scholarly journals Hydrogen bonding and protein perturbation in β-lactam acyl-enzymes of Streptococcus pneumoniae penicillin-binding protein PBP2x

1999 ◽  
Vol 338 (1) ◽  
pp. 153-159 ◽  
Author(s):  
Roger S. CHITTOCK ◽  
Simon WARD ◽  
Alan-Shaun WILKINSON ◽  
Patrick CASPERS ◽  
Barbara MENSCH ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Streptococcus Pneumoniae ◽  
Carbonyl Oxygen ◽  
Ethyl Esters ◽  
Soluble Form ◽  
Difference Spectra ◽  
Ester Carbonyl ◽  
Small Band ◽  
The Difference ◽  
Β Sheet

A soluble form of Streptococcus pneumoniae PBP2x, a molecular target of penicillin and cephalosporin antibiotics, has been expressed and purified. IR difference spectra of PBP2x acylated with benzylpenicillin, cloxacillin, cephalothin and ceftriaxone have been measured. The difference spectra show two main features. The ester carbonyl vibration of the acyl-enzyme is ascribed to a small band between 1710 and 1720 cm-1, whereas a much larger band at approx. 1640 cm-1 is ascribed to a perturbation in the structure of the enzyme, which occurs on acylation. The protein perturbation has been interpreted as occurring in β-sheet. The acyl-enzyme formed with benzylpenicillin shows the lowest ester carbonyl vibration frequency, which is interpreted to mean that the carbonyl oxygen is the most strongly hydrogen-bonded in the oxyanion hole of the antibiotics studied. The semi-synthetic penicillin cloxacillin is apparently less well organized in the active site and shows two partially overlapping ester carbonyl bands. The penicillin acyl-enzyme has been shown to deacylate more slowly than that formed with cloxacillin. This demonstrates that the natural benzylpenicillin forms a more optimized and better-bonded acyl-enzyme and that this in turn leads to the stabilization of the acyl-enzyme required for effective action in the inhibition of PBP2x. The energetics of hydrogen bonding in the several acyl-enzymes is discussed and comparison is made with carbonyl absorption frequencies of model ethyl esters in a range of organic solvents. A comparison of hydrolytic deacylation with hydroxaminolysis for both chymotryspin and PBP2x leads to the conclusion that deacylation is uncatalysed.

scholarly journals Hydrogen-bonding in enzyme catalysis. Fourier-transform infrared detection of ground-state electronic strain in acyl-chymotrypsins and analysis of the kinetic consequences

1990 ◽  
Vol 270 (3) ◽  
pp. 627-637 ◽  
Author(s):  
A J White ◽  
C W Wharton
Keyword(s):  
Hydrogen Bonding ◽  
Oxygen Atom ◽  
Difference Spectrum ◽  
Binding Mode ◽  
Carbonyl Oxygen ◽  
Carbonyl Oxygen Atom ◽  
Rate Theory ◽  
Active Centre ◽  
Ester Carbonyl ◽  
Bond Strengths

I.r. difference spectra are presented for 3-(indol-3-yl)acryloyl-, cinnamoyl-, 3-(5-methylthien-2-yl)acryloyl-, dehydrocinnamoyl- and dihydrocinnamoyl-chymotrypsins at low pH, where the acyl-enzymes are catalytically inactive. At least two absorption bands are seen in each case in the ester carbonyl stretching region of the spectrum. Cinnamoyl-chymotrypsin substituted at the carbonyl carbon atom with 13C was prepared. A difference spectrum in which 13C-substituted acyl-enzyme was subtracted from [12C]acyl-enzyme shows two bands in the ester carbonyl region and thus confirms the assignment of the features to the single ester carbonyl group. The frequencies of the ester carbonyl bands are interpreted in terms of differential hydrogen-bonding. In each case a lower-frequency relatively narrow band is assigned to a productive potentially reactive binding mode in which the carbonyl oxygen atom is inserted in the oxyanion hole of the enzyme active centre. The higher-frequency band, which is broader, is assigned to a non-productive binding mode in each case, where a water molecule bridges from the carbonyl oxygen atom to His-57; this mode is equivalent to the crystallographically determined structure of 3-(indol-3-yl)acryloyl-chymotrypsin, i.e. the Henderson structure. A difference spectrum of dihydrocinnamoyl-chymotrypsin taken at higher pH shows resolution of a feature centred upon 1731 cm-1, which is assigned to a non-bonded conformer in which the carbonyl oxygen atom is not hydrogen-bonded. Perturbation of the protein spectrum in the presence of acyl groups is interpreted in terms of enhanced structural rigidity. It is reported that the ester carbonyl region of the difference spectrum of cinnamoyl-subtilisin is complicated by overlap of features that arise from protein perturbation. Measurements of carbonyl absorption frequencies in a number of solvents of the methyl esters of the acyl groups used to make acyl-enzymes have permitted determination of the apparent dielectric constants experienced by carbonyl groups in the enzyme active centre as well as a discussion of the effects of polarity. The ester carbonyl bond strengths of the various conformations were estimated by using simple harmonic oscillator theory and an empirical relation between the force constants and bond strengths. The fractional bond breaking induced by hydrogen-bonding was used to calculate rate enhancement factors by using absolute reaction rate theory.(ABSTRACT TRUNCATED AT 400 WORDS)

