Nuclear magnetic resonance of labile protons in the basic pancreatic trypsin inhibitor

Assignment of the 1H nuclear magnetic resonance spectrum of the trypsin inhibitor homologue K from Dendroaspis polylepis polylepis. Two-dimensional nuclear magnetic resonance at 360 and 500 MHz

The assignment of the 1H nuclear magnetic resonance (n.m.r.) spectrum of the trypsin inhibitor homologue K from the venom of Dendroaspis polylepis polylepis is described and documented. The assignments are based entirely on the amino acid sequence and on 2-dimensional n.m.r. experiments at 360 and 500 M Hz. Individual assignments were obtained for the backbone and C beta protons of all 57 residues of the inhibitor homologue K, with the exceptions of the N-terminal amino group, the amide protons of Arg16, Gly37 and Gly40 and the C beta protons of Arg16 and Pro19. The assignments for the non-labile protons of the amino acid side-chains are complete, with the exception of Gln29, Glu49 and all the proline, lysine and arginine residues. For Asn and Trp the labile side-chain protons have also been assigned. The chemical shifts for the assigned resonances are listed for an aqueous solution at 50 degrees C and pH 3.4.

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.

Protein dynamics investigated by the neutron diffraction-hydrogen exchange technique

A new approach, using neutron diffraction and the hydrogen exchange (H/D) technique, has been used to study the extent and nature of the inherent conformational fluctuations in the protein, trypsin. The observed pattern of exchange was used to investigate systematic relationships between exchangeable sites and structural and chemical properties of the molecule. Results of this analysis indicate that hydrogen-bonding structure is the dominant factor governing rates of exchange. The model of conformational mobility which best explains the experimental findings involves a localized disruption of the secondary structure within different regions of the protein molecule, each limited in extent to the breaking of a small number of hydrogen bonds.

Individual assignments of the amide proton resonances involved in the triple-stranded antiparallel pleated beta-sheet structure of a long neurotoxin, Laticauda semifasciata III from Laticauda semifasciata

THe characteristic feature of the crystal structure of erabutoxin b, a short neurotoxin from Laticauda semifasciata, and alpha-cobratoxin, a long neurotoxin from Naja naja siamensis, is the presence of a triple-stranded antiparallel pleated beta-sheet structure formed by the central and the third peptide loops. In the present study, we have studied the assignment of slowly exchangeable amide protons of Laticauda semifasciata III from L. semifasciata, using nuclear Overhauser effects (NOE) and spin-decoupling methods. The results show that nearly all of the slowly exchangeable amide protons are to be assigned to the back-bone amide protons, involved in the triple-stranded antiparallel pleated beta-sheet structure, indicating that this sheet is stable in 2H2O solution. In contrast, the amide protons in short neurotoxins are readily exchangeable under the same experimental condition, suggesting that long neurotoxins have a more rigid sheet structure than short ones. This rigidity may come from the hydrophobic and hydrogen bond interaction between the central loop and the tail, which is not present in short neurotoxins. Since the functionally important residues are located on this beta-sheet, the different kinetic properties of the neurotoxins are well correlated with the difference in the rigidity of the beta-sheet.

Proton-nuclear-magnetic-resonance study on molecular conformations of long neurotoxins. alpha-Bungarotoxin from Bungarus multicinctus and Toxin B from Naja naja

The 270-MHz proton NMR spectra were analyzed of the long neurotoxins alpha-bungarotoxin from Bungarus multicinctus and Toxin B from Naja naja. The aromatic proton resonances were completely assigned to individual nuclei for alpha-bungarotoxin and in part for toxin B. The pH dependences of proton chemical shifts were analyzed by the nonlinear least-square method, for obtaining pKa values and protonation shifts. The pKa values of Tyr-25, an invariant residue of neurotoxins, are 12.1 for alpha-bungarotoxin and 11.3 for toxin B, suggesting the presence of a strong hydrogen bond involving Tyr-25 in alpha-bungarotoxin. The Trp-29 residues of both toxins show a common titration shift due to the carboxylate group of Asp-31 and a similar structural arrangement of functionally invariant pair of Trp-29 and Asp-31 is implied. From the temperature dependences of the chemical shifts of His-68 and a methyl group of alpha-bungarotoxin, the local structure around His-68 near the tail part is shown to be more flexible than the other part. The six main-chain amide protons of alpha-bungarotoxin exchange most slowly with solvent deuterons and are found by interproton nuclear Overhauser effects to be in the beta-sheet near the aromatic ring of Tyr-25 residue. Hydrogen leads to deuterium exchange rates in 2H2O solution at 37 degrees C were measured of slowly exchanging amide protons of alpha-bungarotoxin, toxin B, and two short neurotoxins, namely cobrotoxin and erabutoxin b. The two long neurotoxins have amide protons with relatively long half-times spanning as long as 10-100 h, but the two short neurotoxins do not have amide protons with half-times longer than 3 h. The distributions of the half-times of amide proton exchange indicate the structural rigidity of neurotoxins in the order, alpha-bungarotoxin greater than toxin B greater than cobrotoxin approximately erabutoxin b, in agreement with the order of neurotoxicity as reported previously by Chicheportiche et al. and by Lee and Chen.

