Solution 1H NMR of the molecular and electronic structure of the heme cavity and substrate binding pocket of high-spin ferric horseradish peroxidase: effect of His42Ala mutation.

Solution 1H NMR has been used to assign a major portion of the heme environment and the substrate-binding pocket of resting state horseradish peroxidase, HRP, despite the high-spin iron(III) paramagnetism, and a quantitative interpretive basis of the hyperfine shifts is established. The effective assignment protocol included 2D NMR over a wide range of temperatures to locate residues shifted by paramagnetism, relaxation analysis, and use of dipolar shifts predicted from the crystal structure by an axial paramagnetic susceptibility tensor normal to the heme. The most effective use of the dipolar shifts, however, is in the form of their temperature gradients, rather than by their direct estimation as the difference of observed and diamagnetic shifts. The extensive assignments allowed the quantitative determination of the axial magnetic anisotropy, Deltachi(ax) = -2.50 x 10(-8) m(3)/mol, oriented essentially normal to the heme. The value of Deltachi(ax) together with the confirmed T(-2) dependence allow an estimate of the zero-field splitting constant D = 15.3 cm(-1), which is consistent with pentacoordination of HRP. The solution structure was generally indistinguishable from that in the crystal (Gajhede, M.; Schuller, D. J.; Henriksen, A.; Smith, A. T.; Poulos, T. L. Nature Structural Biology 1997, 4, 1032-1038) except for Phe68 of the substrate-binding pocket, which was found turned into the pocket as found in the crystal only upon substrate binding (Henriksen, A.; Schuller, D. J.; Meno, K.; Welinder, K. G.; Smith, A. T.; Gajhede, M. Biochemistry 1998, 37, 8054-8060). The reorientation of several rings in the aromatic cluster adjacent to the proximal His170 is found to be slow on the NMR time scale, confirming a dense, closely packed, and dynamically stable proximal side up to 55 degrees C. Similar assignments on the H42A-HRP mutant reveal conserved orientations for the majority of residues, and only a very small decrease in Deltachi(ax) or D, which dictates that five-coordination is retained in the mutant. The two residues adjacent to residue 42, Ile53 and Leu138, reorient slightly in the mutant H42A protein. It is concluded that effective and very informative 1H NMR studies of the effect of either substrate binding or mutation can be carried out on resting state heme peroxidases.

Study of interactions between food phenolics and aromatic flavors using one- and two-dimensional (1)H NMR spectroscopy.

Changes in flavor release and aroma characteristics in a medium including food phenolics may be attributed to an intermolecular interaction between flavor compounds and phenolics. To investigate the interaction, one- and two-dimensional NMR studies have been carried out on the binding of two phenolics, gallic acid and naringin, with three aroma compounds, 2-methylpyrazine, vanillin, and ethyl benzoate. Evaluation of thermodynamic parameters and intermolecular nuclear Overhauser effects reveals that gallic acid can interact more strongly with aromatic flavors than naringin. The supramolecular complexation is also dependent on the structural nature of the flavors, with 2-methylpyrazine and vanillin interacting more strongly than ethyl benzoate. The interaction is principally pi-pi stacking between the galloyl ring and the aromatic ring of the aroma compounds, but secondary hydrogen-bonding effects help to stabilize the complex and enhance the specificity.

Solution 1H NMR investigation of the heme cavity and substrate binding site in cyanide-inhibited horseradish peroxidase.

Solution two-dimensional 1H NMR studies have been carried out on cyanide-inhibited horseradish peroxidase isozyme C (HRPC-CN) to explore the scope and limitations of identifying residues in the heme pocket and substrate binding site, including those of the "second sphere" of the heme, i.e. residues which do not necessarily have dipolar contact with the heme. The experimental methods use a range of experimental conditions to obtain data on residue protons with a wide range of paramagnetic relaxivity. The signal assignment strategy is guided by the recently reported crystal structure of recombinant HRPC and the use of calculated magnetic axes. The goal of the assignment strategy is to identify signals from all residues in the heme, as well as proximal and distal, environment and the benzhydroxamic acid (BHA) substrate binding pocket. The detection and sequence specific assignment of aromatic and aliphatic residues in the vicinity of the heme pocket confirm the validity of the NMR methodologies described herein. Nearly all residues in the heme periphery are now assigned, and the first assignments of several "second sphere" residues in the heme periphery are reported. The results show that nearly all catalytically relevant amino acids in the active site can be identified by the NMR strategy. The residue assignment strategy is then extended to the BHA:HRPC-CN complex. Two Phe rings (Phe 68 and Phe 179) and an Ala (Ala 140) are shown to be in primary dipolar contact to BHA. The shift changes induced by substrate binding are shown to reflect primarily changes in the FeCN tilt from the heme normal. The present results demonstrate the practicality of detailed solution 1H NMR investigation of the manner in which substrate binding is perturbed by either variable substrates or point mutations of HRP.

