scholarly journals Interfacial Water Many-body Effects Drive Structural Dynamics and Allosteric interactions in SARS-CoV-2 Main Protease Dimerization Interface

2021 ◽  
Author(s):  
Dina El Ahdab ◽  
Louis Lagardère ◽  
Theo Jaffrelot Inizan ◽  
Frédéric Célerse ◽  
Chengwen Liu ◽  
...  
Keyword(s):  
Structural Dynamics ◽  
Adaptive Sampling ◽  
Many Body ◽  
Allosteric Site ◽  
Allosteric Interactions ◽  
Main Protease ◽  
Dimerization Interface ◽  
Bond Network ◽  
Dynamics Simulations ◽  
Many Body Interactions

Following our previous work (Chem. Sci., 2021, 12, 4889 – 4907), we study the structural dynamics of the SARS-CoV-2 Main Protease dimerization interface (apo dimer) by means of microsecond adaptive sampling molecular dynamics simulations (50 microseconds) using the AMOEBA polarizable force field (PFF). This interface is structured by a complex H-bond network that is only stable at physiological pH. Structural correlations analysis between its residues and the catalytic site confirms the presence of a buried allosteric site. However, noticeable differences in allosteric connectivity are observed between PFFs and non-PFFs. Interfacial polarizable water molecules are shown to appear at the heart of this discrepancy, since they are connected to the global interface H-bond network and able to adapt their dipole moment (and dynamics) to their diverse local physico-chemical micro-environments. The water-interface many-body interactions appear to drive the interface volume fluctuations and to therefore mediate the allosteric interactions with the catalytic cavity.

scholarly journals Interfacial Water Many-body Effects Drive Structural Dynamics and Allosteric interactions in SARS-CoV-2 Main Protease Dimerization Interface

2021 ◽  
Author(s):  
Dina El Ahdab ◽  
Louis Lagardère ◽  
Theo Jaffrelot Inizan ◽  
Frédéric Célerse ◽  
Chengwen Liu ◽  
...  
Keyword(s):  
Structural Dynamics ◽  
Adaptive Sampling ◽  
Many Body ◽  
Allosteric Site ◽  
Allosteric Interactions ◽  
Main Protease ◽  
Dimerization Interface ◽  
Bond Network ◽  
Dynamics Simulations ◽  
Many Body Interactions

Following our previous work (Chem. Sci., 2021, 12, 4889 – 4907), we study the structural dynamics of the SARS-CoV-2 Main Protease dimerization interface (apo dimer) by means of microsecond adaptive sampling molecular dynamics simulations (50 microseconds) using the AMOEBA polarizable force field (PFF). This interface is structured by a complex H-bond network that is only stable at physiological pH. Structural correlations analysis between its residues and the catalytic site confirms the presence of a buried allosteric site. However, noticeable differences in allosteric connectivity are observed between PFFs and non-PFFs. Interfacial polarizable water molecules are shown to appear at the heart of this discrepancy, since they are connected to the global interface H-bond network and able to adapt their dipole moment (and dynamics) to their diverse local physico-chemical micro-environments. The water-interface many-body interactions appear to drive the interface volume fluctuations and to therefore mediate the allosteric interactions with the catalytic cavity.

scholarly journals Interfacial Water Many-body Effects Drive Structural Dynamics and Allosteric interactions in SARS-CoV-2 Main Protease Dimerization Interface

2021 ◽  
Author(s):  
Dina El Ahdab ◽  
Louis Lagardère ◽  
Theo Jaffrelot Inizan ◽  
Frédéric Célerse ◽  
Chengwen Liu ◽  
...  
Keyword(s):  
Structural Dynamics ◽  
Adaptive Sampling ◽  
Many Body ◽  
Allosteric Site ◽  
Allosteric Interactions ◽  
Main Protease ◽  
Dimerization Interface ◽  
Bond Network ◽  
Dynamics Simulations ◽  
Many Body Interactions

Following our previous work (Chem. Sci., 2021, 12, 4889 – 4907), we study the structural dynamics of the SARS-CoV-2 Main Protease dimerization interface (apo dimer) by means of microsecond adaptive sampling molecular dynamics simulations (50 microseconds) using the AMOEBA polarizable force field (PFF). This interface is structured by a complex H-bond network that is only stable at physiological pH. Structural correlations analysis between its residues and the catalytic site confirms the presence of a buried allosteric site. However, noticeable differences in allosteric connectivity are observed between PFFs and non-PFFs. Interfacial polarizable water molecules are shown to appear at the heart of this discrepancy, since they are connected to the global interface H-bond network and able to adapt their dipole moment (and dynamics) to their diverse local physico-chemical micro-environments. The water-interface many-body interactions appear to drive the interface volume fluctuations and to therefore mediate the allosteric interactions with the catalytic cavity.

