Relaxation of excited normal modes in benzene

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

scholarly journals Insights into the substrate binding mechanism of SULT1A1 through molecular dynamics with excited normal modes simulations

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Balint Dudas ◽  
Daniel Toth ◽  
David Perahia ◽  
Arnaud B. Nicot ◽  
Erika Balog ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Conformational Changes ◽  
Molecular Mechanisms ◽  
Normal Modes ◽  
Md Simulations ◽  
Conformational Space ◽  
Metabolizing Enzymes ◽  
Protein Ligand Interactions ◽  
Ligand Interactions ◽  
Excited Normal Modes

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.

scholarly journals Conformational Equilibrium of CDK/Cyclin Complexes by Molecular Dynamics with Excited Normal Modes

2015 ◽  
Vol 109 (6) ◽  
pp. 1179-1189 ◽  
Author(s):  
Nicolas Floquet ◽  
Mauricio G.S. Costa ◽  
Paulo R. Batista ◽  
Pedro Renault ◽  
Paulo M. Bisch ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Conformational Equilibrium ◽  
Normal Modes ◽  
Excited Normal Modes

Effects of pH and aggregation in the human prion conversion into scrapie form: a study using molecular dynamics with excited normal modes

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 ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Normal Modes ◽  
Effects Of Ph ◽  
Prion Conversion ◽  
Excited Normal Modes

ChemInform Abstract: Relaxation of Excited Normal Modes in Benzene.

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

A New Strategy for Atomic Flexible Fitting in Cryo-EM Maps by Molecular Dynamics with Excited Normal Modes (MDeNM-EMfit)

2020 ◽  
Vol 60 (5) ◽  
pp. 2419-2423 ◽  
Author(s):  
Mauricio G. S. Costa ◽  
Charline Fagnen ◽  
Catherine Vénien-Bryan ◽  
David Perahia
Keyword(s):  
Molecular Dynamics ◽  
Normal Modes ◽  
New Strategy ◽  
Fitting In ◽  
Excited Normal Modes

Filtering methods for finite-time normal modes and atmospheric error growth

2000 ◽  
Vol 42 ◽  
pp. 1482
Author(s):  
Mozheng Wei ◽  
Jorgen S. Frederiksen ◽  
Steve Kepert
Keyword(s):  
Finite Time ◽  
Normal Modes ◽  
Error Growth
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