NMR structures of thioredoxin m from the green alga Chlamydomonas reinhardtii.

Chloroplast thioredoxin m from the green alga Chlamydomomas reinhardtii is very efficiently reduced in vitro and in vivo in the presence of photoreduced ferredoxin and a ferredoxin dependent ferredoxin-thioredoxin reductase. Once reduced, thioredoxin m has the capability to quickly activate the NADP malate dehydrogenase (EC 1.1.1.82) a regulatory enzyme involved in an energy-dependent assimilation of carbon dioxide in C4 plants. This activation is the result of the reduction of two disulfide bridges by thioredoxin m, that are located at the N- and C-terminii of the NADP malate dehydrogenase. The molecular structure of thioredoxin m was solved using NMR and compared to other known thioredoxins. Thioredoxin m belongs to the prokaryotic type of thioredoxin, which is divergent from the eukaryotic-type thioredoxins also represented in plants by the h (cytosolic) and f (chloroplastic) types of thioredoxins. The dynamics of the molecule have been assessed using (15)N relaxation data and are found to correlate well with regions of disorder found in the calculated NMR ensemble. The results obtained provide a novel basis to interpret the thioredoxin dependence of the activation of chloroplast NADP-malate dehydrogenase. The specific catalytic mechanism that takes place in the active site of thioredoxins is also discussed on the basis of the recent new understanding and especially in the light of the dual general acid-base catalysis exerted on the two cysteines of the redox active site. It is proposed that the two cysteines of the redox active site may insulate each other from solvent attack by specific packing of invariable hydrophobic amino acids.

Overall rotational diffusion and internal mobility in domain II of protein G from Streptococcus determined from 15N relaxation data.

The backbone dynamics and overall tumbling of protein G have been investigated using 15N relaxation. Comparison of measured R2/R1 relaxation rate ratios with known three-dimensional coordinates of the protein show that the rotational diffusion tensor is significantly asymmetric, exhibiting a prolate axial symmetry. Extensive Monte Carlo simulations have been used to estimate the uncertainty due to experimental error in the relaxation rates to be D(parallel)/D(perpendicular) = 1.68 +/- 0.08, while the dispersion in the NMR ensemble leads to a variation of D(parallel)/D(perpendicular) = 1.65 +/- 0.03. Incorporation of this tensorial description into a Lipari-Szabo type analysis of internal motion has allowed us to accurately describe the local dynamics of the molecule. This analysis differs from an earlier study where the overall rotational diffusion was described by a spherical top. In this previous analysis, exchange parameters were fitted to many of the residues in the alpha helix. This was interpreted as reflecting a small motion of the alpha helix with respect to the beta sheet. We propose that the differential relaxation properties of this helix compared to the beta sheet are due to the near-orthogonality of the NH vectors in the two structural motifs with respect to the unique axis of the diffusion tensor. Our analysis shows that when anisotropic rotational diffusion is taken into account NH vectors in these structural motifs appear to be equally rigid. This study underlines the importance of a correct description of the rotational diffusion tensor if internal motion is to be accurately investigated.

NMR structures of the C-terminal end of human complement serine protease C1s.

Synthetic peptides derived from the C-terminal end of the human complement serine protease C1s were analysed by circular dichroism and nuclear magnetic resonance (NMR) spectroscopy. Circular dichroism indicates that peptides 656-673 and 653-673 are essentially unstructured in water and undergo a coil-to-helix transition in the presence of increasing concentrations of trifluoroethanol. Two-dimensional NMR analyses performed in water/trifluoroethanol solutions provide evidence for the occurrence of a regular alpha-helix extending from Trp659 to Ser668 (peptide 656-673), and from Tyr656 to Ser668 (peptide 653-673), the C-terminal segment of both peptides remaining unstructured under the conditions used. Based on these and other observations, we propose that the serine protease domain of C1s ends in a 13-residue alpha-helix (656Tyr-Ser668) followed by a five-residue C-terminal extension. The latter appears to be flexible and is probably locked within C1s through a salt bridge involving Glu672.

