An overview of the Amber biomolecular simulation package

Salomón-Ferrer, Romelia; Case, David A.; Walker, Ross C.

doi:10.1002/wcms.1121

Cited by 2,093 publications

(1,812 citation statements)

References 81 publications

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“…Mixed-sequence 25-bp DNA and RNA duplexes were simulated using the AMBER14 suite of programs (27,28) with the parm10 force field, which includes parmbsc0 and parmbsc0_chiOL3 refinements (29,30) for DNA and RNA, respectively. Spermine molecules were simulated using the general Amber force field (GAFF version 1.7).…”

Section: All-atom MD Simulationsmentioning

confidence: 99%

Spermine Condenses DNA, but Not RNA Duplexes

Katz

Tolokh

Pabit

et al. 2017

Biophysical Journal

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Interactions between the polyamine spermine and nucleic acids drive important cellular processes. Spermine condenses DNA and some RNAs, such as poly(rA):poly(rU). A large fraction of the spermine present in cells is bound to RNA but apparently does not condense it. Here, we study the effect of spermine binding to short duplex RNA and DNA, and compare our findings with predictions of molecular-dynamics simulations. When small numbers of spermine are introduced, RNA with a designed sequence containing a mixture of 14 GC pairs and 11 AU pairs resists condensation relative to DNA of an equivalent sequence or to 25 bp poly(rA):poly(rU) RNA. A comparison of wide-angle x-ray scattering profiles with simulation results suggests that spermine is sequestered deep within the major groove of mixed-sequence RNA. This prevents condensation by limiting opportunities to bridge to other molecules and stabilizes the RNA by locking it into a particular conformation. In contrast, for DNA, simulations suggest that spermine binds externally to the duplex, offering opportunities for intermolecular interaction. The goal of this study is to explain how RNA can remain soluble and available for interaction with other molecules in the cell despite the presence of spermine at concentrations high enough to precipitate DNA.

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Section: All-atom MD Simulationsmentioning

confidence: 99%

Spermine Condenses DNA, but Not RNA Duplexes

Katz

Tolokh

Pabit

et al. 2017

Biophysical Journal

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“…The structures were immersed in a rectangular box filled with TIP3P water molecules, 46 imposing a minimum distance between the solute and the box of 14 Å, and the charges were neutralized adding Mg 2+ counterions to the solvated systems in favorable positions, as implemented in the tLeap program. 43 For each structure, a minimization run was performed for 2500 steps using the steepest descent algorithm, imposing a harmonic constraint of 50 kcal·mol −1 · Å −2 , to remove any unfavorable interaction and to prevent irreversible Mg 2+ binding to DNA. The systems were gradually heated from 0 to 300 K in the NVT ensemble over a period of 500 ps using the Langevin thermostat, 47 with a coupling coefficient of 1.0 ps and a weak constraint of 15 kcal·mol −1 ·Å −2 on nucleotides.…”

Section: ■ Experimental Sectionmentioning

confidence: 99%

Simulative and Experimental Characterization of a pH-Dependent Clamp-like DNA Triple-Helix Nanoswitch

