Three-dimensional structure and position of porcine motilin in sodium dodecyl sulfate micelles determined by 1H NMR

The solution structure of the porcine gastrointestinal peptide hormone motilin was determined in the presence of sodium dodecyl sulfate (SDS) micelles at 28 degrees C using 1H nuclear magnetic resonance, full relaxation matrix analysis, and structure calculations based on restrained molecular dynamics. The structure of motilin in SDS micelles is described by a reverse gamma-turn and a beta-turn of type II in the N terminal end, an alpha-helical region in the middle of the molecule, and an extended structure at the C terminus. The position of the motilin molecule relative to the SDS micelles was probed by adding spin-labeled stearic acids, containing 12-doxyl or 5-doxyl spin-labels. We observed selective broadening of the proton resonances of residues 3-5 and concluded that they must be located in the interior of the micelle. These experiments suggest a structural model in which the hydrophobic N terminus consists of two well-defined turns buried in the interior of the micelle, whereas the amphiphilic alpha-helical part is located at the surface of the micelle. Spectral density mapping using a 13C label on the alphaC of Leu10 gave overall rotational correlation times taum of 6.6 and 4.5 ns at 35 and 45 degrees C, respectively. The long correlation time in combination with a high order parameter (S = 0.92) indicates that motilin has a rigid structure in the complex with the SDS micelle.

Cloning and characterization of the R1 and R2 subunits of ribonucleotide reductase from Trypanosoma brucei

Ribonucleotide reductase (RNR) catalyzes the rate limiting step in the de novo synthesis of deoxyribonucleotides by directly reducing ribonucleotides to the corresponding deoxyribonucleotides. To keep balanced pools of deoxyribonucleotides, all nonviral RNRs studied so far are allosterically regulated. Most eukaryotes contain a class I RNR, which is a heterodimer of two nonidentical subunits called proteins R1 and R2. We have isolated cDNAs encoding the R1 and R2 proteins from Trypanosoma brucei. The amino acid sequence identities with the mouse R1 and R2 subunits are 58% and 63%, respectively. Recombinant active trypanosome R1 and R2 proteins were expressed in Escherichia coli and purified. The R2 protein contains an iron-tyrosyl free radical center verified by EPR spectroscopy and iron analyses. Measurement of cytidine 5'-diphosphate reduction by the trypanosome RNR in the presence of various allosteric effectors showed that the activity is highest with dTTP, dGTP, or dATP and considerably lower with ATP. The effect of dGTP is either activating (alone) or inhibitory (in the presence of ATP). Filter binding studies indicated that there are two classes of allosteric effector binding sites that bind ATP or dATP (low-affinity dATP site) and ATP, dATP, dGTP, or dTTP (high-affinity dATP site), respectively. Therefore, the structural organization of the allosteric sites is very similar to the mammalian RNRs, whereas the allosteric regulation of cytidine 5'-diphosphate reduction is unique. Hopefully, this difference can be used to target the trypanosome RNR for therapeutic purposes.

Kinetics of transient radicals in Escherichia coli ribonucleotide reductase. Formation of a new tyrosyl radical in mutant protein R2

Reconstitution of the tyrosyl radical in ribonucleotide reductase protein R2 requires oxidation of a diferrous site by oxygen. The reaction involves one externally supplied electron in addition to the three electrons provided by oxidation of the Tyr-122 side chain and formation of the mu-oxo-bridged diferric site. Reconstitution of R2 protein Y122F, lacking the internal pathway involving Tyr-122, earlier identified two radical intermediates at Trp-107 and Trp-111 in the vicinity of the di-iron site, suggesting a novel internal transfer pathway (Sahlin, M., Lassmann, G., Pötsch, S., Sjöberg, B. -M., and Gräslund, A. (1995) J. Biol. Chem. 270, 12361-12372). Here, we report the construction of the double mutant W107Y/Y122F and its three-dimensional structure and demonstrate that the tyrosine Tyr-107 can harbor a transient, neutral radical (Tyr-107(.)). The Tyr-107(.) signal exhibits the hyperfine structure of a quintet with coupling constants of 1.3 mT for one beta-methylene proton and 0.75 mT for each of the 3 and 5 hydrogens of the phenyl ring. Rapid freeze quench kinetics of EPR-visible intermediates reveal a preferred radical transfer pathway via Trp-111, Glu-204, and Fe-2, followed by a proton coupled electron transfer through the pi-interaction of the aromatic rings of Trp-(Tyr-)107 and Trp-111. The kinetic pattern observed in W107Y/Y122F is considerably changed as compared with Y122F: the Trp-111(.) EPR signal has vanished, and the Tyr-107(.) has the same formation rate as does Trp-111(.) in Y122F. According to the proposed consecutive reaction, Trp-111(.) becomes very short lived and is no longer detectable because of the faster formation of Tyr-107(.). We conclude that the phenyl rings of Trp-111 and Tyr-107 form a better stacking complex so that the proton-coupled electron transfer is facilitated compared with the single mutant. Comparison with the formation kinetics of the stable tyrosyl radical in wild type R2 suggests that these protein-linked radicals are substitutes for the missing Tyr-122. However, in contrast to Tyr-122(.) these radicals lack a direct connection to the radical transfer pathway utilized during catalysis.

