Water in Biology, Chemistry and Physics

Robinson, G. W.; Singh, Samrendra; Zhu, S-B; Evans, M. W.

doi:10.1142/2923

Cited by 219 publications

(52 citation statements)

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“…The volume of the box was such that there was a distance of 9 Å from every wall to the nearest part of the complex. Water molecules were represented applying the SPC (46,47) model. Counterions were added to ensure the overall electric neutrality of the system.…”

Section: Molecular Dynamicsmentioning

confidence: 99%

Stability and structural recovery of the tetramerization domain of p53-R337H mutant induced by a designed templating ligand

Gordo

Martos

Santos

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

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Protein p53 is a transcription factor crucial for cell cycle and genome integrity. It is able to induce both cell arrest when DNA is damaged and the expression of DNA repair machinery. When the damage is irreversible, it triggers apoptosis. Indeed, the protein, which is a homotetramer, is mutated in most human cancers. For instance, the inherited mutation p53-R337H results in destabilization of the tetramer and, consequently, leads to an organism prone to tumor setup. We describe herein a rational designed molecule capable of holding together the four monomers of the mutated p53-R337H protein, recovering the tetramer integrity as in the wild-type structure. Two ligand molecules, based on a conical calix[4]arene with four cationic guanidiniomethyl groups at the wider edge (upper rim) and hydrophobic loops at the narrower edge (lower rim), fit nicely and cooperatively into the hydrophobic clefts between two of the monomers at each side of the protein and keep the tetrameric structure, like molecular templates, by both ion-pair and hydrophobic interactions. We found a good agreement between the structure of the complex and the nature of the interactions involved by a combination of theory (molecular dynamics) and experiments (circular dichroism, differential scanning calorimetry and 1 H saturation transfer difference NMR). molecular recognition ͉ multivalent calix[4]arene ligands ͉ oligoprotein stabilization ͉ protein-protein interactions

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Section: Molecular Dynamicsmentioning

confidence: 99%

Stability and structural recovery of the tetramerization domain of p53-R337H mutant induced by a designed templating ligand

Gordo

Martos

Santos

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

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“…1 As the most common solution for biological processes, a water model is always the starting point for any force field development effort toward a full description of biomolecular systems. 2 Biomolecular force fields are based on simple parametric energy functions, and the quality of the force field parameters determines the reliability of the computational results. An ideal force field model of water should correctly reproduce the structural, thermodynamic, and dynamic behavior of water.…”

Section: Introductionmentioning

confidence: 99%

Six-site polarizable model of water based on the classical Drude oscillator

Lopes

Roux

et al. 2013

The Journal of Chemical Physics

117

151

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A polarizable water model, SWM6, was developed and optimized for liquid phase simulations under ambient conditions. Building upon the previously developed SWM4-NDP model, additional sites representing oxygen lone-pairs were introduced. The geometry of the sites is assumed to be rigid. Considering the large number of adjustable parameters, simulated annealing together with polynomial fitting was used to facilitate model optimization. The new water model was shown to yield the correct self-diffusion coefficient after taking the system size effect into account, and the dimer geometry is better reproduced than in the SWM4 models. Moreover, the experimental oxygen-oxygen radial distribution is better reproduced, indicating that the new model more accurately describes the local hydrogen bonding structure of bulk phase water. This was further validated by its ability to reproduce the experimental nuclear magnetic shielding and related chemical shift of the water hydrogen in the bulk phase, a property sensitive to the local hydrogen bonding structure. In addition, comparison of the liquid properties of the SWM6 model is made with those of a number of widely used additive and polarizable models. Overall, improved balance between the description of monomer, dimer, clustered, and bulk phase water is obtained with the new model compared to its SWM4-NDP polarizable predecessor, though application of the model requires an approximately twofold increase on computational resources.

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“…Because of the large number of papers regarding simulations of water, the reader is referred to a couple of excellent reviews currently available. 19,20 In general, the properties of water can be expressed fairly accurately over a narrow range of temperatures and pressures. One major problem has been the failure of these potentials to reproduce the density versus temperature curve over the liquid-state range from 273 to 373 K. 13 Even in cases where the temperature of maximum density is well reproduced, the potentials often fail at reproducing the rest of the densitytemperature curve.…”

Section: Introductionmentioning

confidence: 99%

Dissociative Water Potential for Molecular Dynamics Simulations

2007

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A new interatomic potential for dissociative water was developed for use in molecular dynamics simulations. The simulations use a multibody potential, with both pair and three-body terms, and the Wolf summation method for the long-range Coulomb interactions. A major feature in the potential is the change in the shortrange O-H repulsive interaction as a function of temperature and/or pressure in order to reproduce the densitytemperature curve between 273 K and 373 at 1 atm, as well as high-pressure data at various temperatures. Using only the change in this one parameter, the simulations also reproduce room-temperature properties of water, such as the structure, cohesive energy, diffusion constant, and vibrational spectrum, as well as the liquid-vapor coexistence curve. Although the water molecules could dissociate, no dissociation is observed at room temperature. However, behavior of the hydronium ion was studied by introduction of an extra H + into a cluster of water molecules. Both Eigen and Zundel configurations, as well as more complex configurations, are observed in the migration of the hydronium.

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Water in Biology, Chemistry and Physics

Cited by 219 publications

References 0 publications

Stability and structural recovery of the tetramerization domain of p53-R337H mutant induced by a designed templating ligand

Stability and structural recovery of the tetramerization domain of p53-R337H mutant induced by a designed templating ligand

Six-site polarizable model of water based on the classical Drude oscillator

Dissociative Water Potential for Molecular Dynamics Simulations

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