Dissolution of Amyloid Aggregates in Aqueous Ionic Liquid Solutions: A Case Study of Insulin Amyloid

2019 ◽  
Vol 72 (2) ◽  
pp. 81 ◽  
Author(s):  
Takahiro Takekiyo ◽  
Yuka Ishikawa ◽  
Erika Yamaguchi ◽  
Natsuki Yamada ◽  
Yukihiro Yoshimura
Keyword(s):  
Ionic Liquid ◽  
Hydrogen Bonding ◽  
Ionic Liquids ◽  
Bovine Insulin ◽  
Future Design ◽  
Amyloid Aggregates ◽  
Liquid Solutions ◽  
The Difference ◽  
Β Sheet

Dissolution of amyloid aggregates with high β-sheet content is required for the correct refolding of ordered protein aggregates. The dissolution of bovine insulin amyloid aggregates in five different ionic liquids (ILs) is investigated. These were comprised of three 1-butyl-3-methylimidazolium ([bmim])-based ILs, containing either SCN−, NO3−, or Cl− anions, and two alkylammonium nitrate-based ILs, ethyl- and propylammonium nitrate (EAN and PAN). A broad IL concentration range (x=0–30mol-% IL) was analysed using FTIR spectroscopy combined with the Congo red assay. On the whole, the [bmim]-based ILs showed a higher dissolution ability than EAN and PAN for all concentrations of x. It is notable that the dissolution ability of dilute aqueous IL solutions (x<15) for insulin amyloid was different to that of concentrated aqueous IL solutions (x>15). The former condition for insulin amyloid may affect dissolution based on the denaturant effect of cations and anions in the ILs. The latter condition may affect this dissolution based on the hydrogen-bonding ability (α and β values) of the ILs, as described by the Kamlet–Taft parameters. Moreover, the difference between these α and β values (α–β) was found to be a good indicator of the dissolution ability of ILs for insulin amyloid aggregates in concentrated conditions above x=20 (α–β<0, strong dissolution ability; α–β>0, weak dissolution ability). These findings may assist the future design of aqueous IL-based dissolution agents for ordered aggregated proteins.

scholarly journals Free water molecules and hydrogen bonding form the basis of variation in homeopathic potencies as revealed by vibrational spectroscopy

2021 ◽  
Vol 14 (4) ◽  
pp. 08-15
Author(s):  
Tandra Sarkar ◽  
Atheni Konar ◽  
Nirmal Chandra Sukul ◽  
Anirban Sukul ◽  
Indrani Chakraborty ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Free Water ◽  
Difference Spectrum ◽  
Wave Number ◽  
Water Molecules ◽  
Distilled Water ◽  
Half Maximum ◽  
Difference Spectra ◽  
The Difference ◽  
Wave Number Region

