Nuclear magnetic resonance titration curves of histidine ring protons. Conformational transition affecting three of the histidine residues of ribonuclease

A new arylating agent, 2-carboxy-4,6-dinitrochlorobenzene. Reaction with model compounds and bovine pancreatic ribonuclease

The reagent 2-carboxy-4,6-dinitrochlorobenzene (CDNCB) reacts with the imino, amino and sulfhydryl groups of model compounds. At pH 8.2, sulfhydryl groups react much faster than do amines. N alpha-Acetylhistidine, N alpha-acetyltyrosine and N alpha-acetyltryptophan do not react. Poly(L-Lysine) and poly(DL-lysine) react about 50 times as fast as does N alpha-acetyllysine. A dichloroanalog, 6-carboxy-2,4-dinitro-1,3-dichlorobenzene, shows stepwise reactivity with amines. With bovine pancreatic ribonuclease, which contains no sulfhydryl, CDNCB reacts preferentially with the epsilon-amino of Lys-41 at 450 times the rate with the epsilon-amino of N alpha-acetyllysine. The preferential reactivity at Lys-41 is discussed in relation to the pK of Ly-41, the cationic character of the active site cleft, and the mechanism of RNAase action on substrates.

Regeneration studies of an analog of ribonuclease A missing disulfide bonds 65-72 and 40-95

Mutants of bovine pancreatic ribonuclease A (RNase A) that contain four of the eight cysteine residues found in the wild-type protein were prepared. Cysteine residues 40, 65, 72, and 95 were replaced by serine to form [C40S,C65S,C72S,C95S] RNase A or by alanine to form [C40A,C65A,C72A,C95A] RNase A, which contain the following four cysteine residues: 26, 58, 84, and 110. The substitutions resulted in deletion of wild-type disulfide bonds, 65-72 and 40-95. These mutants were prepared to investigate interactions that may be important for the folding and unfolding of the wild-type protein. The mutant protein was expressed and purified in an unfolded sulfonated form. Upon regeneration of the native form from the reduced mutant with DTTox, all three of the possible two-disulfide pairings, including the native one, formed. One-dimensional 1H NMR spectra demonstrated that the conformations of these three species are similar and are predominantly disordered; however, there is evidence of local structure in the vicinity of one histidine residue. It was also shown that disulfide pairing is not completely random and that both entropic factors and enthalpic interactions contribute to the formation of the native-disulfide bonds. The presence of more than a statistical population of native-disulfide pairings indicates that specific local interactions present in the reduced protein direct the preferential formation of native-disulfide bonds in the two-disulfide mutant.

H-n.m.r. studies on the specificity of the interaction between bovine pancreatic ribonuclease A and dideoxynucleoside monophosphates

The titration curves of the C-2 histidine protons of bovine pancreatic ribonuclease A in the presence of several dideoxynucleoside monophosphates (dNpdN) were studied by means of proton nuclear magnetic resonance at 270 MHz in order to obtain information on the ligand--RNase A interaction. The changes in the chemical shift and pKs of the C-2 proton resonances of His-12, -48, -119 in the complexes RNase A--dNpdN were smaller than those previously found when the enzyme interacted with mononucleotides. The pK2 of His-12 was not affected by the interaction of the enzyme with these ligands, whereas, the perturbation of the pK2 of His-119 was clearly dependent on the nature of the ligand. If there is a pyrimidine nucleoside at the 3' side of the dideoxynucleoside monophosphates, as in TpdA and TpT, an enhancement due to the well known interaction of the phosphate in p1, the catalytic site, was found. However, when there is a purine nucleoside, as in dApT and dApdA, a decrease in the pK2 value was observed and we propose that in such cases the phosphate group interacts in a secondary phosphate binding site, p2. The results obtained suggest the existence of different specific interactions depending on the structure of the dideoxynucleoside monophosphate studied.

