scholarly journals Water structure of a hydrophobic protein at atomic resolution: Pentagon rings of water molecules in crystals of crambin

1984 ◽  
Vol 81 (19) ◽  
pp. 6014-6018 ◽  
Author(s):  
M. M. Teeter
2017 ◽  
Author(s):  
Tetsuya Masuda ◽  
Mamoru Suzuki ◽  
Shigeyuki Inoue ◽  
Changyong Song ◽  
Takanori Nakane ◽  
...  

AbstractAtomic resolution structures (beyond 1.20 Å) at ambient temperature, which is usually hampered by the radiation damage in synchrotron X-ray crystallography (SRX), will add to our understanding of the structure-function relationships of enzymes. Serial femtosecond crystallography (SFX) has attracted surging interest by providing a route to bypass such challenges. Yet the progress on atomic resolution analysis with SFX has been rather slow. In this report, we describe the 1.20 Å resolution structure of proteinase K using 13 keV photon energy. Hydrogen atoms, water molecules, and a number of alternative side-chain conformations have been resolved. The increase in the value of B-factor in SFX suggests that the residues and water molecules adjacent to active sites were flexible and exhibited dynamic motions at specific substrate-recognition sites.


2018 ◽  
Vol 115 (20) ◽  
pp. E4569-E4576 ◽  
Author(s):  
Mahmoud Moqadam ◽  
Anders Lervik ◽  
Enrico Riccardi ◽  
Vishwesh Venkatraman ◽  
Bjørn Kåre Alsberg ◽  
...  

The pH of liquid water is determined by the infrequent process in which water molecules split into short-lived hydroxide and hydronium ions. This reaction is difficult to probe experimentally and challenging to simulate. One of the open questions is whether the local water structure around a slightly stretched OH bond is actually initiating the eventual breakage of this bond or whether this event is driven by a global ordering that involves many water molecules far away from the reaction center. Here, we investigated the self-ionization of water at room temperature by rare-event ab initio molecular dynamics and obtained autoionization rates and activation energies in good agreement with experiments. Based on the analysis of thousands of molecular trajectories, we identified a couple of local order parameters and show that if a bond stretch occurs when all these parameters are around their ideal range, the chance for the first dissociation step (double-proton jump) increases from 10−7 to 0.4. Understanding these initiation triggers might ultimately allow the steering of chemical reactions.


Author(s):  
Mohamad K. M. Zainol ◽  
Robert J. C. Linforth ◽  
Donald J. Winzor ◽  
David J. Scott

AbstractThis investigation of the temperature dependence of DppA interactions with a subset of three dipeptides (AA. AF and FA) by isothermal titration calorimetry has revealed the negative heat capacity ($$\Delta {C}_{p}^{o}$$ Δ C p o ) that is a characteristic of hydrophobic interactions. The observation of enthalpy–entropy compensation is interpreted in terms of the increased structuring of water molecules trapped in a hydrophobic environment, the enthalpic energy gain from which is automatically countered by the entropy decrease associated with consequent loss of water structure flexibility. Specificity for dipeptides stems from appropriate spacing of designated DppA aspartate and arginine residues for electrostatic interaction with the terminal amino and carboxyl groups of a dipeptide, after which the binding pocket closes to become completely isolated from the aqueous environment. Any differences in chemical reactivity of the dipeptide sidechains are thereby modulated by their occurrence in a hydrophobic environment where changes in the structural state of entrapped water molecules give rise to the phenomenon of enthalpy–entropy compensation. The consequent minimization of differences in the value of ΔG0 for all DppA–dipeptide interactions thus provides thermodynamic insight into the biological role of DppA as a transporter of all dipeptides across the periplasmic membrane.


2018 ◽  
Vol 38 (3) ◽  
Author(s):  
Irina V. Zueva ◽  
Sofya V. Lushchekina ◽  
Patrick Masson

The role of water in oxime-mediated reactivation of phosphylated cholinesterases (ChEs) has been asked with recurrence. To investigate oximate water structure changes in this reaction, reactivation of paraoxon-inhibited human acetylcholinesterase (AChE) was performed by the oxime asoxime (HI-6) at different pH in the presence and absence of lyotropic salts: a neutral salt (NaCl), a strong chaotropic salt (LiSCN) and strong kosmotropic salts (ammonium sulphate and phosphate HPO42−). At the same time, molecular dynamic (MD) simulations of enzyme reactivation under the same conditions were performed over 100 ns. Reactivation kinetics showed that the low concentration of chaotropic salt up to 75 mM increased the percentage of reactivation of diethylphosphorylated AChE whereas kosmotropic salts lead only to a small decrease in reactivation. This indicates that water-breaker salt induces destructuration of water molecules that are electrostricted around oximate ions. Desolvation of oximate favors nucleophilic attack on the phosphorus atom. Effects observed at high salt concentrations (>100 mM) result either from salting-out of the enzyme by kosmotropic salts (phosphate and ammonium sulphate) or denaturing action of chaotropic LiSCN. MDs simulations of diethylphosphorylated hAChE complex with HI-6 over 100 ns were performed in the presence of 100 mM (NH4)2SO4 and 50 mM LiSCN. In the presence of LiSCN, it was found that protein and water have a higher mobility, i.e. water is less organized, compared with the ammonium sulphate system. LiSCN favors protein solvation (hydrophobic hydration) and breakage of elelectrostricted water molecules around of oximate ion. As a result, more free water molecules participated to reaction steps accompanying oxime-mediated dephosphorylation.