Circular dichroism spectroscopy of bovine pancreatic trypsin inhibitor and five altered conformational states. Relationship of conformation and the refolding pathway of the trypsin inhibitor

As part of a conformational study of the pathway of unfolding and refolding of bovine pancreatic trypsin inhibitor that accompanies breakage and formation of its three disulfide bonds, circular dichroism spectra have been measured for several limiting conformational states: native and refolded, with the three correct disulfide bonds; the (30--51, 5--55) two-disulfide species trapped during unfolding and refolding, which have a stable nativelike conformation; the fully reduced protein, with no disulfide bonds. Refolded protein with the three correct disulfide bonds has been found to be slightly different from the native protein; this conformational difference could be removed by gently heating the refolded protein. The same difference appears to be present between the two-disulfide intermediates, lacking the 14--38 disulfide bond, produced during unfolding and refolding. The conformational difference appear to be introduced at an early stage of refolding. The fully reduced protein, with no disulfides, exists as a flexible polypeptide chain with no detectable fixed conformation. The near-ultraviolet portions of the spectra are resolved into probable contributions by tyrosine, disulfide, and phenylalanine side-chain electronic transitions. The probable contributions to the native protein spectrum by tyrosines were also elucidated by observing the spectral shifts caused by their ionization at pH 12.5, where the folded conformation is maintained. The rotational strengths of the isolated transitions provide a measure of conformational flexibilities for the chromophores. Resolution of the far-ultraviolet spectrum of the native protein into contributions of its known secondary structures was not successful.

Preliminary spectroscopic characterization of six toxins from Latin American scorpions

This paper reports on spectroscopic studies of six toxins from the Latin American scorpions Centruroides noxius Hoffmann, Centruroides elegans Thorell and Tityus serrulatus Lutz and Mello. The isolation and purification of five of these toxins was described previously. The preparation of toxin II.9.2.2 from the venom of C. noxius is first described here. Circular dichroism and nuclear magnetic resonance spectra indicate similarities and differences between these scorpion toxins and previously characterized snake toxins. While there is evidence that the toxins from scorpions and snakes both contain extended beta-sheet secondary structures, the spectral properties of the scorpion toxins are overall of a different type from those of snake toxins. Among the six scorpion toxins those from T. serrulatus have spectral properties markedly different from those of the Centruroides species. Furthermore, thermal denaturation and amide proton exchange measurements showed that the globular structures of the Tityus toxins were markedly less stable and less rigid than those of the Centruroides toxins.

High-resolution proton nuclear magnetic resonance studies of the exchangeable resonances of the lac repressor headpiece

The exchangeable hydrogens of the N-terminal 51 amino acid headpiece (HP) of the lac repressor have been examined with high-resolution 1H NMR. Resonances from 35 +/- 3 protons are observable in 2H2O solutions at p2H 4.2. The exchange rates for some of these have been measured over the p2H range 1.5-5. In H2O, resonances from 70 +/- 6 protons are observable at pH 3.2 and 35 +/- 5 protons at pH 7.1. The temperature dependence of the spectrum at neat neutral pH shows the existence of a group of approximately 22 protons particularly slow to exchange. The pH dependence of the spectrum in H2O solution over the range 1-11 is discussed. Results are compared with NMR studies of the nonexchanging protons and CD and IR results.

Genetic assignment of resonances in the NMR spectrum of a protein: lac repressor

By using a systematic genetic approach, the resonances in the 19F NMR spectrum of 3-fluorotyrosine-substituted lac repressor protein have been assigned. The NMR data indicate that each monomer of the repressor consists of two distinct and independent domains. One domain, the NH2-terminal sixth of the primary sequence, which has been shown to be very important for DNA binding, is very mobile. The remaining COOH-terminal sequence is more rigid. Ligands of the repressor, which affect its DNA binding capability, lead to conformational changes in the COOH-terminal domain. The approach to the assignment of spectral features taken here can be extended to other systems.

