Molecular Dynamics Simulations of Zinc Ions in Water Using CHARMM

Obst, Stefan; Bradaczek, H.

doi:10.1007/s008940050034

Cited by 21 publications

(20 citation statements)

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“…2͒, predict 14 water molecules in the second shell region ͑3.5-4.7 Å͒ and nearly within the large range of values obtained from the analysis of the x-ray data, 45-50 7.6-13.2 waters. This number also agrees well with the results from several prior MD and QM/MM simulations 40,44,[51][52][53][54][55] and within the range of values of the conventional MD simulations. However, compared to these prior simulations our second shell maximum is found to be 5%-10% smaller.…”

Section: A the Hydration Shell Structuresupporting

confidence: 90%

Structure and dynamics of the hydration shells of the Zn2+ ion from ab initio molecular dynamics and combined ab initio and classical molecular dynamics simulations

Cauët

Bogatko

Weare

et al. 2010

The Journal of Chemical Physics

101

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Results of ab initio molecular dynamics ͑AIMD͒ simulations ͑density functional theory+ PBE96͒ of the dynamics of waters in the hydration shells surrounding the Zn 2+ ion ͑T Ϸ 300 K, Ϸ 1 gm/ cm 3 ͒ are compared to simulations using a combined quantum and classical molecular dynamics ͓AIMD/molecular mechanical ͑MM͔͒ approach. Both classes of simulations were performed with 64 solvating water molecules ͑ϳ15 ps͒ and used the same methods in the electronic structure calculation ͑plane-wave basis set, time steps, effective mass, etc.͒. In the AIMD/MM calculation, only six waters of hydration were included in the quantum mechanical ͑QM͒ region. The remaining 58 waters were treated with a published flexible water-water interaction potential. No reparametrization of the water-water potential was attempted. Additional AIMD/MM simulations were performed with 256 water molecules. The hydration structures predicted from the AIMD and AIMD/MM simulations are found to agree in detail with each other and with the structural results from x-ray data despite the very limited QM region in the AIMD/MM simulation. To further evaluate the agreement of these parameter-free simulations, predicted extended x-ray absorption fine structure ͑EXAFS͒ spectra were compared directly to the recently obtained EXAFS data and they agree in remarkable detail with the experimental observations. The first hydration shell contains six water molecules in a highly symmetric octahedral structure is ͑maximally located at 2.13-2.15 Å versus 2.072 Å EXAFS experiment͒. The widths of the peak of the simulated EXAFS spectra agree well with the data ͑8.4 Å 2 versus 8.9 Å 2 in experiment͒. Analysis of the H-bond structure of the hydration region shows that the second hydration shell is trigonally bound to the first shell water with a high degree of agreement between the AIMD and AIMD/MM calculations. Beyond the second shell, the bonding pattern returns to the tetrahedral structure of bulk water. The AIMD/MM results emphasize the importance of a quantum description of the first hydration shell to correctly describe the hydration region. In these calculations the full d 10 electronic structure of the valence shell of the Zn 2+ ion is retained. The simulations show substantial and complex charge relocation on both the Zn 2+ ion and the first hydration shell. The dipole moment of the waters in the first hydration shell is 3.4 D ͑3.3 D AIMD/MM͒ versus 2.73 D bulk. Little polarization is found for the waters in the second hydration shell ͑2.8 D͒. No exchanges were seen between the first and the second hydrations shells; however, many water transfers between the second hydration shell and the bulk were observed. For 64 waters, the AIMD and AIMD/MM simulations give nearly identical results for exchange dynamics. However, in the larger particle simulations ͑256 waters͒ there is a significant reduction in the second shell to bulk exchanges.

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Section: A the Hydration Shell Structuresupporting

confidence: 90%

Structure and dynamics of the hydration shells of the Zn2+ ion from ab initio molecular dynamics and combined ab initio and classical molecular dynamics simulations

Cauët

Bogatko

Weare

et al. 2010

The Journal of Chemical Physics

101

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“…Contrary to the classical simulation, both QM/MM-MD simulations showed a sixfold coordination with 100% occurrence, which is in good agreement with experimental values ͑6͒ ͑Refs. In all cases two peaks located at ϳ90°and ϳ173°are shown, as already obtained from the classical MD simulations by Obst et al, 10 and indicating an almost perfect octahedral arrangement of the ͓Zn͑H 2 O͒ 6 ͔ 2+ species ͑Fig. 13 and 48͒ and MC simulations ͑5.6͒.…”

