Hydration water molecules seen by NMR and by X-ray crystallography

The 1:1 proton-transfer brucinium compounds from the reaction of the alkaloid brucine with 5-nitrosalicylic acid, 3,5-dinitrosalicylic acid, and 5-sulfosalicylic acid, namely anhydrous brucinium 5-nitrosalicylate (1), brucinium 3,5-dinitrosalicylate monohydrate (2), and brucinium 5-sulfosalicylate trihydrate (3) have been prepared and their crystal structures determined by X-ray crystallography. All structures further demonstrate the selectivity of brucine for meta-substituted benzoic acids and comprise three-dimensional hydrogen-bonded framework polymers. Two of the compounds (1 and 3) have the previously described undulating brucine sheet host-substructures which incorporate interstitially hydrogen-bonded salicylate anion guest species and additionally in 3 the water molecules of solvation. The structure of 2 differs in having a three-centre brucinium–salicylate anion bidentate N+–H···O(carboxyl) hydrogen-bonding association linking the species through interstitial associations involving also the water molecules of solvation. A review of the crystallographic structural literature on strychnine and brucine is also given.

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Water–protein interactions from high–resolution protein crystallography

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2004.1498 ◽

2004 ◽

Vol 359 (1448) ◽

pp. 1191-1206 ◽

Cited By ~ 111

Author(s):

Masayoshi Nakasako

Keyword(s):

Hydrogen Bond ◽

Conformational Changes ◽

Protein Interactions ◽

Three Dimensional ◽

Water Molecules ◽

Aqueous Environment ◽

Hydration Water ◽

X Ray Crystallography ◽

Physico Chemical ◽

Domain Motions

To understand the role of water in life at molecular and atomic levels, structures and interactions at the protein–water interface have been investigated by cryogenic X–ray crystallography. The method enabled a much clearer visualization of definite hydration sites on the protein surface than at ambient temperature. Using the structural models of proteins, including several hydration water molecules, the characteristics in hydration structures were systematically analysed for the amount, the interaction geometries between water molecules and proteins, and the local and global distribution of water molecules on the surface of proteins. The tetrahedral hydrogen–bond geometry of water molecules in bulk solvent was retained at the interface and enabled the extension of a three–dimensional chain connection of a hydrogen–bond network among hydration water molecules and polar protein atoms over the entire surface of proteins. Networks of hydrogen bonds were quite flexible to accommodate and/or to regulate the conformational changes of proteins such as domain motions. The present experimental results may have profound implications in the understanding of the physico–chemical principles governing the dynamics of proteins in an aqueous environment and a discussion of why water is essential to life at a molecular level.

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Mechanochemical Synthesis and Structure of the Tetrahydrate and Mesoporous Anhydrous Metforminium(2+)-N,N’-1,4-Phenylenedioxalamic Acid Cocrystal Salt: The Role of Hydrogen Bonding and N→π* Charge Assisted Interactions

10.20944/preprints202009.0660.v1 ◽

2020 ◽

Author(s):

Sayuri Chong-Canto ◽

Efrén V. García-Báez ◽

Francisco J. Martínez-Martínez ◽

Ángel Ramos-Organillo ◽

Itzia I. Padilla-Martínez

Keyword(s):

Hydrogen Bonding ◽

Mechanochemical Synthesis ◽

Water Molecules ◽

X Ray ◽

X Ray Crystallography ◽

Adsorption Desorption ◽

First Time ◽

Selective Formation ◽

Crystallization From Solution

A new cocrystal salt of metformin, an antidiabetic drug, and N,N’-(1,4-phenylene)dioxalamic acid, was synthesized by mechanochemical synthesis, purified by crystallization from solution and characterized by single X-ray crystallography. The structure revealed a salt-type cocrystal composed of one dicationic metformin unit, two monoanionic units of the acid and four water molecules namely H2Mf(HpOXA)2∙4H2O. X-ray powder, IR, 13C-CPMAS, thermal and BET adsorption-desorption analyses were performed to elucidate the structure of the molecular and supramolecurar structure of the anhydrous microcrystalline mesoporous solid H2Mf(HpOXA)2. The results suggest that their structures, conformation and hydrogen bonding schemes are very similar between them. To the best of our knowledge, the selective formation of the monoanion HpOXA⁻, as well as its structure in the solid, is herein reported for the first time. Regular O(-)∙∙∙C(), O(-)∙∙∙N+ and bifacial O(-)∙∙∙C()∙∙∙O(-) of n→* charge-assisted interactions are herein described in H2MfA cocrystal salts which could be responsible of the interactions of metformin in biologic systems. The results, support the participation of n→* charge-assisted interactions independently, and not just as a short contact imposed by the geometric constraint due to the hydrogen bonding patterns.

