Hydrogen Exchange

Englander, S. W.; Downer, Nancy W.; Teitelbaum, H

doi:10.1146/annurev.bi.41.070172.004351

Cited by 483 publications

(358 citation statements)

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“…Many models describing the protein dynamics that lead to hydrogen exchange in folded proteins have been proposed. These have all been described extensively in several reviews including the breathing model, the penetration model, the mobile defect model, the local unfolding model, and the global unfolding model (Hvidt & Nielsen, 1966;Englander et al, 1972;Englander, 1975: Richards, 1979Wagner & Wuthrich, 1979;Wood-ward & Hilton, 1979;Barksdale & Rosenberg, 1982;Wagner, 1982;Woodward et al, 1982).…”

Section: Hydrogen Exchangementioning

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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Section: Hydrogen Exchangementioning

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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“…1 this is indicated by the step-shaped efficiency curve. For the rotational motions of the aromatic side chains the critical reaction time is determined essentially by the moment of inertia of the aromatic ring, and for the isotope exchange this quantity is given by the intrinsic exchange rates (see Englander, Downer & Teitelbaum, 1972). This estimation of the critical reaction times is valid, however, only for amplitudes of fluctuations much larger than the minimum necessary amplitude.…”

Section: (B) Reactions Of Probes With the Solventmentioning

confidence: 99%

Characterization of the distribution of internal motions in the basic pancreatic trypsin inhibitor using a large number of internal NMR probes

Wagner

1983

Quart. Rev. Biophys.

274

197

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The experimental observations described in this article indicated that a distribution of many different fluctuations is present in a globular protein. These fluctuations were characterized by observation of many natural internal probes such as the labile peptide protons and the aromatic side chains. The conditions which are necessary to get reactions of the internal probes have been discussed in detail. The structural interpretation of the data was facilitated by the development and the use of new NMR techniques which provided the identification of the resonances of all the labile peptide protons. With NOE measurements a distinction between correlated and uncorrelated exchange events was obtained. This enabled us to elucidate the exchange mechanism over a wide range of p2H and temperature and to classify different subsets of fluctuations with respect to their lifetimes. It was further demonstrated that a change of external conditions such as temperature, p2H or pressure can change the distribution of fluctuations in the protein. The mechanisms responsible for rotation of internal aromatic side chains were also found to change with temperature, and mechanistic aspects of these fluctuations were discussed.

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“…However, the valuable information inherent in the rates for the fastest members of the slow-exchange group would be lost in the increased lag time between sample resolubilization and spectral acquisition. Fortunately, small differences in pH may be easily corrected for in the base-catalyzed regime of amide exchange by assuming a 10-fold increase in rate for every unit increase in pH (Englander et al, 1972). The actual rate dependence on pH may be somewhat less, because the pH dependence of the equilibrium constant of the exchange reaction often decreases slightly from pH 4 to pH 8 in cases where pHdependent protein stabilization occurs (Richarz et al, 1979).…”

Section: Structure Of the Recognition Modulementioning

confidence: 99%

“…At 35 "C, however, the exchange for many amide protons of Cd-GAL4 is too rapid to be measured accurately by the exchange-out method. Amide exchange was instead measured at 25 "C for Cd-GAL4, and temperature effects corrected for by assuming a threefold decrease in rate for the 10 "C decrease in temperature, as previously observed for amide exchange in peptides (Englander et al, 1972). The threefold decrease may be a slight undercompensation because proteins are often structurally sensitive to temperature.…”

Section: Structure Of the Recognition Modulementioning

confidence: 99%

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Effects of DNA binding and metal substitution on the dynamics of the GAL4 DNA‐binding domain as studied by amide proton exchange

Mau¹,

Baleja²,

Wagner³

1992

Protein Science

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Backbone amide proton exchange rates in the DNA-binding domain of GAL4 have been determined using 'H-''N heteronuclear correlation NMR spectroscopy. Three forms of the protein were studied-the native Zn-containing protein, the Cd-substituted protein, and a Zn-GAL4/DNA complex. Exchange rates in the Zncontaining protein are significantly slower than in the Cd-substituted protein. This shows that Cd-substituted GAL4 is destabilized relative to the native Zn-containing protein. Upon DNA binding, global retardation of amidz proton exchange with solvent was observed, indicating that internal fluctuations of the DNA-recognition module are significantly reduced by the presence of DNA. In all forms of the protein, the internal dyad symmetry of the DNArecognition module of GAL4 is reflected by the backbone amide proton exchange rates.

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Hydrogen Exchange

Cited by 483 publications

References 0 publications

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

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

Characterization of the distribution of internal motions in the basic pancreatic trypsin inhibitor using a large number of internal NMR probes

Effects of DNA binding and metal substitution on the dynamics of the GAL4 DNA‐binding domain as studied by amide proton exchange

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