Objective: Using Fourier Transform Infrared spectroscopy (FTIR) we have demonstrated that homeopathic potencies of Natrum mur, Cantharis, Nux vomica and Sulphur show differences with respect to the number of free water molecules and strength of hydrogen bonding. The purpose of the present study is to confirm this phenomenon in three potencies of two more drugs Calcarea carb and Silicea. Design: The potencies used for each of the two drugs were 30cH, 200cH and 1000cH. The control was 90% ethanol as also the potentized drugs. The control, as well as the potencies, were diluted with distilled water to reduce the level of ethanol to 0.03 molar fraction in each of them. FTIR spectra of all the potentized drugs, control and sterile distilled water (reference water) were taken in the wave number region of 4000-2800 cm-1. The full width at half maximum (fwhm) of OH band was measured for each spectrum. The width was divided into two in the middle. The difference spectrum (absorbance of drug solution - absorbance of reference water) for each potency and the control was obtained after normalization of the spectrum at 3410 cm-1. One difference spectrum so obtained for a potency was subtracted from another to find out if there is a difference between two different potencies. Results: The half width half maximum (hwhm) in both the high and low-frequency sides of the OH band is far less narrow in potencies than in the control as compared to that in water. The difference spectra for different potencies show different levels of fall in intensity at the wave number region of dip at 3630 cm-1. The level of dip at 3630 cm-1 and subsequent rise in intensity in the lower frequency region represent the quantity of free water molecules and strong alcoholic OH bond around 3250 cm-1, respectively. The results of subtraction between two different potencies are not zero but have marked positive or negative values. Conclusion (i) Potencies have stronger intermolecular interactions and a higher number of chemical environments than the control, as revealed by the data on hwhm. (ii) The three potencies of each of the two drugs show distinct variation in the number of free water molecules and strength of hydrogen bonding. (iii) There exists both inter-drug and inter-potency variation as revealed by the difference spectra and results of subtraction between two difference spectra.

scholarly journals Analysis and elimination of protein perturbation in infrared difference spectra of acyl-chymotrypsin ester carbonyl groups by using 13C isotopic substitution

1992 ◽  
Vol 287 (1) ◽  
pp. 317-323 ◽  
Author(s):  
A J White ◽  
K Drabble ◽  
S Ward ◽  
C W Wharton
Keyword(s):  
Hydrogen Bonding ◽  
Carbonyl Group ◽  
Ground State ◽  
Difference Method ◽  
Deuterium Oxide ◽  
Spectral Features ◽  
Difference Spectra ◽  
Oxyanion Hole ◽  
Ester Carbonyl ◽  
Ester Carbonyl Group

I.r. spectroscopy has been applied to the study of hydrogen-bonding of the unique ester carbonyl group of acylchymotrypsins in the oxyanion hole of the enzyme. This catalytic device provides electrophilic stabilization of negative charge in the transition states and tetrahedral intermediates along the reaction pathway. The use of 13C isotope substitution of the ester carbonyl group reinforces the previous observation [White & Wharton (1990) Biochem. J. 270, 627-637] that the ester carbonyl group is significantly polarized in the ground state by hydrogen bonding in the oxyanion hole. I.r. difference spectra of [carbonyl-12C]-minus [carbonyl-13C]-cinnamoyl-chymotrypsin as well as each of these acylenzymes minus free enzyme are reported. These spectra show that the contribution of protein perturbation (i.e. spectral features that arise from the enzyme which is distorted on acylation) in [carbonyl-12C]cinnamoyl-chymotrypsin minus free enzyme spectra is significant. The contribution of the perturbation components of the spectra is pH-dependent and can represent up to 50% of the total absorbance in the spectral region from 1690 to 1740 cm-1. Use of the isotopic difference method has allowed problems associated with protein perturbation to be eliminated. Similar difference spectra are presented for dihydrocinnamoyl-chymotrypsin. In this case the effect of perturbation is very marked and leads to the cancellation of the band assigned to the non-bonded conformation of the acyl group which has previously only been observed at higher pH. The isotopic difference method again proves reliable and shows that the frequency difference previously used to calculate the ground-state electronic strain induced by the oxyanion-hole catalytic device is not affected by the perturbation, although the amplitudes of the spectral features are different. A study of the deacylation of cinnamoyl-chymotrypsin in water and deuterium oxide using both u.v. and i.r. spectroscopies has confirmed that the use of deuterium oxide as solvent has no serious effect on the deacylation behaviour of the enzyme. I.r. bands assigned to nonproductive and productive conformers decline identically during deacylation, which shows that the conformers are in dynamic exchange on the reaction time-scale.