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Correlation Between Water Molecules Identified in Atomic Models of Beta-Galactosidase Determined by Cryo-EM and X-Ray Crystallography

10.26434/chemrxiv.12449297 ◽

2020 ◽

Author(s):

Florentina Tofoleanu ◽

Lesley Earl ◽

Frank Pickard ◽

Bernard Brooks

Keyword(s):

Crystal Structures ◽

Binding Sites ◽

Md Simulations ◽

Water Molecules ◽

Water Residence Time ◽

Solvent Exposure ◽

X Ray ◽

Protein Residues ◽

X Ray Crystallography ◽

Beta Galactosidase

<p>We start from the water placement in cryo-EM maps and in X-ray crystal structures of beta-galactosidase. We apply MD simulations to analyze the behavior of the placed water, and how they are bound to the protein residues. We analyze the solvent exposure of binding sites for water, and the water residence time at these locations. Through a statistical analysis, we conclude that water placed by cryo-EM has a similar behavior to conserved water across multiple crystal structures.</p>

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UHR PX and NPC studies of H-FABP water network with tiny perdeuterated crystals

Acta Crystallographica Section A Foundations and Advances ◽

10.1107/s2053273314087993 ◽

2014 ◽

Vol 70 (a1) ◽

pp. C1200-C1200

Author(s):

Alberto Podjarny ◽

Matthew Blakeley ◽

Michael Haertlein ◽

Andre Mitschler ◽

Alexandra Cousido-Siah ◽

...

Keyword(s):

Fatty Acid ◽

Charge Distribution ◽

Binding Pocket ◽

Internal Cavity ◽

Water Molecules ◽

Fatty Acid Binding ◽

X Ray ◽

X Ray Crystallography ◽

Internal Water ◽

Dynamics Simulations

We have obtained very detailed information about the internal water molecules in the large internal cavity inside fatty acid binding (FABP) proteins , in the presence of bound fatty acids (FA), by Ultra High Resolution X-Ray Crystallography (UHR) to 0.7 Å and Neutron Protein Crystallography (NPC) to 1.9 Å using a "radically small" (V=0.05 mm3) crystal. These waters form a very well ordered dense cluster of 12 molecules, positioned between the hydrophilic internal wall of the cavity and the fatty acid molecule. This information has been used for a detailed electrostatic analysis based on the charge distribution description modeled in the multipole formalism and on the Atoms in Molecules theory. This information is also being used in molecular dynamics simulations of H-FABP and its complex with FA in order to quantify the energetic contribution of these internal waters to the binding energy. The experiment has been done with oleic acid, coming with the protein expressed in E. Coli. The results have been analyzed in order to understand the interactions between the FA, the internal water and the protein, and in particular the role played by the water molecules in determining the potency and specificity of FA binding to FABPs. The major tool for visualizing the water molecules inside the H-FABP cavity is UHR X-Ray Crystallography combined with NPC. UHR crystallographic structures give the positions of hydrogen and oxygen atoms for well-ordered water molecules. NPC determines hydrogen atom positions, particularly of water molecules which have multiple conformations, leading to the best possible crystallographic model. This model was then complemented by a transferred charge distribution to accurately determine the electrostatic and topological properties in the binding pocket, providing a description of the way water molecules in hydration layer contribute to the binding of ligand, which is essential to understand and model ligand binding.

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Synthesis, Characterization and Single Crystal X–ray Crystallography of Nd(III) and Pr(III) Complexes with the Tridentate Schiff Base Ligand N'–(1–(pyridin–2–yl)ethylidene)nicotinohydrazide

Earthline Journal of Chemical Sciences ◽

10.34198/ejcs.6121.99117 ◽

2021 ◽

pp. 99-117

Author(s):

Moussa Faye ◽

Papa Aly Gaye ◽

Mouhamadou Moustapha Sow ◽

Moussa Dieng ◽

Farba Bouyagui Tamboura ◽

...

Keyword(s):

