Redox control of the P450cam catalytic cycle: effects of Y96F active site mutation and binding of a non-natural substrate

Spectroelectrochemistry measurements are used to demonstrate that active site mutation and binding of an non-natural substrate to P450cam (CYP101) reduces the shift in the redox potential caused by substrate-binding, and thereby results in slower catalytic turnover rate relative to wild-type enzyme with the natural camphor substrate.     

Analysis of quaternary carbon resonances of vinylidene chloride/methyl acrylate copolymers

Analysis of the quaternary carbon resonance signals of vinylidene chloride in vinylidene chloride (V)/methyl acrylate (M) copolymers at pentad level of compositional sensitivity is presented in this paper. The analysis has been done by resolving overlapped and complex resonance signals using an approach based on the intensities of resonances, chemical shift prediction and spectral simulation. Intensities of the resonance signals were calculated using the reactivity ratios optimized from the dyad and triad fractions, obtained from the ¹³C ¹H NMR data, by applying genetic algorithm. Joint confidence interval was obtained for the optimized reactivity ratios. The chemical shift modeling of the quaternary carbon resonance signals in terms of empirical additive parameters was done. The chemical shifts of overlapping pentad resonances were predicted from the empirical additive parameters optimized using genetic algorithm. Comparison of the intensities of pentad resonances assigned by chemical shift modeling and experimental intensities of resonances has been done to ascertain the assignments made. Comparison between simulated and experimental spectra at pentad level of sensitivity has been done.     

Microenvironmental and conformational structure of triblock copolymers in aqueous solution by 1H and 13C NMR spectroscopy

1H and 13C nuclear magnetic resonance (NMR) spectra of poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide) (PEO-PPO-PEO) triblock copolymers in D2O solutions have been systematically investigated. The detailed assignments of various 1H and 13C NMR signals are presented. The hyperfine structure of PO -CH2- protons was clearly assigned, the arising reason of this hyperfine structure was attributed to the influence of the chiral center of -CHCH3- groups and the direct coupling between the PO -CH2- and -CH3 protons. The external standard 2,2-dimethyl-2-silapentane-5-sulfonate sodium salt (DSS) was firstly applied in this system. Accurate chemical shift values referenced to the external standard DSS were obtained. 1H NMR chemical shift of PO -CH2- and -CH3 signals shows a larger decrease in ppm values than that of EO -CH2- signal with the increase of PPO/PEO ratio or temperature indicating that PO segments exist in a more hydrophobic microenvironment. A new resonance signal assigned to the PO -CH2- protons appeared when the temperature is above the CMT, which is attributed to the breakdown of the intra-molecular (C-H)...O hydrogen bond between the PO -CH2- protons and the ester oxygens. The breakdown of this intra-molecular hydrogen bond may result in a decrease of gauche conformers of the PPO chain. The increase of 13C NMR chemical shift of block copolymers validates this conformational change assumption. It can be inferred that the amount of gauche conformers decreases whereas that of trans conformers increases in both PO and EO chains when elevating the PPO/PEO ratio or temperature. The observed 13C NMR chemical shifts of PO segments show a bigger increase than those of EO segments, supporting the formation of a nonpolar microenvironment around PO segments.     

Multinuclear two-dimensional NMR: Assignments of natural abundance polypeptide 13C, 1H and 15N chemical shifts and demonstration of isomer interconversion