15N- and 1H-NMR investigations of the active-site amino acids in semisynthetic RNase S' and RNase A

Extensive 15N-NMR investigations of active-site amino acids were made possible by the solid-phase synthesis of the N-terminal pentadecapeptide of RNase A with selectively 15N-enriched amino acids. On complexation with S-protein a fully active RNase S' complex was obtained. The 15N resonances of the side chains of lysine-7 (N epsilon), glutamine-11 (N gamma), and histidine-12 (N pi, tau) were studied in the free synthetic peptide, in the RNase S' complex and in the nucleotide complexes RNase S' with 2'CMP, 3'CMP, and 5'AMP. The analysis of the 15N-1H couplings, the 15N line broadenings due to proton exchange, and the chemical shift values showed that, while the imidazole ring is directly involved in the peptide-protein interaction, the side chains of Lys-7 and Gln-11 do not contribute to this interaction. In the nucleotide complexes the resonances of His-12 and Gln-11 are shifted downfield. In the 2'CMP complex a doublet for the N tau signal of His-12 indicates a stable H bond between this nitrogen and the phosphate group of nucleotide. The other nucleotide influence the resonances of the imidazole group much less, possibly due to a slightly different orientation of the phosphate group. The downfield shift of the Gln-11 resonance indicates an interaction between the carbonyl oxygen of the amide group and the phosphate moiety of the nucleotide. The only observable effect of nucleotide complexation on the Lys-7 signal is line broadening due to reduced proton exchange. For comparison with the 15N-NMR titration curves of His-12 in RNase S' the 1H-NMR titration curves of RNase A were also recorded. Both shape and pK values were very similar for the 15N and the 1H titration curves. An extensive analysis of the protonation equilibria with several fitting models showed that a mutual interaction of the imidazole groups of the active-site histidines results in flat titration curves. The Hill plots of all resonances of the imidazole rings, including the 15N resonances, show a small inflection in the pH range 5.8-6.4. Since the existence of a diimidazole system is most likely in this pH range, the inflection could be interpreted as a disturbance of the mutual electrostatic interaction of the active-site histidines by a partial H-bond formation between the imidazole groups.

Nuclear magnetic resonance and neutron diffraction studies of the complex of ribonuclease A with uridine vanadate, a transition-state analogue

The complex of ribonuclease A (RNase A) with uridine vanadate (U-V), a transition-state analogue, has been studied with 51V and proton NMR spectroscopy in solution and by neutron diffraction in the crystalline state. Upon the addition of aliquots of U-V at pH 6.6, the C epsilon-H resonances of the two active-site histidine residues 119 and 12 decrease in intensity while four new resonances appear. Above pH 8 and below pH 5, these four resonances decrease in intensity as the complex dissociates. These four resonances are assigned to His-119 and His-12 in protonated and unprotonated forms in the RNase-U-V complex. These resonances do not titrate or change in relative area in the pH range 5-8, indicating a slow protonation process, and the extent of protonation remains constant with ca. 58% of His-12 and ca. 26% of His-119 being protonated. The results of diffraction studies show that both His-12 and His-119 occupy well-defined positions in the RNase-U-V complex and that both are protonated. However, while the classic interpretation of the mechanism of action of RNase based on the proposal of Findlay et al. [Findlay, D., Herries, D. G., Mathias, A. P., Rabin, B. R., & Ross, C. A. (1962) Biochem. J. 85, 152-153] requires both His-12 and His-119 to be in axial positions relative to the pentacoordinate transition state, in the diffraction structure His-12 is found to be in an equatorial position, while Lys-41 is close to an axial position. Hydrogen exchange data show that the mobility and accessibility of amides in the RNase-U-V complex do not significantly differ from what was observed in the native enzyme. The results of both proton NMR in solution and neutron diffraction in the crystal are compared and interpreted in terms of the mechanism of action of RNase.

