excited normal modes
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2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Balint Dudas ◽  
Daniel Toth ◽  
David Perahia ◽  
Arnaud B. Nicot ◽  
Erika Balog ◽  
...  

AbstractSulfotransferases (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.



2020 ◽  
Vol 60 (5) ◽  
pp. 2419-2423 ◽  
Author(s):  
Mauricio G. S. Costa ◽  
Charline Fagnen ◽  
Catherine Vénien-Bryan ◽  
David Perahia


2018 ◽  
Vol 47 (5) ◽  
pp. 583-590 ◽  
Author(s):  
Angelica Nakagawa Lima ◽  
Ronaldo Junio de Oliveira ◽  
Antônio Sérgio Kimus Braz ◽  
Maurício Garcia de Souza Costa ◽  
David Perahia ◽  
...  


2015 ◽  
Vol 109 (6) ◽  
pp. 1179-1189 ◽  
Author(s):  
Nicolas Floquet ◽  
Mauricio G.S. Costa ◽  
Paulo R. Batista ◽  
Pedro Renault ◽  
Paulo M. Bisch ◽  
...  


2015 ◽  
Vol 11 (6) ◽  
pp. 2755-2767 ◽  
Author(s):  
Mauricio G. S. Costa ◽  
Paulo R. Batista ◽  
Paulo M. Bisch ◽  
David Perahia


ChemInform ◽  
1988 ◽  
Vol 19 (25) ◽  
Author(s):  
Y. GUAN ◽  
D. L. THOMPSON


1988 ◽  
Vol 88 (4) ◽  
pp. 2355-2360 ◽  
Author(s):  
Yuhua Guan ◽  
Donald L. Thompson


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