Water catalysis of peptide hydrogen isotope exchange

Gregory, Roger B.; Crabo, Lars G.; Percy, Amy J.; Rosenberg, Andreas

doi:10.1021/bi00273a031

Cited by 50 publications

(39 citation statements)

References 23 publications

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“…Water catalysis has been measured before. 3,4,25 The water rate found for NHs adjacent to apolar blocking side chains is smaller than for alanine and increases when the peptide group basicity is increased due to neighboring polar side chains (see below). Figure 7a shows that water rates found for the dipeptide NHs (L NHs) correlate with the side chain inductive effect measured by the shift in pD min .…”

Section: Water-catalyzed Ratementioning

confidence: 99%

“…(3). (3) We recommend use of the activation energies specified below Table III, obtained from available results 3,4,25 and the present work weighted to account for different levels of accuracy in the various data sets. These are 14, 17, and 19 kcal/mol for k A , k B , and k w , respectively.…”

Section: Temperature Dependencementioning

confidence: 99%

“…In aqueous solutions, peptide group HX is catalyzed by hydroxide and hydronium ions 2 in pH-dependent reactions and by water in a pHindependent way. 3,4 The contribution of all other potential catalysts is negligible. 5 HX rates are, however, significantly influenced by neighboring side chains even in the absence of folded structure.…”

Section: Introductionmentioning

confidence: 99%

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Primary structure effects on peptide group hydrogen exchange

et al. 1993

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The rate of exchange of peptide group NH hydrogens with the hydrogens of aqueous solvent is sensitive to neighboring side chains. To evaluate the effects of protein side chains, all 20 naturally occurring amino acids were studied using dipeptide models. Both inductive and steric blocking effects are apparent. The additivity of nearest-neighbor blocking and inductive effects was tested in oligo-and polypeptides and, surprisingly, confirmed. Reference rates for alanine-containing peptides were determined and effects of temperature considered. These results provide the information necessary to evaluate measured protein NH to ND exchange rates by comparing them with rates to be expected for the same amino acid sequence is unstructured oligo-and polypeptides. The application of this approach to protein studies is discussed.

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Section: Water-catalyzed Ratementioning

confidence: 99%

Section: Temperature Dependencementioning

confidence: 99%

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Primary structure effects on peptide group hydrogen exchange

et al. 1993

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“…The reaction scheme is then change process, which in practice is a pseudo first order reaction and k3(i) is the rate constant. The exchange reaction of an amide hydrogen can take place in a reaction directly with water or it can be catalyzed by acid (hydroxonium ions) or base (hydroxide ions) (Gregory et al, 1983;Perrin, 1989), such that the observed exchange rate k,(i) is the sum of contributions from each of these three reactions.…”

Section: And O N H ( I )mentioning

confidence: 99%

Mapping the lifetimes of local opening events in a native state protein

Kragelund¹,

Heinemann²,

Knudsen³

et al. 1998

Protein Science

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The rate constants for the processes that lead to local opening and closing of the structures around hydrogen bonds in native proteins have been determined for most of the secondary structure hydrogen bonds in the four-helix protein acyl coenzyme A binding protein. In an analysis that combines these results with the energies of activation of the opening processes and the stability of the local structures, three groups of residues in the protein structure have been identified. In one group, the structures around the hydrogen bonds have frequent openings, every 600 to 1,500 s, and long lifetimes in the open state, around 1 s. In another group of local structures, the local opening is a very rare event that takes place only every 15 to 60 h. For these the lifetime in the open state is also around 1 s. The majority of local structures have lifetimes between 2,000 and 20,000 s and relatively short lifetimes of the open state in the range between 30 and 400 ms. Mapping of these groups of amides to the tertiary structure shows that the openings of the local structures are not cooperative at native conditions, and they rarely if ever lead to global unfolding. The results suggest a mechanism of hydrogen exchange by progressive local openings.

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“…The term k3 is the rate constant for exchange once the labile site contacts the catalyst. This second step is primarily base catalyzed above pH 4 (McDonald & Phillips, 1973;Patel & Canuel, 1976;Englander & Kallenbach, 1984), but water itself can also react directly (Gregory et al, 1983). Acid catalysis occurs at lower pH (Perrin, 1989).…”

mentioning

confidence: 99%

Amide proton exchange rates of oxidized and reduced saccharomyces cerevisiae iso‐1‐cytochrome c

et al. 1993

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Proton NMR spectroscopy was used to determine the rate constant, kobs, for exchange of labile protons in both oxidized (Fe(II1)) and reduced (Fe(I1)) iso-1-cytochrome c. We find that slowly exchanging backbone amide protons tend to lack solvent-accessible surface area, possess backbone hydrogen bonds, and are present in regions of regular secondary structure as well as in Q-loops. Furthermore, there is no correlation between k,, and the distance from a backbone amide nitrogen to the nearest solvent-accessible atom. These observations are consistent with the local unfolding model. Comparisons of the free energy change for denaturation, A G d , at 298 K to the free energy change for local unfolding, AG,, at 298 K for the oxidized protein suggest that certain conformations possessing higher free energy than the denatured state are detected at equilibrium. Reduction of the protein results in a general increase in AG,. Comparisons of AGd to AG, for the reduced protein show that the most open states of the reduced protein possess more structure than its chemically denatured form. This persistent structure in high-energy conformations of the reduced form appears to involve the axially coordinated heme.

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Water catalysis of peptide hydrogen isotope exchange

Cited by 50 publications

References 23 publications

Primary structure effects on peptide group hydrogen exchange

Primary structure effects on peptide group hydrogen exchange

Mapping the lifetimes of local opening events in a native state protein

Amide proton exchange rates of oxidized and reduced saccharomyces cerevisiae iso‐1‐cytochrome c

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