Anomalous pH dependence of the heme-bound carbon monoxide spectroscopic properties in the Glycera dibranchiata monomer hemoglobin fraction compared to vertebrate hemoglobins

The pH dependence of infrared and NMR spectroscopic parameters for carbon monoxide bound to human, equine, rabbit and Glycera dibranchiata monomer fraction hemoglobins has been examined. In all cases, the vertebrate hemoglobins exhibit CO vibrations and 13CO chemical shifts which are pH dependent, whereas the invertebrate hemoglobin does not. The Glycera dibranchiata monomer fraction exhibits the highest wavenumber CO vibration (1970 cm-1) and the most shielded chemical shift (206.2 ppm). The pH behavior of the vertebrate CO-hemoglobins is that the heme-coordinated carbon monoxide chemical shifts and principal infrared vibrations tend toward the values observed for the G. dibranchiata CO-hemoglobin fraction. These results are interpreted as originating in protonation of the distal histidine (E-7) in the vertebrate hemoglobins. The anomalous values for Glycera dibranchiata are concluded to be due to the absence of a distal histidine (E-7 His----Leu) in the heme pocket and not to gross structural dissimilarities between the proteins of the different species examined. Primary sequence similarity matrices have been constructed to compare the functional classes of amino acids at homologous positions for the CD and E helices and for the primary heme contacts in human, equine, sperm whale myoglobin, and the Glycera dibranchiata monomer hemoglobin to illustrate this point. They reveal a high correspondence for all globins and do not correlate with the spectroscopic parameters of heme-coordinated CO.

Exchange behavior of the H-bonded amide protons in the 3 to 13 helix of ribonuclease S

The preceding article shows that there are eight highly protected amide protons in the S-peptide moiety of RNAase S at pH 5, 0 degrees C. The residues with protected NH protons are 7 to 13, whose amide protons are H-bonded in the 3 to 13 alpha-helix, and Asp 14, whose NH proton is H-bonded to the CO group of Val47. We describe here the exchange behavior of these eight protected protons as a function of pH. Exchange rates of the individual NH protons are measured by 1H nuclear magnetic resonance in D2O. A procedure is used for specifically labeling with 1H only these eight NH protons. The resonance assignments of the eight protons are made chiefly by partial exchange, through correlating the resonance intensities in spectra taken when the peptide is bound and when it is dissociated from S-protein in 3.5 M-urea-d4, in D2O, pH 2.3, -4 degrees C. The two remaining assignments are made and some other assignments are checked by measurements of the nuclear Overhauser effect between adjacent NH protons of the alpha-helix. There is a transition in exchange behavior between pH 3, where the helix is weakly protected against exchange, and pH 5 where the helix is much more stable. At pH 3.1, 20 degrees C, exchange rates are uniform within the helix within a factor of two, after correction for different intrinsic exchange rates. The degree of protection within the helix is only 10 to 20-fold at this pH. At pH 5.1, 20 degrees C, the helix is more stable by two orders of magnitude and exchange occurs preferentially from the N-terminal end. At both pH values the NH proton of Asp 14, which is just outside the helix, is less protected by an order of magnitude than the adjacent NH protons inside the helix. Opening of the helix can be observed below pH 3.7 by changes in chemical shifts of the NH protons in the helix. At pH 2.4 the changes are 25% of those expected for complete opening. Helix opening is a fast reaction on the n.m.r. time scale (tau much less than 1 ms) unlike the generalized unfolding of RNAase S which is a slow reaction. Dissociation of S-peptide from S-protein in native RNAase S at pH 3.0 also is a slow reaction. Opening of the helix below pH 3.7 is a two-state reaction, as judged by comparing chemical shifts with exchange rates. The exchange rates at pH 3.1 are predicted correctly from the changes in chemical shift by assuming that helix opening is a two-state reaction. At pH values above 3.7, the nature of the helix opening reaction changes. These results indicate that at least one partially unfolded state of RNAase S is populated in the low pH unfolding transition.

