking (molecular)
Excited state
Biophysics
Protein structure predictions
Medicine
Protein Binding
Subjects
Details
- ISSN :
- 20452322
- Volume :
- 11
- Issue :
- 1
- Database :
- OpenAIRE
- Journal :
- Scientific reports
- Accession number :
- edsair.doi.dedup.....ae77d4624bb8eff13dbc10be1400c8f8