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

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

Normal modes of crambin and molecular dynamics for structure prediction

Proteins ◽  
1991 ◽  
pp. 220-228 ◽  
Author(s):  
Martha M. Teeter ◽  
Usha Rao ◽  
David Case
Keyword(s):  
Molecular Dynamics ◽  
Structure Prediction ◽  
Normal Modes

Discrete breathers modeling from first principles in graphene and in classical approximation in fcc Ni: Comparison

2019 ◽  
Vol 04 (02) ◽  
pp. 1950002 ◽  
Author(s):  
Ivan P. Lobzenko
Keyword(s):  
Molecular Dynamics ◽  
First Principles ◽  
High Frequency ◽  
Normal Modes ◽  
Nonlinear Normal Modes ◽  
First Principles Calculations ◽  
Discrete Breathers ◽  
Points Of View ◽  
Nonlinear Normal ◽  
Dynamics Simulations

Properties of discrete breathers are discussed from two points of view: (I) the ab initio modeling in graphene and (II) classical molecular dynamics simulations in the ace-centered cubic (fcc) Ni. In the first (I) approach, the possibility of exciting breathers depends on the strain applied to the graphene sheet. The uniaxial strain leads to opening the gap in the phonon band and, therefore, the existence of breathers with frequencies within the gap. In the second (II) approach, the structure of fcc Ni supports breathers of another kind, which possess a hard nonlinearity type. It is shown that particular high frequency normal mode can be used to construct the breather by means of overlaying a spherically symmetrical function, the maximum of which coincides with the breather core. The approach of breathers excitation based on nonlinear normal modes is independent of the level of approximation. Even though breathers could be obtained both in classical and first-principles calculations, each case has advantages and shortcomings, that are compared in the present work.

Analysis of Heat Conduction in Silicon Using Molecular Dynamics Simulations

2006 ◽  
Author(s):  
Asegun S. Henry ◽  
Gang Chen
Keyword(s):  
Molecular Dynamics ◽  
Lattice Dynamics ◽  
Crystalline Silicon ◽  
Relaxation Times ◽  
Normal Modes ◽  
Md Simulations ◽  
Dynamics Simulations ◽  
Technological Significance ◽  
Fitting Parameters ◽  
Phonon Properties

Silicon's material properties, have been studied extensively because of its technological significance in a variety of industries, including microelectronics. Yet, questions surrounding the phonon relaxation times in silicon continue to linger.1,2 Previous theoretical works3-5 have generated qualitative expressions for phonon relaxation times, however these approaches require fitting parameters that cannot be determined reliably. This paper first discusses implementation issues associated with using the Green-Kubo method in molecular dynamics (MD) simulations. We compare various techniques used in similar works and discusses several implementation issues that have arisen in the literature. We then describe an alternative procedure for analyzing the normal modes of a crystal to extract phonon relaxation times. As an example material we study bulk crystalline silicon using equilibrium MD simulations and lattice dynamics. The environment dependent interatomic potential6 is used to model the interactions and frequency dependent phonon properties are extracted from the MD simulations.

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