scholarly journals Conversion of Core Oxos to Water Molecules by 4e-/4H+Reductive Dehydration of the Mn4O26+Core in the Manganese−Oxo Cubane Complex Mn4O4(Ph2PO2)6:  A Partial Model for Photosynthetic Water Binding and Activation.

2000 ◽  
Vol 39 (18) ◽  
pp. 4186-4186 ◽  
Author(s):  
Wolfgang F. Ruettinger ◽  
G. Charles Dismukes
Keyword(s):  
Water Molecules ◽  
Water Binding ◽  
Partial Model

Water molecules at protein–drug interfaces: computational prediction and analysis methods

2021 ◽  
Author(s):  
Marley L. Samways ◽  
Richard D. Taylor ◽  
Hannah E. Bruce Macdonald ◽  
Jonathan W. Essex
Keyword(s):  
Computational Prediction ◽  
Water Molecules ◽  
Protein Drug ◽  
Water Binding ◽  
Computational Approaches ◽  
Analysis Methods

In this review we examine computational approaches to explore the structure and thermodynamics of water binding in protein–drug complexes

scholarly journals WT and A53T α-synuclein systems: Melting Diagram and its new interpretation

2019 ◽  
Author(s):  
M. Bokor ◽  
Á. Tantos ◽  
P. Tompa ◽  
K.-H. Han ◽  
K. Tompa
Keyword(s):  
Secondary Structure ◽  
Structural Disorder ◽  
Water Molecules ◽  
Hydration Water ◽  
Wild Type ◽  
Water Binding ◽  
Potential Barriers ◽  
Intrinsically Disordered ◽  
Mobile Water ◽  
Binding Interfaces

AbstractParkinson’s disease is connected with abnormal α-synuclein (αS) aggregation. Energetics of potential barriers governing motions of hydration water is examined. Information about the distributions and heights of potential barriers is gained by a thermodynamical approach. The ratios of the heterogeneous water-binding interfaces measure proteins’ structural disorder. All αS forms possess secondary structural elements though they are intrinsically disordered. Monomers are functional at the lowest potential barriers, where mobile hydration water exists, with monolayer coverage of mobile hydration. The αS monomer contains 33% secondary structure and is more compact than a random coil. A53T αS monomer has a more open structure than the wild type. Monomers realize all possible hydrogen bonds. Half of the mobile hydration water amount for monomers is missing in αS oligomers and αS amyloids. Oligomers are ordered by 66%. Mobile water molecules in the first hydration shell of amyloids are the weakest bound compared to other forms. Wild type and A53T amyloids show identical, low-level hydration, and are considered as disordered to 75%.Statement of SignificanceAggregation of α-synuclein into oligomers, amyloid fibrils is a hallmark of Parkinson’s disease. A thermodynamic approach provides information on the heterogeneity of protein-water bonds in the wild type and A53T mutant monomers, oligomers, amyloids. This information can be related to ratios of heterogeneous water-binding interfaces, which measure the proteins’ structural disorder. Both α-synuclein monomers are intrinsically disordered. The monomers nevertheless have 33% secondary structure. They are functional as long as mobile water molecules surround them. They realize every possible H-bonds with water. Oligomers are like globular proteins with 66% ordered structure. Amyloids are disordered to 75% and are poorly hydrated with loosely bound water. Their hydration is identical. Oligomers, amyloids have only half as much hydrating mobile water as monomers.

Deep learning model can predict water binding sites on the surface of proteins using limited-resolution data

2020 ◽  
Author(s):  
Jan Zaucha ◽  
Charlotte A. Softley ◽  
Michael Sattler ◽  
Grzegorz M. Popowicz
Keyword(s):  
Deep Learning ◽  
High Resolution ◽  
Electron Density ◽  
Binding Sites ◽  
Hot Spots ◽  
Water Molecules ◽  
X Ray Diffraction ◽  
Water Binding ◽  
X Ray ◽  
Deep Learning Model