The polypeptide carbobenzoxy-glycyl-L -prolyl-L -leucyl-L -alanyl-L -proline (0.2 M in DMSO-d₆) was investigated using ¹³C, ¹H and ¹⁵N NMR in natural abundance at 4.7 tesla. The existence of cis–trans-Gly-Pro and -Ala-Pro bonds permits up to four isomers, and all four were observed (in a 60:30:7:3 ratio). ¹³C shifts of the proline β-CH₂ resonances are consistent only with the 60% form being trans–trans. The 30% form is either trans–cis or cis–trans (order as above) and was tentatively assigned as cis-trans on the basis of relaxation behavior. Refocused INEPT studies aided the ¹³C assignments. The ¹⁵N data were obtained using both NOE and INEPT excitation, with signals evident for the three major isomers. The spectra were analysed by starting from the ¹³C data, which were assigned based on known regularities in peptide spectra. A ¹³C? ¹H heteronuclear two-dimensional chemical shift correlation experiment allowed direct assignment of proton shifts for major and minor isomers. The NH proton shifts were assigned by running a homonuclear two-dimensional chemical shift correlation experiment and noting the correlation with the previously assigned α-CH protons. The ¹⁵N resonances were then assigned from a ¹⁵N? ¹H heteronuclear two-dimensional chemical shift correlation experiment, relating the ¹⁵N signals directly to the NH proton resonances. Isomer interconversion between the two major isomers was demonstrated by performing a magnetization transfer homonuclear 2D experiment. Off-diagonal intensity was noted relating the major and minor isomer alanine NH proton, as well as for the major and minor isomer leucine NH protons.     

Nuclear magnetic resonance studies of the microscopic protonation of L-cysteine

The protonation scheme of L-cysteine has been investigated by nuclear magnetic resonance. Chemical shift data as a function of pH are given for L-cysteine, L-cysteine methyl ester and S-methyl-L-cysteine. Use of derivatives of L-cysteine permits determination of the effect of protonation of the amino, sulfhydryl and carboxylic sites on the chemical shift of the -CH and -CH₂ protons. On the basis of these results, a set of simultaneous equations was written whose solution yielded the fraction of protonation of each site upon the addition of n equivalents of acid to the initially completely deprotonated molecule.     

The four-electron diamagnetic ring current of porphycene

Porphycene, an isomer that can replace porphin in chemical and biochemical contexts, is predicted by ab initio calculation to exhibit a global diatropic pi ring current with bifurcation across the four pyrrole units of the macrocycle. Analysis of the orbital contributions to the current density in porphycene reveals that the global current, with its bifurcation feature, is attributable to the four electrons of the near-degenerate HOMO levels, the same set of active electrons that feature in the well-known four-orbital model of the electronic spectra of porphyrins. Integration of the current density gives 1H, 13C and 15N NMR shieldings that are compatible with the observed low-field shifts of peripheral and bridge protons and high-field shift of the internal NH protons, assignment of the 13C NMR spectrum and the single average 15N chemical shift resulting from rapid NH tautomerism. Geometries were calculated with the DFT B3LYP functional, the current density maps were calculated with the ipsocentric coupled-Hartree-Fock CTOCD-DZ method, and the shieldings with the CTOCD-PZ2 variant, all in the same 6-31G** basis.     

Solid-state NMR studies of the molecular structure of Taxol

Solid-state 13C{1H} cross-polarization/magic angle spinning spectroscopy (CP/MAS) has been utilized to extract the molecular structure information of Taxol, which is an anti-tumor therapeutic medicine extracted from the yew bark. The 13C signals have chemical shift values quite consistent with those measured in solution phase, and the overall chemical shift range is over 200 ppm. Notably, most of the 13C resonances of the taxane ring have two clearly resolved spectral components except the resonance peaks of C-15, C-16 and C-17, which are located at the central part of the taxane ring. On the basis of our NMR data, we propose that these doublets originate from two slightly different molecular conformations of the taxane ring and still the central part of the ring remains structurally similar. Furthermore, it is demonstrated that the 13C chemical shift difference deduced from the doublet splittings can serve as a direct measure of the structural difference between the two conformations, which could possibly correlate with the anti-tumor activity of Taxol.     

Computerunterstützte Zuordnung von13C-NMR-Spektren

A computer program for the assignment of¹³C resonances to the respective carbons of a known structure is presented. The algorithm is based on the prediction of chemical shift ranges from a data base containing carbon-centered substructural environments and their corresponding chemical shifts. The method permits a stepwise solution of the assignment problem using chemical shift arguments up to a five-bond radius.     

