Common conformational changes in flavodoxins induced by FMN and anion binding: the structure of Helicobacter pylori apoflavodoxin

Flavodoxins, noncovalent complexes between apoflavodoxins and flavin mononucleotide (FMN), are useful models to investigate the mechanism of protein/flavin recognition. In this respect, the only available crystal structure of an apoflavodoxin (that from Anabaena) showed a closed isoalloxazine pocket and the presence of a bound phosphate ion, which posed many questions on the recognition mechanism and on the potential physiological role exerted by phosphate ions. To address these issues we report here the X-ray structure of the apoflavodoxin from the pathogen Helicobacter pylori. The protein naturally lacks one of the conserved aromatic residues that close the isoalloxazine pocket in Anabaena, and the structure has been determined in a medium lacking phosphate. In spite of these significant differences, the isoallozaxine pocket in H. pylori apoflavodoxin appears also closed and a chloride ion is bound at a native-like FMN phosphate site. It seems thus that it is a general characteristic of apoflavodoxins to display closed, non-native, isoalloxazine binding sites together with native-like, rather promiscuous, phosphate binding sites that can bear other available small anions present in solution. In this respect, both binding energy hot spots of the apoflavodoxin/FMN complex are initially unavailable to FMN binding and the specific spot for FMN recognition may depend on the dynamics of the two candidate regions. Molecular dynamics simulations show that the isoalloxazine binding loops are intrinsically flexible at physiological temperatures, thus facilitating the intercalation of the cofactor, and that their mobility is modulated by the anion bound at the phosphate site.     

The long and short flavodoxins: I. The role of the differentiating loop in apoflavodoxin structure and FMN binding

Flavodoxins are well known one-domain alpha/beta electron-transfer proteins that, according to the presence or absence of a approximately 20-residue loop splitting the fifth beta-strand of the central beta-sheet, have been classified in two groups: long and short-chain flavodoxins, respectively. Although the flavodoxins have been extensively used as models to study electron transfer, ligand binding, protein stability and folding issues, the role of the loop has not been investigated. We have constructed two shortened versions of the long-chain Anabaena flavodoxin in which the split beta-strand has been spliced to remove the original loop. The two variants have been carefully analyzed using various spectroscopic and hydrodynamic criteria, and one of them is clearly well folded, indicating that the long loop is a peripheral element of the structure of long flavodoxins. However, the removal of the loop (which is not in contact with the cofactor in the native structure) markedly decreases the affinity of the apoflavodoxin-FMN complex. This seems related to the fact that, in long flavodoxins, the adjacent tyrosine-bearing FMN binding loop (which is longer and thus more flexible than in short flavodoxins) is stabilized in its competent conformation by interactions with the excised loop. The modest role played by the long loop of long flavodoxins in the structure of these proteins (and in its conformational stability, see Lopez-Llano, J., Maldonado, S., Jain, S., Lostao, A., Godoy-Ruiz, R., Sanchez-Ruiz, Cortijo, M., Fernandez-Recio, J., and Sancho, J. (2004) J. Biol. Chem. 279, 47184-47191) opens the possibility that its conservation in so many species is related to a functional role yet to be discovered. In this respect, we discuss the possibility that the long loop is involved in the recognition of some flavodoxin partners. In addition, we report on a structural feature of flavodoxins that could indicate that the short flavodoxins derive from the long ones.     

pH-dependent changes in mitochondrial membrane structure

The pH-dependent changes in structure of submitochondrial vesicles prepared from rat liver have been investigated by a variety of structural probes. The main changes are: (a) the volume of the vesicles as assessed by electron microscopy and packed volume is dependent upon pH, being a minimum at pH 5. Between pH 5 and pH 9 the changes are reversible; (b) the accompanying light-scattering changes are also sensitive to divalent cations; (c) the binding characteristics of 8-anilinonaphthalene-1-sulfonic acid indicate pH-dependent changes in the amount of net charge on the membrane; (d) above pH 4, circular dichroism spectra show alterations characteristic of changes in quaternary protein structure; (e) below pH 4, infrared studies indicate changes in protein secondary conformation are also taking place. From these results, the nature and limits of conformational (molecular) and configurational (morphological) changes in mitochondrial membranes following changes in H⁺ activity are better defined. In the physiological range, pH-dependent conformational changes are confined to reversible changes in quaternary structure resulting from alterations in membrane charge.     