ABSTRACTThe surfaces of proteins are generally hydrophilic but there have been reports of sites that exhibit an exceptionally high affinity for individual water molecules. Not only do such molecules often fulfil critical biological functions, but also, they may alter the binding of newly designed drugs. In crystal structures, sites consistently occupied in each unit cell yield electron density clouds that represent water molecule presence. These are recorded in virtually all high-resolution structures obtained through X-ray diffraction. In this work, we utilized the wealth of data from the RCSB Protein Data Bank to train a residual deep learning model named ‘hotWater’ to identify sites on the surface of proteins that are most likely to bind water, the so-called water hot spots. The model can be used to score existing water molecules from a PDB file to provide their ranking according to the predicted binding strength or to scan the surface of a protein to determine the most likely water hot-spots de novo. This is computationally much more efficient than currently used molecular dynamics simulations. Based on testing the model on three example proteins, which have been resolved using both high-resolution X-ray crystallography (providing accurate positions of trapped waters) as well as low-resolution X-ray diffraction, NMR or CryoEM (where structure refinement does not yield water positions), we were able to show that the hotWater method is able to recover in the “water-free” structures many water binding sites known from the high-resolution structures. A blind test on a newly solved protein structure with waters removed from the PDB also showed good prediction of the crystal water positions. This was compared to two known algorithms that use electron density and was shown to have higher recall at resolutions >2.6 Å. We also show that the algorithm can be applied to novel proteins such as the RNA polymerase complex from SARS-CoV-2, which could be of use in drug discovery. The hotWater model is freely available at (https://pypi.org/project/hotWater/).

scholarly journals QM/MM computational studies of substrate water binding to the oxygen-evolving centre of photosystem II

2007 ◽  
Vol 363 (1494) ◽  
pp. 1149-1156 ◽  
Author(s):  
Eduardo M Sproviero ◽  
Katherine Shinopoulos ◽  
José A Gascón ◽  
James P McEvoy ◽  
Gary W Brudvig ◽  
...  
Keyword(s):  
Photosystem Ii ◽  
Exchange Rates ◽  
Water Exchange ◽  
Metal Cluster ◽  
Bound Water ◽  
Water Molecules ◽  
Computational Studies ◽  
Water Binding ◽  
Model Complexes ◽  
Oxygen Evolving

This paper reports computational studies of substrate water binding to the oxygen-evolving centre (OEC) of photosystem II (PSII), completely ligated by amino acid residues, water, hydroxide and chloride. The calculations are based on quantum mechanics/molecular mechanics hybrid models of the OEC of PSII, recently developed in conjunction with the X-ray crystal structure of PSII from the cyanobacterium Thermosynechococcus elongatus . The model OEC involves a cuboidal Mn 3 CaO 4 Mn metal cluster with three closely associated manganese ions linked to a single μ 4 -oxo-ligated Mn ion, often called the ‘dangling manganese’. Two water molecules bound to calcium and the dangling manganese are postulated to be substrate molecules, responsible for dioxygen formation. It is found that the energy barriers for the Mn(4)-bound water agree nicely with those of model complexes. However, the barriers for Ca-bound waters are substantially larger. Water binding is not simply correlated to the formal oxidation states of the metal centres but rather to their corresponding electrostatic potential atomic charges as modulated by charge-transfer interactions. The calculations of structural rearrangements during water exchange provide support for the experimental finding that the exchange rates with bulk 18 O-labelled water should be smaller for water molecules coordinated to calcium than for water molecules attached to the dangling manganese. The models also predict that the S 1 →S 2 transition should produce opposite effects on the two water-exchange rates.

scholarly journals Aqueous Micro-hydration of Na+(H2O)n=1-7 Clusters: DFT Study

2019 ◽  
Vol 17 (1) ◽  
pp. 260-269 ◽  
Author(s):  
Tahoon M.A. ◽  
Gomaa E.A. ◽  
Suleiman M.H.A.
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Hydration Number ◽  
Sodium Ion ◽  
Water Molecules ◽  
Functional Theory ◽  
Water Binding ◽  
X Ray ◽  
X Ray Scattering ◽  
Scattering Study