et al. 2017

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Here we couple experimental and simulative techniques to characterize the structural/dynamical behavior of a pH-triggered switching mechanism based on the formation of a parallel DNA triple helix. Fluorescent data demonstrate the ability of this structure to reversibly switch between two states upon pH changes. Two accelerated, half microsecond, MD simulations of the system having protonated or unprotonated cytosines, mimicking the pH 5.0 and 8.0 conditions, highlight the importance of the Hoogsteen interactions in stabilizing the system, finely depicting the time-dependent disruption of the hydrogen bond network. Urea-unfolding experiments and MM/ GBSA calculations converge in indicating a stabilization energy at pH 5.0, 2-fold higher than that observed at pH 8.0. These results validate the pH-controlled behavior of the designed structure and suggest that simulative approaches can be successfully coupled with experimental data to characterize responsive DNA-based nanodevices. ■ INTRODUCTIONDNA nanotechnology allows us to design and engineer smart nanomaterials and nanodevices using synthetic DNA sequences. 1−6 For example, current methodologies and synthetic strategies, such as DNA tiles, origami, or supramolecular assembly, allowed the production of complex nanostructures of different shapes and dimensions. 7−11 The unparalleled versatility of these approaches allows precise positioning of molecule-responsive switching elements in specific locations of DNA nanostructures, leading to the construction of more complex functional nanodevices. 12−14 Similarly, enzyme−DNA nanostructures have been demonstrated to enhance enzyme catalytic activity and stability. 15 DNA motifs that rely on noncanonical DNA interactions, such as G-quadruplex, triplex, i-motif, hairpin, and aptamers, can be used to design such nanodevices due to their dynamic-responsive behavior toward chemical and environmental stimuli. 16,17 These responsive units often respond to specific chemical inputs through a bindinginduced conformational change mechanism that leads to a measurable output or function. The efficiency of this class of responsive nanodevices strongly depends on the designed structure-switching mechanism that controls their activity or functionality. Therefore, there is an urgent need to understand the energies involved in these responsive systems and the relationship between their structure and dynamics. 16 Among such functional DNA nanodevices, those based on the triple-helix motif are attracting interest for their strong and programmable pH dependence. 18−20 By rationally incorporating triplex-forming portions into DNA nanodevices, it is possible to trigger conformational changes and functions using pH as a chemical input. 21−24 Despite the fair amount of knowledge of the basic design principles and mechanism of action of triplex-based nanodevices, no reports describing the connection between their structural and dynamical properties are available. Toward this aim, simulative approaches represent valuable tools to shed ...

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“…Finally, we calculated LRF of trialanine peptide system with α-helix structure in order to show whether and how the nearsightedness holds for usual molecular systems that are treated with QM/MM calculations. The quasi-equilibrium geometry at 300 K is obtained with using the Amber molecular dynamics simulations program [30]. The umbrella sampling [31] with WHAM scheme [32] is employed.…”

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confidence: 99%

Theoretical Investigation on Nearsightedness of Finite Model and Molecular Systems Based on Linear Response Function Analysis

et al. 2014

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Abstract:We examined nearsightedness of electronic matter (NEM) of finite systems on the basis of linear response function (LRF). From the computational results of a square-well model system, the behavior of responses obviously depends on the number of electrons (N): as N increases, LRF, δρ(r)/δv(r′), decays rapidly for the distance, |r−r′|. This exemplifies that the principle suggested by Kohn and Prodan holds even for finite systems: the cause of NEM is destructive interference among electron density amplitudes. In addition, we examined double-well model systems, which have low-lying degenerate levels. In this case, there are two types of LRF: the cases of the half-filled and of full-filled in low-lying degenerate levels. The response for the former is delocalized, while that of the later is localized. These behaviors of model systems are discussed in relation to the molecular systems' counterparts, H2, He2 2+, and He2 systems. We also see that NEM holds for the dissociated limit of H2, of which the mechanism is similar to that of the insulating state of solids as suggested by Kohn. We also examined LRF of alanine tripeptide system as well as butane and butadiene molecules, showing that NEM of the polypeptide system is caused by sp3 junctions at Cα atoms that prevent propagation of amplitudes of LRF, which is critically different from that of NEM for finite and infinite homogeneous systems.

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An overview of the Amber biomolecular simulation package

Cited by 2,093 publications

References 81 publications

Spermine Condenses DNA, but Not RNA Duplexes

Spermine Condenses DNA, but Not RNA Duplexes

Simulative and Experimental Characterization of a pH-Dependent Clamp-like DNA Triple-Helix Nanoswitch

Theoretical Investigation on Nearsightedness of Finite Model and Molecular Systems Based on Linear Response Function Analysis

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