pH-dependent conformational changes in thrombocyte proteins

A study was made of the medium pH influence on structural states of platelets by optical methods. Within the pH range (6-8), two pH induced reversible changes of platelet state were observed. A conclusion is made that the structural rearrangements in platelets induced in the medium by changes in hydrogen ion concentration may involve some rearrangements in platelet proteins, and thus acting as a factor regulating platelet function.     

pH-dependent changes of 2,3-bisphosphoglycerate.

A systematic study of the pH dependent changes in the range 6.6--7.4 of 2,3 bisphosphoglycerate (2,3-DPG) was performed in the presence and absence of glucose during transitional and steady states. The results indicate that 2,3-DPGase breaks down 2,3-DPG nealy independent of pH at a rate of 480 mu moles 2,3-DPG/1 cells.h. The 2,3-DPG mutase is practically completely inhibited below pH 6.9. The 2,3-DPG level in the presence of glucose reaches a pH dependent steady state after about 18 h. The share of the 2,3-DPG bypass in the steady state decreases from 24% at pH 7.4 to 12% at pH 7.0. The formation of pyruvate corresponds to the beadkdown of 2,3-DPG after consumption of an unknown reducing substance.     

pH-dependent conformational changes of wheat germ calmodulin

Fluorescence energy transfer measurements were carried out between landmarks on wheat germ calmodulin to measure the interdomain distance. Tb3+ ions bound at the four Ca2+-binding sites were used as energy donors, and an organic chromophore, [4-(dimethylamino)-phenyl-4'-azophenyl]maleimide, attached to the single cysteine residue at position 27, was used as the acceptor. At pH's near neutrality all bound Tb3+ ions emit luminescence with shortened lifetimes as a result of energy transfer to the acceptor; at pH 5, however, part of the metal emission becomes unquenched. When the protein is subjected to limited digestion with trypsin in the presence of Ca2+, resulting in the formation of two fragments, each corresponding to half of the molecule, the decay of Tb3+ emission is no longer pH sensitive. These results suggest that, like rabbit skeletal troponin C [Wang, C.-L. A., Zhan, Q., Tao, T., & Gergely, J. (1987) J. Biol. Chem. 257, 8372-8375], wheat germ calmodulin exists in a relatively compact conformation at neutral pH's, but becomes more elongated at pH 5.     

Inverse pH-dependent shape changes of erythrocytes in the presence of albumin

A comparative study on the shape of human erythrocytes suspended in 7 different media showed, contrary to the well-known albumin-free case, an enhancement of the number of discocytes and stomatocytes for pH rising in all HSA containing media applied. At the same time, the transmembrane potential as determined by extra- and intracellular pH was lowered in all of 6 media tested. Consequently, there is no simple relationship between the pH-dependent behaviour of cell shape and corresponding changes of transmembrane potential.     

Wattles in goats are associated with the FMN1/GREM1 region on chromosome 10

The presence of congenital appendages (wattles) on the throat of goats is supposed to be under genetic control with a dominant mode of inheritance. Wattles contain a cartilaginous core covered with normal skin resembling early stages of extremities. To map the dominant caprine wattles (W) locus, we collected samples of 174 goats with wattles and 167 goats without wattles from nine different Swiss goat breeds. The samples were genotyped with the 53k goat SNP chip for a subsequent genome‐wide association study. We obtained a single strong association signal on chromosome 10 in a region containing functional candidate genes for limb development and outgrowth. We sequenced the whole genomes of an informative family trio containing an offspring without wattles and its heterozygous parents with wattles. In the associated goat chromosome 10 region, a total of 1055 SNPs and short indels perfectly co‐segregate with the W allele. None of the variants were perfectly associated with the phenotype after analyzing the genome sequences of eight additional goats. We speculate that the causative mutation is located in one of the numerous gaps in the current version of the goat reference sequence and/or represents a larger structural variant which influences the expression of the FMN1 and/or GREM1 genes. Also, we cannot rule out possible genetic or allelic heterogeneity. Our genetic findings support earlier assumptions that wattles are rudimentary developed extremities.     

