p2H dependence of the exchange with the solvent of interior amide protons in basic pancreatic trypsin inhibitor modified by reduction of the disulfide bone 14--38

Detection of intermolecular chemical exchange through decorrelation of two-spin order

An initial correlation between two spins is lost when they are separated by intermolecular chemical exchange. This effect, termed "decorrelation by chemical exchange," manifests itself in a decay of the corresponding two-spin modes. It can be used for monitoring intermolecular chemical exchange, as is demonstrated for l-tryptophan where the decay of 1H15N two-spin order provides information on the exchange of indole protons with solvent water.

On the pH dependence of amide proton exchange rates in proteins

We have analyzed the pH dependencies of published amide proton exchange rates (kex) in three proteins: bovine pancreatic trypsin inhibitor (BPTI), bull seminal plasma proteinase inhibitor IIA (BUSI IIA), and calbindin D9K. The base-catalyzed exchange rate constants (kOH) of solvent exposed amides in BPTI are lower for residues with low peptide carbonyl exposure, showing that the environment around the carbonyl oxygen influences kOH. We also examined the possible importance of an exchange mechanism that involves formations of imidic acid intermediates along chains of hydrogen-bonded peptides in the three proteins. By invoking this "relayed imidic acid exchange mechanism," which should be essentially acid-catalyzed, we can explain the surprisingly high pHmin (the pH value at which kex reaches a minimum) found for the non-hydrogen-bonded amide protons in the beta-sheet in BPTI. The successive increase of pHmin along a chain of hydrogen-bonded peptides from the free amide to the free carbonyl, observed in BPTI, can be explained as an increasing contribution of the proposed mechanism in this direction of the chain. For BUSI IIA (pH 4-5) and calbindin D9K (pH 6-7) the majority of amide protons with negative pH dependence of kex are located in chains of hydrogen-bonded peptides; this situation is shown to be consistent with the proposed mechanism.

Hydrogen exchange kinetics of surface peptide amides in bovine pancreatic trypsin inhibitor

The acid and base catalytic rate constants, kH, obs and kOH, obs and the pH at the minimum rate, pHmin, of 25 rapidly exchanging protons in bovine pancreatic trypsin inhibitor have been determined. Here we report the labeling procedure giving 1H nuclear magnetic resonance spectral resolution of seven additional rapidly exchanging NH protons and the pH dependence of their chemical shifts. Values of kH,obs kOH,obs and pHmin are given for Ala16, Gly28 and Arg53 NH groups, the only backbone amide protons with static accessibility of more than zero in the crystal structure not previously reports, and for Gly56 NH, buried at the C terminus of an alpha-helix. All four protons reported here have pH min greater than or equal to 3. Conclusions of the previous study predict that peptide protons with pHmin higher than those of model compounds have greater static accessibility of the peptide O than of the peptide N atom. The locations in the crystal structure of the four NH groups whose exchange rates are reported here are in qualitative agreement with these predictions. The ionic strength dependence of Ala16 at pH 5.5 shows a sharp increase in the exchange rate with decreasing salt concentration, as expected for base-catalyzed exchange in a positive electrostatic field.

Identification of an allosterically sensitive unfolding unit in hemoglobin

Hydrogen-exchange studies locate a set of seven allosterically sensitive amide NH protons side by side around two turns of the F-FG helical segment in the hemoglobin beta chain. Some of these protons are on the aqueous protein surface and some deeply inside, yet they all exchange with solvent protons at similar rates. Further, they move in unison to a new common rate when hemoglobin changes its allosteric form. These observations and analogous results for other proteins appear to be inconsistent with penetration-dependent models which relate H-exchange rate to solvent accessibility in the native state. Rather, these results point to sizeable fluctuational distortions that make small sets of protons more or less equally accessible in some transient H-exchange transition state, as visualized in the local unfolding model. The set of allosterically sensitive protons studied here exchanges 30-fold faster in liganded hemoglobin than in the deoxy form. In terms of the unfolding model, this means that the F-FG structure is relatively destabilized in oxyhemoglobin, so that the allosterically linked change in structural free energy at F-FG favors the deoxy state. The 30-fold change in H-exchange rate suggests a contribution to the allosteric free energy by this segment of 2 kcal (1 cal = 4.184 J). These experiments utilized a labeling technique, described earlier, that selectively places tritium on sites whose H-exchange rates are sensitive to the protein functional state, and used a method introduced by Rosa & Richards (1979,1981) to locate this label in the protein. The latter method, which rapidly separates protein fragments under conditions that can preserve exchangeable label, was here brought to a more quantitative level. Taken together, these techniques provide a "functional labeling" method capable of selectively labeling and identifying protein segments that participate in functional interactions.

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

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. This demonstration of a manifold of spatial fluctuations in a small protein provides an impression on the kind of fluctuations which have to be expected for larger proteins. When studying protein reactions one should therefore consider the presence of a large number of different, transiently formed, spatial structures available for the partner in the reaction, which may pick out only that structure which will optimally perform a particular reaction with the highest efficiency.

Hydrogen exchange and the dynamic structure of proteins

In native proteins, buried, labile protons undergo isotope exchange with solvent hydrogens, but the kinetics of exchange are markedly slower than in unfolded polypeptides. This indicates that, whereas buried protein atoms are shielded from solvent, the protein fluctuates around the time average structure and occasionally exposes buried sites to solvent. Generally, hydrogen exchange studies are designed to characterize the nature of the fluctuations between conformational substates, to monitor the shift in conformational equilibria among protein substates due to ligand binding or other factors, or to monitor the major cooperative denaturation transition. In this article, we review the recent reports of hydrogen exchange in proteins, focusing on recent advances in methodology, especially with regard to the implications of the results for the mechanism of hydrogen exchange in folded proteins.