Matrix-isolation IR studies on the basic interaction sites in esters and thiolesters towards proton donors

Maes, Guido; Smolders, A; Vandevyvere, P; Vanderheyden, L.; Zeegers‐Huyskens, Th.

doi:10.1016/0022-2860(88)80066-8

Cited by 13 publications

(3 citation statements)

References 19 publications

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“…This large shift corresponds to a change in bond length of only 0Á02 Å ! Formation of a single hydrogen bond to a C==O group leads to a 20 cm x1 downshift for the methyl acetatewater complex in an argon matrix (Maes & Zeegers-Huyskens, 1983 ;Maes et al 1988) and of 25 cm x1 for propionic acid in an ethanol/hexane (1 : 200 ) mixture (Dioumaev & Braiman, 1995).…”

Section: Information That Can Be Derived From the Vibrational Spectrummentioning

confidence: 99%

What vibrations tell about proteins

Barth

Zscherp

2002

Quart. Rev. Biophys.

1,859

123

2,185

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This review deals with current concepts of vibrational spectroscopy for the investigation of protein structure and function. While the focus is on infrared (IR) spectroscopy, some of the general aspects also apply to Raman spectroscopy. Special emphasis is on the amide I vibration of the polypeptide backbone that is used for secondary-structure analysis. Theoretical as well as experimental aspects are covered including transition dipole coupling. Further topics are discussed, namely the absorption of amino-acid side-chains, 1H/2H exchange to study the conformational flexibility and reaction-induced difference spectroscopy for the investigation of reaction mechanisms with a focus on interpretation tools.

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Section: Information That Can Be Derived From the Vibrational Spectrummentioning

confidence: 99%

What vibrations tell about proteins

Barth

Zscherp

2002

Quart. Rev. Biophys.

1,859

123

2,185

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“…In model compound studies it was observed that the carbonyl stretching vibration may be reduced by 20 cm À1 due to the formation of a CQO group of methylacetate with water. [67][68][69] Several reports further show a linear relationship between the enthalpy of hydrogen bond formation (DH) and the change in frequency of the stretching vibration. 65,[70][71][72][73][74] It is known that the carbonyl group of methylacetate, which is often used as a model for Lys and Glu, shows a B1 cm À1 shift to a low frequency of CQO stretching with a favorable binding enthalpy of 1.7 kJ mol À1 .…”

Section: Ft-ir Studymentioning

confidence: 99%

Hydrogen bonding plays a significant role in the binding of coomassie brilliant blue-R to hemoglobin: FT-IR, fluorescence and molecular dynamics studies

Maity

Dolui

Maiti

2015

Phys. Chem. Chem. Phys.

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An analog of coomassie brilliant blue-R (CBB-R) was recently found to act as an antagonist to ATP-sensitive purinergic receptors (P2X7R) and has potential to be used in medicine. With the aim of understanding its transportation and distribution through blood, in this investigation, we measured the binding parameters of CBB-R with bovine hemoglobin (BHG). The molecule specifically bound to a single binding site of the protein with a stoichiometric ratio of 1 : 1 and the observed binding constant Ka was 3.5, 2.5, 2.0 and 1.5 × 10(5) M(-1) at 20 °C, 27 °C, 37 °C and 45 °C, respectively. The measured respective ΔG(0) values of the binding at four temperatures were -30.45, -22.44, -18.04 and -11.95 kJ mol(-1). The ΔH(0) (change in enthalpy) and ΔS(0) (change in entropy) values were -23.6 kJ mol(-1) and -70.66 J mol(-1) respectively in the binding process. The negative value of ΔH(0) and ΔS(0) indicated that the binding of the molecule was thermodynamically favorable. The best energy structure in the molecular docking analysis revealed that CBB-R preferred to be intercalated in the cavity among the α2, β1 and β2 subunits and the binding location was 7.4 Å away from Trp37 in the β2 subunit. The binding of the molecule with the protein was stabilized by hydrogen bonds involving the side chain of two amino acid residues. The residues were Lys104 and Glu101 in the β2 subunit. The binding was further stabilized via hydrogen bond formation between the amide group of the peptide backbone (residue Tyr145 of the β1 subunit) and CBB-R. A shift of the amide I (-C=O stretching) band frequency of ∼8 cm(-1) to low energy was ascribed to the hydrogen bond interaction involving the polypeptide carbonyl of the protein and the CBB-R molecule. In addition, two π-cation interactions between Lys99 of the α2 subunit and Lys104 of the β2 subunit and CBB-R contributed favorably in the binding processes. No substantial change in the soret and Q absorption bands of BHG could be observed in the presence of CBB-R. It indicated that the oxygen binding domain or the heme proximity was not blocked or substantially perturbed due to the binding of CBB-R. The circular dichroism and the molecular dynamics analysis further established that the binding interaction caused no significant alteration in the protein long range secondary structure.

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“…An infrared spectrum contains a wealth of information on a molecule and its environment, such as bond lengths, bond strengths (22,(48)(49)(50)(51)(52)(53)(54)(55)(56), conformational freedom (5,(57)(58)(59)(60)(61)(62), and hydrogen bonding (63)(64)(65)(66)(67)(68)(69)(70)(71)(72). Anything that changes the electron distribution of the bonds or the environment will change the vibrational frequency and therefore appear in the infrared spectrum.…”

Section: Information From Infrared Spectramentioning

confidence: 99%

Infrared Difference Spectroscopy as a Physical Tool to Study Biomolecules

Kumar

2013

Applied Spectroscopy Reviews

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Matrix-isolation IR studies on the basic interaction sites in esters and thiolesters towards proton donors

Cited by 13 publications

References 19 publications

What vibrations tell about proteins

What vibrations tell about proteins

Hydrogen bonding plays a significant role in the binding of coomassie brilliant blue-R to hemoglobin: FT-IR, fluorescence and molecular dynamics studies

Infrared Difference Spectroscopy as a Physical Tool to Study Biomolecules

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