Clare Woodward

Hydrogen exchange and the dynamic structure of proteins.

SummaryIn 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.

Structure of form III crystals of bovine pancreatic trypsin inhibitor.

The structure of bovine pancreatic trypsin inhibitor has been solved in a new crystal form III. The crystals belong to space group P2(1)2(1)2 with a = 55.2 A, b = 38.2 A, c = 24.05 A. The structure was solved on the basis of co-ordinates of forms I and II of the inhibitor by molecular replacement, and the X-ray data extending to 1.7 A were used in a restrained least-squares refinement. The final R factor was 0.16, and the deviation of bonded distances from ideality was 0.020 A. Root-mean-square discrepancy between C alpha co-ordinates of forms III and I are 0.47 A, whilst between forms II and III the discrepancy is 0.39 A. These deviations are about a factor of 3 larger than the expected experimental errors, showing that true differences exist between the three crystal forms. Two residues (Arg39 and Asp50) were modeled with two positions for their side-chains. The final model includes 73 water molecules and one phosphate group bound to the protein. Sixteen water molecules occupy approximately the same positions in all three crystal forms studied to date, indicating their close association with the protein molecule. Temperature factors also show a high degree of correlation between the three crystal forms.

Hydrogen exchange rates and protein folding

Abstract Transient folding intermediates have been monitored in 11 proteins by pulsed hydrogen exchange methods. Standard hydrogen isotope exchange kinetics have also been measured for several molten globules. Taken together with folding kinetics detected by optical techniques, and with hydrogen exchange kinetics in native proteins, the results permit conclusions about time constants, structure and stability of folding intermediates, and about parallel versus serial folding pathways.

Crystal structure of a Y35G mutant of bovine pancreatic trypsin inhibitor.

The structure of a Y35G mutant of bovine pancreatic trypsin inhibitor (BPTI) was solved by molecular replacement and was refined by both simulated annealing and restrained least-squares at 1.8 A resolution. The crystals belong to the space group P42212, with unit cell dimensions a = b = 46.75 A, c = 50.61 A. The final R-factor is 0.159 and the deviation from ideality for bond distances is 0.02 A. The structure of the mutant differs from that of the native protein, showing an overall root-mean-square (r.m.s.) difference of 1.86 A for main-chain atoms. However, the change is mostly localized in the two loops (respective r.m.s. values of 2.04 A and 3.93 A) and the C terminus (r.m.s. 6.79 A), while the core of the protein is well conserved (r.m.s. 0.45 A). The change in the loop regions can be clearly attributed to the mutation while the difference in the C terminus might be only due to a different crystal packing. Seventy water molecules were included in the model but only seven of them are shared with the native structure. Thermal parameters are showing a good correlation with those for the wild-type of BPTI.

Hydrogen kinetics of peptide amide protons at the bovine pancreatic trypsin inhibitor protein-solvent interface

Hydrogen exchange rate constants of the 25 most rapidly exchanging peptide amide protons in bovine pancreatic trypsin inhibitor have been determined over a range of pH that spans pH min, the pH of minimum rate. Most of these are on the protein surface, exposed to solvent and not hydrogen bonded in the crystal structure. Contrary to commonly held assumptions, the exchange kinetics of surface NH groups are not equivalent to the kinetics of NH groups in peptides in the extended configuration. All surface NH groups exchange more slowly than NH groups in model peptides, with rate constants distributed over a range of more than two orders of magnitude. In addition, their pH min values vary widely. For most of the surface NH groups, pH min is lower than in model compounds and, for several, pH min is less than 1. These results indicate that the local environment of the surface peptide groups when the exchange event occurs is very different from that of extended peptides. Analysis based on consideration of an O-protonation mechanism for acid catalysis and of electrostatic effects on exchange kinetics further indicates (see the accompanying paper) that, in general, exchange of surface NH groups occurs from a conformation of the protein approximated by the crystal structure. The 1H-2H exchange rate constants were measured from 300 MHz nuclear magnetic resonance spectra in which assigned surface N1H resonances are resolved by the use of partially deuterated protein samples. A marked pH dependence of the chemical shifts observed in the pH range 1 to 4.5 for several surface NH groups reflects the titration of nearby carboxyl groups.

Mechanism of surface peptide proton exchange in bovine pancreatic trypsin inhibitor salt effects and O-protonation☆