Participation of 19-ester groups in the cleavage of 2α,3α- and 5α,6α-steroid epoxides. A case of competition between participation and external nucleophile attack

1979 ◽  
Vol 44 (5) ◽  
pp. 1496-1509 ◽  
Author(s):  
Pavel Kočovský ◽  
Václav Černý
Keyword(s):  
Perchloric Acid ◽  
Hydrobromic Acid ◽  
Ester Group ◽  
Carbonyl Oxygen ◽  
Cyclic Carbonate ◽  
Cyclic Ether ◽  
Normal Reaction ◽  
Neighboring Group ◽  
Ether Oxygen ◽  
The Difference

Acid cleavage of the acetoxy epoxide IIIa with aqueous perchloric acid or hydrobromic acid gave two types of products, i.e. the diol Va or the bromohydrin VIa, and the cyclic ether VIII. The latter compound arises by participation of ether oxygen of the ester group. On reaction with perchloric acid the epoxide IVa gave the diol XIIIa as a product of a normal reaction and the isomeric diol Xa as a product arising by intramolecular participation of the carbonyl oxygen of the 19-acetoxy group. Participation of the 19-ester group is confirmed by the formation of the cyclic carbonate XI when the 19-carbonate IVb is treated analogously. On reaction with hydrobromic acid, the epoxide IVa gave solely the bromohydrin XIVa as a product of the normal reaction course. Discussed is the similarity of these reactions with electrophilic additions to the related 19-acetoxy olefins I and II, the mechanism, the difference in behavior of both epoxides III and IV, the dependence of the product ratio on the nucleophility of the attacking species, and the competition between participation of an ambident neighboring group and an external nucleophile attack.

scholarly journals Theoretical Study of the Structures of 4-(2,3,5,6-Tetrafluoropyridyl)Diphenylphosphine Oxide and Tris(Pentafluorophenyl)Phosphine Oxide: Why Does the Crystal Structure of (Tetrafluoropyridyl)Diphenylphosphine Oxide Have Two Different P=O Bond Lengths?

Molecules ◽  
2020 ◽  
Vol 25 (12) ◽  
pp. 2778
Author(s):  
Joseph R. Lane ◽  
Graham C. Saunders
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Phosphine Oxide ◽  
Density Functional ◽  
Lone Pair ◽  
Diphenylphosphine Oxide ◽  
Functional Theory ◽  
Weak Hydrogen Bonding ◽  
Independent Molecules ◽  
The Difference

The crystal structure of 4-(2,3,5,6-tetrafluoropyridyl)diphenylphosphine oxide (1) contains two independent molecules in the asymmetric unit. Although the molecules are virtually identical in all other aspects, the P=O bond distances differ by ca. 0.02 Å. In contrast, although tris(pentafluorophenyl)phosphine oxide (2) has a similar crystal structure, the P=O bond distances of the two independent molecules are identical. To investigate the reason for the difference, a density functional theory study was undertaken. Both structures comprise chains of molecules. The attraction between molecules of 1, which comprises lone pair–π, weak hydrogen bonding and C–H∙∙∙arene interactions, has energies of 70 and 71 kJ mol−1. The attraction between molecules of 2 comprises two lone pair–π interactions, and has energies of 99 and 100 kJ mol−1. There is weak hydrogen bonding between molecules of adjacent chains involving the oxygen atom of 1. For one molecule, this interaction is with a symmetry independent molecule, whereas for the other, it also occurs with a symmetry related molecule. This provides a reason for the difference in P=O distance. This interaction is not possible for 2, and so there is no difference between the P=O distances of 2.

The interaction of bovine milk caseins with the detergent sodium dodecyl sulphate. II. The effect of detergent binding on spectral properties of caseins

1970 ◽  
Vol 37 (2) ◽  
pp. 259-267 ◽  
Author(s):  
G. C. Cheeseman ◽  
Dorothy J. Knight
Keyword(s):  
Sodium Dodecyl Sulphate ◽  
Sodium Dodecyl ◽  
Bovine Milk ◽  
Difference Spectrum ◽  
Temperature Dependent ◽  
Difference Spectra ◽  
Negative Change ◽  
Tryptophan Residues ◽  
Hydrophobic Binding ◽  
The Difference

