Dynamical aspects of supercooled TIP3P–water in the grooves of DNA

Santos, Maike A. F. dos; Habitzreuter, Marco A.; Schwade, M H; Borrasca, R; Gonzatti, Guilherme K.; Netz, Paulo Augusto; Barbosa, Márcia C.

doi:10.1063/1.5100601

Cited by 13 publications

(18 citation statements)

References 72 publications

(80 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In the ILC nanochannels, water molecule diffuses faster than the ammonium-based cation and BF 4 anion, and the self-diffusion coefficient D w is of the order of 10 −12 to 10 −10 m 2 /s depending on c w . The low diffusivity is sufficiently reasonable since confined water in electrolytes gives slow mobility as observed in ionic liquids ( 25 , 46 ) and in the vicinity of rod-like polyelectrolytes ( 64 , 65 ). The counterion condensation ( 32 , 33 ) also supports the present results that the ILC nanochannels slow down the dynamics of confined waters due to the existence of condensed and tightly bound counterions via the high ion density of nanochannels (see section S4).…”

Section: Resultsmentioning

confidence: 95%

Molecular insights on confined water in the nanochannels of self-assembled ionic liquid crystal

et al. 2021

View full text Add to dashboard Cite

Self-assembled ionic liquid crystals can transport water and ions via the periodic nanochannels, and these materials are promising candidates as water treatment membranes. Molecular insights on the water transport process are, however, less investigated because of computational difficulties of ionic soft matters and the self-assembly. Here we report specific behavior of water molecules in the nanochannels by using the self-consistent modeling combining density functional theory and molecular dynamics and the large-scale molecular dynamics calculation. The simulations clearly provide the one-dimensional (1D) and 3D-interconnected nanochannels of self-assembled columnar and bicontinuous structures, respectively, with the precise mesoscale order observed by x-ray diffraction measurement. Water molecules are then confined inside the nanochannels with the formation of hydrogen bonding network. The quantitative analyses of free energetics and anisotropic diffusivity reveal that, the mesoscale geometry of 1D nanodomain profits the nature of water transport via advantages of dissolution and diffusion mechanisms inside the ionic nanochannels.

show abstract

Section: Resultsmentioning

confidence: 95%

Molecular insights on confined water in the nanochannels of self-assembled ionic liquid crystal

et al. 2021

View full text Add to dashboard Cite

show abstract

“…Two software packages, VMD 1.9.2 and NAMD 2.12 [ 43 , 44 ], were used for visualization and modeling, respectively. The complex was soaked with TIP3P [ 45 , 46 ] water molecules in a rectangular box (165.6 Å × 96.8 Å × 95.6 Å) with walls at least 15 Å away from any protein atom. The system was neutralized with 150 mM NaCl to mimic the actual physiological environment [ 47 ], being consisted of 145,099 atoms ( Figure S1 ).…”

Section: Methodsmentioning

confidence: 99%

Biphasic Force-Regulated Phosphorylation Site Exposure and Unligation of ERM Bound with PSGL-1: A Novel Insight into PSGL-1 Signaling via Steered Molecular Dynamics Simulations

