Heats of Hydrolysis of Amide and Peptide Bonds

Dobry, Alan; Sturtevant, Julian M.

doi:10.1016/s0021-9258(19)50882-1

Cited by 35 publications

(6 citation statements)

References 8 publications

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“…The solutions were pumped at flow rates of 0.198 cm3 min"1 (insulin) and 0.206 cm3 min"1 (DTT). number of protons released from the buffer, n0, were determined from the intercept and the slope of the plots according to the relation described in the literature (Dobry & Sturtevant, 1952;Hinz et al, 1971). In this procedure, it was assumed that the enthalpies of ionization of the buffers are independent of temperature.…”

Section: Resultsmentioning

confidence: 99%

Enthalpy and heat capacity changes for the reduction of insulin

Fukada¹,

Takahashi²

1982

Biochemistry

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The enthalpy changes for the reduction of three disulfide bonds of insulin by dithiothreitol (DTT) were calorimetrically measured at various temperatures ranging from 289 to 308 K. The reduction was performed in three different buffer solutions of pH 9.6, and the observed heat changes were corrected for the ionization heats of the buffer components to obtain the net heats of reduction of insulin with DTT. By subtracting the enthalpy of DTT oxidation reported in the previous paper [Fukada, H., & Takahashi, K. (1980a) J. Biochem. (Tokyo) 87, 1105-1110], we determined the standard enthalpy of reduction of insulin to be delta Hr = 93.4 +/- 7.8 kJ (mol of insulin-1 at 298 K. The heat capacity change with delta Cp,r = 3.2 +/- 0.3 kJ mol-1 K-1. Using the heat of oxidation of the cysteine residue, we estimated the enthalpy change for the conformational transition of insulin induced by the cleavage of three disulfide bonds to be delta H conf = 91 kJ mol-1 at 298 K. The heat capacity change was 2.1 kJ mol-1 K-1. These results imply that the conformational transition taking place during the reduction of three disulfide bonds is thermodynamically of the same nature as the thermal denaturation observed for other globular proteins.

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Section: Resultsmentioning

confidence: 99%

Enthalpy and heat capacity changes for the reduction of insulin

Fukada¹,

Takahashi²

1982

Biochemistry

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“…Earlier studies investigated the heat generated by a catalytic reaction of some enzymes: [52] – [54] The heat increased the enzyme's diffusivity, [52] , [53] and the energy of the heat was about 5 kcal/mol. [54] The results raise the question of why the resultant heat does not cause severe denaturation of the active site. We speculated that if the heat dissipates into the hydration water molecules in D 1 , the active site may not be intensely perturbed.…”

Section: Resultsmentioning

confidence: 99%

Asymmetric dynamics of dimeric SARS-CoV-2 and SARS-CoV main proteases in an apo form: Molecular dynamics study on fluctuations of active site, catalytic dyad, and hydration water

Iida¹,

Fukunishi²

2021

BBA Advances

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been widely spread around the world. It is necessary to examine the viral proteins that play a notorious role in the invasion of our body. The main protease (3CL pro ) facilitates the maturation of the coronavirus. It is thought that the dimerization of 3CL pro leads to its catalytic activity; the detailed mechanism has, however, not been suggested. Furthermore, the structural differences between the predecessor SARS-CoV 3CL pro and SARS-CoV-2 3CL pro have not been fully understood. Here, we show the structural and dynamical differences between the two main proteases, and demonstrate the relationship between the dimerization and the activity via atomistic molecular dynamics simulations. Simulating monomeric and dimeric 3CL pro systems for each protease, we show that (i) global dynamics between the two different proteases are not conserved, (ii) the dimerization stabilizes the catalytic dyad and hydration water molecules behind the dyad, and (iii) the substrate-binding site (active site) and hydration water molecules in each protomer fluctuate asymmetrically. We then speculate the roles of hydration water molecules in their catalytic activity.

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“…The heat of formation of the peptide bond is 10.67 kJ mol À1 , and that of an amide bond is 24.43 kJ per mole. [22] The stability and properties that make DMF an attractive solvent would suggest that the molecule contains a very stable amide bond. The binding of water to Fe 3+ would make it a better nucleophile to attack the C À N bond of the formamide.…”

Section: Methodsmentioning

confidence: 99%

“…We compared this strain energy to the energy of a relaxed system (Figure 3 D). Electronic energies were calculated using density functional theory (DFT) with the B3LYP functional [20][21][22] and the 6-311G(d) basis set in Gaus-sian16 23 (Figure S8). The difference in the energies obtained between the strained and relaxed octahedral states with Fe 3+ ions is À222.01 kJ mol À1 (Table S3 in the Supporting information).…”

Section: A Distinctive Metal Sitementioning

confidence: 99%

A 2‐Tyr‐1‐carboxylate Mononuclear Iron Center Forms the Active Site of a Paracoccus Dimethylformamidase

et al. 2020

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N,N‐dimethyl formamide (DMF) is an extensively used organic solvent but is also a potent pollutant. Certain bacterial species from genera such as Paracoccus, Pseudomonas, and Alcaligenes have evolved to use DMF as a sole carbon and nitrogen source for growth via degradation by a dimethylformamidase (DMFase). We show that DMFase from Paracoccus sp. strain DMF is a halophilic and thermostable enzyme comprising a multimeric complex of the α2β2 or (α2β2)2 type. One of the three domains of the large subunit and the small subunit are hitherto undescribed protein folds of unknown evolutionary origin. The active site consists of a mononuclear iron coordinated by two Tyr side‐chain phenolates and one carboxylate from Glu. The Fe3+ ion in the active site catalyzes the hydrolytic cleavage of the amide bond in DMF. Kinetic characterization reveals that the enzyme shows cooperativity between subunits, and mutagenesis and structural data provide clues to the catalytic mechanism.

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Heats of Hydrolysis of Amide and Peptide Bonds

Cited by 35 publications

References 8 publications

Enthalpy and heat capacity changes for the reduction of insulin

Enthalpy and heat capacity changes for the reduction of insulin

Asymmetric dynamics of dimeric SARS-CoV-2 and SARS-CoV main proteases in an apo form: Molecular dynamics study on fluctuations of active site, catalytic dyad, and hydration water

A 2‐Tyr‐1‐carboxylate Mononuclear Iron Center Forms the Active Site of a Paracoccus Dimethylformamidase

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