Identification of residues in the aromatic substrate binding site of horseradish peroxidase by 1H NMR studies on isozymes.

The cyanide-inhibited complexes of two horseradish peroxidase acidic isozymes, A1 (HRPA1, unsequenced) and A2 (HRPA2, sequenced), have been examined by solution two-dimensional 1H NMR methods, and the active site molecular and electronic structure compared to that of the well-characterized isozyme C (HRPC) (Chen, Z., de Ropp, J.S., Hernández, G., & La Mar, G.N. (1994) J. Am. Chem. Soc. 116, 8772-8783), as well as to that of cytochrome c peroxidase. The identity and alignment of catalytically relevant residues near the active site for HRPA1-CN and HRPA2-CN are determined, and key residue replacements implicated in the differential catalytic properties of the acidic vs C isozymes are identified. Heme and axial His contact shift patterns, as well as dipolar contacts of residues with the heme and with each other, confirm a highly conserved structure among the three isozymes, including for the distal pocket residues involved in the activation of the enzyme. The remarkable dynamic stability of the heme pocket, as reflected in NH exchange with solvent, is also conserved for the three isozymes. An additional heme contact, Ile 148, is identified in HRPC-CN. Four residues in contact with the heme in HRPC-CN are replaced in HRPA2-CN, two of which are likely functionally neutral, Gly 169-->Ala and Ile 148-->Leu. However, two substitutions in the acidic isozymes in the aromatic substrate binding pocket on the heme edge, Ile 244-->Leu and Phe 179 or 221-->aliphatic residue, could well account for the dramatic decrease (approximately 10(3) in aromatic substrate binding in the A1 and A2 isozymes vs the C isozyme of HRP.(ABSTRACT TRUNCATED AT 250 WORDS)

H NMR investigation of the influence of interacting sites on the dynamics and thermodynamics of substrate and ligand binding to horseradish peroxidase.

The influence of substrate benzhydroxamic acid (BHA) and iron ligand (cyanide) on the thermodynamics and dynamics of each of the two binding sites of horseradish peroxidase (HRP) isozyme C has been investigated by 1H NMR spectroscopy. A combination of line-width analysis and saturation transfer spectroscopy has allowed the direct determination of the off-rate of substrate and ligand in the absence or presence of the other. These off-rates, together with available dissociation constants obtained by optical spectroscopy (Schonbaum, 1973), provide estimates for kon. The dissociation constant for cyanide binding to the BHA.HRP complex was also directly determined by NMR. In all cases the 1H NMR determined dynamic and thermodynamic data agree well with those values available in the literature. BHA binding leads to a 200-fold decrease in CN- affinity that arises from a factor greater than 10 decrease in koff(CN-) and greater than 2 x 10(3) decrease in kon(CN-). While a portion of the decrease in kon(CN-) can be rationalized by water coordination of the iron in the BHA.HRP complex, the additional decrease in kon(CN-) and that in koff(CN-) indicates that BHA in the binding pocket blocks the CN- ligation channel and serves as a "gate" to CN- exchange. This view is supported by observing a factor greater than 4 decrease in distal His labile proton exchange with bulk water in HRP-CN upon BHA binding. The ternary complex BHA.HRP-CN is shown to be heterogeneous. While the thermodynamics of BHA and CN- binding appear similar in the two ternary complexes, the BHA on- and off-rates for the two complexes differ by a factor of approximately 10. The two heterogeneous forms interconvert at 25 degrees C at approximately 2 x 10(2) s-1, precluding the determination of any difference in the CN- binding rates by saturation transfer. The greater lability of one of the two ternary complexes is attributed to an alternate orientation of some distal residue that blocks the substrate binding channel in one of the forms. Transferred nuclear Overhauser effects from the heme to BHA in the ternary complex reveal that the BHA substrate is in contact not only with the heme pyrrole D substituents but also with the distal His 42, indicating that the polar side chain of BHA extends well into the distal heme pocket.(ABSTRACT TRUNCATED AT 400 WORDS)

NMR study of the active site of resting state and cyanide-inhibited lignin peroxidase from Phanerochaete chrysosporium. Comparison with horseradish peroxidase.

