Reorientation of water molecules in solid hydrates. Correlation with spectroscopic and structural data

1991 ◽  
Vol 87 (8) ◽  
pp. 1193 ◽  
Author(s):  
Karin Larsson ◽  
J�rgen Tegenfeldt ◽  
Kersti Hermansson
Keyword(s):  
Structural Data ◽  
Water Molecules

scholarly journals The role of conserved surface hydrophobic residues in the carbapenemase activity of the class D β-lactamases

2017 ◽  
Vol 73 (8) ◽  
pp. 692-701 ◽  
Author(s):  
Marta Toth ◽  
Clyde A. Smith ◽  
Nuno T. Antunes ◽  
Nichole K. Stewart ◽  
Lauren Maltz ◽  
...  
Keyword(s):  
Water Molecule ◽  
Active Site ◽  
Clinical Importance ◽  
Catalytic Efficiency ◽  
Structural Data ◽  
Molecular Surface ◽  
Water Molecules ◽  
Hydrophobic Residues ◽  
Class D ◽  
Life Threatening

Carbapenem-hydrolyzing class D β-lactamases (CHDLs) produce resistance to the last-resort carbapenem antibiotics and render these drugs ineffective for the treatment of life-threatening infections. Here, it is shown that among the clinically important CHDLs, OXA-143 produces the highest levels of resistance to carbapenems and has the highest catalytic efficiency against these substrates. Structural data demonstrate that acylated carbapenems entirely fill the active site of CHDLs, leaving no space for water molecules, including the deacylating water. Since the entrance to the active site is obstructed by the acylated antibiotic, the deacylating water molecule must take a different route for entry. It is shown that in OXA-143 the movement of a conserved hydrophobic valine residue on the surface opens a channel to the active site of the enzyme, which would not only allow the exchange of water molecules between the active site and the milieu, but would also create extra space for a water molecule to position itself in the vicinity of the scissile bond of the acyl-enzyme intermediate to perform deacylation. Structural analysis of the OXA-23 carbapenemase shows that in this enzyme movement of the conserved leucine residue, juxtaposed to the valine on the molecular surface, creates a similar channel to the active site. These data strongly suggest that all CHDLs may employ a mechanism whereupon the movement of highly conserved valine or leucine residues would allow a water molecule to access the active site to promote deacylation. It is further demonstrated that the 6α-hydroxyethyl group of the bound carbapenem plays an important role in the stabilization of this channel. The recognition of a universal deacylation mechanism for CHDLs suggests a direction for the future development of inhibitors and novel antibiotics for these enzymes of utmost clinical importance.

RAMAN AND FTIR SPECTRA OF RE(BrO3)3·9H2O(RE = Eu, Tb) AND ELECTRONIC TRANSITIONS IN Eu(BrO3)3·9H2O

2001 ◽  
Vol 15 (18) ◽  
pp. 2499-2507 ◽  
Author(s):  
M. J. BUSHIRI ◽  
V. U. NAYAR
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Raman Spectra ◽  
Structural Data ◽  
Ftir Spectra ◽  
Free State ◽  
Electronic Transitions ◽  
Water Molecules ◽  
Spectral Pattern ◽  
Bending Modes

Raman, FTIR spectra of Eu ( BrO 3)3·9 H 2 O and Tb ( BrO 3)3·9 H 2 O are recorded and analyzed. The observed bands are assigned on the basis of [Formula: see text] and H 2 O vibrations. Electronic transitions observed in the Raman spectra of Eu ( BrO 3)3· 9 H 2 O are also investigated. In Tb ( BrO 3)3·9 H 2 O the symmetry of [Formula: see text] anion is lowered from C 3 v to C s due to distortion. The wavenumber value of the ν1 mode of [Formula: see text] anion is found to be decreased from that of free state and is due to hydrogen bonding in the crystal. The decrease in wavenumber values of stretching modes and the increase in wavenumber values of the bending modes of water molecules from free state values confirm that they form hydrogen bonds with oxygen atoms are bromate ions in agreement with the structural data. Further the spectral pattern of water molecules indicates the presence of hydrogen bonds of varying strengths. The electronic transitions observed in Eu ( BrO 3)3·9 H 2 O suggest that Eu 3+ ions are situated in the crystal at sites having symmetry higher than C 2 or C 1.

scholarly journals Structure of plant Photosystem I-plastocyanin complex reveals strong hydrophobic interactions