Structural interpretation of vicinal proton-proton coupling constants 3JH alpha H beta in the basic pancreatic trypsin inhibitor measured by two-dimensional J-resolved NMR spectroscopy

Two-dimensional J-resolved 1H NMR spectroscopy was used to measure the vicinal spin-spin coupling constants 3JH alpha H beta for numerous, previously individually assigned amino acid residues in the basic pancreatic trypsin inhibitor at various temperatures between 30 and 85 degrees JC. An analysis of this data is proposed which enables one to compare the spatial arrangements of individual amino acid side chains in solution and in single crystals of the protein, and which also provides information on the mobility of the side chains in the solution conformation. As a rule, the amino acid side chains in the interior of the protein were found to be locked into unique spatial orientations, with the mobility restricted to rapid rotational fluctuations about this unique value for the dihedral angle chi 1. In most, but not all, instances the data for the interior amino acids indicate identical average conformations for the amino acid side chains in single crystals and in solution. For residues on the protein surface structural rearrangements between crystal and solution appear to be common, and the mobility in the solution conformation may include rapid averaging between two or several distinct, preferentially populated values of chi 1, analogous to the gauche-trans-gauche isomerization in isolated amino acids.

Combined use of proton-proton Overhauser enhancements and a distance geometry algorithm for determination of polypeptide conformations. Application to micelle-bound glucagon

In a new approach for the determination of polypeptide conformation, experimental data on intramolecular distances between pairs of hydrogen atoms obtained from nuclear Overhauser enhancement studies are used as input for a distance geometry algorithm. The algorithm determines the limits of the conformation space occupied by the polypeptide chain. The experimental data are used in such a way that the real conformation should in all cases be within these limits. Two important features of the method are that the results do not depend critically on the accuracy of the distance measurements by nuclear Overhauser enhancement studies and that internal mobility of the polypeptide conformation is explicitly taken into consideration. The use of this new procedure is illustrated with a structural study of the region 19-27 of glucagon bound to perdeuterated dodecylphosphocholine micelles.

Systematic application of two-dimensional 1H nuclear-magnetic-resonance techniques for studies of proteins. 2. Combined use of correlated spectroscopy and nuclear Overhauser spectroscopy for sequential assignments of backbone resonances and elucidation of polypeptide secondary structures

This paper describes a new nuclear magnetic resonance approach for the determination of secondary structure in globular proteins. To illustrate the practical application of the new procedure, two-dimensional correlated spectroscopy and two-dimensional nuclear Overhauser enhancement spectroscopy were used to obtain individual assignments for all the backbone protons of the beta-sheet secondary structures in the basic pancreatic trypsin inhibitor. First, combined connectivity diagrams of these two methods recorded in both 2H2O solution and H2O solution of the inhibitor were employed to obtain sequential, individual resonance assignments for the separate strands in the beta sheet. Second, a 2D nuclear Overhauser enhancement spectrum recorded with a long mixing time was used to determine how the separate, extended polypeptide strands are linked by hydrogen bonds in the sheet structures. By combination of these results with the identifications of the amino acid side-chain resonances described in the preceding paper, the beta-sheet structures can, without reference to data on the spatial structure obtained with other techniques, be localized in the amino acid sequence. This investigation confirms results on limited regions of the beta sheet in the inhibitor obtained previously with one-dimensional nuclear magnetic resonance experiments and demonstrates that the entire beta-sheet structure seen in single crystals of the inhibitor is preserved in aqueous solution.

Systematic application of two-dimensional 1H nuclear-magnetic-resonance techniques for studies of proteins. 1. Combined use of spin-echo-correlated spectroscopy and J-resolved spectroscopy for the identification of complete spin systems of non-labile protons in amino-acid residues

This and the following paper describe the practical application of recently developed, two-dimensional nuclear magnetic resonance techniques for studies of proteins. In the present report spin-echo-correlated spectroscopy and two-dimensional J-resolved spectroscopy are used to identify complete spin systems of non-labile, aliphatic protons in the basic pancreatic trypsin inhibitor. Overall, 41 out of the 58 aliphatic spin systems in this protein were identified; for the first time the spin systems of all the glycyl residues in a protein have been identified in the 1H NMR spectrum. Combined with the following paper, the present data yield new individual assignments for numerous amino acid residues and provide a new avenue, based on accurate measurements of spin-spin coupling constants in the two-dimensional J-resolved spectra, for studying changes of static and dynamic aspects of protein conformation between single crystals and solution, or between different conditions of solvent and temperature.