Density functional calculations on model tyrosyl radicals

A gradient-corrected density functional theory approach (PWP86) has been applied, together with large basis sets (IGLO-III), to investigate the structure and hyperfine properties of model tyrosyl free radicals. In nature, these radicals are observed in, e.g., the charge transfer pathways in photosystem II (PSII) and in ribonucleotide reductases (RNRs). By comparing spin density distributions and proton hyperfine couplings with experimental data, it is confirmed that the tyrosyl radicals present in the proteins are neutral. It is shown that hydrogen bonding to the phenoxyl oxygen atom, when present, causes a reduction in spin density on O and a corresponding increase on C4. Calculated proton hyperfine coupling constants for the beta-protons show that the alpha-carbon is rotated 75-80 degrees out of the plane of the ring in PSII and Salmonella typhimurium RNR, but only 20-30 degrees in, e.g., Escherichia coli, mouse, herpes simplex, and bacteriophage T4-induced RNRs. Furthermore, based on the present calculations, we have revised the empirical parameters used in the experimental determination of the oxygen spin density in the tyrosyl radical in E. coli RNR and of the ring carbon spin densities, from measured hyperfine coupling constants.

Radiolytic reduction of methane monooxygenase dinuclear iron cluster at 77 K. EPR evidence for conformational change upon reduction or binding of component B to the diferric state

The soluble form of methane monooxygenase (MMO) consists of three components: reductase, hydroxylase (MMOH), and "B" (MMOB). Resting MMOH contains a diferric bis-mu-hydroxodinuclear iron "diamond core" cluster which is the site of oxygen activation chemistry after reduction. Here it is shown that gamma-irradiation of MMOH at 77 K results in reduction of the diiron cluster to an EPR active Fe(II). Fe(III) mixed valence state. At this temperature, the conformation of the enzyme remains essentially unchanged during reduction, so the EPR-spectrum becomes a probe of the conformation of the diferric state. The gamma-irradiated MMOH exhibits EPR spectra that differ in lineshape and saturation properties from those of the mixed valence MMOH generated by chemical reduction in solution; annealing the gamma-irradiated sample at 230 K yields the spectra of the chemically reduced sample. This demonstrates that the conformation of diferric MMOH in the vicinity of the diiron cluster changes during reduction to the mixed valence state. The analogous experiment for the MMOB.MMOH complex gives a new mixed valence species following gamma-irradiation that differs from all previously reported mixed valence species. Thus, binding of MMOB also causes a change in the conformation of diferric MMOH. It is hypothesized that the structural changes observed for the first time here may involve conversion of the dihydroxo-bridged diamond core structure to one with more readily dissociable bridging oxygen ligands to facilitate reaction with O2 following cluster reduction.

High field EPR studies of mouse ribonucleotide reductase indicate hydrogen bonding of the tyrosyl radical

Ribonucleotide reductase catalyzes by free radical chemistry the reduction of ribonucleotides to deoxyribonucleotides. The R2 protein of a class 1 ribonucleotide reductase contains a stable tyrosyl radical of neutral phenoxy character, which is necessary for normal enzymatic activity. Here we present the EPR spectra from the tyrosyl free radical in the R2 protein from mouse at 9.62, 115, and 245 GHz. We show that the g-value anisotropy of the mouse R2 radical, when precisely determined from high field EPR spectra, is similar to that of the hydrogen bonded dark stable YD middle dot tyrosyl radical of photosystem II and different from that of the Escherichia coli R2 radical. Because the g-value anisotropy is an important indicator of the hydrogen bonding status of the tyrosyl radical, this result suggests that the mouse R2 radical has its tyrosylate oxygen hydrogen bonded with a D2O exchangeable proton, whereas this hydrogen bond is absent in the E. coli enzyme. It is suggested that the observed proton may be derived from the tyrosine that will become a tyrosyl radical.