1H-NMR study of the structural influence of Y64 substitution in Desulfovibrio vulgaris Hildenborough cytochrome c553.

Y64 has been replaced in cytochrome c553 from Desulfovibrio vulgaris Hildenborough by phenylalanine, leucine, valine, serine and alanine residues. An NMR study of structural variation induced in both oxidoreduction states of the molecule has been carried out by analysing observed chemical-shift variations. Dynamic changes were evidenced using NH exchange. We have observed that the substitution has a drastic effect on the stability of the molecule in the reduced state, although there is no effect on the reduction potential of the cytochrome. Y64-->F substitution induces particular effects on the NH exchange at the N-terminal, C-terminal and central alpha-helices and increases the stability of the oxidized molecule.

NMR solution structure of an oxidised thioredoxin h from the eukaryotic green alga Chlamydomonas reinhardtii.

NMR solution structures of a cytosolic plant thioredoxin h (112 amino acids, 11.7 kDa) from the green alga Chlamydonmonas reinhardtii have been calculated on the basis of 1904 NMR distance restraints, which include 90 distances used to restrain 45 hydrogen bonds, and 44 phi dihedral restraints. The structure of C. reinhardtii thioredoxin h was solved in its oxidised form, and the ensemble of 23 converged structures superpose to the geometric average structure with an atomic rmsd of 0.080 nm +/- 0.016 for the (N, C(alpha), C) backbone atoms of residues 4-110. Comparisons with other thioredoxins, such as thioredoxin from the bacterium Escherichia coli, thioredoxin 2 from a cyanobacterium of the Anabaena genus, and human thioredoxin, showed that thioredoxin h models share more structural features with human thioredoxin than with other bacterial thioredoxins. Examination of the accessible surface around the redoxactive peptide sequence indicates that a potent thioredoxin-h-substrate interaction could be similar to the vertebrate thioredoxin-substrate interactions.

Solution structure of the cellulose-binding domain of the endoglucanase Z secreted by Erwinia chrysanthemi.

Two-dimensional proton nuclear magnetic resonance spectroscopy has been used to determine the three-dimensional structure of the 62 amino acid C-terminal cellulose-binding domain (CBD) of the endoglucanase Z (CBDEGZ), secreted by Erwinia chrysanthemi. An experimental data set comprising 958 interproton nOe-derived restraints was used to calculate 23 structures. The calculated structures have an average root-mean-square deviation between Cys4 and Cys61 of 0.91 +/- 0.11 A for backbone atoms and 1.18 +/- 0.12 A for the heavy atoms. The CBDEGZ exhibits a skiboot shape based mainly on a triple antiparallel beta-sheet perpendicular to a less-ordered summital loop. Three aromatic rings (Trp18, Trp43, and Tyr44) are localized on one face of the protein and are exposed to the solvent in a conformation compatible with a cellulose-binding site. Based on its original folding, we have been able to relate the CBD sequence to those of several domains of unknown function occurring in several bacterial chitinases as well as other proteins. This study also provides a structural basis for analyzing the secretion-related information specific to the CBDEGZ.

Ectothiorhodospira halophila ferrocytochrome c551: solution structure and comparison with bacterial cytochromes c.

The solution structure of the Ectothiorhodospira halophila ferrocytochrome c551 has been determined. This molecule belongs to a separate class of small bacterial cytochromes c for which no 3D structure has been reported so far. It is characterized by a very low redox potential (58 mV) and is isolated from the periplasm of halophilic purple phototrophic bacteria. For the 78 residue protein, 1445 NOE derived distance constraints were used in a combined simulated annealing/restrained molecular dynamics calculation. The final ensemble of 37 structures presents a backbone r.m.s.d. of less than 0.5 A compared to the mean structure. The physical viability of these structures was investigated by subjecting eight of them to a constraint free molecular dynamics simulation. No systematic conformational change was observed and the average backbone r.m.s.d. compared to the initial structures was less than 1.5 A. The structure of the E. halophila cytochrome c551 shows a striking resemblance to Azotobacter vinelandii cytochrome c5. Significant differences in backbone conformations occur in three small regions which are implicated in solvent protection of the heme propionates and thiomethyl-8(1). Comparison with Pseudomonas aeruginosa cytochrome c551 reveals that only the common cytochrome c core, i.e. three helices, is conserved. The folding of the protein chain around the heme propionates is very different and results in more efficient solvent protection in Ps. aeruginosa. The electrostatic surface of E. halophila cytochrome c551 was found to be significantly different from mitochondrial cytochromes c and bacterial cytochromes c2 but similar to that of Ps. aeruginosa cytochrome c551.