Hydrogen isotope exchange kinetics of single protons in bovine pancreatic trypsin inhibitor

The exchange kinetics of the slowest exchanging BPTI beta-sheet protons are complex compared to model peptides; the activation energy, E alpha, and the pH dependence are temperature dependent. We have measured the exchange kinetics in the range pH 1--11, 33--71 degrees C, particularly the temperature dependence. The data are fit to a model in which exchange of each proton is determined by two discrete dynamical processes, one with E alpha approximately 65 kcal/mol and less than first order dependence on catalyst ion, and one with E alpha 20--30 kcal/mol and approaching first order in catalyst ion. The low activation energy process is the mechanism of interest in the native conformation of globular proteins and involves low energy, small amplitude fluctuations; the high activation energy process involves major unfolding. The model is simple, has a precedent in the hydrogen exchange literature, and explains quantitatively the complex feature of the exchange kinetics of single protons in BPTI, including the following. For the slowest exchanging protons, in the range 36 degrees--68 degrees C, E alpha is approximately 65 kcal/mol at pH approximately 4, 20--30 kcal/mol at pH greater than 10, and rises to approximately 65 kcal/mol with increasing temperature at pH 6--10; the Arrhenius plots converge around 70 degrees C; the pH of minimum rate, pHmin, is greater than 1 pH unit higher at 68 degrees C than for model compounds; and at high pH, the pH-rate profiles shift to steeper slope; the exchange rates around pHmin are correlated to the thermal unfolding temperature in BPTI derivatives (Wagner and Wüthrich, 1979, J. Mol. Biol. 130:31). For the more rapidly exchanging protons in BPTI the model accounts for the observation of normal pHmin and E alpha of 20--30 kcal/mol at all pH's. The important results of our analysis are (a) rates for exchange from the folded state of proteins are not correlated to thermal lability, as proposed by Wuthrich et al. (1979, J. Mol. Biol. 134:75); (b) the unfolding rate for the BPTI cooperative thermal transition is equal to the observed exchange rates of the slowest exchanging protons between pH 8.4--9.6, 51 degrees C; (c) the rates for exchange of single protons from folded BPTI are consistent with our previous hydrogen-tritium exchange results and with a penetration model of the dynamic processes limiting hydrogen exchange.

Correlations between internal mobility and stability of globular proteins

The recent work is surveyed which leads to the suggestions that the conformation of globular proteins in solution corresponds to a dynamic ensemble of rapidly interconverting spatial structures, that clusters of hydrophobic amino acid side chains have an important role in the architecture of protein molecules, and that mechanistic aspects of protein denaturation can be correlated with internal mobility seen in the native conformation. These conclusions resulted originally from high resolution 1H nuclear magnetic resonance (NMR) studies of aromatic ring mobility, exchange of interior amide protons and thermal denaturation of the basic pancreatic trypsin inhibitor and a group of related proteins. Various new approaches to further characterize proteins in solution have now been taken and preliminary data are presented. These include computer graphics to outline hydrophobic clusters in globular protein structures, high resolution 1H-NMR experiments at variable hydrostatic pressure and 13C-NMR relaxation measurements. At the present early stage of these new investigations it appears that the hydrophobic cluster model for globular proteins is compatible with the data obtained.

A conformational isomer of bovine pancreatic trypsin inhibitor protein produced by refolding

Refolding of the bovine pancreatic trypsin inhibitor protein (BPTI) after reduction of its three cysteine disulphide linkages can occur when the reduced protein is placed in a suitable oxidizing medium (ref. 1 and refs therein). The refolding process has been studied by trapping chemically intermediates which contain only one or two disulphide bonds (ref. 1 and refs therein). We report here that during structural studies of these intermediates by NMR, we have found that complete re-oxidation of the protein results in substantial quantities of a metastable folded species which is identical to native BPTI in its covalent bonding (including the disulphide bonds) but possesses a somewhat different conformation. The existence of such a species is supported by circular dichroism measurements on refolded BPTI. This novel form of BPTI is of considerable interest because it can be used to provide information about the folding mechanism and conformational stability of the protein.