1H-NMR studies on the binding subsites of bovine pancreatic ribonuclease A

The titration curves of the C-2 histidine protons of an RNAase derivative (a covalent derivative obtained by reaction of bovine pancreatic RNAase A (EC 3.1.27.5) with 6-chloropurine 9-beta-D-ribofuranosyl 5'-monophosphate) were studied by means of 1H-NMR spectroscopy at 270 MHz. The interaction of natural (5'AMP, 5'GMP, 5'IMP) and halogenated purine mononucleotides (cl6RMP, br8AMP) with RNAase A was also monitored by using the same technique. The slight change observed in the pK values of the active centre histidine residues of the RNAase derivative, with respect to those in the native enzyme, can be considered as evidence that the phosphate of the label does not interact directly either with His-12 or 119 in the p1 site, but the p2 site as proposed previously (Parés, X., Llorens, R., Arús, C. and Cuchillo, C.M. (1980) Eur. J. Biochem. 105, 571--579). Lys-7 and/or Arg-10 are proposed as part of the p2 phosphate-binding subsite. The pK values of His-12 and 119 and the shift of an aromatic resonance of the native enzyme found on interaction with some purine nucleotides, can be interpreted by postulating that the interaction of 5'AMP, 5'GMP and 5'IMP takes place not only in the so-called purine-binding site B2R2p1 but also in the primary pyrimidine-binding site B1R1 and p0 of RNAase A.

Effects of coenzyme binding on histidine residues of Lactobacillus casei dihydrofolate reductase

The effects of coenzyme binding on the seven histidine C2 proton resonances of Lactobacillus casei dihydrofolate reductase have been determined. Binary complexes containing NADP+, NADPH, and their hypoxanthine, thionicotinamide, and acetylpyridine analogues, together with ternary complexes containing the inhibitors trimethoprim or methotrexate, have been examined. Four of the histidine residues are affected by coenzyme binding. The largest effect-a marked upfield shift (0.85 ppm) of the C2 proton resonance-is seen for His-64. The hypoxanthine analogue of the coenzyme was found to produce a smaller upfield shift and, in addition, a decrease in the pK of His-64. The effects on this reductase are discussed in the light of the crystal structure [Matthews, D. A., Alden, R. A., Bolin, J. T., Filman, D. J., Freer, S. T., Hamlin, R., Hol, W. G. J., Kisliuk, R. L., Pastore, E. J., Plante, L. T., Xuong, N., & Kraut, J. (1978) J. Biol. Chem. 253, 6946], and it is concluded that His-64 is close to a carboxyl group in the free enzyme and that the hypoxanthine ring binds in a somewhat different orientation to the adenine ring. The effects on histidine resonances A, E, and G are significantly different for oxidized and reduced coenzymes. The changes in pK of the histidines giving rise to resonances A and E (probably His-22 and His-18) are discussed in terms of ligand-induced conformational changes, which differ for NADP+ and NADPH.

Guanyl-specific ribonuclease from the fungus Penicillium chrysogenum strain 152 and its complex with guanosine 3'-phosphate studied by nuclear magnetic resonance

The method of proton magnetic resonance was used to obtain information on the active site of the guanyl-specific ribonuclease from Penicillium chrysogenum, strain 152A. Four pH-dependent signals in the aromatic region of the proton NMR spectrum of the enzyme were assigned to the C-2 and C-4 protons of the two histidine residues. To determine the pK values and the environment of the histidine residues the pH dependence of their chemical shifts was studied and experimental curves thus obtained were analyzed taking into account the effect of other dissociating groups of the enzyme. The pK values of the histidine residues were found to be equal to 7.92 +/- 0.04 and 7.86 +/- 0.09. The results of the calculations indicate that each histidine residue should interact with an acidic group (carboxylic) of the protein (pK 4.33 and 3.48) and the distance between two histidine residues does not exceed 0.85 nm. The rate constants for the quasi-first order reaction of deuterium exchange of the histidine residues (11.2 s-1 and 3.7 x-1) suggest that both residues are accessible, though to a different degree to solvent. Formation of a complex between the enzyme and guanosine 3'-phosphate (Guo3'P) is accompanied by the shift of the histidine pK toward the alkaline region by 0.5. The existence of the complex is controlled by dissociation of a histidine residue with pK 8.7 in alkaline medium and by protonation of the N-7 of Guo3'P (pK 2.4) in acid medium. Nuclear Overhauser effect measurements were used to determine the glycosidic torsion angle for the Guo3'P in the complex and to estimate the distances between the histidine residues of the enzyme and ribose ring of Guo-3'P. The results obtained suggest that the nucleotide in the complex has an anti conformation and the least exposed histidine is spaced not more than 0.5 nm from the C-1' proton of the nucleotide ribose ring. A model for the enzyme-nucleotide complex is presented.