Electron paramagnetic resonance and nuclear magnetic resonance studies of class I ribonucleotide reductase

Ribonucleotide reductase catalyses the reduction of ribonucleotides to the corresponding deoxyribonucleotides needed for DNA synthesis. This review describes recent studies on the iron/tyrosyl free radical site in the R2 protein of iron-containing (class I) ribonucleotide reductases. The active enzyme is composed of two homodimeric proteins, R1 and R2. Active protein R2 contains a diiron-oxygen site and a neighboring free radical on a tyrosyl residue per polypeptide chain. The properties of the different redox states of the diiron center in protein R2 are discussed, as well as the formation of the iron/radical site and its possible involvement in long range electron transfer from the substrate binding site in protein R1. The EPR properties of oxidized neutral tyrosyl free radicals are described, and also of tryptophan free radicals found in studies of a mutant of the R2 protein, which lacks the tyrosyl radical site. NMR studies on protein R2 include observations of paramagnetically shifted resonances. Structural NMR studies have been performed on its highly mobile C-terminal domain as well as the corresponding oligopeptide which interacts with protein R1.

Effect of the tyrosyl radical on the reduction and structure of the Escherichia coli ribonucleotide reductase protein R2 diferric site as probed by EPR on the mixed-valent state

It was recently shown by EPR that high yields of a sterically constrained mixed-valent species may be formed in radical free protein metR2 of Escherichia coli ribonucleotide reductase by gamma-irradiation at 77 K [Davydov, R., Kuprin, S., Gräslund, A., & Ehrenberg, A. (1994) J. Am. Chem. Soc. 116, 11120]. This species, with S = 1/2, essentially retains the ligand geometry of the original diferric center and should be a sensitive probe for structural changes in the diferric centers. Here we apply this probe and demonstrate that there is a structural difference between the diferric iron center of the complete site of protein R2, with a tyrosyl radical, and that of metR2, without radical. The EPR spectrum of the mixed-valent species of metR2 shows pure axial symmetry, while complete sites show rhombic distortion and a shifted high-field turning point. Differences also remain in the EPR of the first S = 9/2 species obtained by annealing at 165 K, but disappear after relaxation at 200 K. In addition, the diferric center of a complete site is not reduced radiolytically until the associated tyrosyl radical has been reduced, indicating that an electron first reaching the iron center may be transferred to the radical. This route of electron transfer and the influence of the radical on the structure of the iron center are likely to have functional roles for the formation of the proposed substrate radical and regulation of redox processes within the enzyme. The sensitivity of the structure of the iron site to the structure of the Tyr-122 site is also demonstrated by the strong influence the mutation Y122F has on the EPR spectra of the corresponding mixed-valent species.

A synthetic model for triple-helical domains in self-splicing group I introns studied by ultraviolet and circular dichroism spectroscopy

Structural studies were performed on synthetic oligonucleotides with sequences corresponding to the P4/P6 and J3/4, J6/7 regions of the self-splicing group I intron of the bacteriophage T4 nrdB pre-mRNA, which correspond to the proposed triple-helical domain in the Tetrahymena thermophila intron. A 23-mer RNA was synthesized as a mixed ribo-deoxyribo oligonucleotide, modeling an expected base-paired region of P4 along with the J3/4 and P6 (5'-end bases of P6) regions. strand modeling the 3'-end bases of P6 and J6/7 regions, with which a triple helix may form, was synthesized as a pure oligoribonucleotide (7-mer RNA). The interactions of these oligonucleotides have been characterized by UV and circular dichroism (CD) spectroscopy. The results show that the 23-mer RNA forms a stable hairpin modeling the P4 base-paired region. Triple helix association between the 23-mer RNA hairpin and the 7-mer RNA single strand was detected by CD in the presence of Mg2+ (>5mM) but not in presence of a monovalent cation like Na+ (up to 500 mM). Studies on selected variants of both 7-mer and 23-mer RNAs were carried out. The results show that for the association of the two partner strands not only the formation of P6 helix but also triplet interactions between two strands are required. The association of the two strands in general follow a pattern predicted by comparative sequence analysis. Parallel studies on pure oligoribonucleotides having base sequence corresponding to those of the oligoribonucleotides showed no evidence of association under similar conditions, which could indicate that the 2'-hydroxyl groups of the riboses might play an important role in hydrogen bonding to form the required nucleoside triples. Molecular modeling studies on the proposed "plaited triple helix" formed by the association of the 23-mer RNA hairpin and 7-mer RNA single strand showed that the structure is sterically and energetically feasible.