AbstractSodium ion micro-solvated clusters, [Na(H2O) n]+, n = 1–7, were completed by (DFT) density functional theory at B3LYP/6-311+G(d,p) level in the gaseous phase. At the ambient situation, the four, five and six micro-solvated configurations can convert from each other. The investigation of the sequential water binding energy on Na+ obviously indicates that the influence of Na+ on the neighboring water molecules goes beyond the first solvation layer with the hydration number of 5. The hydration number of Na+ is 5 and the hydration space (rNa-O) is 2.43 Å. The current study displays that all our simulations have an brilliant harmony with the diffraction result from X-ray scattering study. The vibration frequency of H2O solvent was also determined. This work is important for additional identification of the Na+(H2O)n clusters in aqueous medium.

scholarly journals Reveal the Relationship Between Hyaluronic Acid and Water Using Aquaphotomics

2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Weilu Tian ◽  
Qin Dong ◽  
Boran Lin ◽  
Xiangchun Yang ◽  
Hui Zhang ◽  
...  
Keyword(s):  
Hyaluronic Acid ◽  
The Body ◽  
Water Molecules ◽  
Binding Ability ◽  
Water Binding ◽  
Living Body ◽  
Ongoing Work ◽  
Biological Environment ◽  
The Relationship ◽  
Water Species

Hyaluronic acid (HA) is a kind of biological macromolecule with strong water binding ability. It has rich biological functions and plays an important role in the living body. It has extremely high application value in the fields of medical beauty, medicine, medical treatment and food. In the past, the thinking of studying HA was rather rigid, which is reflected in the direct study of HA itself, which is quite difficult in a complex system because there are too many influencing factors in the real biological environment. The proposal of aquaphotomics allows researchers to focus on the water molecules in complex biological systems, which leads us to shift the angle of thinking about HA-related issues to the water molecules that are closely bound to it. In previous and ongoing work, we use spectroscopy technology and aquaphotomics to study water species, focus on the widely used HA and its derivatives on the market, and apply multivariate analysis methods to analyze the interaction between HA and water molecules to further clarify the material properties of HA form the basis for monitoring its process of binding water in the body. This paper briefly reviews important knowledge concerning the relationship between HA and water, and explains our past and ongoing related research in this field. Key words: hyaluronic acid, water, aquaphotomics, spectroscopy

scholarly journals Asymmetric Solvation of the Zinc Dimer Cation Revealed by Infrared Multiple Photon Dissociation Spectroscopy of Zn2+(H2O)n (n = 1–20)

2021 ◽  
Vol 22 (11) ◽  
pp. 6026
Author(s):  
Ethan M. Cunningham ◽  
Thomas Taxer ◽  
Jakob Heller ◽  
Milan Ončák ◽  
Christian van der Linde ◽  
...  
Keyword(s):  
Metal Ion ◽  
Density Functional ◽  
Metal Corrosion ◽  
Water Molecules ◽  
Functional Theory ◽  
Irmpd Spectroscopy ◽  
Water Binding ◽  
Binding Motifs ◽  
Metal Centers ◽  
Infrared Multiple Photon Dissociation

Investigating metal-ion solvation—in particular, the fundamental binding interactions—enhances the understanding of many processes, including hydrogen production via catalysis at metal centers and metal corrosion. Infrared spectra of the hydrated zinc dimer (Zn2+(H2O)n; n = 1–20) were measured in the O–H stretching region, using infrared multiple photon dissociation (IRMPD) spectroscopy. These spectra were then compared with those calculated by using density functional theory. For all cluster sizes, calculated structures adopting asymmetric solvation to one Zn atom in the dimer were found to lie lower in energy than structures adopting symmetric solvation to both Zn atoms. Combining experiment and theory, the spectra show that water molecules preferentially bind to one Zn atom, adopting water binding motifs similar to the Zn+(H2O)n complexes studied previously. A lower coordination number of 2 was observed for Zn2+(H2O)3, evident from the highly red-shifted band in the hydrogen bonding region. Photodissociation leading to loss of a neutral Zn atom was observed only for n = 3, attributed to a particularly low calculated Zn binding energy for this cluster size.

The accumulation of solutes and water binding strength in durum wheat

1994 ◽  
Vol 90 (4) ◽  
pp. 715-721 ◽  
Author(s):  
A. Rascio ◽  
C. Platani ◽  
G. Scalfati ◽  
A. Tonti ◽  
N. Di Fonzo
Keyword(s):  
Durum Wheat ◽  
Water Binding ◽  
Binding Strength
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