The aromatic residues of bovine pancreatic ribonuclease studied by 1H nuclear magnetic resonance

1. The aromatic proton resonances in the 360-MHz 1H nuclear magnetic resonance (NMR) spectrum of bovine pancreatic ribonuclease were divided into histidine, tyrosine and phenylalanine resonances by means of pH titrations and double resonance experiments. 2. Photochemically induced dynamic nuclear polarization spectra showed that one histidine (His-119) and two tyrosines are accessibly to photo-excited flavin. This permitted the identification of the C-4 proton resonance of His-119. 3. The resonances of the ring protons of Tyr-25, Tyr-76 and Tyr-115 and the C-4 proton of His-12 were identified by comparison with subtilisin-modified and nitrated ribonucleases. Other resonances were assigned tentatively to Tyr-73, Tyr-92 and Phe-46. 4. On addition of active-site inhibitors, all phenylalanine resonances broadened or disappeared. The resonance that was most affected was assigned tentatively to Phe-120. 5. Four of the six tyrosines of bovine RNase, identified as Tyr-76, Tyr-115 and, tentatively, Tyr-73 and Tyr-92, are titratable above pH 9. The rings of Tyr-73 and Tyr-115 are rapidly rotating or flipping by 180 degrees about their C beta--C gamma bond and are accessible to flavin in photochemically induced dynamic nuclear polarization experiments. Tyr-25 is involved in a pH-dependent conformational transition, together with Asp-14 and His-48. A scheme for this transition is proposed. 6. Binding of active-site inhibitors to bovine RNase only influences the active site and its immediate surroundings. These conformational changes are probably not connected with the pH-dependent transition in the region of Asp-14, Tyr-25 and His-48. 7. In NMR spectra of RNase A at elevated temperatures, no local unfolding below the temperature of the thermal denaturation was observed. NMR spectra of thermally unfolded RNase A indicated that the deviations from a random coil are small and might be caused by interactions between neighbouring residues.

Carbon-13 NMR investigations on ribonuclease A

The proposed interaction between the amino acid residues Asp 14 and His 48 of ribonuclease A has been confirmed by 13C-NMR spectroscopy. The titration behaviour of the resonance of the side-chain carboxyl group of Asp 14 suggests a pKa of 6.5--7.0 for His 48. An equilibrium between different conformation process of His 48. Upon this deprotonation a hydrogen bond between the side-chains of Asp 14 or His 48 and Tyr 25 seems to be formed as is suggested by the behaviour of a tyrosine C zeta resonance assigned to Tyr 25. One phenylalanine resonance broadens and moves upfield on the addition of the inhibitor Cyd-2'-P, being therefore assigned to Phe 120. The behaviour of this resonance suggests that the upfield shift results from the anisotropy of the cytidine ring. Three signals are assigned to the three Phe residues.