Single Crystal ◽

Metal Ion ◽

Water Molecules ◽

Monoclinic Space Group ◽

Space Group ◽

X Ray ◽

X Ray Crystallography ◽

Coordinated Water ◽

Tridentate Schiff Base ◽

Nitrate Anions

The use of N'–(1–(pyridin–2–yl)ethylidene)nicotinohydrazide (HL) in lanthanide(III) chemistry has yielded one mononuclear and one dinuclear complexes. The 1:1 Nd(NO3)3.6H2O or Pr(CH3COO)3.6H2O/HL in methanol afforded the complexes [Nd (HL)2(NO3)2(H2O)2].(NO3) (1) and {[Pr(L)(h2–OOCCH3)(H2O)](h1:h2:m–OOCCH3)2[Pr (L)(h2–OOCCH3)(H2O)]} (2). The structures of the complexes were solved by single crystal X–ray crystallography. In the mononuclear complex, the Nd3+ atom is coordinated by two neutral molecules of ligand acting in tridentate fashion, two nitrate anions acting in bidentate manner and two coordinated water molecules yielding a twelve–coordinated Nd atom. In the complex (2) the Pr3+ atoms are doubly bridged by two acetates anions and each metal ion is coordinated by one tridentate monodeprotonated molecule ligand, one bidentate acetate group and one coordinated water molecule. Each Pr3+ atom is nine–coordinated with an environment best described as a tricapped prismatic geometry. Complex 1 crystallizes in the monoclinic space group C2/c with the following parameters: a = 22.7657(8) Å, b = 8.4276(3) Å, c = 18.0831(7) Å, b = 114.851(2)°, V = 3148.2(2) Å3, Z = 4, R1 = 0.032, wR2 = 0.098. Complex 2 crystallizes in the monoclinic space group P21/n with the following parameters: a = 11.5388(6) Å, b = 14.1087(8) Å, c = 12.2833(6) Å, b = 102.211(2)°, V = 1954.45(18) Å3, Z = 2, R1 = 0.029, wR2 = 0.066. The supramolecular structures are consolidated by multiple hydrogen bonds.

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Preparation and Crystal Structure of a Mixed Metal Assembly [Ni(phen)3][Cu(H-1pap)]2(NO3) · 8 H2O Featuring Octahedral Cationic and Square-planar Anionic Modules

Zeitschrift für Naturforschung B ◽

10.1515/znb-2000-1013 ◽

2000 ◽

Vol 55 (10) ◽

pp. 966-970 ◽

Cited By ~ 3

Author(s):

Igor O. Fritsky ◽

Jolanta Świątek-Kozlowska ◽

Anatoliy A. Kapshuk ◽

Henryk Kozłowski ◽

Tatiana Yu. Sliva ◽

...

Keyword(s):

Crystal Structure ◽

Water Molecules ◽

Aromatic Rings ◽

Triclinic Space Group ◽

X Ray ◽

Mixed Metal ◽

X Ray Crystallography ◽

Square Planar ◽

Different Types ◽

Nitrate Anions

AbstractThe new mixed metal assembly [Ni(phen)3][Cu(H-1pap)]2(NO3 ) · 8 H2O (2) (H2pap = CH3- C(=NO H)-C(O )-NH-(CH2)3-NH-C(O )-C(=NOH)-CH3) was obtained by co-crystallisation of [Li(H2O)4][Cu(H-1pap)] · 2 H2O (1) and tris(1,10-phenanthroline)nickel(II) nitrate and studied by means of X-ray crystallography (triclinic, space group P1, a = 13.471(3), b = 13.641(3), c = 15.401(3) Å, α = 108.21(3), β = 97.73(3), γ = 107.74(3)°, V = 2476.6(9) Å , Z = 2 ,R1 = 0.0677 for 4672 unique reflections with I > 2σ(I)). The assembly indicates a network structure and consists of isolated cationic and anionic modules (octahedral [Ni(phen)3]2+ and square-planar [Cu(H-1pap)]-), non-coordinated nitrate anions and solvating water molecules. The elements of the crystal structure are linked by interactions of different types: by an extended system of H bonds, stacking interactions between aromatic rings, long apical Cu-N contacts and specific π-π interaction between a deprotonated oxime group of the complex anion and a phenanthroline ligand

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Crystal structures of highly simplified BPTIs provide insights into hydration-driven increase of unfolding enthalpy

Scientific Reports ◽

10.1038/srep41205 ◽

2017 ◽

Vol 7 (1) ◽

Cited By ~ 4

Author(s):

Mohammad Monirul Islam ◽

Masafumi Yohda ◽

Shun-ichi Kidokoro ◽

Yutaka Kuroda

Keyword(s):

Thermal Denaturation ◽

Water Molecules ◽

Scanning Calorimetry ◽

X Ray ◽

X Ray Crystallography ◽

Hydration Shells ◽

Initial Expectation ◽

Pancreatic Trypsin Inhibitor ◽

Packed Structure ◽

Water Hydrogen

Abstract We report a thermodynamic and structural analysis of six extensively simplified bovine pancreatic trypsin inhibitor (BPTI) variants containing 19–24 alanines out of 58 residues. Differential scanning calorimetry indicated a two-state thermal unfolding, typical of a native protein with densely packed interior. Surprisingly, increasing the number of alanines induced enthalpy stabilization, which was however over-compensated by entropy destabilization. X-ray crystallography indicated that the alanine substitutions caused the recruitment of novel water molecules facilitating the formation of protein–water hydrogen bonds and improving the hydration shells around the alanine’s methyl groups, both of which presumably contributed to enthalpy stabilization. There was a strong correlation between the number of water molecules and the thermodynamic parameters. Overall, our results demonstrate that, in contrast to our initial expectation, a protein sequence in which over 40% of the residues are alanines can retain a densely packed structure and undergo thermal denaturation with a large enthalpy change, mainly contributed by hydration.

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