New tricks for modelers from the crystallography toolkit: the particle mesh Ewald algorithm and its use in nucleic acid simulations

Darden, Tom; Perera, Lalith; Li, Leping; Pedersen, Lee G.

doi:10.1016/s0969-2126(99)80033-1

Cited by 591 publications

(416 citation statements)

References 54 publications

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“…Typical Ewald simulations employ Cartesian boundary conditions where the system is periodically replicated in the three spatial dimensions, and divides the long range Coulombic interactions into a short range part that is evaluated in real space (as a direct sum over atomic positions) and a long range part evaluated in reciprocal space. Practical implementations are usually based on particle mesh Ewald method 152 .…”

Section: Classical and Quantum Simulations Of Water Structurementioning

confidence: 99%

Water Structure from Scattering Experiments and Simulation

2002

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Section: Classical and Quantum Simulations Of Water Structurementioning

confidence: 99%

Water Structure from Scattering Experiments and Simulation

2002

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“…Periodic boundary conditions using the Particle Mesh Ewald method 29,30 were applied to calculate long-range Coulomb interactions. For non-bonded interactions, the cutoff was 10 Å.…”

Section: Simulationmentioning

confidence: 99%

Molecular dynamics simulation of telomeric single-stranded DNA and POT1

Kaburagi

Yamada

Miyakawa

et al. 2015

Polym J

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Telomeres, which consist of single-, double-and four-stranded DNA, shorten after each round of cell division. The repeated telomeric DNA sequence 5′-TTAGGG-3′ does not encode genetic information and is not replicated completely. We performed molecular dynamics (MD) simulations of telomeric single-stranded DNA (ssDNA) and protection of telomere 1 (POT1) for 100 ns. We calculated the distance between C α (POT1) and O5' (telomeric ssDNA) to verify the binding system for 100 ns MD. We then calculated the distance between the bases of the telomeric DNA ends and the root-mean-square deviation and gyration radius in the single and binding states. Moreover, we compared the root-mean-square fluctuations (RMSFs) between the single and binding states and calculated the number of hydrogen bonds between POT1 and telomeric DNA. There are many hydrogen bonds between Gln94 and the first guanine of the closest 5′-TTAGGG-3′ sequence in telomeric single-stranded DNA, and the RMSF between the single and binding states has a large difference between Gln94 and guanine. Overall, we found that Gln94 and guanine are important components of the binding system and are related to the stability of this system.

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“…Molecular Dynamics (MD) simulations were subsequently performed with the GROMACS [11] package by using GROMOS96 force field with an integration time step of 2 fs. Non-bonded interactions were accounted for by using the particle-mesh Ewald method (grid spacing 0.12 nm) [19] for the electrostatic contribution and cut-off distances of 1.4 nm for Van der Waals terms. Bonds were constrained by LINCS [20] algorithm.…”

Section: Atomistic Molecular Dynamicsmentioning

confidence: 99%

Multi-Scale Simulations Provide Supporting Evidence for the Hypothesis of Intramolecular Protein Translocation in GroEL/GroES Complexes

Coluzza¹,

Simone²,

Fraternali³

et al. 2005

PLoS Comput Biol

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The biological function of chaperone complexes is to assist the folding of non-native proteins. The widely studied GroEL chaperonin is a double-barreled complex that can trap non-native proteins in one of its two barrels. The ATP-driven binding of a GroES cap then results in a major structural change of the chamber where the substrate is trapped and initiates a refolding attempt. The two barrels operate anti-synchronously. The central region between the two barrels contains a high concentration of disordered protein chains, the role of which was thus far unclear. In this work we report a combination of atomistic and coarse-grained simulations that probe the structure and dynamics of the equatorial region of the GroEL/GroES chaperonin complex. Surprisingly, our simulations show that the equatorial region provides a translocation channel that will block the passage of folded proteins but allows the passage of secondary units with the diameter of an alpha-helix. We compute the free-energy barrier that has to be overcome during translocation and find that it can easily be crossed under the influence of thermal fluctuations. Hence, strongly non-native proteins can be squeezed like toothpaste from one barrel to the next where they will refold. Proteins that are already fairly close to the native state will not translocate but can refold in the chamber where they were trapped. Several experimental results are compatible with this scenario, and in the case of the experiments of Martin and Hartl, intra chaperonin translocation could explain why under physiological crowding conditions the chaperonin does not release the substrate protein.

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New tricks for modelers from the crystallography toolkit: the particle mesh Ewald algorithm and its use in nucleic acid simulations

Cited by 591 publications

References 54 publications

Water Structure from Scattering Experiments and Simulation

Water Structure from Scattering Experiments and Simulation

Molecular dynamics simulation of telomeric single-stranded DNA and POT1

Multi-Scale Simulations Provide Supporting Evidence for the Hypothesis of Intramolecular Protein Translocation in GroEL/GroES Complexes

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