Ring current effects in the active site of medium-chain Acyl-CoA dehydrogenase revealed by NMR spectroscopy

Medium-chain acyl-CoA dehydrogenase (MCAD) catalyzes the flavin-dependent oxidation of fatty acyl-CoAs to the corresponding trans-2-enoyl-CoAs. The interaction of hexadienoyl-CoA (HD-CoA), a product analogue, with recombinant pig MCAD (pMCAD) has been studied using (13)C NMR and (1)H-(13)C HSQC spectroscopy. Upon binding to oxidized pMCAD, the chemical shifts of the C1, C2, and C3 HD carbons are shifted upfield by 12.8, 2.1, and 13.8 ppm, respectively. In addition, the (1)H chemical shift of the C3-H is also shifted upfield by 1.31 ppm while the chemical shift of the C4 HD-CoA carbon is unchanged upon binding. These changes in chemical shift are unexpected given the results of previous Raman studies which revealed that the C3=C2-C1=O HD enone fragment is polarized upon binding to MCAD such that the electron density at the C3 and C1 carbons is reduced, not increased (Pellet et al. Biochemistry 2000, 39, 13982-13992). To investigate the apparent discrepancy between the NMR and Raman data for HD-CoA bound to MCAD, (13)C NMR spectra have been obtained for HD-CoA bound to enoyl-CoA hydratase, an enzyme system that has also previously been studied using Raman spectroscopy. Significantly, binding to enoyl-CoA hydratase causes the chemical shifts of the C1 and C3 HD carbons to move downfield by 4.8 and 5.6 ppm, respectively, while the C2 resonance moves upfield by 2.2 ppm, in close agreement with the alterations in electron density at these carbons predicted from Raman spectroscopy (Bell, A. F.; Wu, J.; Feng, Y.; Tonge, P. J. Biochemistry 2001, 40, 1725-33). The large increase in shielding experienced by the C1 and C3 HD carbons in the HD-CoA/MCAD complex is proposed to arise from the ring current field from the isoalloxazine portion of the flavin cofactor. The flavin ring current, which is only present when the enzyme is placed in an external magnetic field, also explains the differences in (13)C NMR chemical shifts for acetoacetyl-CoA when bound as an enolate to MCAD and enoyl-CoA hydratase and is used to rationalize the observation that the line widths of the C1 and C3 resonances are narrower when the ligands are bound to MCAD than when they are free in the protein solution.     

Interaction of bleomycin with deoxyribonucleic acid oligomer: proton nuclear magnetic resonance titration study using novel bleomycin complexes with Ni2+ and VO3+.

Two metal complexes of bleomycin (BLM), BLM-Ni2+ and BLM-VO3+ are used for studying interactions between BLM and deoxyribonucleic acid (DNA) by nuclear magnetic resonance. Although these BLMs do not mediate DNA strand scission under the usual conditions, they bind to DNA in the same manner as the active metal complexes of bleomycin (BLM-Fe2+ and BLM-Co3+). A self-complementary dodecanucleotide, d(CCCCAGCTGGGG), having a single site for cleavage was synthesized. d(CCCCAATTGGGG), which contains no -GpC- sequence, was also synthesized. The BLM-metal complexes were shown to bind specifically to the GpC site by circular dichroism and fluorescence titration studies. We assigned all the resonances for imino protons and phosphorus, and most of the nonexchangeable proton resonances of d(CCCCAGCTGGGG). No substantial change in the chemical shifts of these signals was observed upon titration with either BLM-Ni2+ or BLM-VO3+. This result is not consistent with a model of the strong intercalation of the BLMs between the base-pairs. The BLMs bind to DNA in a different manner, and DNA does not change its conformation upon binding with BLMs.     

Assignment of the carbon-13 chemical shifts of quinacrine,chloroquine and related compounds in D2O solution

The carbon resonances of quinacrine, chloroquine, acranil, 4-aminopyridine and 9-aminoacridine in D₂O solution have been assigned. Resonance assignments were made using empirical shift parameters, partial proton decoupling, selective proton decoupling and by interpretation of the fully coupled spectra. The effect of pD on the carbon chemical shifts for quinacrine and chloroquine over the range of about 4.5 to 8.5 was observed. Characteristic chemical shifts for the aromatic ring carbons for deprotonation of the heteroaromatic nitrogen were observed.     

