Canonical sampling through velocity rescaling

Bussi, Giovanni; Donadio, Davide; Parrinello, Michele

doi:10.1063/1.2408420

Cited by 13,990 publications

(10,528 citation statements)

References 22 publications

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“…Subsequently, three 1-μs production runs were performed. The temperature of the systems was maintained at 310 K using the v-rescale method 39 with a coupling time of 0.1 ps. The pressure was kept at 1 bar using the Parrinello-Rahman 40 with τ p = 1.0 ps and a compressibility of 4.5 × 10 −5 bar −1 .…”

Section: Methodsmentioning

confidence: 99%

Structure of the full-length glucagon class B G-protein-coupled receptor

Zhang

Qiao

Yang

et al. 2017

Nature

190

172

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The human glucagon receptor (GCGR) belongs to the class B G protein-coupled receptor (GPCR) family and plays a key role in glucose homeostasis and the pathophysiology of type 2 diabetes. Here we report the 3.0 Å crystal structure of full-length GCGR containing both extracellular domain (ECD) and transmembrane domain (TMD) in an inactive conformation. The two domains are connected by a 12-residue segment termed the ‘stalk’, which adopts a β-strand conformation, instead of forming an α-helix as observed in the previously solved structure of GCGR-TMD. The first extracellular loop (ECL1) exhibits a β-hairpin conformation and interacts with the stalk to form a compact β-sheet structure. Hydrogen/deuterium exchange, disulfide cross-linking and molecular dynamics studies suggest that the stalk and ECL1 play critical roles in modulating peptide ligand binding and receptor activation. These insights into the full-length GCGR structure deepen our understanding about the signaling mechanisms of class B GPCRs.

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Section: Methodsmentioning

confidence: 99%

Structure of the full-length glucagon class B G-protein-coupled receptor

Zhang

Qiao

Yang

et al. 2017

Nature

190

172

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“…The temperature is controlled by using the velocityscaling method. 44 Density-Functional Theory Calculations and ab Initio Molecular Dynamics Simulations. Density functional theory (DFT) calculations and ab initio MD (AIMD) simulations are performed by using QUICKSTEP module implemented in the CP2K package.…”

Section: Methodsmentioning

confidence: 99%

Spontaneous Formation of One-Dimensional Hydrogen Gas Hydrate in Carbon Nanotubes

et al. 2014

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We present molecular dynamics simulation evidence of spontaneous formation of quasi-one-dimensional (Q1D) hydrogen gas hydrates within single-walled carbon nanotubes (SW-CNTs) of nanometer-sized diameter (1−1.3 nm) near ambient temperature. Contrary to conventional 3D gas hydrates in which the guest molecules are typically contained in individual and isolated cages in the host lattice, the guest H 2 molecules in the Q1D gas hydrates are contained within a 1D nanochannel in which the H 2 molecules form a molecule wire. In particular, we show that in the (15,0) zigzag SW-CNT, the hexagonal H 2 hydrate tends to form, with one H 2 molecule per hexagonal prism, while in the (16,0) zigzag SW-CNT, the heptagonal H 2 hydrate tends to form, with one H 2 molecule per heptagonal prism. In contrast, in the (17,0) zigzag SW-CNT, the octagonal H 2 hydrate can form, with either one H 2 or two H 2 molecules per pentagonal prism (single or double occupancy). Interestingly, in the hexagonal or heptagonal ice nanotube, the H 2 wire is solid-like as the axial diffusion constant is very low (<5 × 10 −10 cm 2 /s), whereas in the octagonal ice nanotube, the H 2 wire is liquid-like as its axial diffusion constant is comparable to 10 −5 cm 2 /s.

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“…70 Temperatures were controlled by the Bussi−Donadio−Parrinello velocity rescaling thermostat found to sample the canonical ensemble. 71 Exchanges between neighboring replicas were attempted every 2 ps, leading to an average acceptance ratio of 39.4%. The REMD simulation ran for 250 ns.…”

Section: ■ Methodsmentioning

confidence: 99%

Atomic and Dynamic Insights into the Beneficial Effect of the 1,4-Naphthoquinon-2-yl-l-tryptophan Inhibitor on Alzheimer’s Aβ1–42 Dimer in Terms of Aggregation and Toxicity

Zhang

et al. 2013

ACS Chem. Neurosci.

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Aggregation of the amyloid β protein (Aβ) peptide with 40 or 42 residues is one key feature in Alzheimer's disease (AD). The 1,4-naphthoquinon-2-yl-L-tryptophan (NQTrp) molecule was reported to alter Aβ self-assembly and reduce toxicity. Though nuclear magnetic resonance experiments and various simulations provided atomic information about the interaction of NQTrp with Aβ peptides spanning the regions of residues 12−28 and 17−42, none of these studies were conducted on the fulllength Aβ1−42 peptide. To this end, we performed extensive atomistic replica exchange molecular dynamics simulations of Aβ1−42 dimer with two NQTrp molecules in explicit solvent, by using a force field known to fold diverse proteins correctly. The interactions between NQTrp and Aβ1−42, which change the Aβ interface by reducing most of the intermolecular contacts, are found to be very dynamic and multiple, leading to many transient binding sites. The most favorable binding residues are Arg5, Asp7, Tyr10, His13, Lys16, Lys18, Phe19/Phe20, and Leu34/Met35, providing therefore a completely different picture from in vitro and in silico experiments with NQTrp with shorter Aβ fragments. Importantly, the 10 hot residues that we identified explain the beneficial effect of NQTrp in reducing both the level of Aβ1−42 aggregation and toxicity. Our results also indicate that there is room to design more efficient drugs targeting Aβ1−42 dimer against AD.

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Canonical sampling through velocity rescaling

Cited by 13,990 publications

References 22 publications

Structure of the full-length glucagon class B G-protein-coupled receptor

Structure of the full-length glucagon class B G-protein-coupled receptor

Spontaneous Formation of One-Dimensional Hydrogen Gas Hydrate in Carbon Nanotubes

Atomic and Dynamic Insights into the Beneficial Effect of the 1,4-Naphthoquinon-2-yl-l-tryptophan Inhibitor on Alzheimer’s Aβ1–42 Dimer in Terms of Aggregation and Toxicity

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