Roles of hydration water molecules in molecular packing of the killer toxin from Pichia farinosa in its crystalline state investigated by cryogenic X-ray crystallography

2002 ◽  
Vol 95 (3) ◽  
pp. 211-225 ◽  
Author(s):  
Masayoshi Nakasako ◽  
Fumihiko Tsuchiya ◽  
Yoji Arata
2003 ◽  
Vol 185 (14) ◽  
pp. 4195-4203 ◽  
Author(s):  
Stephanie Ravaud ◽  
Patrice Gouet ◽  
Richard Haser ◽  
Nushin Aghajari

ABSTRACT The psychrophilic alkaline metalloprotease (PAP) produced by a Pseudomonas bacterium isolated in Antarctica belongs to the clan of metzincins, for which a zinc ion is essential for catalytic activity. Binding studies in the crystalline state have been performed by X-ray crystallography in order to improve the understanding of the role of the zinc and calcium ions bound to this protease. Cocrystallization and soaking experiments with EDTA in a concentration range from 1 to 85 mM have resulted in five three-dimensional structures with a distinct number of metal ions occupying the ion-binding sites. Evolution of the structural changes observed in the vicinity of each cation-binding site has been studied as a function of the concentration of EDTA, as well as of time, in the presence of the chelator. Among others, we have found that the catalytic zinc ion was the first ion to be chelated, ahead of a weakly bound calcium ion (Ca 700) exclusive to the psychrophilic enzyme. Upon removal of the catalytic zinc ion, the side chains of the active-site residues His-173, His-179 and Tyr-209 shifted ∼4, 1.0, and 1.6 Å, respectively. Our studies confirm and also explain the sensitivity of PAP toward moderate EDTA concentrations and propose distinct roles for the calcium ions. A new crystal form of native PAP validates our previous predictions regarding the adaptation of this enzyme to cold environments as well as the proteolytic domain calcium ion being exclusive for PAP independent of crystallization conditions.


2006 ◽  
Vol 59 (5) ◽  
pp. 320 ◽  
Author(s):  
Graham Smith ◽  
Urs D. Wermuth ◽  
Peter C. Healy ◽  
Jonathan M. White

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.


2004 ◽  
Vol 359 (1448) ◽  
pp. 1191-1206 ◽  
Author(s):  
Masayoshi Nakasako

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.


Author(s):  
Sayuri Chong-Canto ◽  
Efrén V. García-Báez ◽  
Francisco J. Martínez-Martínez ◽  
Ángel Ramos-Organillo ◽  
Itzia I. Padilla-Martínez

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.


2020 ◽  
Author(s):  
Florentina Tofoleanu ◽  
Lesley Earl ◽  
Frank Pickard ◽  
Bernard Brooks

<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>


2003 ◽  
Vol 86 (5) ◽  
pp. 1352-1358 ◽  
Author(s):  
Terufumi Takayama ◽  
Masaki Kawano ◽  
Hidehiro Uekusa ◽  
Yuji Ohashi ◽  
Tadashi Sugawara

1997 ◽  
Vol 53 (1) ◽  
pp. 112-113 ◽  
Author(s):  
N. Kunishima ◽  
T. Kashiwagi ◽  
C. Suzuki ◽  
S. Nikkuni ◽  
F. Tsuchiya ◽  
...  

2014 ◽  
Vol 13 (11) ◽  
pp. 1509-1520 ◽  
Author(s):  
Barnali Mondal ◽  
Tingting Zhang ◽  
Rajeev Prabhakar ◽  
Burjor Captain ◽  
V. Ramamurthy

A combination of water molecules and chloride ions pre-orient protonated stilbazole molecules towards photodimerization the solid state.


2021 ◽  
Author(s):  
Joshua Clark ◽  
David O'Hagan ◽  
Stefan Guldin ◽  
Alexandra Slawin ◽  
David Bradford Cordes ◽  
...  

This study uses X-ray crystallography, theory and Langmuir isotherm analysis to explore the conformations and molecular packing of alkyl all-cis 2,3,4,5,6-pentafluorocyclohexyl motifs, which are prepared by direct aryl hydrogenations from...


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