2021 ◽  
Author(s):  
Ido Caspy ◽  
Mariia Fadeeva ◽  
Sebastian Kuhlgert ◽  
Anna Borovikova-Sheinker ◽  
Daniel Klaiman ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Genetic Engineering ◽  
Photosystem I ◽  
Ternary Complex ◽  
Hydrophobic Interactions ◽  
Structural Data ◽  
Water Molecules ◽  
Ferredoxin Oxidoreductase ◽  
Complex Forms ◽  
Oxidized Pc

Photosystem I is defined as plastocyanin-ferredoxin oxidoreductase. Taking advantage of genetic engineering, kinetic analyses and cryo-EM, our data provide novel mechanistic insights into binding and electron transfer between PSI and Pc. Structural data at 2.74 Å resolution reveals strong hydrophobic interactions in the plant PSI-Pc ternary complex, leading to exclusion of water molecules from PsaA-PsaB / Pc interface once the PSI-Pc complex forms. Upon oxidation of Pc, a slight tilt of bound oxidized Pc allows water molecules to accommodate the space between Pc and PSI to drive Pc dissociation. Such a scenario is consistent with the six times larger dissociation constant of oxidized as compared to reduced Pc and mechanistically explains how this molecular machine optimized electron transfer for fast turnover.

scholarly journals Structure of plant PSI-plastocyanin complex reveals strong hydrophobic interactions

2021 ◽  
Author(s):  
Ido Caspy ◽  
Mariia Fadeeva ◽  
Sebastian Kuhlgert ◽  
Anna Borovikova-Sheinker ◽  
Daniel Klaiman ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Genetic Engineering ◽  
Hydrophobic Interactions ◽  
Structural Data ◽  
Oxygenic Photosynthesis ◽  
Water Molecules ◽  
Major Step ◽  
Ferredoxin Oxidoreductase ◽  
Complex Forms ◽  
Oxidized Pc

AbstractPhotosystem I is defined as plastocyanin-ferredoxin oxidoreductase. Taking advantage of genetic engineering, kinetic analyses and cryo-EM, our data provide novel mechanistic insights into binding and electron transfer between PSI and Pc. Structural data at 2.74 Å resolution reveals strong hydrophobic interactions in the plant PSI-Pc ternary complex, leading to exclusion of water molecules from PsaA-PsaB / Pc interface once the PSI-Pc complex forms. Upon oxidation of Pc, a slight tilt of bound oxidized Pc allows water molecules to accommodate the space between Pc and PSI to drive Pc dissociation. Such a scenario is consistent with the six times larger dissociation constant of oxidized as compared to reduced Pc and mechanistically explains how this molecular machine optimized electron transfer for fast turnover.One Sentence SummaryGenetic engineering, kinetics and cryo-EM structural data reveal a mechanism in a major step of oxygenic photosynthesis

scholarly journals VERY LOW H–O–H BENDING FREQUENCIES. VI. VIBRATIONAL SPECTRA OF CdCl2·H2O

2017 ◽  
Vol 38 (1) ◽  
pp. 91
Author(s):  
Viktor Stefov ◽  
Metodija Najdoski ◽  
Bernward Engelen ◽  
Zlatko Ilievski ◽  
Adnan Cahil
Keyword(s):  
Hydrogen Bonds ◽  
Water Molecule ◽  
Gas Phase ◽  
Raman Spectra ◽  
Structural Data ◽  
Liquid Nitrogen Temperature ◽  
Water Molecules ◽  
Deuterium Content ◽  
Infrared And Raman Spectra ◽  
The Difference

The infrared and Raman spectra of CdCl2·H2O as well as those of a series of its partially deuterated analogues were recorded at room and at liquid-nitrogen temperature (RT and LNT, respectively). The combined results from the analysis of the spectra were used to assign the observed bands. In the difference IR spectrum of the compound with low deuterium content (≈ 4 % D) recorded at RT, one broad bands is observed at around 2590 cm–1 while in the LNT spectrum two bands appear (at 2584 cm–1 and 2575 cm–1). The appearance in the LNT spectrum of these two bands which are due to the stretching OD modes of the isotopically isolated HDO molecules points to the existance of two crystallographically different hydrogen bonds and is in accordance with the structural data for this compound. In the LNT infrared and Raman spectra of the protiated compound, one band, at 1583 cm-1, is observed in the region of the bending НОН vibrations with a frequency that is decreasing with lowering the temperature. An interesting finding related to this band is that its frequency is lower than that for the water molecule in the gas phase (1594 cm–1). In the RT and LNT IR spectra, only one strong band (at 560 cm–1) is observed in the region of the librations of water molecules (700 cm–1 – 400 cm–1).