13C NMR investigations on Npi-[13C1]carboxymethyl-histidine-119 ribonuclease

The ribonuclease A derivative Npi-[13C1]carboxymethyl-histine-119 ribonuclease prepared by using [13C1]bromoacetate as alkylating reagent has been investigated with high resolution 13C NMR spectroscopy. In the 13C NMR spectra two carbon resonances of relatively high intensity appear which can be assigned to carboxyl groups attached to His-119 and Met-30, their intensity ratio being 10 : 1. The pH dependence of the carbon resonance of the carboxy-methyl group bound to the Npi of His-119 differs in the absence and presence of Cyd-2'-P, thus indicating that the catalytically inactive derivative does bind nucleotides. A mechanism of the alkylation reaction at pH 5.6 is proposed in which the epsilon-amino group of Lys-41 acts as the binding site for the carboxyl group of bromoacetate pushing the bromomethylene group towards the Npi of His-119 or the Ntau of His-12.

1H NMR studies of the binding of EDTA to bovine pancreatic ribonuclease

EDTA binds at the active site of ribonuclease causing a selective downfield shift of the C2 proton resonance of His 12 at pH 5.5 (pH denotes an uncorrected glass electrode pH meter reading of a 2H2O solution). A dissociation constant for EDTA binding to ribonuclease of 1.70 mM was calculated from this chemical shift change. The pKa of His 12 increased from 5.79 in ribonuclease alone to 6.73 in the RNAase . EDTA complex. Compared to these effects, the other histidine residues were not significantly affected by EDTA. EDTA was shown to act as a competitive inhibitor of cytidine 2',3'-cyclic phosphate hydrolysis by ribonuclease with a Ki of 1.37 mM at pH 5.5, 25 degrees C. Molecular model building suggests that three of the four carboxyl groups of EDTA could simultaneously interact with histidine 12, lysine 41 and lysine 7. A complex of this type would account for the data described herein.

Nuclear-magnetic-resonance study of the histidine residues of S-peptide and S-protein and kinetics of 1H-2H exchange of ribonuclease A

1H NMR spectroscopy at 100 MHz was used to determine the first-order rate constants for the 1H-2H exchange of the H-2 histidine resonances of RNase-A in 2H2O at 35 degrees C and pH meter readings of 7, 9, 10 and 10.5. Prolonged exposure in 2H2O at 35 degrees C and pH meter reading 11 caused irreversible denaturation of RN-ase-A. The rate constants at pH 7 and 9 agreed reasonably well with those obtained in 1H-3H exchange experiments by Ohe, J., Matsuo, H., Sakiyama, F. and Narita, K. [J. Biochem, (Tokyo) 75, 1197-1200 (1974)]. The rate data obtained by various authors is summarised and the reasons for the poor agreement between the data is discussed. The first-order rate constant for the exchange of His-48 increases rapidly from near zero at pH 9 (due to its inaccessibility to solvent) with increase of pH to 10.5 The corresponding values for His-119 show a decrease and those for His-12 a small increase over the same pH range. These changes are attributed to a conformational change in the hinge region of RNase-A (probably due to the titration of Tyr-25) which allows His-48 to become accessible to solvent. 1H NMR spectra of S-protein and S-peptide, and of material partially deuterated at the C-2 positions of the histidine residues confirm the reassignment of the histidine resonances of RNase-A [Bradbury, J. H. & Teh, J. S. (1975) Chem. Commun., 936-937]. The chemical shifts of the C-2 and C-4 protons of histidine-12 of S-peptide are followed as a function of pH and a pK' value of 6.75 is obtained. The reassignment of the three C-2 histidine resonances of S-protein is confirmed by partial deuteration studies. The pK' values obtained from titration of the H-2 resonances of His-48, His-105 and His-119 are 5.3, 6.5 and 6.0, respectively. The S-protein is less stable to acid than RNase-A since the former, but not the latter, shows evidence of reversible denaturation at pH 3 and 26 degrees C. His-48 in S-protein titrates normally and has a lower pK than in RN-ase-A probably because of the absence of Asp-14, which in RN-ase-A forms a a hydrogen bond with His-48 and causes it to be inaccessible to solvent, at pH values below 9.