Data-Driven Many-Body Models with Chemical Accuracy for CH4/H2O Mixtures

2020 ◽  
Author(s):  
Marc Riera ◽  
Alan Hirales ◽  
Raja Ghosh ◽  
Francesco Paesani
Keyword(s):  
Liquid Phase ◽  
Quantitative Description ◽  
Liquid Mixtures ◽  
Many Body ◽  
Energy Functions ◽  
Potential Energy Functions ◽  
Dynamics Simulations ◽  
Body Potential ◽  
Small Clusters ◽  
Many Body Interactions

<div> <div> <div> <p>Many-body potential energy functions (PEFs) based on the TTM-nrg and MB-nrg theoretical/computational frameworks are developed from coupled cluster reference data for neat methane and mixed methane/water systems. It is shown that that the MB-nrg PEFs achieve subchemical accuracy in the representation of individual many-body effects in small clusters and enables predictive simulations from the gas to the liquid phase. Analysis of structural properties calculated from molecular dynamics simulations of liquid methane and methane/water mixtures using both TTM-nrg and MB-nrg PEFs indicates that, while accounting for polarization effects is important for a correct description of many-body interactions in the liquid phase, an accurate representation of short-range interactions, as provided by the MB-nrg PEFs, is necessary for a quantitative description of the local solvation structure in liquid mixtures. </p> </div> </div> </div>

scholarly journals High-resolution mining of the SARS-CoV-2 main protease conformational space: supercomputer-driven unsupervised adaptive sampling

2021 ◽  
Author(s):  
Théo Jaffrelot Inizan ◽  
Frédéric Célerse ◽  
Olivier Adjoua ◽  
Dina El Ahdab ◽  
Luc-Henri Jolly ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
High Resolution ◽  
Adaptive Sampling ◽  
Force Fields ◽  
Sampling Strategy ◽  
Md Simulations ◽  
Conformational Space ◽  
Many Body ◽  
Polarizable Force Fields ◽  
Main Protease

We provide an unsupervised adaptive sampling strategy capable of producing μs-timescale molecular dynamics (MD) simulations of large biosystems using many-body polarizable force fields (PFFs).

Dislocation Generation and Crack Propagation in Metals Examined in Molecular Dynamics Simulations

1992 ◽  
Vol 278 ◽  
Author(s):  
J. A. Rifkin ◽  
C. S. Becquart ◽  
D. Kim ◽  
P. C. Clapp
Keyword(s):  
Crack Propagation ◽  
Atomistic Simulations ◽  
Many Body ◽  
Dislocation Generation ◽  
Embedded Atom ◽  
Stress Levels ◽  
Different Temperatures ◽  
The Many ◽  
Dynamics Simulations ◽  
Many Body Interactions

AbstractWe have carried out a series of atomistic simulations on arrays of about 10,000 atoms containing an atomically sharp crack and subjected to increasing stress levels. The ordered stoichiometric alloys B2 NiAl, B2 RuAl and A15 Nb3AI have been studied at different temperatures and stress levels, as well as the elements Al, Ni, Nb and Ru. The many body interactions used in the simulations were derived semi-empirically, using techniques related to the Embedded Atom Method. Trends in dislocation generation rates and crack propagation modes will be discussed and compared to experimental indications where possible, and some of the simulations will be demonstrated in the form of computer movies.

scholarly journals High-Resolution Mining of SARS-CoV-2 Main Protease Conformational Space: Supercomputer-Driven Unsupervised Adaptive Sampling

2021 ◽  
Author(s):  
Theo Jaffrelot Inizan ◽  
Frédéric Célerse ◽  
Olivier Adjoua ◽  
Dina El Ahdab ◽  
Luc-Henri Jolly ◽  
...  
Keyword(s):  
High Resolution ◽  
Adaptive Sampling ◽  
Dipole Moments ◽  
Sampling Strategy ◽  
Md Simulations ◽  
Conformational Space ◽  
Many Body ◽  
Main Protease ◽  
Comparison Results ◽  
Wide Range