Investigation of oxidation state-dependent conformational changes in Desulfovibrio vulgaris Hildenborough cytochrome c553 by two-dimensional H-NMR spectra.

Two-dimensional nuclear magnetic resonance spectroscopy (2D-NMR) was used to assign the proton resonances of ferricytochrome C553 from Desulfovibrio vulgaris Hildenborough. The spin systems of 76 out of 79 amino acids were identified by J-correlation spectroscopy (COSY and HOHAHA) in H20 and D20 and correlated by nuclear Overhauser effect spectroscopy (NOESY). The proton chemical shifts are compared in both oxidized and reduced states of the protein at 23 degrees C and pH 5.9. Chemical shift variations between reduced and oxidized states are due to the paramagnetic contribution. Medium and long-range nOe demonstrate the lack of major changes between the two redox states. NMR data provide evidence that in this low oxidoreduction potential cytochrome, the oxidized state is more rigid than the reduced state.

Comparison of low oxidoreduction potential cytochrome c553 from Desulfovibrio vulgaris with the class I cytochrome c family.

The cytochrome c553 from Desulfovibrio vulgaris (DvH c553) is of importance in the understanding of the relationship of structure and function of cytochrome c due to its lack of sequence homology with other cytochromes, and its abnormally low oxido-reduction potential. In evolutionary terms, this protein also represents an important reference point for the understanding of both bacterial and mitochondrial cytochromes c. Using the recently determined nuclear magnetic resonance (NMR) structure of the reduced protein we compare the structural, dynamic, and functional characteristics of DvH c553 with members of both the mitochondrial and bacterial cytochromes c to characterize the protein in the context of the cytochrome c family, and to understand better the control of oxide-reduction potential in electron transfer proteins. Despite the low sequence homology, striking structural similarities between this protein and representatives of both eukaryotic [cytochrome c from tuna (tuna c)] and prokaryotic [Pseudomonas aeruginosa c551 (Psa c551)] cytochromes c have been recognized. The previously observed helical core is also found in the DvH c553. The structural framework and hydrogen bonding network of the DvH c553 is most similar to that of the tuna c, with the exception of an insertion loop of 24 residues closing the heme pocket and protecting the propionates, which is absent in the DvH c553. In contrast, the Psa c551 protects the propionates from the solvent principally by extending the methionine ligand arm. The electrostatic distribution at the recognized encounter surface around the heme in the mitochondrial cytochrome is reproduced in the DvH c553, and corresponding hydrogen bonding networks, particularly in the vicinity of the heme cleft, exist in both molecules. Thus, although the cytochrome DvH c553 exhibits higher primary sequence homology to other bacterial cytochromes c, the structural and physical homology is significantly greater with respect to the mitochondrial cytochrome c. The major structural and functional difference is the absence of solvent protection for the heme, differentiating this cytochrome from both reference cytochromes, which have evolved different mechanisms to cover the propionates. This suggests that the abnormal redox potential of the DvH c553 is linked to the raised accessibility of the heme and supports the theory that redox potential in cytochromes is controlled by heme propionate solvent accessibility.

NMR and restrained molecular dynamics study of the three-dimensional solution structure of toxin FS2, a specific blocker of the L-type calcium channel, isolated from black mamba venom.

