Moltemplate: A Tool for Coarse-Grained Modeling of Complex Biological Matter and Soft Condensed Matter Physics

Jewett, Andrew I.; Stelter, David; Lambert, Jason; Saladi, Shyam; Roscioni, Otello Maria; Ricci, Matteo; Autin, Ludovic; Maritan, Martina; Bashusqeh, Saeed Momeni; Keyes, T.; Dame, Remus T.; Shea, Joan–Emma; Jensen, Grant J.; Goodsell, David S.

doi:10.1016/j.jmb.2021.166841

Cited by 254 publications

(164 citation statements)

References 42 publications

(46 reference statements)

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“…changes in a twist, extension, conformation) correlate with HU movement (e.g. sliding, pause, or hopping) are required to be able to better understand and ultimately adequately include HU behavior in whole nucleoid models 48 , 49 .…”

Section: Discussionmentioning

confidence: 99%

Direct visualization of the effect of DNA structure and ionic conditions on HU–DNA interactions

Lin

Dame

Wuite

2021

Sci Rep

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Architectural DNA–binding proteins are involved in many important DNA transactions by virtue of their ability to change DNA conformation. Histone-like protein from E. coli strain U93, HU, is one of the most studied bacterial architectural DNA–binding proteins. Nevertheless, there is still a limited understanding of how the interactions between HU and DNA are affected by ionic conditions and the structure of DNA. Here, using optical tweezers in combination with fluorescent confocal imaging, we investigated how ionic conditions affect the interaction between HU and DNA. We directly visualized the binding and the diffusion of fluorescently labelled HU dimers on DNA. HU binds with high affinity and exhibits low mobility on the DNA in the absence of Mg2+; it moves 30-times faster and stays shorter on the DNA with 8 mM Mg2+ in solution. Additionally, we investigated the effect of DNA tension on HU–DNA complexes. On the one hand, our studies show that binding of HU enhances DNA helix stability. On the other hand, we note that the binding affinity of HU for DNA in the presence of Mg2+ increases at tensions above 50 pN, which we attribute to force-induced structural changes in the DNA. The observation that HU diffuses faster along DNA in presence of Mg2+ compared to without Mg2+ suggests that the free energy barrier for rotational diffusion along DNA is reduced, which can be interpreted in terms of reduced electrostatic interaction between HU and DNA, possibly coinciding with reduced DNA bending.

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Section: Discussionmentioning

confidence: 99%

Direct visualization of the effect of DNA structure and ionic conditions on HU–DNA interactions

Lin

Dame

Wuite

2021

Sci Rep

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“…We used sixth power mixing rules and a long-range VanderWaals “correction” to the energy and pressure. The molecules were constructed with a MOLTEMPLATE utility [ 58 ]. The ethanol molecule was constructed based on the following script [ 59 ] and CO 2 molecule from the following example [ 60 ].…”

Section: Methodsmentioning

confidence: 99%

The Anomalous Behavior of Thermodynamic Parameters in the Three Widom Deltas of Carbon Dioxide-Ethanol Mixture

Mareev

Sviridov

Gordienko

2021

IJMS

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Using molecular dynamics, we demonstrated that in the mixture of carbon dioxide and ethanol (25% molar fraction) there are three pronounced regions on the p-T diagram characterized by not only high-density fluctuations but also anomalous behavior of thermodynamic parameters. The regions are interpreted as Widom deltas. The regions were identified as a result of analyzing the dependences of density, density fluctuations, isobaric thermal conductivity, and clustering of a mixture of carbon dioxide and ethanol in a wide range of pressures and temperatures. Two of the regions correspond to the Widom delta for pure supercritical carbon dioxide and ethanol, while the third region is in the immediate vicinity of the critical point of the binary mixture. The origin of these Widom deltas is a result of the large mixed linear clusters formation.

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“…Auxiliary MD simulations were performed using periodic boundary conditions and a time step of 1 fs using the atomistic simulation mode of LAMMPS software (Plimpton, 1995). We used the open-source platform Moltemplate (Jewett et al, 2021) to model 5 and 10 wt% NaCl(aq), with 1,680 and 1,056 water molecules and 27 and 36 ion pairs, respectively. The water molecules were characterized by the SPC/E potential (Joung & Cheatham, 2008), and the NaCl ions were modeled as charged Lennard-Jones particles.…”

Section: Simulationsmentioning

confidence: 99%

Electrical Conductivity of Aqueous NaCl at High Pressure and Low Temperature: Application to Deep Subsurface Oceans of Icy Moons

Pan

Yong

2021

Geophysical Research Letters

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Moltemplate: A Tool for Coarse-Grained Modeling of Complex Biological Matter and Soft Condensed Matter Physics

Cited by 254 publications

References 42 publications

Direct visualization of the effect of DNA structure and ionic conditions on HU–DNA interactions

Direct visualization of the effect of DNA structure and ionic conditions on HU–DNA interactions

The Anomalous Behavior of Thermodynamic Parameters in the Three Widom Deltas of Carbon Dioxide-Ethanol Mixture

Electrical Conductivity of Aqueous NaCl at High Pressure and Low Temperature: Application to Deep Subsurface Oceans of Icy Moons

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