The NMR spectra of the porphyrins: 24—The NMR spectra of some tetraarylchlorins

The synthesis and complete assignment of the ¹H NMR spectra of 5-(o-pivaloylaminophenyl)-10,15,20-triphenylporphyrin (PIVTPP) and its two chiral dihydro adducts 3,4-dihydro-(PIVPTPC-I)- and 7,8-dihydr- (PIVPTPC-II)-porphyrins are reported. The use of the zinc complexes of the chlorins as chiral shift reagents with optically active bases is discussed. Comparison of the observed shift differences between the chlorins and the parent porphyrin with those calculated by a ring current model shows that a decrease in the ring current occurs on chlorin formation, and also specific effects occur at the reduced pyrrole ring, presumably reflecting different steric constraints.     

NMR assignment methods for the aromatic ring resonances of phenylalanine and tyrosine residues in proteins

The unambiguous assignment of the aromatic ring resonances in proteins has been severely hampered by the inherently poor sensitivities of the currently available methodologies developed for uniformly 13C/15N-labeled proteins. Especially, the small chemical shift differences between aromatic ring carbons and protons for phenylalanine residues in proteins have prevented the selective observation and unambiguous assignment of each signal. We have solved all of the difficulties due to the tightly coupled spin systems by preparing regio-/stereoselectively 13C/2H/15N-labeled phenylalanine (Phe) and tyrosine (Tyr) to avoid the presence of directly connected 13C-1H pairs in the aromatic rings. The superiority of the new labeling schemes for the assignment of aromatic ring signals is clearly demonstrated for a 17 kDa calcium binding protein, calmodulin.     

光活性聚甲基丙烯酸三苯甲酯链结构的研究——PTrMA的~(13)C液体和固体NMR谱

<正> 80年代出现的光活性高聚物—聚甲基丙烯酸三苯甲酯(PTrMA)是由非手性单体经不对称阴离子聚合得到的。近年来,PTrMA作为手性固定相在分离手性化合物方面得到了越来越多的实际应用。由于聚合物侧基上的三个苯基产生的大位阻,使它具     

Increasing the Chemical‐Shift Dispersion of Unstructured Proteins with a Covalent Lanthanide Shift Reagent

The study of intrinsically disordered proteins (IDPs) by NMR often suffers from highly overlapped resonances that prevent unambiguous chemical‐shift assignments, and data analysis that relies on well‐separated resonances. We present a covalent paramagnetic lanthanide‐binding tag (LBT) for increasing the chemical‐shift dispersion and facilitating the chemical‐shift assignment of challenging, repeat‐containing IDPs. Linkage of the DOTA‐based LBT to a cysteine residue induces pseudo‐contact shifts (PCS) for resonances more than 20 residues from the spin‐labeling site. This leads to increased chemical‐shift dispersion and decreased signal overlap, thereby greatly facilitating chemical‐shift assignment. This approach is applicable to IDPs of varying sizes and complexity, and is particularly helpful for repeat‐containing IDPs and low‐complexity regions. This results in improved efficiency for IDP analysis and binding studies.     

Paramagnetic 1H NMR spectrum of nickel(II) pseudoazurin: investigation of the active site structure and the acid and alkaline transitions