The three-dimensional solution structure of toxin FS2, a 60-residue polypeptide isolated from the venom of black mamba snake (Dendroaspis polylepis polylepis), has been determined by nuclear magnetic resonance spectroscopy. Using 600 NOE constraints and 55 dihedral angle constraints, a set of 20 structures obtained from distance-geometry calculations was further refined by molecular dynamics calculations using a combined simulated annealing-restrained MD protocol. The resulting 20 conformers, taken to represent the solution structure, give an average rmsd of 1.2 A for their backbone atoms, relative to the average structure. The overall resulting three-fingered structure is similar to those already observed in several postsynaptic neurotoxins, cardiotoxins, and fasciculins, which all share with toxin FS2 the same network of four disulfide bridges. The overall concavity of the molecule, considered as a flat bottomed dish, is oriented toward the C-terminal loop of the molecule. This orientation is similar to that of fasciculins and cardiotoxins but opposite to that of neurotoxins. On the basis of the local rms displacements between the 20 conformers, the structure of the first loop appears to be less well defined in FS2 than in the previously reported neurotoxin structures, but fasciculin 1 shows a similar trend with particularly high temperature factors for this part of the X-ray structure. The concave side which presents most of the positively charged residues is quite similar in FS2 and fasciculin 1. The main difference is shown by the convex side of the third loop, mostly hydrophobic in FS2, in contrast to the pair of negatively charged aspartates in fasciculin 1. This difference could be one of the factors leading to the distinct pharmacological properties-L-type calcium channel blocker for FS2 and cholinesterase inhibitor for fasciculin--observed for these two subgroups of the "angusticeps-type" toxins.

Structure and dynamics of ferrocytochrome c553 from Desulfovibrio vulgaris studied by NMR spectroscopy and restrained molecular dynamics.

The solution structure of Desulfovibrio vulgaris Hildenborough (DvH) ferrocytochrome c553 has been determined by nuclear magnetic resonance spectroscopy and combined simulated annealing/high temperature restrained molecular dynamics calculations. This three-stage protocol consists of an initial determination of overall fold from randomised co-ordinates, followed by a 20 picosecond exploratory stage, during which the non-bonded terms are simplified to facilitate as broad a sampling of conformational space as possible, and a 26 picosecond refinement stage, using the full AMBER force field. This latter stage systematically improved the energetic and convergence characteristics of the ensemble, while still satisfying the experimental restraints. Forty structures have been obtained from a total of 875 distance constraints for this protein of 79 amino acid residues. The root-mean-square deviation over all residues with respect to the mean is 0.70(+/- 0.12)A for the backbone (N, C alpha and C') atoms. Two conformations of the turn motif at the solvent/heme cleft interface have been identified, both fulfilling the experimental data and having equally viable energetic characteristics. The stability of the ensemble and the dynamic characteristics have been further investigated by subjecting ten of the structures to constraint-free molecular dynamics calculations (130 picoseconds) in vacuo. The structures were found to be stable to within 1.5 A of the initial backbone conformation. Comparison with the dynamic behaviour of the restrained molecular dynamics calculations has been used to identify regions of inherent flexibility in the molecule.

Conformational backbone dynamics of the cyclic decapeptide antamanide. Application of a new multiconformational search algorithm based on NMR data.

A general procedure for the analysis of biomolecular structures by NMR in the presence of rapid conformational dynamics has been applied to the study of the cyclic decapeptide antamanide. Two-dimensional experiments, relaxation measurements in the rotating frame, and homo- and heteronuclear coupling constant determinations have been used to characterize the dynamic properties of the molecule, in combination with a novel search algorithm for investigating multiconformational equilibria. Direct evidence for the presence of a conformational exchange process with an activation energy of approximately 20 kJ mol-1 and an exchange lifetime of approximately 25 microseconds at 320 K has been obtained from rotating frame relaxation measurements. This evidence is combined with the information derived from the multiconformational search algorithm MEDUSA to propose sets of structures that coexist in a dynamic exchange equilibrium.

Spatially localized magnetic resonance spectroscopy of the brains of normal and asphyxiated newborns.