SummaryThe dissociation of casein aggregates by the detergent sodium dodecyl sulphate (SDS) gave rise to difference spectra and these spectra were characteristic for each of the different types of casein. Increase in absorption by the chromophore groups, tyrosine and tryptophan, when αs1- and β-casein aggregates were dissociated indicated binding of the detergent at regions of the molecule containing these residues. A decrease in absorption when κ-casein was dissociated indicated that the tyrosine and tryptophan residues were not in the region of the molecule to which the detergent was bound and that in the κ-casein aggregate these residues were in a more hydrophobic environment. Peaks on the difference spectra were obtained at 280 and 288 nm for αs1-casein and 284 and 291 nm for β-casein and troughs at 278 and 286 nm for κ-casein. The difference spectrum reached a maximum value when the αsl- and β-casein aggregates were dissociated and the further binding of SDS did not alter this value. The large negative change in the difference spectrum of κ-casein did not occur until after most of the aggregates were dissociated and did not reach a maximum until binding with SDS was complete. The value obtained for ΔOD was found to be temperature-dependent for β-casein-SDS interaction, but not for αs1- and κ-casein. Changes in spectra were also observed when αs1- and κ-casein interacted to form aggregates. The data obtained confirmed the importance of hydrophobic binding in casein aggregate formation and indicated the possible involvement of tyrosine and tryptophan residues in this binding.

scholarly journals Probing the Role of Backbone Hydrogen Bonding in a Critical β Sheet of the Extracellular Domain of a Cys-Loop Receptor

ChemBioChem ◽  
2009 ◽  
Vol 10 (8) ◽  
pp. 1385-1391 ◽  
Author(s):  
Kristin R. Gleitsman ◽  
Henry A. Lester ◽  
Dennis A. Dougherty
Keyword(s):  
Hydrogen Bonding ◽  
Extracellular Domain ◽  
Β Sheet

The antioxidant methyl 3-(3,5-di-tert-butyl-4-hydroxyphenyl)propionate

2014 ◽  
Vol 70 (11) ◽  
pp. 1050-1053 ◽  
Author(s):  
Xiang Li ◽  
Zhi-Gang Wang ◽  
Hou-He Chen ◽  
Sheng-Gao Liu
Keyword(s):  
Hydrogen Bonding ◽  
Dimethyl Sulfoxide ◽  
Methyl Acrylate ◽  
Title Compound ◽  
Intermolecular Hydrogen Bonding ◽  
Tert Butyl ◽  
Ester Carbonyl ◽  
Compound C ◽  
Steric Crowding

The title compound, C18H28O3, was prepared by the reaction of 2,6-di-tert-butylphenol with methyl acrylate under basic conditions using dimethyl sulfoxide as the promoter. The structure of this antioxidant indicates significant strain between theortho tert-butyl substituents and the phenolic OH group. In spite of the steric crowding of the OH group, it participates in intermolecular hydrogen bonding with the ester carbonyl O atom.

scholarly journals Assessment of Conformational Changes in Low-Sulphur S-Carboxymethylkerateine from Wool

1967 ◽  
Vol 20 (4) ◽  
pp. 827 ◽  
Author(s):  
GM Bhatnagar ◽  
WG Crewther
Keyword(s):  
Absorption Spectrum ◽  
Conformational Changes ◽  
Guanidine Hydrochloride ◽  
Ultraviolet Absorption Spectrum ◽  
Spectral Measurements ◽  
Characteristic Difference ◽  
Concentrated Solutions ◽  
Difference Spectra ◽  
The Difference ◽  
Negative Difference

The effects of urea and guanidine hydrochloride on the ultraviolet absorption spectrum of the low-sulphur S-carboxymethylkerateine fraction of wool have been measured. In concentrated solutions of urea characteristic difference spectra were obtained with maxima of negative absorbance at 288, 280, and 240 miL. The addition of guanidine hydrochloride or an increase in temperature gave similar negative difference maxima at the higher wavelengths. Calculation of the extent of unfolding of the protein chains from the difference in absorbance at all three maxima showed that the unfolding was 50% complete at a urea concentration of about 1� 8M whereas a urea concep.tration of about 4� 3M was required to decrease the helix content by 50%. Similar measurements on components 7 and 8, the two major constituents of SCMKA, showed that a 50% decrease in helix content was obtained with 2�8M and O� 8M urea respectively whereas the corresponding values for 50 % unfolding assessed from difference spectral measurements were 2� 2M and 1� 2M urea respectively. It is suggested that the helical regions of components 7 and 8 aggregate specifically and that spectral measurements relate largely to non-helical portions of the chains.

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