Insights into the substrate binding mechanism of SULT1A1 through molecular dynamics with excited normal modes simulations
| Autor: | Maria A. Miteva, Erika Balog, David Perahia, Dániel J. Tóth, Balint Dudas, Arnaud Nicot |
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| Rok vydání: | 2021 |
| Předmět: |
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 |
| Zdroj: | Scientific Reports Scientific Reports, Vol 11, Iss 1, Pp 1-13 (2021) |
| ISSN: | 2045-2322 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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