Phase-modulated rotating frame imaging is a modification of magnetic resonance spectroscopy, which uses a linear radiofrequency field gradient to obtain spatially localized biochemical information. Phase-modulated rotating frame imaging was used to study regional cerebral energy metabolism in the brains of 9 normal newborns and 25 newborns after birth asphyxia. Relative concentrations of phosphorus-containing metabolites and intracellular pH were determined for brain tissue at three specified depths below the brain surface for all neonates. Wide variations in metabolite ratios were seen among normal neonates, and considerable metabolic heterogeneity was demonstrated in individual neonates by depth-resolved spectroscopy. Asphyxiated neonates with severe hypoxic-ischemic encephalopathy and a poor neurodevelopmental outcome showed the expected rise in inorganic orthophosphate and fall in phosphocreatine concentrations in both global and spatially localized spectra. Phase-modulated rotating frame imaging showed that metabolic derangement was less in superficial than in deeper brain tissue. The inorganic orthophosphate-adenosine triphosphate ratio from 1 to 2 cm below the brain surface was more accurate than any global metabolite ratio for the identification of neonates with a poor short-term outcome. These data are consistent with the known vulnerability of subcortical brain tissue to hypoxic-ischemic injury in the full-term neonate.

Cardiac metabolism during exercise in healthy volunteers measured by 31P magnetic resonance spectroscopy.

A technique was devised for individuals to exercise prone in a magnet during magnetic resonance spectroscopy of the heart and phosphorus-31 magnetic resonance spectra of the heart were obtained by the phase modulated rotating frame imaging technique in six healthy volunteers during steady state dynamic quadriceps exercise. During prone exercise heart rate, blood pressure, and total body oxygen consumption were measured at increasing loads and the results were compared with those during Bruce protocol treadmill exercise. During prone exercise with a 5 kg load the heart rate was similar and the systolic and diastolic blood pressures were higher than those during stage 1 of the Bruce protocol. The rate-pressure products were similar but the total body oxygen consumption was lower during prone exercise. There was no difference in the ratio of phosphocreatine to adenosine triphosphate during rest and exercise.Thus during exercise that produced a local cardiac stress equal to or greater than that during stage 1 of the Bruce protocol treadmill exercise, the energy requirements of the normal human myocardium were adequately supplied by oxidative phosphorylation.

Spatially resolved changes in diabetic rat skeletal muscle metabolism in vivo studied by 31P-n.m.r. spectroscopy.

Phase-modulated rotating-frame imaging (p.m.r.f.i.), a localization technique for 31P-n.m.r. spectroscopy, has been applied to obtain information on the heterogeneity of phosphorus-containing metabolites and pH in the skeletal muscle of control and streptozotocin-diabetic rats. Using this method, the metabolic changes in four spatially resolved longitudinal slices (where slice I is superficial and slice IV is deep muscle) through the ankle flexor muscles have been investigated at rest and during steady-state isometric twitch-contraction at 2 Hz. At rest, intracellular pH was lower, and phosphocreatine (PCr)/ATP was higher, throughout the muscle mass in diabetic compared with control animals. The change in PCr/ATP in diabetic muscle correlated with a decrease in the chemically determined ATP concentration. During the muscle stimulation period, the decrease in pH observed in diabetic muscle at rest was maintained, but not exacerbated, by the contractile stimulus. Stimulation of muscle contraction caused more marked changes in PCr/(PCr + Pi), PCr/ATP and Pi/ATP in the diabetic group. These changes were most evident in slice III, which contains the greatest proportion of fast glycolytic-oxidative (type IIa) fibres, in which statistically significant differences were observed for all metabolite ratios. The results presented suggest that some degree of heterogeneity occurs in diabetic skeletal muscle in vivo with respect to the extent of metabolic dysfunction caused by the diabetic insult and that regions of the muscle containing high proportions of type IIa fibres appear to be most severely affected.

Imaging of human brain creatine kinase activity in vivo.

