A Leap-frog Algorithm for Stochastic Dynamics

Gunsteren, Wilfred F. van; Berendsen, H.J.C.

doi:10.1080/08927028808080941

Cited by 1,158 publications

(840 citation statements)

References 16 publications

Supporting

Mentioning

826

Contrasting

Unclassified

Order By: Relevance

“…The protein was protonated and solvated using GROMACS (22). The charge was neutralized with Na ϩ , and NaCl was added to the solvent for a concentration of 0.15 M. "Steepest descents" in GROMACS was used to energy minimize the system (23). Once minimized, the proteinsolvent system was heated to a simulated temperature of 310 K, and the system was stabilized using Berendsen temperature and pressure coupling (24).…”

Section: Methodsmentioning

confidence: 99%

High Accuracy in Silico Sulfotransferase Models

Cook

Wang

Falany

et al. 2013

Journal of Biological Chemistry

View full text Add to dashboard Cite

Background: Human sulfotransferases (SULTs) regulate the bioactivities of hundreds of compounds in vivo. Results:The in silico models of SULTs developed here proved remarkably accurate in identifying SULT substrates in a 1,455-compound library containing all FDA-approved drugs. Conclusion: Highly accurate in silico SULT models are now available. Significance: The elision of mechanism and modeling can produce remarkably accurate in silico tools for the study of biology.

show abstract

Section: Methodsmentioning

confidence: 99%

High Accuracy in Silico Sulfotransferase Models

Cook

Wang

Falany

et al. 2013

Journal of Biological Chemistry

View full text Add to dashboard Cite

show abstract

“…The GROMACS Ver. 4.5.3 [16][17][18][19] was used for the MD simulations, which include the temperature increase from 0 to 300 K, followed by the structural relaxation and the ensemble process at 300 K. The temperature increasing process was performed under the NVT ensemble, by using the leap-frog integral method [25,26] and the particle mesh Ewald method [27,28] for evaluating long-range electrostatic interactions. The integration step was 2 fs, as allowed by the application of the LINCS [29] and SETTLE [30] algorithms to constrain the bond lengths of H atoms in the peptides of CAP and the water molecules, respectively.…”

Section: Search For Stable Structure Of Solvated Cap+camp+dna Complexmentioning

confidence: 99%

Specific interactions between DNA and regulatory protein controlled by ligand-binding: Ab initio molecular simulation

Matsushita

Murakawa

Shimamura

et al. 2015

AIP Conference Proceedings

View full text Add to dashboard Cite

Abstract. The catabolite activator protein (CAP) is one of the regulatory proteins controlling the transcription mechanism of gene. Biochemical experiments elucidated that the complex of CAP with cyclic AMP (cAMP) is indispensable for controlling the mechanism, while previous molecular simulations for the monomer of CAP+cAMP complex revealed the specific interactions between CAP and cAMP. However, the effect of cAMP-binding to CAP on the specific interactions between CAP and DNA is not elucidated at atomic and electronic levels. We here considered the ternary complex of CAP, cAMP and DNA in solvating water molecules and investigated the specific interactions between them at atomic and electronic levels using ab initio molecular simulations based on classical molecular dynamics and ab initio fragment molecular orbital methods. The results highlight the important amino acid residues of CAP for the interactions between CAP and cAMP and between CAP and DNA.

show abstract

“…The temperature was controlled at 293.15 K using a stochastic dynamics integrator (τ = 0.1 ps) 56 . No cut-offs were applied to the Lennard-Jones or Coulomb interactions, and the droplet was simulated in vacuum (without periodic boundary conditions).…”

Section: Pmf Calculationsmentioning

confidence: 99%

Organic molecules on the surface of water droplets – an energetic perspective

Hub

Caleman

Spoel

2012

Phys. Chem. Chem. Phys.

100

View full text Add to dashboard Cite

The solubility of organic molecules is a well established property, founded on decades of measurements, the results of which have been tabulated in handbooks. Under atmospheric conditions water droplets may form containing small amounts of other molecules. Such droplets typically have a very large area to volume ratio, which may shift the solvation equilibrium towards molecules residing on the droplet surface. The presence of organic molecules on droplet surfaces is extremely important for reactivity -it is well established that certain chemical reactions are more prevalent under atmospheric conditions than in bulk. Here we present a thermodynamic rationalization of the surface solvation properties of methanol, ethanol, propanoic acid, nbutylamine, diethyl ether, and neopentane based on potential of mean force (PMF) calculations -we have previously demonstrated that an energetic description is a very powerful means of disentangling the factors governing solvation (Caleman et al., Proc. Natl. Acad. Sci. U.S.A. 108 (2011) 6838-6842). All organic molecules investigated here are preferentially solvated on the surface of the droplets rather than in the inside, yet the magnitude of surface preference may differ by orders of magnitude. In order to dissect the energetic contributions that govern surface preference, we decompose the PMF into enthalpic and entropic components, and, in a second step, into contributions from water-water and solute-water interactions. The analysis demonstrates that surface preference is primarily an enthalpic effect, but the magnitude of surface preference of solutes containing large apolar groups is enhanced due to entropy. We introduce an analysis of the droplet PMFs that allows one to extrapolate the results to larger droplets. From this we can estimate the solubility of the solutes in water droplets, demonstrating that the solubility in droplets can be orders of magnitude larger than in bulk water. Our findings have implications for understanding the process of electrospray ionization, an important technique in biological mass spectrometry, since our work strongly suggests that in equilibrium biomolecules would be adsorbed on the droplet surface as well.

show abstract

A Leap-frog Algorithm for Stochastic Dynamics

Cited by 1,158 publications

References 16 publications

High Accuracy in Silico Sulfotransferase Models

High Accuracy in Silico Sulfotransferase Models

Specific interactions between DNA and regulatory protein controlled by ligand-binding: Ab initio molecular simulation

Organic molecules on the surface of water droplets – an energetic perspective

Contact Info

Product

Resources

About