The paramagnetic (1)H NMR spectrum of Ni(II) pseudoazurin [(PA)Ni(II)] possesses a number of resonances exhibiting sizable Fermi-contact shifts. These have been assigned to protons associated with the four ligating amino acids, His40, Cys78, His81, and Met86. The shifts experienced by the C(gamma)H protons of the axial Met86 ligand are unprecedented compared to other Ni(II)- and Co(II)-substituted cupredoxins (the C(gamma)(1)H signal is found at 432.5 ppm at 25 degrees C). The large shift of protons of the axial Met86 ligand highlights a strong Ni(II)-S(Met) interaction in (PA)Ni(II). The paramagnetic (1)H NMR spectrum of (PA)Ni(II) is altered by decreasing and increasing the pH value from 8.0. At acidic pH a number of the hyperfine-shifted resonances undergo limited changes in their chemical shift values. This effect is assigned to the surface His6 residue whose protonation results in a structural modification of the active site. Increasing the pH value from 8.0 has a more significant effect on the paramagnetic (1)H NMR spectrum of (PA)Ni(II), and the alkaline transition can now be assigned to two surface lysine residues close to the active site of the protein. The effect of altering pH on the (1)H NMR spectrum of Ni(II) pseudoazurin is smaller than that previously observed in the Cu(II) protein indicating more limited structural rearrangements at the non-native metal site.     

Pyrene.pyrene complexes at the active site of cytochrome P450 3A4: evidence for a multiple substrate binding site

Cytochrome P450 monooxygenases (CYPs) metabolize nearly all drugs and toxins. Recently, it has become clear that CYPs exhibit both homotropic and heterotropic allosteric kinetics for many substrates. However, the mechanism of cooperative kinetics has not been established for any specific human CYP/substrate combination. Suggested mechanisms include binding of multiple substrates within distinct, static, subsites of a single large active site or binding of multiple substrates within a single fluid active site. CYP3A4 hydroxylates pyrene with positive cooperativity. Therefore, experiments were designed to exploit the fluorescence properties of pyrene, which diagnostically distinguish between pyrene.pyrene complexes versus spatially separated pyrene substrates. Pyrene complexes (excimers) yield an emission spectrum clearly distinct from pyrene monomers. In lipid-free aqueous/glycerol solutions of CYP3A4, addition of pyrene affords a concentration-dependent low-spin to high-spin conversion of the CYP3A4 heme prosthetic group, indicating occupancy of the active site by pyrene. Under the same conditions, in the presence of CYP3A4 but not other heme proteins, the excimer/monomer ratio (E/M) of pyrene was decreased in emission spectra, compared to pyrene alone. However, excitation spectra indicate a CYP3A4-dependent increase in the wavelength shift for the excimer excitation spectrum versus the monomer excitation spectrum, as well as changes in the excimer excitation peak shape and vibronic structure. These changes are reversed by the CYP3A4 substrate testosterone. Together, the results demonstrate that pyrene.pyrene ground-state complexes occupy the CYP3A4 active site, and they provide the first spectroscopic evidence for substrate complexes within a single fluid active site. Functional implications include the possibility that turnover rate, regioselectivity, and stereoselectivity of the reaction are determined by the substrate.substrate complex rather than individual substrates.     

NMR and EPR studies of the bis(pyridine) and bis(tert-butyl isocyanide) complexes of iron(III) octaethylchlorin