The free radical of the anaerobic ribonucleotide reductase from Escherichia coli is at glycine 681

The anaerobic ribonucleoside triphosphate reductase of Escherichia coli is an iron-sulfur protein carrying an oxygen-sensitive organic radical, which is essential for catalysis. The radical was tentatively proposed to be on glycine 681, based on a comparison with the glycyl radical-containing enzyme pyruvate formate-lyase. By EPR spectroscopy of selectively 2H- and 13C-labeled anaerobic ribonucleotide reductase, the radical was now unambiguously assigned to carbon-2 of a glycine residue. The large 1H hyperfine splitting (1.4 millitesla) was assigned to the alpha-proton. Site-directed mutagenesis was used to change glycine 681 into an alanine residue. In separate experiments, the two adjacent residues, cysteine 680 and tyrosine 682, were changed into serine and phenylalanine, respectively. All mutated proteins were retained on dATP-Sepharose, indicating that the mutant proteins had intact allosteric sites. They also contained amounts of iron comparable with the wild type reductase and showed the same iron-sulfur-related spectrum, suggesting that the mutant proteins were properly folded. Of the three mutant proteins only the G681A protein completely lacked the detectable glycyl radical as well as enzyme activity. Our results identify glycine 681 as the stable free radical site in E. coli anaerobic ribonucleotide reductase.

A study of melittin, motilin and galanin in reversed micellar environments, using circular dichroism spectroscopy

Circular dichroism spectroscopy has been used to study the behaviour of the cytolytic peptide melittin, the intestinal peptide hormone motilin (porcine) and the neuropeptide galanin (porcine) in various reversed micellar systems. The micellar systems used contained sodium dodecyl sulphate, bis(2-ethylhexyl) sulfosuccinate, n-dodecyltrimethylammonium chloride or polyoxyethylene(7) lauryl ether. Various structural changes of the peptides, induced either by varying the water content or the surface charge of the reversed micelles, could be monitored. Melittin has in all micellar systems a large amount of alpha-helix, and is almost unaffected by both water content and the surface charge of the reversed micelles. Motilin on the other hand attains an alpha-helical structure at low water content only. The surface charges seem to be of importance for the association between motilin and the hydrated reversed micellar surface. Galanin has the most complicated behaviour with a large dependence on surface charge and with a water content dependence which varies with the surfactant used. Stabilization of alpha-helical secondary structures was only seen in negatively charged reversed micelles. These observations indicate a specific interaction between galanin and surfactant, probably of electrostatic nature.

Reversible red-ox reactions of the diiron site in the mouse ribonucleotide reductase R2 protein

The red-ox reactions of the dinuclear iron center of mouse R2 protein upon interaction with different reductants (dithionite alone and with mediators) and oxidants (PES, methylene blue, hydrogen peroxide and para-benzoquinone) have been studied by EPR and optical spectroscopy. The obtained results indicate that the transitions between Fe(III)Fe(III), Fe(II)Fe(III) and Fe(II)Fe(II) states of the dinuclear iron center are reversible and the mu-oxo-bridge may be formed upon oxidation by non-oxygen oxidants. In contrast to the case for the E. coli R2 protein, dithionite alone reduces the tyrosyl radical and diiron center in mouse R2 protein.

