Effect of the thermostat in the molecular dynamics simulation on the folding of the model protein chignolin

Fuzo, Carlos Alessandro; Degrève, Léo

doi:10.1007/s00894-011-1282-2

Cited by 10 publications

(5 citation statements)

References 25 publications

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“…It has been rigorously shown that the Berendsen thermostat does not generate the true canonical ensemble, with too narrow a distribution of kinetic, potential, and total energies . An incorrect ensemble of energies can lead to systems being trapped in local energy minima, as seen in one study which found the time required for a protein to fold increased with strong Berendsen coupling . In replica exchange molecular dynamics simulations, the Berendsen thermostat has been shown to alter the distribution of folded and unfolded conformations of different peptides at low temperatures. , Kinetic processes which depend on the thermodynamics of the system can be similarly affected.…”

Section: Introductionmentioning

confidence: 99%

Effects of Temperature Control Algorithms on Transport Properties and Kinetics in Molecular Dynamics Simulations

Basconi

Shirts

2013

J. Chem. Theory Comput.

345

306

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Temperature control algorithms in molecular dynamics (MD) simulations are necessary to study isothermal systems. However, these thermostatting algorithms alter the velocities of the particles and thus modify the dynamics of the system with respect to the microcanonical ensemble, which could potentially lead to thermostat-dependent dynamical artifacts. In this study, we investigate how six well-established thermostat algorithms applied with different coupling strengths and to different degrees of freedom affect the dynamics of various molecular systems. We consider dynamic processes occurring on different times scales by measuring translational and rotational self-diffusion as well as the shear viscosity of water, diffusion of a small molecule solvated in water, and diffusion and the dynamic structure factor of a polymer chain in water. All of these properties are significantly dampened by thermostat algorithms which randomize particle velocities, such as the Andersen thermostat and Langevin dynamics, when strong coupling is used. For the solvated small molecule and polymer, these dampening effects are reduced somewhat if the thermostats are applied to the solvent alone, such that the solute's temperature is maintained only through thermal contact with solvent particles. Algorithms which operate by scaling the velocities, such as the Berendsen thermostat, the stochastic velocity rescaling approach of Bussi and co-workers, and the Nosé-Hoover thermostat, yield transport properties that are statistically indistinguishable from those of the microcanonical ensemble, provided they are applied globally, i.e. coupled to the system's kinetic energy. When coupled to local kinetic energies, a velocity scaling thermostat can have dampening effects comparable to a velocity randomizing method, as we observe when a massive Nose-Hoover coupling scheme is used to simulate water. Correct dynamical properties, at least those studied in this paper, are obtained with the Berendsen thermostat applied globally, despite the fact that it yields the wrong kinetic energy distribution.

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Section: Introductionmentioning

confidence: 99%

Effects of Temperature Control Algorithms on Transport Properties and Kinetics in Molecular Dynamics Simulations

Basconi

Shirts

2013

J. Chem. Theory Comput.

345

306

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“…All simulations were performed using periodic boundary conditions (PBC), all long range electrostatic interactions were calculated using Ewald summation [12] while the SHAKE algorithm was used to fix hydrogen bonds. Integration of atomic motions (2 fs time step) was done using Newtonian equations, while the Berendsen thermostat and barostat algorithms were used in temperature and pressure controls respectively [13].…”

Section: Methodsmentioning

confidence: 99%

Monoclonal Antibody-Light chain CDR1/Spike Glycoprotein Receptor Binding Domain Dissociation Explains Antibody Escape Mechanism in L452R-SARS-CoV-2

omotuyi,

Nash,

Oyinloye

et al. 2024

Preprint

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Most of the well-characterized innate antibodies elicited by exposure to SARS-CoV-2 or a vaccine targets the spike glycoprotein receptor-binding domain (RDB) which doubles as the angiotensin-converting enzyme 2 (ACE2, receptor) binding. RBD mutation is therefore a potential health concern in COVID-19 pandemic. RBD-L452R-SARS-CoV-2 exhibits increased transmissibility and immune evasion with an unknown underlying mechanisms. The immune evasion mechanism was investigated here. in R452, loss of hydrophobic interaction between RBD-L452/HCDR3-I103 disrupts RBD-E484/heavy-chain-R112 salt-bridge, and cation-π interaction between RBD-E484/mAB-Y32(LcCDR1). Unburied RBD flips ~64° from the antibody plane, losing all interaction with the mAB light chain-CDR; thus, making ternary complex thermodynamically unstable.

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“…Finally, the production run was carried out considering an NVT ensemble with Nosè-Hoover thermal coupling. This thermostat (target temperature: 300 K; time constant coupling: 0.2 ps) was applied to the three groups of atoms that build up the system (water, PLGA, curcumin) to avoid any hot solvent-cold solute issue [ 53 ]. Production runs lasted 5 ns to have enough statistics to extrapolate results.…”

Section: Methodsmentioning

confidence: 99%

Diffusion of curcumin in PLGA-based carriers for drug delivery: a molecular dynamics study

De Giorgi,

Bellussi,

Parlani

et al. 2024

J Mol Model

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Context: The rapid growth and diversification of drug delivery systems have been significantly supported by advancements in micro- and nano-technologies, alongside the adoption of biodegradable polymeric materials like poly(lactic-co-glycolic acid) (PLGA) as microcarriers. These developments aim to reduce toxicity and enhance target specificity in drug delivery. The use of in silico methods, particularly molecular dynamics (MD) simulations, has emerged as a pivotal tool for predicting the dynamics of species within these systems. This approach aids in investigating drug delivery mechanisms, thereby reducing the costs associated with design and prototyping. In this study, we focus on elucidating the diffusion mechanisms in curcumin-loaded PLGA particles, which are critical for optimizing drug release and efficacy in therapeutic applications. Methods: We utilized MD to explore the diffusion behavior of curcumin in PLGA drug delivery systems. The simulations, executed with GROMACS, modeled curcumin molecules in a representative volume element of PLGA chains and water, referencing molecular structures from the Protein Data Bank and employing the CHARMM force field. We generated PLGA chains of varying lengths using the Polymer Modeler tool and arranged them in a bulk-like environment with Packmol. The simulation protocol included steps for energy minimization, T and p equilibration, and calculation of the isotropic diffusion coefficient from the mean square displacement. The Taguchi method was applied to assess the effects of hydration level, PLGA chain length, and density on diffusion. Results: Our results provide insight into the influence of PLGA chain length, hydration level, and polymer density on the diffusion coefficient of curcumin, offering a mechanistic understanding for the design of efficient drug delivery systems. The sensitivity analysis obtained through the Taguchi method identified hydration level and PLGA density as the most significant input parameters affecting curcumin diffusion, while the effect of PLGA chain length was negligible within the simulated range. We provided a regression equation capable to accurately fit MD results. The regression equation suggests that increases in hydration level and PLGA density result in a decrease in the diffusion coefficient.

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Effect of the thermostat in the molecular dynamics simulation on the folding of the model protein chignolin

Cited by 10 publications

References 25 publications

Effects of Temperature Control Algorithms on Transport Properties and Kinetics in Molecular Dynamics Simulations

Effects of Temperature Control Algorithms on Transport Properties and Kinetics in Molecular Dynamics Simulations

Monoclonal Antibody-Light chain CDR1/Spike Glycoprotein Receptor Binding Domain Dissociation Explains Antibody Escape Mechanism in L452R-SARS-CoV-2

Diffusion of curcumin in PLGA-based carriers for drug delivery: a molecular dynamics study

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