One- and two-dimensional 1H NMR spectroscopy has been used to probe the active site of the high spin ferric resting state and the low spin, cyanide-inhibited derivative of isozyme H2 of the lignin peroxidase, LiP, from Phanerochaete chrysosporium strain BKM 1767. One-dimensional NMR revealed a resting state LiP that is five coordinate at 25 degrees C with an electronic structure similar to that of horseradish peroxidase, HRP. Differential paramagnetic relaxivity was used to identify the C beta H signals of the axial His177. A combination of bond correlation spectroscopy and nuclear Overhauser effect spectroscopy of cyanide-inhibited LiP (LiP-CN) has allowed the assignment of all resolved heme resonances without recourse to isotope labeling, as well as those of the proximal His177 and the distal His48. The surprising effectiveness of the two dimensional NMR methods on such a large and paramagnetic protein indicates that such two dimensional experiments can be expected to have major impact on solution structure determination of diverse classes of heme peroxidases. The two dimensional NMR data of LiP-CN reveal a heme contact shift pattern that reflects a close similarity to that of HRP-CN, including the unusual in-plane trans and cis orientation of the 2- and 4-vinyls. The axial His177 also exhibits the same orientation relative to the heme as in HRP-CN. The proximal His177 contact shifted resonances of both the low spin LiP-CN and high spin LiP are shown to reflect significantly reduced hydrogen bond donation by, or imidazolate character for, the axial histidine in LiP relative to HRP, which may explain the higher redox potential of LiP. The signals are identified for a distal residue that originates from the protonated His48 with disposition relative to the heme similar to that found for the distal His42 in HRP-CN. In contrast, the absence of any resolved signals attributable to an Arg44 in LiP-CN suggest that this distal residue has an altered orientation relative to the heme compared with that of the conserved Arg38 in HRP-CN (Thanabal, V., de Ropp, J. S., and La Mar, G. N. (1987) J. Am. Chem. Soc. 109, 7516-7525).

2D NMR of paramagnetic metalloenzymes: cyanide-inhibited horseradish peroxidase.

Two-dimensional (2D) proton NMR correlation spectroscopy, COSY, and nuclear Overhauser spectroscopy, NOESY, have been used to explore the applicability of these methods for the moderately large (42 KDa), paramagnetic cyanide-inhibited derivative of horseradish peroxidase, HRP-CN. The target resonances are those in the active site of HRP-CN which experience substantial hyperfine shifts and paramagnetic relaxation. The magnitude COSY experiment was found to yield cross peaks for all known spin-coupled heme substituents, as well as for the majority of non-heme hyperfine shifted protons, in spite of line widths of the order of approximately 100 Hz. Moreover, the rapid relaxation of the hyperfine-shifted resonances allows the extremely rapid collection of useful 2D NMR data sets without the loss of information. For the heme, the combination of COSY cross peaks for the vinyl and propionate substituents, and NOESY cross peaks among these substituent protons and heme methyls, allows assignment of heme resonances without recourse to deuterium labeling of the heme. A seven-proton coupled spin system was identified in the upfield region that is consistent with originating from the proposed catalytic Arg38 residue in the distal heme pocket, with orientation relative to the heme similar to that found in cytochrome c peroxidase. The upfield hyperfine-shifted methyl group in the substrate binding pocket previously proposed to arise from Leu237 is shown to arise instead from an as yet unidentified Ile. NOESY spectra collected at very short (3 ms) and intermediate (20 ms) mixing times indicate that build-up curves can be obtained that should yield estimates of distances in the heme cavity. It is concluded that 2D NMR studies should be able to provide the heme assignments, aid in identifying the catalytic residues, and provide information on the spatial disposition of such residues in the active site for cyanide complexes of a number of intermediate to large paramagnetic heme peroxidases, as well as for other paramagnetic metalloenzymes with line widths of approximately 100 Hz. Moreover, paramagnetic-induced hyperfine shifts and linewidths to approximately 100 Hz need not interfere with the complete solution structure determination of a small paramagnetic protein solely on the basis of 2D NMR data.

Conformational analysis of PKI(5-22)amide, the active inhibitory fragment of the inhibitor protein of the cyclic AMP-dependent protein kinase.