Synthesis and characterization of adducts derived from the syn-diastereomer of benzo[a]pyrene 7,8-dihydrodiol 9,10-epoxide and the 5'-d(CCTATAGATATCC) oligonucleotide

5'-d(CCTATAGATATCC) was reacted with each syn-enantiomer of trans-7,8-dihydroxy 9,10-epoxy 7,8,9,10-tetrahydrobenzo[a]pyrene (syn-BPDE). The (-)-enantiomer yielded one dominating adduct, whereas the (+)-enantiomer resulted in two major adducts. As indicated by optical spectroscopic methods, the major adduct derived from both (-)- and (+)-syn-BPDE involves cis addition of the C-10 position of the diol epoxide to the exocyclic amino group of deoxyguanosine [(-)-syn-BPDEc-N2-dG and (+)-syn-BPDEc-N2-dG, respectively], whereas the minor (+)-syn-BPDE adduct is identical to a trans adduct [(+)-syn-BPDEt-N2-dG]. The cis adducts as well as the (+)-syn-BPDEt-N2-dG adduct are chemically stable for several weeks when stored at < or = 4 degrees C in darkness. In duplexes composed of (-)-syn-BPDEc-N2-dG or (+)-syn-BPDEc-N2-dG modified 5'-d(CCTATAGATATCC) and the complement 5'-d(GGATATCTATAGG), the presence of an adduct, in particular the latter, substantially decreased the Tm value relative to the corresponding unmodified duplex. Addition of 5'-d(GGATATCTATAGG) or strands in which dC was replaced with dT, dG, or dA to (-)-syn-BPDEc-N2-dG modified 5'-d(CCTATAGATATCC) decreased the fluorescence intensity in all cases (25-45%). In similar experiments with the (+)-syn-BPDEc-N2-dG adduct, dC or dT opposite the adduct decreased the fluorescence intensity, whereas dA and dG caused an increase. With the (+)-syn-BPDEt-N2-dG adduct, duplex formation had no effect on the intensity with dC or dG opposite the adduct, while an increase could be noted with dT or dA. Acrylamide had no significant effect on the fluorescence intensity of duplexes with cis adducts in contrast to the marked quenching of the fluorescence of (+)-syn-BPDEt-N2-dG oligonucleotide duplexes. In single stranded form, both the cis adducts exhibited absorption and fluorescence excitation maxima at 352-353 nm while the (+)-syn-BPDEt-N2-dG adduct was around 350-351 nm. Addition of the complement or the sequence in which dA replaced dC to the (+)-syn-BPDEt-N2-dG adduct shifted the maxima to 347-349 nm, whereas addition of sequences containing dT or dG opposite the adduct affected the fluorescence maxima but had no effect on absorption maxima. Formation of duplexes with the cis adducts had no or very little effect on the absorption and fluorescence maxima. In conclusion, the results of this study imply an intercalative mode of interaction of the pyrenyl chromophores of the cis adducts and external localization of the (+)-syn-BPDEt-N2-dG adduct.

Formation of a free radical of the sulfenylimine type in the mouse ribonucleotide reductase reaction with 2'-azido-2'-deoxycytidine 5'-diphosphate

Mouse and Escherichia coli ribonucleotide reductases (RR) both belong to the same class of RR, where the enzyme consists of two non-identical subunits, proteins R1 and R2. A transient free radical was observed by EPR spectroscopy in the mouse RR reaction with the suicidal inhibitor 2'-azido-2'-deoxycytidine 5'-diphosphate. The detailed hyperfine structure of the EPR spectrum of the transient radical is somewhat different for the mouse and previously studied E. coli enzymes. When the positive allosteric effector ATP was replaced by the negative effector dATP, no transient radical was observed, showing that 'normal' binding of the inhibitor to the substrate binding site is required. Using the mouse protein R2 mutants W103Y and D266A, where the mutations have been shown to specifically block long range electron transfer between the active site of the R1 protein to the iron/radical site in protein R2, no evidence of transient radical was found. Taken together, the data suggest that the radical is located at the active site in protein R1, and is probably of the sulfenylimine type.

Nonideality of water-hexafluoropropanol mixtures as studied by X-ray small angle scattering

Strong temperature dependent low angle X-ray scattering by trifluoroethanol- and hexafluoro-2-propanol-water mixtures was observed in conditions commonly used in NMR work on peptides. At least two types of molecular effects may contribute to the observed scattering: formation of clathrate hydrate-like aggregates of alcohol with water as have been proposed for the similar system tert-butanol-water (Iwasaki, K. and Fujiyama, T. (1976) J. Phys. Chem. 81, 1908-1912) and a further heterogeneity of the solution resulting from immiscibility of the two components.