The acid-catalyzed hydrogen exchange rate constants kH, and the base-catalyzed rate constants kOH, have been determined (in the preceding paper) for the 25 most rapidly exchanging NH groups of bovine pancreatic trypsin inhibitor. Most of these NH groups are at the protein-solvent interface. The correlation of kH, but not kOH, with the static accessibility and hydrogen bonding of the peptide carbonyl O atom indicates that the mechanism of acid catalysis in proteins involves O-protonation. Agreement between the ionic strength dependence observed for kH and kOH and the ionic strength dependence calculated for an O-protonation mechanism supports this conclusion. N-protonation for acid catalysis, as well as N-deprotonation for base catalysis, have traditionally been assumed in the mechanism of the chemical step in peptide amide proton exchange. A preference for the alternative O-protonation mechanism has far-reaching implications in the interpretation of protein hydrogen exchange kinetics. With an O-protonation mechanism, acid-catalyzed rates of surface NH groups are primarily a function of the average solvent accessibility of the carbonyl O atoms in the dynamic solution structure, while base-catalyzed rates of surface NH groups measure solvent accessibility of the peptide N. The relative dynamic accessibilities of peptide O atoms, as measured by relative values of kH (corrected for electrostatic effects), correlate with O static accessibilities in the crystal structure. A lower correlation of static accessibility of N atoms with kOH is observed for surface NH groups in peptide groups in which the carbonyl O is not hydrogen bonded. For some surface NH groups, the observed pH of minimum rate, pHmin, deviates widely from the pHmin of model compounds. This is explained as the combined result of electrostatic effects and of the differences in accessibility of the carbonyl O and N atoms that result in a change in the relative values of kH and kOH as compared to those of model peptides. A mechanism whereby exchange of interior sites is catalyzed by interactions of catalysis ions with protein surface atoms via charge transfer is suggested.

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.

Dynamic solvent accessibility in the soybean trypsin inhibitor--trypsin complex.

The effect of complex formation on the hydrogen-tritium exchange kinetics of trypsin and soybean trypsin inhibitor has been determined by a comparison of the exchange kinetics of the complex to those of the unassociated proteins. Approximately one-third of the exchangeable protons in the inhibitor and in trypsin have slowed exchange rates as a result of association at pH 6·5, 0°C. The effect extends beyond the immediate vicinity of the protein-protein contact region and includes a large number of both solvent-shielded and freely accessible protons. This effect is apparently due to a widespread decrease in low energy fluctuations in trypsin and in the inhibitor as a result of complex formation. The hydrogen exchange kinetics of the inhibitor-trypsin complex interface were studied by partial labeling techniques. The temperature and pH dependence indicates that, although exchange in the interface region is greatly restricted, there are in the complexed dimer low energy processes through which all interface protons are accessible to H2O and OH ions without complex dissociation or protein unfolding.

Rapid internal dynamics of BPTI is insensitive to pressure: 15N spin relaxation at 2 kbar

Pressure effects on the backbone dynamics of a native basic pancreatic trypsin inhibitor (BPTI) have been measured by 15N spin relaxation and chemical shifts at 30 and 2000 bar. The experiments utilized the on‐line variable pressure cell nuclear magnetic resonance system on 15N‐uniformly labeled BPTI at a proton frequency of 750.13 MHz at 36°C. Longitudinal (R 1) and transverse (R 2) 15N relaxation times and (1H)–15N nuclear Overhauser effects were measured for 41 protonated backbone nitrogens at both pressures. The model free analysis of the internal dynamics gave order parameters for individual H–N vectors at both pressures. The results indicate that rapid internal dynamics in the ps–ns range for the polypeptide backbone is not significantly affected by pressure in the range between 30 bar and 2 kbar. The result is consistent with the linear pressure dependence of 1H and 15N chemical shifts of BPTI, which suggests that local compressibilities and amplitudes of associated conformational fluctuation are nearly invariant in the same pressure range. Overall, we conclude that at 2 kbar BPTI remains within the same native ensemble as at 1 bar, with a small shift of population from that at 1 bar.

Unfolded BPTI variants with a single disulfide bond have diminished non-native structure distant from the crosslink.

BACKGROUND NMR studies of denatured states, both fully unfolded and partially folded, give insight into the conformations and interactions favored in initial stages of folding, and in early intermediates formed during folding. We have characterized non-random structures favored in unfolded, reduced BPTI [1], and in partially folded BPTI [2]. Here, we report NMR-detected structure of two analogs of unfolded BPTI with one native 14-38 disulfide bond. RESULTS Analogs Y21A[14-38]Abu and Y23A[14-38]Abu, obtained by chemical synthesis of [14-38]Abu with Y21 or Y23 replaced by alanine, are models for unfolded BPTI with 14-38 the only disulfide. Compared to unfolded BPTI with all three disulfides broken, the unfolded 14-38 BPTI analogs have numerous differences, including loss of non-native, turn-like conformations for beta 2 residues, diminished non-native aromatic-aliphatic NOEs, and increased intermediate chemical exchange of residues that have native-like conformations in partially folded BPTI. Although the Y21A and Y23A analogs have similar CD and NMR properties, specific differences in NOE patterns and in exchange broadening are observed. CONCLUSIONS Changes in unfolded BPTI associated with formation of the 14-38 disulfide bond are consistent with less non-native structure, and more native-like structure, in residues composing the stable core of antiparallel beta-sheet in partially folded BPTI. Specific differences between Y21A[14-38]Abu and Y23A[14-38]Abu indicate that replacement of Y23 results in less ordered structure than replacement of Y21.