Accurate Biomolecular Simulations Account for Electronic Polarization

Melcr, Josef; Piquemal, Jean‐Philip

doi:10.3389/fmolb.2019.00143

Cited by 76 publications

(91 citation statements)

References 127 publications

(377 reference statements)

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“…[14][15][16] Briefly, these ion models account for electronic polarizability in a mean field manner by adapting the electronic continuum correlation (ECC) approach. [23][24][25][26] Effectively, the charges of the ions are scaled by a factor of 0.75 and the Lennard-Jones σ parameter is fine-tuned to agree with neutron scattering data. Finally, the OPC water model 18 was recently demonstrated by us to provide good agreement with experimental isotherms of lipid monolayers 19,20 and was hence adapted to this work.…”

Section: Simulation Models and Methodsmentioning

confidence: 99%

Structural Effects of Cation Binding to DPPC Monolayers

Javanainen¹,

Wang²,

Ticháček³

et al. 2020

Preprint

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Ions at the two sides of the plasma membrane maintain the transmembrane potential, participate in signaling, and affect the properties of the membrane itself. The extracellular leaflet is particularly enriched in phosphatidylcholine lipids an under the influence of Na+, Ca2+, and Cl− ions. In this work, we combined molecular dynamics simulations performed using state-of-the-art models with vibrational sum frequency generation (VSFG) spectroscopy to study the effects of these key ions on the structure of dipalmitoylphosphatidylcholine. We used lipid monolayers as a proxy for membranes, as this approach enabled a direct comparison between simulation and experiment. We find that the effects of Na+ are minor. Ca2+, on the other hand, strongly affects the lipid head group conformations and induces a tighter packing of lipids, thus promoting the liquid condensed phase. It does so by binding to both the phosphate and carbonyl oxygens via direct and water-mediated binding modes, the ratios of which depend on the monolayer packing. Clustering analysis performed on simulation data revealed that changes in area per lipid or CaCl2 concentration both affect the head group conformations, yet their effects are anti-correlated. Cations at the monolayer surface also attract Cl−, which at large CaCl2 concentrations penetrates deep to the monolayer. This phenomenon coincides with a radical change in the VSFG spectra of the phosphate group, thus indicating the emergence of a new binding mode.

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Section: Simulation Models and Methodsmentioning

confidence: 99%

Structural Effects of Cation Binding to DPPC Monolayers

Javanainen¹,

Wang²,

Ticháček³

et al. 2020

Preprint

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show abstract

“…While classical computational mechanics is adequate for describing most of the properties of these systems (e.g. with molecular dynamics), the incorporation of quantum effects is instrumental in understanding some physical processes at the microscopic level [64]. The incorporation of many-body quantum effects then allows us to refine models and better understand the reactivity of some molecules, by providing a more complete modelling of the electronic degrees of freedom of the molecules' active sites.…”

Section: Applications Of Quantum Simulationmentioning

confidence: 99%

Quantum computing with neutral atoms

Henriet¹,

Béguin²,

Signoles³

et al. 2020

Quantum

340

167

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The manipulation of neutral atoms by light is at the heart of countless scientific discoveries in the field of quantum physics in the last three decades. The level of control that has been achieved at the single particle level within arrays of optical traps, while preserving the fundamental properties of quantum matter (coherence, entanglement, superposition), makes these technologies prime candidates to implement disruptive computation paradigms. In this paper, we review the main characteristics of these devices from atoms / qubits to application interfaces, and propose a classification of a wide variety of tasks that can already be addressed in a computationally efficient manner in the Noisy Intermediate Scale Quantum\cite{Preskill_NISQ} era we are in. We illustrate how applications ranging from optimization challenges to simulation of quantum systems can be explored either at the digital level (programming gate-based circuits) or at the analog level (programming Hamiltonian sequences). We give evidence of the intrinsic scalability of neutral atom quantum processors in the 100-1,000 qubits range and introduce prospects for universal fault tolerant quantum computing and applications beyond quantum computing.

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“…Force fields encompassed empirically derived energy terms that approximate torsional potentials and interatomic interactions, namely bonded and non-bonded interactions, in a condensed phase. The establishment of a force field that realistically represents the PES of a system is one of the main concerns in MD simulation that developers try to ameliorate through several alterations such as the inclusion of the polarization effect of proteins and solvent, refinement of torsional parameters, and improvement of water models [ 123 , 124 ]. Of particular interest in force field development efforts is the reparameterization of electrostatic interactions (non-bonded) that are governed by the Coulomb’s law equation to characterize interactions between charged atoms [ 125 ].…”

Section: Limitations and Improvements In Current Computational Appmentioning

confidence: 99%

“…However, the use of fixed point charges overlooked the intrinsic traits of charged atoms to assume lower energy states through the distortion of their electron density cloud and charge redistribution when approached by oppositely charged atoms or in the presence of an external dielectric field. This limitation has been actively rectified over the years through explicit consideration of polarizability, which consequently permitted a more precise electrostatic description of protein atoms in a non-homogeneous natural environment [ 123 , 126 ].…”

Section: Limitations and Improvements In Current Computational Appmentioning

confidence: 99%

Advances in Molecular Dynamics Simulations and Enhanced Sampling Methods for the Study of Protein Systems

Lazim

Suh

Choi

2020

IJMS

117

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Molecular dynamics (MD) simulation is a rigorous theoretical tool that when used efficiently could provide reliable answers to questions pertaining to the structure-function relationship of proteins. Data collated from protein dynamics can be translated into useful statistics that can be exploited to sieve thermodynamics and kinetics crucial for the elucidation of mechanisms responsible for the modulation of biological processes such as protein-ligand binding and protein-protein association. Continuous modernization of simulation tools enables accurate prediction and characterization of the aforementioned mechanisms and these qualities are highly beneficial for the expedition of drug development when effectively applied to structure-based drug design (SBDD). In this review, current all-atom MD simulation methods, with focus on enhanced sampling techniques, utilized to examine protein structure, dynamics, and functions are discussed. This review will pivot around computer calculations of protein-ligand and protein-protein systems with applications to SBDD. In addition, we will also be highlighting limitations faced by current simulation tools as well as the improvements that have been made to ameliorate their efficiency.

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Accurate Biomolecular Simulations Account for Electronic Polarization

Cited by 76 publications

References 127 publications

Structural Effects of Cation Binding to DPPC Monolayers

Structural Effects of Cation Binding to DPPC Monolayers

Quantum computing with neutral atoms

Advances in Molecular Dynamics Simulations and Enhanced Sampling Methods for the Study of Protein Systems

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