NMR studies and restrained-molecular-dynamics calculations of a long A+T-rich stretch in DNA. Effects of phosphate charge and solvent approximations

The nonamer duplex d(GCAAAAACG).d(CGTTTTTGC) was studied by 1H-NMR at 500 MHz. With the exception of the H5' and H5" sugar protons, all protons were assigned by two-dimensional NMR experiments [NOE spectroscopy (NOESY), double-quantum-filtered J-correlated spectroscopy (DQF-COSY) and total correlation spectroscopy (TOCSY)]. The exchange kinetics of the imino protons of the Watson-Crick base pairing were studied at 15 degrees C by measuring inversion-recovery rates under conditions of extensive ammonia base catalysis. Extrapolation to infinite base concentration gave anomalous long lifetimes for the A-tract in accordance with previous results [Leroy, J.-L., Charettier, E., Kochoyan, M. & Guéron, M. (1988) Biochemistry 27, 8894-8898]. On average, 11 NOESY distance constraints/nucleotide were evaluated using the complete relaxation matrix approach. Deoxyribose coupling constants were obtained from simulations of the DQF-COSY cross-peaks, assuming a rapid two-state equilibrium between a C2'-endo and C3'-endo conformer. The sugars were found to be predominantly in the C2'-endo conformation. The NMR-derived distance and torsion constraints were implemented into three different restrained-molecular-dynamics (rMD) protocols, two in vacuo, with different charges on the phosphate group and the third with the solvent explicitly included. All protocols displayed good convergence from different starting structures. The structures derived from the three protocols satisfied experimental restraints equally well and had similar final energies. Although the overall pattern of sequence dependence of helical parameters shows some resemblance in all structures, we find that the absolute amplitudes of the parameters are largely dependent on the rMD protocols, particularly the twist parameters. The minor groove distance P(n + 2)-P(m + 2) varies from 0.7 nm to 1.2 nm in the three protocols. Still the NOESY-derived anomalously short distances AH2(n)-H1'(m + 1) and AH2(n)-H1'(n + 1), n and m denote complementary residues, which are assumed to be indicative of a compressed minor groove, are kept in all calculated structures.

Reduction of the tyrosyl radical and the iron center in protein R2 of ribonucleotide reductase from mouse, herpes simplex virus and E. coli by p-alkoxyphenols

The rate of reduction of the tyrosyl radical in the small subunit of ribonucleotide reductase (protein R2) from E. coli, mouse, and herpes simplex virus (HSV-2) by a series of p-alkoxyphenols with different alkyl chains, have been studied by stopped-flow UV-vis and stopped-flow EPR spectroscopy. The reduction and release of iron in R2 by the inhibitors was followed using bathophenanthroline as chelator of Fe2+. p-Alkoxyphenols reduce the mouse R2 tyrosyl radical 1-2 orders of magnitude faster than the HSV-2 and E. coli radical. In contrast to E. coli, the iron center in R2 from mouse and HSV-2 is reduced by the inhibitors. For mouse R2, the rate of reduction of the tyrosyl radical increases in parallel with increasing alkyl chain length of the inhibitor, an observation which may be important for the design of new antiproliferative drugs.

Solvent stabilized solution structures of galanin and galanin analogs, studied by circular dichroism spectroscopy

Circular dichroism spectroscopy has been used to study how different solvents stabilize secondary structure in the neuropeptide galanin (rat), two N-terminal fragments of galanin, galanin(1-12) and galanin(1-16), and six other differently charged analogs. Among these analogs, the peptide M40, galanin(1-13)-Pro-Pro-Ala-Leu-Ala-Leu-Ala amide, is a high affinity, receptor subtype specific galanin receptor antagonist. The different solvents include sodium dodecyl sulfate (SDS) micelle solutions, 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and 1,2-dioleoyl-sn-glycero-3-phosphoglycerol (DOPG) vesicle solutions. 100% 1,1,1,3,3,3-hexafluoro-2-propanol (HFP) and 100% 2,2,2-trifluoroethanol (TFE). DOPC vesicles did not change the structure of the peptides as compared to aqueous solvent. The negatively charged DOPG vesicles and SDS micelles induced similar changes towards alpha-helical structures in all peptides. The HFP and TFE solvents have an even stronger tendency to stabilize alpha-helical conformations in these peptides. Since DOPG vesicles can be considered as a model system for negatively charged biological membranes, the solution structures observed in the presence of DOPG or SDS may be the most relevant for the in vivo situation. Correlations between the binding affinity of the peptides to hippocampal galanin receptors and their observed structures in the DOPG solvent were investigated.

