scholarly journals The properties of buried ion pairs are governed by the propensity of proteins to reorganize

2020 ◽  
Author(s):  
Christos M. Kougentakis ◽  
Lauren Skerritt ◽  
Ananya Majumdar ◽  
Jamie L. Schlessman ◽  
Bertrand García-Moreno E.
Keyword(s):  
Ion Pairs ◽  
Experimental Studies ◽  
Ph Sensing ◽  
Coulomb Interactions ◽  
Structural Reorganization ◽  
Alternative Conformation ◽  
Spectroscopy Studies ◽  
Α Helix ◽  
Structural Adaptations ◽  
Electrostatic Calculations

AbstractCharges are incompatible with the hydrophobic interior of proteins, yet proteins use buried charges, often in pairs or networks, to drive energy transduction processes, catalysis, pH-sensing, and ion transport. The structural adaptations necessary to accommodate interacting charges in the protein interior are not well understood. According to continuum electrostatic calculations, the Coulomb interaction between two buried charges cannot offset the highly unfavorable penalty of dehydrating two charges. This was investigated experimentally with two variants of staphylococcal nuclease (SNase) with Glu:Lys or Lys:Glu pairs introduce at internal i, i+4 positions on an α-helix. Contrary to expectations from previous theoretical and experimental studies, the proteins tolerated the charged ion pairs in both orientations. Crystal structures and NMR spectroscopy studies showed that in both variants, side chains or backbone are reorganized. This leads to the exposure of at least one of the two buried groups to water. Comparison of these ion pairs with a highly stable buried ion pair in SNase shows that the location and the amplitude of structural reorganization can vary dramatically between ion pairs buried in the same general region of the protein. The propensity of the protein to populate alternative conformation states in which internal charges can contact water appears to be the factor that governs the magnitude of electrostatic effects in hydrophobic environments. The net effect of structural reorganization is to weaken the Coulomb interactions between charge pairs; however, the reorganized protein no longer has to pay the energetic penalty for burying charges. These results provide the framework necessary to understand the interplay between the dehydration of charges, Coulomb interactions and protein reorganization that tunes the functional properties of proteins.

Fourier transform infrared spectroscopy studies of cyanide ion solutions of dimethylformamide and aqueous dimethylformamide

1993 ◽  
Vol 71 (9) ◽  
pp. 1353-1361 ◽  
Author(s):  
David J. Jobe ◽  
Kenneth Charles Westaway
Keyword(s):  
Fourier Transform ◽  
Infrared Spectroscopy ◽  
Fourier Transform Infrared Spectroscopy ◽  
Ion Pairs ◽  
Fourier Transform Infrared ◽  
Phase System ◽  
Cyanide Ion ◽  
Two Phase ◽  
Solvated Ions ◽  
Spectroscopy Studies

Fourier transform infrared spectroscopy has been used to investigate the behaviour of HCN and alkali metal and tetraethylammonium cyanides in DMF and aqueous DMF. The cyanide ion exists as free ions and ion pairs in pure DMF but as water-solvated and DMF-solvated ions in aqueous DMF. The aqueous DMF solutions can be treated as a pseudo two-phase system with a distribution coefficient of 0.018 between the aqueous and DMF-rich pseudo phases. A kinetic analysis of the cyanide ion – benzyl chloride reaction in DMF and aqueous DMF has shown that the rate constant for the SN2 reaction is markedly decreased with the addition of as little as 2.5% water. This decrease is primarily due to changes in transition state solvation. The SN2 reactions between cyanide ion and benzylmethyl-4-substituted phenylsulphonium perchlorates in 20% aqueous DMF have also been investigated.

Double-Chamber Flow Cell for in situ Infrared Spectroscopy Studies of Chemical Reactions in Ziegler-Natta Catalyst Systems

1994 ◽  
Vol 48 (8) ◽  
pp. 985-993 ◽  
Author(s):  
Øystein Bache ◽  
Martin Ystenes
Keyword(s):  
Experimental Studies ◽  
Flow Cell ◽  
Infrared Transmission ◽  
Chemical Systems ◽  
Operation Conditions ◽  
Natta Catalyst ◽  
Catalyst Systems ◽  
Spectroscopy Studies ◽  
Solid Liquid

A complete experimental setup for in situ infrared transmission spectroscopy studies of solid/liquid reactions in Ziegler-Natta catalysts has been developed. The main part of the apparatus, the flow cell, facilitates separate recording of the liquid-phase spectrum and the superimposed solid/liquid spectrum, and thus allows solid and dissolved species during reactions to be distinguished. Addition of solutes and exchange of solution during the experiments are made possible, thus allowing subsequent reactions to be studied. The setup is suited also for liquid reactions, and, in principle, for other chemical systems as well. The construction of the flow cell and the operation conditions are based on pressure-drop calculations of the flow in the apparatus. Two experimental studies are included to demonstrate the use and to document the performance of the setup: (1) the reaction of MgCl2 with dissolved ethyl benzoate and AlEt3 in succession, and (2) the interaction of a MgCl2/ethyI benzoate support during TiCl4 treatment. In the latter, a hitherto unknown TiCl4/EB complex is discovered in the TiCl4 solution.