The NMR and EPR spectra of a series of pyridine complexes [(OEC)Fe(L)2]+ (L = 4-Me2NPy, Py, and 4-CNPy) have been investigated. The EPR spectra at 4.2 K suggest that, with a decrease of the donor strength of the axial ligands, the complexes change their ground state from (d(xy))2 (d(xz)d(yz))3 to (d(xz)d(yz))4 (d(xy))1. The NMR data from 303 to 183 K show that at any temperature within this range the chemical shifts of pyrrole-8,17-CH2 protons increase with a decrease in the donor strength of the axial ligands. The full peak assignments of the [(OEC)Fe(L)2]+ complexes of this study have been made from COSY and NOE difference experiments. The pyrrole-8,17-CH2 and pyrroline protons show large chemical shifts (hence indicating large pi spin density on the adjacent carbons which are part of the pi system), while pyrrole-12,13-CH2 and -7,18-CH2 protons show much smaller chemical shifts, as predicted by the spin densities obtained from molecular orbital calculations, both Hückel and DFT; the DFT calculations additionally show close energy spacing of the highest five filled orbitals (of the Fe(II) complex) and strong mixing of metal and chlorin character in these orbitals that is sensitive to the donor strength of the axial substituents. The pattern of chemical shifts of the pyrrole-CH2 protons of [(OEC)Fe(t-BuNC)2]+ looks somewhat like that of [(OEC)Fe(4-Me2NPy)2]+, while the chemical shifts of the meso-protons are qualitatively similar to those of [(OEP)Fe(t-BuNC)2]+. The temperature dependence of the chemical shifts of [(OEC)Fe(t-BuNC)2]+ shows that it has a mixed (d(xz)d(yz))4 (d(xy))1 and (d(xy))2 (d(xz),d(yz))3 electron configuration that cannot be resolved by temperature-dependent fitting of the proton chemical shifts, with a S = 5/2 excited state that lies somewhat more than 2kT at room temperature above the ground state; the observed pattern of chemical shifts is the approximate average of those expected for the two S = 1/2 electronic configurations, which involve the a-symmetry SOMO of a planar chlorin ring with the unpaired electron predominantly in the d(yz) orbital and the b-symmetry SOMO of a ruffled chlorin ring with the unpaired electron predominantly in the d(xy) orbital. A rapid interconversion between the two, with calculated vibrational frequency of 22 cm(-1), explains the observed pattern of chemical shifts, while a favoring of the ruffled conformation explains the negative chemical shift (and thus the negative spin density at the alpha-pyrroline ring carbons), of the pyrroline-H of [TPCFe(t-BuNC)2]CF3SO3 (Simonneaux, G.; Kobeissi, M. J. Chem. Soc., Dalton Trans. 2001, 1587-1592). Peak assignments for high-spin (OEC)FeCl have been made by saturation transfer techniques that depend on chemical exchange between this complex and its bis-4-Me2NPy adduct. The contact shifts of the pyrrole-CH2 and meso protons of the high-spin complex depend on both sigma and pi spin delocalization due to contributions from three of the occupied frontier orbitals of the chlorin ring.     

Solid-state NMR study of amyloid nanocrystals and fibrils formed by the peptide GNNQQNY from yeast prion protein Sup35p

Sup35p is a prion protein found in yeast that contains a prion-forming domain characterized by a repetitive sequence rich in Gln, Asn, Tyr, and Gly amino acid residues. The peptide GNNQQNY7-13 is one of the shortest segments of this domain found to form amyloid fibrils, in a fashion similar to the protein itself. Upon dissolution in water, GNNQQNY displays a concentration-dependent polymorphism, forming monoclinic and orthorhombic crystals at low concentrations and amyloid fibrils at higher concentrations. We prepared nanocrystals of both space groups as well as fibril samples that reproducibly contain three (coexisting) structural forms and examined the specimens with magic angle spinning (MAS) solid-state nuclear magnetic resonance. 13C and 15N MAS spectra of both nanocrystals and fibrils reveal narrow resonances indicative of a high level of microscopic sample homogeneity that permitted resonance assignments of all five species. We observed variations in chemical shift among the three dominant forms of the fibrils which were indicated by the presence of three distinct, self-consistent sets of correlated NMR signals. Similarly, the monoclinic and orthorhombic crystals exhibit chemical shifts that differ from one another and from the fibrils. Collectively, the chemical shift data suggest that the peptide assumes five conformations in the crystals and fibrils that differ from one another in subtle but distinct ways. This includes variations in the mobility of the aromatic Tyr ring. The data also suggest that various structures assumed by the peptide may be correlated to the "steric zipper" observed in the monoclinic crystals.     

Assignments of the chemical shifts of carbon-13 nuclear magnetic resonance spectra of some 2-methyl-3-(3,4-dimethoxy/dihydroxyphenylethyl)-4-quinazolones

The ¹³C nmr chemical shifts of a series of 2-methyl-3-(3,4-dimethoxy/dihydroxyphenylethyl)-4-quinazolones are reported. The carbon resonances have been assigned on the basis of chemical shift theory, intensity of the signals, multiplicities generated in SFORD spectra and the comparison with the structurally related compounds.