Feng

Zhang

et al. 2020

IJMS

View full text Add to dashboard Cite

The PSGL-1-actin cytoskeleton linker proteins ezrin/radixin/moesin (ERM), an adaptor between P-selectin glycoprotein ligand-1 (PSGL-1) and spleen tyrosine kinase (Syk), is a key player in PSGL-1 signal, which mediates the adhesion and recruitment of leukocytes to the activated endothelial cells in flow. Binding of PSGL-1 to ERM initials intracellular signaling through inducing phosphorylation of Syk, but effects of tensile force on unligation and phosphorylation site exposure of ERM bound with PSGL-1 remains unclear. To answer this question, we performed a series of so-called “ramp-clamp” steered molecular dynamics (SMD) simulations on the radixin protein FERM domain of ERM bound with intracellular juxtamembrane PSGL-1 peptide. The results showed that, the rupture force of complex pulled with constant velocity was over 250 pN, which prevented the complex from breaking in front of pull-induced exposure of phosphorylation site on immunoreceptor tyrosine activation motif (ITAM)-like motif of ERM; the stretched complex structure under constant tensile forces <100 pN maintained on a stable quasi-equilibrium state, showing a high mechano-stabilization of the clamped complex; and, in consistent with the force-induced allostery at clamped stage, increasing tensile force (<50 pN) would decrease the complex dissociation probability but facilitate the phosphorylation site exposure, suggesting a force-enhanced biophysical connectivity of PSGL-1 signaling. These force-enhanced characters in both phosphorylation and unligation of ERM bound with PSGL-1 should be mediated by a catch-slip bond transition mechanism, in which four residue interactions on binding site were involved. This study might provide a novel insight into the transmembrane PSGL-1 signal, its biophysical connectivity and molecular structural basis for cellular immune responses in mechano-microenvironment, and showed a rational SMD-based computer strategy for predicting structure-function relation of protein under loads.

show abstract

“…MD simulations of cubic simulation cells with 4096 rigid water molecules were performed for four different three-body water models (SPC/E, OPC3, TIP3P, and TIP3P-FB), four different four-body water models (OPC, TIP4P-Ew, TIP4P-2005, and TIP4P-FB), and the coarse-grained mW model using the LAMMPS simulation package . SPC/E, TIP3P, TIP4P-2005, and TIP4P-Ew are well-established models that have all been used to study supercooled water. ,,, By contrast, the force balance (TIP3P-FB and TIP4P-FB) and optimal point charge (OPC and OPC3) models are recent reparameterizations with more optimization degrees of freedom (i.e., more fitting parameters). Recently, there has been increasing interest in using the mW model for deeply supercooled simulations, , as its computational efficiency allows sufficiently long simulations to probe extremely slow relaxations.…”

Section: Methodsmentioning

confidence: 99%

“…40 SPC/E, TIP3P, TIP4P-2005, and TIP4P-Ew are wellestablished models that have all been used to study supercooled water. 14,24,36,41 By contrast, the force balance (TIP3P-FB and TIP4P-FB) and optimal point charge (OPC and OPC3) models are recent reparameterizations with more optimization degrees of freedom (i.e., more fitting parameters).…”

Section: ■ Computational Methodsmentioning

confidence: 99%

Dynamical Accuracy of Water Models on Supercooling

Farmer

Markvardsen

Rod³

et al. 2020

J. Phys. Chem. Lett.

View full text Add to dashboard Cite

Molecular dynamics (MD) simulations are commonly used to explore the structural and dynamical properties of supercooled bulk water in the so-called "no man's land" (NML) (150−227 K), where crystallization occurs almost instantaneously. This approach has provided significant insight into experimentally inaccessible phenomena. In this paper, we compare the dynamics of simulations using one-, three-, and four-body water models to experimentally measured quasielastic neutron scattering spectra. We show that the agreement between simulated and experimental data becomes substantially worse with a decrease in temperature toward the deeply supercooled regime. It was found that it is mainly the nature of the local dynamics that is poorly reproduced, as opposed to the macroscopic properties such as the diffusion coefficient. This strongly implies that the molecular mechanism describing the water dynamics is poorly captured in the MD models, and simulated structural and dynamical properties of supercooled water in NML must be interpreted with care.

show abstract

Dynamical aspects of supercooled TIP3P–water in the grooves of DNA

Cited by 13 publications

References 72 publications

Molecular insights on confined water in the nanochannels of self-assembled ionic liquid crystal

Molecular insights on confined water in the nanochannels of self-assembled ionic liquid crystal

Biphasic Force-Regulated Phosphorylation Site Exposure and Unligation of ERM Bound with PSGL-1: A Novel Insight into PSGL-1 Signaling via Steered Molecular Dynamics Simulations

Dynamical Accuracy of Water Models on Supercooling

Contact Info

Product

Resources

About