Creatine kinase activity and high-energy phosphate concentration have been investigated using localized 31P spectroscopy in the human brain in vivo. The phase-modulated rotating frame imaging technique, incorporating magnetization transfer and inversion recovery, has been used to produce a 1-dimensional rate profile map of steady-state enzyme activity. Large differences in the flux from phosphocreatine (PCr) to ATP have been discovered between volumes of human brain consisting of predominantly gray (2.0 cm) and white (4.5 cm) matter. The concentration of PCr changes slightly (2.0 cm = 5.20 +/- 0.45 mmol.l-1, 4.5 cm = 4.63 +/- 0.31 mmol.l-1), while the ATP concentration remains within limits (3.30 +/- 0.4 mmol.l-1). No change in pHi was detected between the two regions in normal volunteers (n = 6). The forward rate constant of the PCr----ATP reaction in regions of predominantly gray matter (0.30 +/- 0.04 s-1) was twice that of white matter (0.16 +/- 0.02 s-1) in vivo.

Human primary brain tumour metabolism in vivo: a phosphorus magnetic resonance spectroscopy study.

Magnetic resonance spectroscopy was used to study intracellular pH and compounds which contain phosphorus in normal human brain and primary brain tumours non-invasively. In normal subjects (n = 7) intracellular pH (pHi) of the brain was 7.03 +/- 0.02 (mean +/- s.e.m.). The pHi did not vary between superficial (2 cm, majority grey matter) and deep brain (5 cm, majority white matter). The relative concentrations of phosphocreatine (PCr) and phosphomonoesters (PME) to ATP were also constant with depth. The relative concentration of phosphodiesters (PDE) increased from superficial to deep in normal brain. The astrocytomas (n = 7, grade II-IV) were significantly more alkaline (pHi = 7.08 +/- 0.03), and contained more PCr and PME, with respect to ATP, than normal brain at similar depth. The meningiomas (n = 4) were also more alkaline (pHi = 7.19 +/- 0.02) with a raised PME level but reduced PCr. The reduction in meningioma PCr may be due to the significant necrosis (greater than 20%) seen in the surgical biopsies. No significant necrosis was seen in the gliomas. Previous in vitro studies suggest that increased PME may be due to accumulation of phosphoethanolamine (PE), a phospholipid precursor. These results suggest that human primary brain tumours characteristically are more alkaline with increased PME than normal brain.

31P NMR magnetization-transfer measurements of ATP turnover during steady-state isometric muscle contraction in the rat hind limb in vivo.

31P NMR magnetization-transfer measurements have been used to measure the flux between ATP and inorganic phosphate during steady-state isometric muscle contraction in the rat hind limb in vivo. Steady-state contraction was obtained by supramaximal sciatic nerve stimulation. Increasing the stimulation pulse width from 10 to 90 ms, at a pulse frequency of 1 Hz, or increasing the frequency of a 10-ms pulse from 0.5 to 2 Hz resulted in an increase in the flux which was an approximately linear function of the increase in the tension-time integral. The flux showed an approximately linear dependence on the calculated free cytosolic ADP concentration up to an ADP concentration of about 90 microM. The data are consistent with control of mitochondrial ATP synthesis by the cytosolic ADP concentration and indicate that the apparent Km of the mitochondria for ADP is at least 30 microM.

A gated 31P-n.m.r. study of bioenergetic recovery in rat skeletal muscle after tetanic contraction.

1. Gated 31P-n.m.r. spectra were obtained from the ankle flexor muscles of the rat at various times after 3 s isometric tetanic contraction. This allowed the time course of changes in phosphocreatine (PCr), Pi and free ADP concentrations and intracellular pH to be monitored in skeletal muscle in vivo with 1 s time resolution. 2. ATP concentration did not change significantly, either during the recovery from a 3 s tetanus or during the overall protocol. 3. The calculated rate of recovery of ADP towards pre-stimulation levels was very rapid (t1/2 less than 5 s). The rate of Pi disappearance (t1/2 = 14 s) was more rapid than the rate of PCr synthesis (t1/2 = 24 s), resulting in a significant transient decrease in n.m.r.-visible PCr + Pi between 25 and 45 s after tetanic contraction. 4. The rates of PCr, Pi and ADP recovery are higher than those previously reported for recovery from steady-state exercise in humans or twitch isometric contraction in animals.