Transient free radicals in iron/oxygen reconstitution of mutant protein R2 Y122F. Possible participants in electron transfer chains in ribonucleotide reductase

Ferrous iron/oxygen reconstitution of the mutant R2 apoprotein Y122F leads to formation of a diferric center similar to that of the wild-type R2 protein of Escherichia coli ribonucleotide reductase. This reconstitution reaction requires two extra electrons, supplied or transferred by the protein matrix of R2. We observed several transient free radical species using stopped flow and freeze quench EPR and stopped flow UV-visible spectroscopy. Three of the radicals occur in the time window 0.1-2 s, i.e. concomitant with formation of the diferric site. They include a strongly iron-coupled radical (singlet EPR signal) observed only at < or = 77 K, a singlet EPR signal observed only at room temperature, and a radical at Tyr-356 (light absorption at 410 nm), an invariant residue proposed to be part of an electron transfer chain in catalysis. Three additional transient radicals species are observed in the time window 6 s to 20 min. Two of these are conclusively identified, by specific deuteration, as tryptophan radicals. Comparing side chain geometry and distance to the iron center with EPR characteristics of the radicals, we propose certain Trp residues in R2 as likely to harbor these transient radicals.

Evidence by site-directed mutagenesis supports long-range electron transfer in mouse ribonucleotide reductase

Mammalian ribonucleotide reductase consists of two nonidentical subunits, proteins R1 and R2, each inactive alone. The R1 protein binds the ribonucleotide substrates while the R2 protein contains a binuclear iron center and a tyrosyl free radical, essential for activity. The crystal structures of the corresponding Escherichia coli proteins suggest that the distance from the active site in R1 to the tyrosyl radical buried in R2 is about 35 A. Therefore, an electron pathway was suggested between the active site and the tyrosyl radical. Such a pathway could include a conserved tryptophan on the suggested R1 interaction surface of R2 and a conserved aspartic acid hydrogen bonded both to the tryptophan and to a histidine iron ligand. To find experimental support for such an electron pathway, we have replaced the conserved tryptophan in mouse R2 with phenylalanine or tyrosine and the aspartic acid with alanine. All the mutated R2 proteins were shown to bind metal with the same affinity as native R2 and to form the binuclear iron center. In addition, the W103Y and D266A proteins formed a normal tyrosyl free radical while only low amounts of radical were observed in the W103F protein. Neither the kinetic rate constants nor the equilibrium dissociation constant of the R1/R2 complex was affected by the mutations as shown by BIAcore biosensor technique. However, all mutant R2 proteins were completely inactive in the enzymatic assay, supporting the hypothesis that the tryptophan and aspartic acid residues are important links in an amino acid residue specific long-range electron transfer.

Mapping of the spectral density function of a C alpha-H alpha bond vector from NMR relaxation rates of a 13C-labelled alpha-carbon in motilin

The peptide hormone motilin was synthesised with a 13C-enriched alpha-carbon in the leucine at position 10. In aqueous solution, six different relaxation rates were measured for the 13C alpha-H alpha fragment as a function of temperature and with and without the addition of 30% (v/v) of the cosolvent d2-1,1,1,3,3,3-hexafluoro-2-propanol (HFP). The relaxation rates were analysed employing the spectral density mapping technique introduced by Peng and Wagner [(1992) J. Magn. Reson., 98, 308-332] and using the model-free approach by Lipari and Szabo [(1982) J. Am. Chem. Soc., 104, 4546-4570]. The fit to various models of dynamics was also considered. Different procedures to evaluate the overall rotational correlation time were compared. A single exponential time correlation function was found to give a good fit to the measured spectral densities only for motilin in 30% (v/v) HFP at low temperatures, whereas at high temperatures in this solvent, and in D2O at all temperatures, none of the considered models gave an acceptable fit. A new empirical spectral density function was tested and found to accurately fit the experimental spectral density mapping points. The application of spectral density mapping based on NMR relaxation data for a specific 13C-1H vector is shown to be a highly useful method to study biomolecular dynamics. Advantages are high sensitivity, high precision and uniform sampling of the spectral density function over the frequency range.