scholarly journals Cooperative Allostery and Structural Dynamics of Streptavidin at Cryogenic- and Ambient-temperature

2021 ◽  
Author(s):  
Esra Ayan ◽  
Busra Yuksel ◽  
Ebru Destan ◽  
Fatma Betul Ertem ◽  
Gunseli Yildirim ◽  
...  
Keyword(s):  
Ambient Temperature ◽  
Structural Dynamics ◽  
Protein Complexes ◽  
Interaction Network ◽  
Structural Data ◽  
Water Molecules ◽  
Protein Assemblies ◽  
X Ray ◽  
Versatile Tool ◽  
Multimeric Protein

Multimeric protein assemblies are abundant in nature. Streptavidin is an attractive protein that provides a paradigm system to investigate the intra- and intermolecular interactions of multimeric protein complexes. Also, it offers a versatile tool for biotechnological applications. Here, we present two apo-streptavidin structures, the first one is an ambient temperature Serial Femtosecond X-ray crystal (Apo-SFX) structure at 1.7 Å resolution and the second one is a cryogenic crystal structure (Apo-Cryo) at 1.1 Å resolution. These structures are mostly in agreement with previous structural data. Combined with computational analysis, these structures provide invaluable information about structural dynamics of apo streptavidin. Collectively, these data further reveal a novel cooperative allostery of streptavidin which binds to substrate via water molecules that provide a polar interaction network and mimics the substrate biotin which displays one of the strongest affinities found in nature.

Crystal structure of ammonium cis-Tetraamminedisulfitocobaltate(III) trihydrate (a redetermination)

1978 ◽  
Vol 31 (5) ◽  
pp. 999 ◽  
Author(s):  
CL Raston ◽  
AH White ◽  
JK Yandell
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Least Squares ◽  
Title Compound ◽  
Structural Data ◽  
Water Molecules ◽  
Hydrogen Atoms ◽  
Full Matrix ◽  
The Difference

The crystal structure of the title compound, NH4 [Co(NH3)4(SO3)2],3H2O, has been redetermined using diffractometer data at 295 K and refined by full-matrix least squares to a residual of 0.056 for 2068 'observed' reflections. Crystals are orthorhombic, P212121, a 10.978(4), b 17.552(7), c 6.828(3)Ǻ, Z 4. The redetermined structure provides accurate structural data for the cobalt environment; as well, it locates all hydrogen atoms and defines cations and water molecules un- ambiguously. Co-S are 2.224(2), 2.221(2) Ǻ. Co-N (trans to S) (1.993(6), 2.023(6) Ǻ) are longer than the mutually trans Co-N (1.970(7), 1.977(6) Ǻ); the difference in the former is a consequence of lattice hydrogen bonding.

The organization and function of water in protein crystals

1977 ◽  
Vol 278 (959) ◽  
pp. 3-32 ◽  
Keyword(s):  
Protein Interactions ◽  
Active Sites ◽  
Structural Integrity ◽  
Bound Water ◽  
Structural Data ◽  
Protein Molecule ◽  
Biologically Active ◽  
Complex Nature ◽  
Water Molecules ◽  
And Function

Dry proteins are dead, or at best asleep. Substitution of D 2 O can drastically alter biological activity. Water is thus essential in maintaining the structural integrity of biologically active macromolecules, and is implicated in their functioning. Such water may occupy a range of dynamical states, from being strongly bound and localized, to more labile and ‘liquid-like’. Spatially ordering the macromolecules aids the search for the more localized water molecules. For example, diffraction experiments on single crystals can resolve ‘bound’ water molecules within a protein molecule - often at active sites, coordinated to metals or ions. Less precise information is obtained on the partially occupied external water sites, which are of importance to the folding and the dynamics of the biomolecule. Orientation of fibrous molecules increases the information obtainable from n.m.r. experiments. Combination of other experimental results on disordered aggregates (e.g. in solution) with chemical and structural data on the macromolecule and water itself yields useful, if circumstantial, information. Statistical and computer techniques may help to elucidate the complex nature of water-protein interactions, and to interpret the results of more complex experiments.

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