Nanodomains and local structure in ternary alkaline-earth hexaborides

2018 ◽  
Vol 51 (5) ◽  
pp. 1445-1454 ◽  
Author(s):  
Robert Koch ◽  
Peter C. Metz ◽  
Oscar Jaime ◽  
C. Ingram Vargas-Consuelos ◽  
Raúl Borja-Urby ◽  
...  
Keyword(s):  
Raman Spectroscopy ◽  
Alkaline Earth ◽  
Experimental Studies ◽  
X Ray ◽  
Transmission Electron ◽  
Sample Composition ◽  
Pdf Analysis ◽  
High Resolution Tem ◽  
Cation Radius ◽  
Spectroscopy Studies

The local structures of ternary alkaline-earth hexaborides (MB6, M = Ca0.5Sr0.5, Ca0.5Ba0.5 and Sr0.5Ba0.5) have been analysed using X-ray pair distribution function (PDF) analysis, Raman spectroscopy and transmission electron microscopy (TEM). The results show significant local deviations from the average cubic structure within the boron sub-lattice and support the conclusion that rapid synthesis processes lead to the formation of coherent nanodomains over length scales of about 10 nm. Reverse Monte Carlo fitting of the PDFs allows for quantification of the displacement disorder within the boron sub-lattice as a function of sample composition. Detailed Raman spectroscopy studies and high-resolution TEM support the models derived from X-ray scattering. The average magnitude of the static displacement disorder varies by sample composition and positively correlates with the cation radius ratios across the three compositions. The new models form a foundation for future computational and experimental studies aimed at understanding and predicting properties of hexaborides.

scholarly journals Structural adaptation of vertebrate endonuclease G for 5-hydroxymethylcytosine recognition and function

2020 ◽  
Vol 48 (7) ◽  
pp. 3962-3974 ◽  
Author(s):  
Crystal M Vander Zanden ◽  
Ryan S Czarny ◽  
Ethan N Ho ◽  
Adam B Robertson ◽  
P Shing Ho
Keyword(s):  
Dna Cleavage ◽  
Holliday Junctions ◽  
Structural Adaptation ◽  
Endonuclease G ◽  
Dna Binding Site ◽  
Modified Dna ◽  
Recombination Processes ◽  
Α Helix ◽  
And Function ◽  
Structural Adaptations

Abstract Modified DNA bases functionally distinguish the taxonomic forms of life—5-methylcytosine separates prokaryotes from eukaryotes and 5-hydroxymethylcytosine (5hmC) invertebrates from vertebrates. We demonstrate here that mouse endonuclease G (mEndoG) shows specificity for both 5hmC and Holliday junctions. The enzyme has higher affinity (>50-fold) for junctions over duplex DNAs. A 5hmC-modification shifts the position of the cut site and increases the rate of DNA cleavage in modified versus unmodified junctions. The crystal structure of mEndoG shows that a cysteine (Cys69) is positioned to recognize 5hmC through a thiol-hydroxyl hydrogen bond. Although this Cys is conserved from worms to mammals, a two amino acid deletion in the vertebrate relative to the invertebrate sequence unwinds an α-helix, placing the thiol of Cys69 into the mEndoG active site. Mutations of Cys69 with alanine or serine show 5hmC-specificity that mirrors the hydrogen bonding potential of the side chain (C–H < S–H < O–H). A second orthogonal DNA binding site identified in the mEndoG structure accommodates a second arm of a junction. Thus, the specificity of mEndoG for 5hmC and junctions derives from structural adaptations that distinguish the vertebrate from the invertebrate enzyme, thereby thereby supporting a role for 5hmC in recombination processes.

Terahertz Spectroscopy Studies of Solid-State Salicylic Acid

2015 ◽  
Vol 1117 ◽  
pp. 65-68
Author(s):  
Kateryna Zelenska ◽  
Hiroko Kimura ◽  
Tetsuo Sasaki ◽  
Toru Aoki ◽  
Volodymyr Gnatyuk
Keyword(s):  
Salicylic Acid ◽  
Solid State ◽  
Density Functional ◽  
Organic Molecules ◽  
Terahertz Spectroscopy ◽  
Experimental Studies ◽  
State Density ◽  
Functional Theory ◽  
Absorbance Spectroscopy ◽  
Spectroscopy Studies

Molecular and lattice vibration frequencies of solid-state salicylic acid were studied in the Terahertz (THz) and Mid-Infrared (Mid-IR) ranges. The calculation of the THz and Mid-IR spectra of salicylic acid which was based on the solid-state density functional theory (DFT) was carried out. Experimental studies were conducted by THz absorbance spectroscopy and Fourier transform infrared spectroscopy (FTIR) methods. Vibrations revealed in “finger-print” spectrum of salicylic acid were compared with the typical vibrations of groups of atoms that make up organic molecules.

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