NIR news ◽  
2019 ◽  
Vol 30 (5-6) ◽  
pp. 22-25 ◽  
Author(s):  
Jelena Muncan ◽  
Shinichiro Kuroki ◽  
Daniela Moyankova ◽  
Hiroyuki Morita ◽  
Stefka Atanassova ◽  
...  

The research team of Kobe University’s Graduate School of Agriculture Science, led by Professor Dr Roumiana Tsenkova and a research group from Agrobioinstitute in Sofia, Bulgaria led by Professor Dr Dimitar Djilianov, recently made a significant step forward in understanding the “drying without dying” phenomenon in resurrection plants – a small group of plant species which are able to survive long periods without water. Using aquaphotomics and near infrared spectroscopy, the entire process of desiccation and subsequent rehydration in one such plant – Haberlea rhodopensis was monitored non-destructively and compared with botanically similar, non-resurrection species Deinostigma eberhardtii. The research found that during drying, resurrection plant performs controlled, organized restructuring of water molecular network in its leaves as a preparation for full desiccation which is characterized by accumulation of water molecular dimers and water molecules with four hydrogen bonds, while free water molecules are drastically diminished. This regulation of water structure in the leaves appears to be the protective mechanism against dehydration-induced damages of the tissues which ensures survival in the absence of water. The discovery that water molecular structure is important for preservation of plant tissues not only opens up new possibilities for bioengineering of crops better adapted to combat climate changes but may also have important implications for food preservation industry, preservation of tissues in medicine and in biomedical applications.


1969 ◽  
Vol 24 (4) ◽  
pp. 375-377 ◽  
Author(s):  
G. Zundel ◽  
A. Murr

The OH stretching vibration of the water molecules in membranes of salts of polystyrene sulfonic acid is investigated by IR spectroscopy. In the series of the alkali ions anomalous behaviour of the position of this band is to be seen. If one compares the position of this band with the corresponding one in pure liquid water this anomality is to be understood like follows: From Li⊕ to Cs⊕ in a progressing degree the molecules of water are not still attached between cation and neighboring anions, but they are present as network of „pure“ water structure cross-linked by hydrogen bonds in the neighbourhood of the ions. A similar situation but to an even greater extend is found in the presence of alkyl ammonium ions. These ions are interacting more strongly with the - SO3⊝ ions. The reasons for this are given. By these results it is understandable that in biological membranes the alkyl ammonium group of the lecithins and sphingomyelines - as postulated by FINEAN - are turned away the surface inwardly in the membran. In the end the different hydration behaviour of the Na⊕ and K⊕ ions is discussed.


2019 ◽  
Author(s):  
Jiarun Zhou ◽  
Nurun Nahar Lata ◽  
Sapna Sarupria ◽  
will cantrell

We studied thin films of water at the mica-air interface using infrared spectroscopy and molecular dynamics simulations. We investigate the influence of ions on interfacial water by exchanging the naturally occurring K<sup>+</sup> ion with H<sup>+</sup>/Na<sup>+</sup>, Ca<sup>2+</sup>, and Mg<sup>2+</sup>. The experiments do not show a difference in the bulk structure (<i>i. e.</i> in the infrared spectra), but indicate that water is more strongly attracted to the Mg<sup>2+</sup> mica. The simulations reveal that the cation-water interactions significantly influence the microscopic arrangement of water on mica. Our results indicate that the divalent cations result in strong water-mica interactions, which leads to longer hydrogen bond lifetimes and larger hydrogen bonded clusters of interfacial water molecules. These results have implications for surface-mediated processes such as heterogeneous ice nucleation, protein assembly and catalysis.


2021 ◽  
Vol 56 (31) ◽  
pp. 17844-17859
Author(s):  
Shin Yagihara ◽  
Hironobu Saito ◽  
Hironori Sugimoto ◽  
Tsubasa Kawaguchi ◽  
Minoru Fukuzaki ◽  
...  

AbstractBroadband dielectric spectroscopy measurements were performed on naturally dried cotton cloth, and a recently developed analytical technique for fractal analysis of water structures was applied to obtain existential states and locations of water molecules in the material. Three relaxation processes observed in GHz, MHz, and kHz frequency regions were attributed to dynamic behaviors of hydrogen bonding networks (HBNs) of water and interacting molecules, polymer chains with interacting ion and water molecules, and ions restricted on the interfaces of larger structures, respectively. Water molecules were heterogeneously distributed in the cotton cloth, and the HBNs remained as a broad GHz frequency process. Fractal analysis suggested that water molecules distributed in the material were characterized by a small value (0.55) of the Cole–Cole relaxation time distribution parameter, indicating spatial distribution of HBN fragments with various sizes in cotton cloth. This result was also supported by the T2 relaxation time obtained from nuclear magnetic resonance for naturally dried cotton yarn. Comparing previous results of dielectric relaxation measurements and fractal analysis with the τ–β diagram for various aqueous systems, the results determined that water molecules cannot exist inside cellulose microfibrils. The fractal analysis employed in this work can be applied to dynamic water structures in any material. The presented analytical technique with a universal τ–β diagram is expected to be an effective tool to clarify water structure detail even for heterogeneous hydrations of the low water content substances. Graphical abstract


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