Structure and oxidation-reduction behavior of 1-deaza-FMN flavodoxins: modulation of redox potentials in flavodoxins

Flavodoxins from Clostridium beijerinckii and from Megasphaera elsdenii with 1-carba-1-deaza-FMN substituted for FMN have been used to study flavin-protein interactions in flavodoxins. The oxidized 1-deaza analogue of FMN binds to apoflavodoxins from M. elsdenii and C. beijerinckii (a.k.a. Clostridium MP) with association constants (Ka) of 1.0 x 10(7) M-1 and 3.1 x 10(6) M-1, values about 10(2) less than the corresponding Ka values for FMN. X-ray structure analysis of oxidized 1-deaza-FMN flavodoxin from C. beijerinckii at 2.5-A resolution shows that the analogue binds with the flavin atoms in the same locations as their equivalents in FMN but that the protein moves in the vicinity of Gly 89 to accommodate the 1-CH group, undergoing displacements which increase the distance between position 1 of the flavin ring and the main-chain atoms of Gly 89 and move the peptide hydrogen of Gly 89 by about 0.6 A. The X-ray analysis implies that protonation of normal flavin at N(1), as would occur in formation of the neutral fully reduced species, would result in a similar structural perturbation. The oxidation-reduction potentials of 1-deaza-FMN flavodoxin from M. elsdenii have been determined in the pH range 4.5-9.2. The oxidized/semiquinone equilibrium (E'0 = -160 mV at pH 7.0) displays a pH dependence of -60 mV per pH unit; the semiquinone/reduced equilibrium (E'0 = -400 mV at pH 7.0) displays a pH dependence of -60 mV per pH unit at low pH and is pH independent at high pH, with a redox-linked pK of 7.4. Spectral changes of fully reduced 1-deaza-FMN flavodoxin with pH suggest that this latter pK corresponds to protonation of the flavin ring system (the pK of free reduced 1-deaza-FMN is 5.6 [Spencer, R., Fisher, J., & Walsh, C. (1977) Biochemistry 16, 3586-3593]. The pK of reduced 1-deaza-FMN flavodoxin provides an estimate of the electrostatic interaction between the protein and the bound prosthetic group; the free energy of binding neutral reduced 1-deaza-FMN is more negative than that for binding the anionic reduced 1-deaza-FMN by 2.4 kcal.(ABSTRACT TRUNCATED AT 250 WORDS)     

pH-dependent changes of ganglioside biosynthesis in neuronal cell culture

Ganglioside biosynthesis was studied in primary cultured murine cerebellar cells after labeling with [14C]galactose. A shift in biosynthesis from "a"-series to "b"-series gangliosides was observed after lowering the pH of the culture medium from 7.4 to 6.2; this effect was fully reversible on changing back to pH 7.4. The observed regulatory effect of pH is in accordance with a recent model of ganglioside biosynthesis. Sialyltransferase II (ST II), the first enzyme for biosynthesis of "b"-series gangliosides, is more active at pH 6.2 than Gal-NAc-transferase, the first enzyme for synthesis of "a"-series gangliosides, which is more active than sialyltransferase II at pH 7.4.     