Fourier-transform i.r. spectroscopy, 1H-n.m.r. spectroscopy and X-ray scattering were used to study the conformation and shape of the peptide PKI(5-22)amide, which contains the active site of the inhibitor protein of the cyclic AMP-dependent protein kinase [Cheng, Van Pattern, Smith & Walsh (1985) Biochem. J. 231, 655-661]. The X-ray-scattering solution studies show that the peptide has a compact structure with Rg 0.9 nm (9.0 A) and a linear maximum dimension of 2.5 nm (25A). Compatible with this, Fourier-transform i.r. and n.m.r. determinations indicate that the peptide contains approx. 26% alpha-helix located in the N-terminal one-third of the molecule. This region contains the phenylalanine residue that is one essential recognition determinant for high-affinity binding to the protein kinase catalytic site.

Solvent isotope effects on NMR spectral parameters in high-spin ferric hemoproteins: an indirect probe for distal hydrogen bonding.

The influence of solvent isotope composition on 1H-NMR resonance position and linewidth of heme methyls has been investigated for a variety of high-spin ferric hemoproteins for the purpose of detecting hydrogen-bonding interactions in the heme cavity. Consistently larger hyperfine shifts and paramagnetic linewidths in 2H2O than 1H2O are observed for metmyoglobins and methemoglobin possessing a coordinated water molecule. The analysis of the dynamics of labile proton exchange in sperm whale metmyoglobin, and the absence of any isotope effects in the five-coordinate Aplysia metmyoglobin, indicate that the significant axial modulation of heme electronic structure by solvent isotope is consistent with arising from distal hydrogen-bonding interactions. The presence or absence of similarly large isotope effects on shifts and linewidths in other hemoproteins, depending on the presence of a bound water in the distal heme pocket, suggests that this isotope effect can serve as a probe for the presence of such bound water. The absence of any detectable isotope effect on either shifts or linewidths in resting-state horseradish peroxidase supports a five-coordinate structure with bound water absent from the vicinity of the iron.

A nuclear Overhauser effect study of the heme crevice in the resting state and compound I of horseradish peroxidase: evidence for cation radical delocalization to the proximal histidine.

The assignment of resolved hyperfine-shifted resonances in high-spin resting state horseradish peroxidase (HRP) and its double-oxidized reactive form, compound I (HRP-I), has been carried out by using the nuclear Overhauser effect (NOE) starting with the known heme methyl assignments in each species. In spite of the efficient spin-lattice relaxation and very broad resonances, significant NOEs were observed for all neighboring pyrrole substituents, which allowed the assignment of the elusive propionate alpha-methylene protons. In the resting state HRP, this leads directly to the identity of the proximal His-170 H beta peaks. The determination that one of the most strongly contact-shifted single proton resonances in HRP-I does not arise from the porphyrin dictates that the cation radical must be delocalized to some amino acid residue. The relaxation properties of the non-heme contact-shifted signal in HRP-I support the identity of this contributing residue as the proximal His-170. Detailed analysis of changes in both contact shift pattern and NOEs indicates that compound I formation is accompanied by a approximately 5 degree rotation of the 6-propionate group. The implication of a porphyrin cation radical delocalized over the proximal histidine for the proposed location of the solely amino acid centered radical in compound I of related cytochrome c peroxidase is discussed.

2H NMR investigation of the organization and dynamics of polyisoprenols in membranes.

The polyisoprenols (PIs) dolichol and undecaprenol function as chemical carriers of glycosyl residues in the membrane-directed synthesis of glycoconjugates in prokaryotic and eukaryotic cells. The molecular details of how these lipid cofactors function is unknown. Presented here are results of deuterium NMR investigations of site specifically 2H-labeled PIs incorporated into model membranes. To complement previous omega-terminal PI labeling schemes, a simple synthesis of head group 2H-labeled PIs is presented in which a PI alcohol is esterified with deuterated acetyl chloride. The 2H-labeled PIs, when incorporated into multilamellar membranes composed of phosphatidylcholine, gave rise to 2H NMR powder patterns interpretable in terms of quadrupole splittings (delta vQ) and spin-lattice relaxation times (T1s). Pure isomers of head group 2H-labeled geraniol (C10) and solanesol (C45) gave rise to single splittings while farnesol (C15) gave rise to two sets of splittings due to cis-trans isomerization at the polar terminal double bond. Membranes containing C45 solanesol exhibited a large isotropic component, indicative of limited partitioning of this poly trans PI into the membrane. T1 measurements revealed high rates of motion for PIs relative to cholesterol in similar membrane hosts and revealed correlation times close to the fatty acyl methyl termini in phosphatidylcholine. The smaller PIs showed higher rates of motion but the T1s of head and tail labels were similar. These data indicate that both ends of the esterified PI molecules see similar environments, probably in the bilayer interior, and suggest that the esterified PIs studied here do not appear to adopt a conventional head group-at-interface orientation of lipids within the bilayer.