We provide an unsupervised adaptive sampling strategy capable of producing microseconds-timescale molecular dynamics (MD) simulations of large biosystems using many-body polarizable force fields (PFF). The global exploration problem is decomposed into a set of separate MD trajectories that can be restarted within a selective process to achieve sufficient phase-space sampling. Accurate statistical properties can be obtained through reweighting. Within this highly parallel setup, the Tinker--HP package can be powered by an arbitrary large number of GPUs on supercomputers, reducing exploration time from years to days. This approach is used to tackle the urgent modeling problem of the SARS--CoV--2 Main Protease (Mpro) producing more than 38 microseconds of all-atom simulations of its apo, ligand-free, dimer using the high-resolution AMOEBA PFF. A first 15.14 microseconds simulation (physiological pH) is compared to available non--PFF long-timescale simulation data. A detailed clustering analysis exhibits striking differences between FFs, AMOEBA showing a richer conformational space. Focusing on key structural markers related to the oxyanion hole stability, we observe an asymmetry between protomers. One of them appears less structured resembling the experimentally inactive monomer for which a 6 microseconds simulation was performed as a basis of comparison. Results highlight the plasticity of Mpro active site. The C--terminal end of its less structured protomer is shown to oscillate between several states, being able to interact with the other protomer, potentially modulating its activity. Active and distal sites volumes are found to be larger in the most active protomer within our AMOEBA simulations compared to non-PFFs as additional cryptic pockets are uncovered. A second 17 microseconds AMOEBA simulation is performed with protonated His172 residues mimicking lower pH. Data show the protonation impact on the destructuring of the oxyanion loop. We finally analyze the solvation patterns around key histidine residues. The confined AMOEBA polarizable water molecules are able to explore a wide range of dipole moments, going beyond bulk values, leading to a water molecule counts consistent with experiment. Results suggest that the use of PFFs could be critical in drug discovery to accurately model the complexity of the molecular interactions structuring Mpro

scholarly journals Allosteric modulation in monomers and oligomers of a G protein-coupled receptor

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Rabindra V Shivnaraine ◽  
Brendan Kelly ◽  
Krishana S Sankar ◽  
Dar'ya S Redka ◽  
Yi Rang Han ◽  
...  
Keyword(s):  
Muscarinic Receptor ◽  
Allosteric Modulation ◽  
Atomic Level ◽  
Allosteric Site ◽  
Allosteric Interactions ◽  
M2 Muscarinic Receptor ◽  
Orthosteric Ligands ◽  
Dynamics Simulations ◽  
G Protein Coupled ◽  
Allosteric Properties

The M2 muscarinic receptor is the prototypic model of allostery in GPCRs, yet the molecular and the supramolecular determinants of such effects are unknown. Monomers and oligomers of the M2 muscarinic receptor therefore have been compared to identify those allosteric properties that are gained in oligomers. Allosteric interactions were monitored by means of a FRET-based sensor of conformation at the allosteric site and in pharmacological assays involving mutants engineered to preclude intramolecular effects. Electrostatic, steric, and conformational determinants of allostery at the atomic level were examined in molecular dynamics simulations. Allosteric effects in monomers were exclusively negative and derived primarily from intramolecular electrostatic repulsion between the allosteric and orthosteric ligands. Allosteric effects in oligomers could be positive or negative, depending upon the allosteric-orthosteric pair, and they arose from interactions within and between the constituent protomers. The complex behavior of oligomers is characteristic of muscarinic receptors in myocardial preparations.

scholarly journals Bond order redefinition needed to reduce inherent noise in molecular dynamics simulations

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ibnu Syuhada ◽  
Nikodemus Umbu Janga Hauwali ◽  
Ahmad Rosikhin ◽  
Euis Sustini ◽  
Fatimah Arofiati Noor ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Bond Order ◽  
Interatomic Potential ◽  
Interatomic Potentials ◽  
Many Body ◽  
Range Interaction ◽  
Dynamics Simulations ◽  
Interaction Approach ◽  
Many Body Interactions

AbstractIn this work, we present the bond order redefinition needed to reduce the inherent noise in order to enhance the accuracy of molecular dynamics simulations. We propose defining the bond order as a fraction of energy distribution. It happens due to the character of the material in nature, which tries to maintain its environment. To show the necessity, we developed a factory empirical interatomic potential (FEIP) for carbon that implements the redefinition with a short-range interaction approach. FEIP has been shown to enhance the accuracy of the calculation of lattice constants, cohesive energy, elastic properties, and phonons compared to experimental data, and can even be compared to other potentials with the long-range interaction approach. The enhancements due to FEIP can reduce the inherent noise, then provide a better prediction of the energy based on the behaviour of the atomic environment. FEIP can also transform simple two-body interactions into many-body interactions, which is useful for enhancing accuracy. Due to implementing the bond order redefinition, FEIP offers faster calculations than other complex interatomic potentials.

Sign in / Sign up

Export Citation Format

Share Document