Section: A Structural Propertiessupporting

confidence: 79%

“…3 Furthermore, zinc is one of the most important basic materials in various industrial processes. [6][7][8][9][10][11][12][13] Salmon et al 14 investigated the dynamics of the zinc hydrate in Zn͑ClO 4 ͒ 2 ͑1.98 and 2.58 mol kg −1 ͒ and ZnCl 2 ͑1.96 mol kg −1 ͒ solution by means of incoherent quasi-elastic neutron scattering ͑IQENS͒. 4,5 Both experimental and theoretical studies have shown the primary hydration number of Zn 2+ in dilute aqueous solution to be 6, forming an octahedral geometry.…”

Section: Introductionmentioning

confidence: 99%

An extended ab initio QM/MM MD approach to structure and dynamics of Zn(II) in aqueous solution

Fatmi

Hofer

Randolf

et al. 2005

The Journal of Chemical Physics

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Structural and dynamical properties of Zn(II) in aqueous solution were investigated, based on an ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulation at double-zeta Hartree-Fock quantum mechanical level including the first and second hydration shells into the QM region. The inclusion of the second shell in the QM region resulted in significant changes in the properties of the hydrate. The first shell coordination number was found to be 6, the second shell consists of approximately 14 water molecules. The structural properties were determined in terms of RDF, ADF, tilt and theta angle distributions, while dynamics were characterized by mean ligand residence times, ion-ligand stretching frequencies and the vibrational and librational motions of water ligands.

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“…The coordination numbers and the global fit parameters that were allowed to vary during the fitting procedure were the distance R(Å), Debye-Waller factor ( 2 ) and the angles of the n contributions which were defined according to atomic structural models constructed using the VMD software (66) . Zinc was solvated based on a published refined structure (67) . For the model containing histidine, the residue was positioned by replacing one coordinating water molecule with it.…”

Section: Methodsmentioning

confidence: 99%

Zinc Determines Dynamical Properties and Aggregation Kinetics of Human Insulin

Pounot

Grime

Longo³

et al. 2020

Preprint

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AbstractProtein aggregation is a widespread process leading to deleterious consequences in the organism, with amyloid aggregates being important not only in biology but also for drug design and biomaterial production. Insulin is a protein largely used in diabetes treatment and its amyloid aggregation is at the basis of the so-called insulin-derived amyloidosis. Here we uncover the major role of zinc in both insulin dynamics and aggregation kinetics at low pH, where the formation of different amyloid superstructures (fibrils and spherulites) can be thermally induced. Amyloid aggregation is accompanied by zinc release and the suppression of water-sustained insulin dynamics, as shown by particle-induced X-ray emission and X-ray absorption spectroscopy and by neutron spectroscopy, respectively. Our study shows that zinc binding stabilizes the native form of insulin by facilitating hydration of this hydrophobic protein and suggests that introducing new binding sites for zinc can improve insulin stability and tune its aggregation propensity.Statement of SignificanceLocalized amyloidosis occurs at insulin injection sites for diabetes treatment, leading to deleterious inflammations known as insulin-derived amyloidosis. Amyloid superstructures are also promising candidates in the field of biomaterials. Here we revealed that zinc, coordinated to insulin in the native form, is released upon amyloid aggregation, when insulin forms superstructures known as fibrils and spherulites. Zinc release leads to a full suppression of functionally essential protein dynamics through a modification of the protein’s hydration properties and completely modifies insulin amyloid kinetics. The results suggest that changes in protein hydration upon zinc binding/release modifies both stability and dynamics of insulin and might then be a general strategy to control protein stability and tune protein aggregation into amorphous and ordered superstructures.

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Molecular Dynamics Simulations of Zinc Ions in Water Using CHARMM

Cited by 21 publications

References 1 publication

Structure and dynamics of the hydration shells of the Zn2+ ion from ab initio molecular dynamics and combined ab initio and classical molecular dynamics simulations

Structure and dynamics of the hydration shells of the Zn2+ ion from ab initio molecular dynamics and combined ab initio and classical molecular dynamics simulations

An extended ab initio QM/MM MD approach to structure and dynamics of Zn(II) in aqueous solution

Zinc Determines Dynamical Properties and Aggregation Kinetics of Human Insulin

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