Chemical synthesis and 2H NMR investigations of polyisoprenols: dynamics in model membranes.

Polyisoprenols (PIs) such as dolichol and undecaprenol have been shown to play an important role as enzymatic cofactors in the synthesis of glycoconjugates of both prokaryotic and eukaryotic cells. Presented here is a synthetic route used for obtaining specifically labeled [omega,omega-(C2H3)2]PIs that initiates with the selective oxidation of the omega-terminal double bond of the PI with N-bromosuccinimide. Continuation of the reaction sequence produces an omega-terminal aldehyde three carbons shorter than the original PI. A Wittig reaction with an appropriate deuterium-labeled phosphonium salt is then used to form an omega-terminal-deuterated PI identical with the starting material except for replacement of 1H with 2H at the two omega-terminal methyls of the PI. Deuterium NMR spectra of [omega, omega-(C2H3)2]geraniol and -farnesol incorporated into phospholipid multilamellar vesicles show powder patterns. The quadrupole splitting of the 2H NMR signals was interpretable in terms of the degree of orderedness of the 2H-labeled site. The pure trans isomer geraniol gave rise to a single set of splittings for each C2H3 group while farnesol, a mixture of isomers, showed multiple quadrupole splittings. The quadrupole splittings of the PIs increased with increasing concentration of label and with lowering of temperature. Deuterium NMR T1 measurements, revealing rates of motion of the 2H-labeled site, showed fast motion for [omega,omega-(C2H3)3]geraniol relative to [omega,omega-(C2H3)2]cholesterol under similar conditions. A correlation time of 5 X 10(-10) s was estimated for [omega,omega-(C2H3)2]geraniol, which was 1 order of magnitude faster than for [26,27-(C2H3)2]cholesterol.(ABSTRACT TRUNCATED AT 250 WORDS)

Axial histidyl imidazole non-exchangeable proton resonances as indicators of imidazole hydrogen bonding in ferric cyanide complexes of heme peroxidases.

Proton NMR spectra of a model of low-spin cyanide complexes of ferric hemoproteins indicate that two broad single-protein resonances from the axial imidazole can be resolved outside the diamagnetic spectral region. Upon deprotonation of the imidazole in the model, the upfield resonance shifts dramatically to higher field, suggesting that its position may reflect the degree of hydrogen bonding or proton donation of the imidazole. Met-cyano myoglobin reveals a pair of such broad peaks in the regions expected for an essentially neutral axial imidazole. In the cyano complexes of horseradish peroxidase and cytochrome c peroxidase, a pair of single-proton resonances are located which are assigned to the same imidazole protons on the basis of their linewidth and shift changes upon altering the heme substituents. The upfiled proton, however, is found at much higher field than in metMbCN. The upfield bias of this resonance is taken as evidence for appreciable imidazolate character for the axial ligand in these heme peroxidases.

Proton nuclear magnetic resonance study of the electronic and molecular structure of the heme crevice in horseradish peroxidase.

High field proton nuclear magnetic resonance spectroscopy was used to investigate the electronic and molecular structure of the ferric heme in the resting state of horseradish peroxidase. Deuterium labeling of selected positions of hemin and deuterohemin which were subsequently reconstituted into apo-horseradish peroxidase yielded hyperfine shift patterns for the prosthetic group which are consistent with a ferric porphyrin exhibiting appreciable S = 3/2 character in a quantum mixed spin state. All resolved resonances with significant hyperfine shifts can be accounted for by the porphyrin and a proximal histidyl imidazole, although a sixth ligand from the protein cannot be definitely eliminated. The extremely slow exchange rate with bulk water of the proximal histidyl imidazole exchangeable proton and the absence of deviations from Curie behavior for the porphyrin vinyl and propionic acid proton hyperfine shifts indicate a buried heme crevice which is more rigid than in metmyoglobin. The observation of significant deviations from Curie behavior of the proximal histidyl imidazole exchangeable proton in horseradish peroxidase but not in metmyoglobins is suggested to arise from strong hydrogen bonding between the coordinated imidazole and some unspecified protein acceptor residue in the former protein.