pH-dependent changes in properties of concanavalin A in the acid pH range

Properties characteristic of the structure and function of dimeric concanavalin A have been studied as a function of pH in the acid pH range using preparations comprising intact subunits or enriched in fragmented chains. For intact subunits, the glycogen binding ability falls to zero with a midpoint of pH 4.7, the release of Mn+2, Ca+2 and the fluorescent ligand 4-methylumbelliferyl-alpha-D-mannopyranoside from the lectin coincides over a pH range centered at pH 3.9, and the CD spectra of the aromatic amino acid residues increase sharply in amplitude between pH 4.0 and 1.5. Nevertheless, the sedimentation coefficient and peptide CD spectrum change insignificantly in the pH range 5 to 2, indicating that dimeric concanavalin A retains its secondary structure and overall hydrodynamic shape essentially unchanged upon acidification. The behavior of concanavalin comprising primarily fragmented chains is not significantly different from that of intact subunits, although it precipitates glycogen less efficiently. It is concluded that dimeric concanavalin A does not undergo a concerted change in structure upon acidification, but rather that it passes through a series of states differing from one another in their local conformations. The distinction in binding between the monosaccharide and the polysaccharide is attributed to participation of a secondary binding site in the latter case. A change in optical activity at 283 nm in the pH range 5-6 is ascribed to disruption of intersubunit interactions of Tyr 67 as the protein undergoes the dimer-tetramer equilibrium.     

pH-dependent changes in the two-stage kinetics of superprecipitation reaction of natural actomyosin

The effect of pH on the two-stage kinetics of the superprecipitation (SPP) reaction of natural actomyosin was investigated. It was shown that the experimental dependencies appear as two intersecting bell-shaped curves reflecting the effects of pH on individual steps of the SPP reaction which are mediated by different molecular mechanisms. It was supposed that the both reaction mechanisms involve actomyosin complexes which have different structural states and differ also by the degree of dissociation in the presence of ATP. The shifts in the dynamic equilibrium between the two states of actomyosin may induce pH-modulations in the two-stage kinetics of SPP and, presumably, ATPase.     

Conformational changes in Chondrus crispus flavodoxin on dissociation of FMN and reconstitution with flavin analogues.

The apoflavodoxin produced by precipitation of Chondrus crispus flavodoxin with trichloroacetic acid migrates as a single molecular species on non-denaturing PAGE, but at a much lower Rm than the flavoprotein. Values of s and D were significantly lower than for the flavodoxin, but their substitution in the Svedberg equation indicated the molecular mass was closely similar to that of the flavodoxin. This was confirmed by meniscus-depletion sedimentation-equilibrium studies. The Stokes radius of the apoflavodoxin was 3.65 nm, compared with 2.33 nm for the flavodoxin, and estimates of frictional coefficient ratio suggested the apoprotein was in extended conformation compared with the roughly globular shape of the flavodoxin. The Ka for FMN binding was 2.8 x 10(8)M, and the electrophoretic and physicochemical properties of the reconstituted flavoprotein were closely similar to those of the native flavodoxin. FAD, iso-FMN and thio-FMN were also bound effectively, but methyl-FMN and riboflavin were bound only weakly, if at all. The reconstituted flavoproteins were active to various extents in mediating electron transfer from NADPH to cytochrome c catalysed by flavodoxin-NADP+ oxidoreductase, the highest activity being with the thio-FMN flavodoxin.     

Elucidation of critical pH-dependent structural changes in Botulinum Neurotoxin E

Botulinum Neurotoxins (BoNT) are the most potent toxins currently known. However, they also have therapeutic applications for an increasing number of motor related conditions due to their specificity, and low diffusion into the system. Although the start- and end- points for the BoNT mechanism of action are well-studied, a critical step remains poorly understood. It is theorised that BoNTs undergo a pH-triggered conformational shift, activating the neurotoxin by priming it to form a transmembrane (TM) channel. To test this hypothesis, we combined molecular dynamics (MD) simulations and small-angle x-ray scattering (SAXS), revealing a new conformation of serotype E (BoNT/E). This conformation was exclusively observed in simulations below pH 5.5, as determined by principal component analysis (PCA), and its theoretical SAXS profile matched an experimental SAXS profile obtained at pH 4. Additionally, a localised secondary structural change was observed in MD simulations below pH 5.5, in a region previously identified as instrumental for membrane insertion for serotype A (BoNT/A). These changes were found at a critical pH value for BoNTs in vivo, and may be relevant for their therapeutic use.     

pH-dependent changes in the tryptophan and porphyrin fluorescence of the apomyoglobin complex with protoporphyrin IX and methemoglobin

The fluorescence of protoporphyrin IX (PPIX) complexed with sperm whale apomyoglobin as well as the tryptophan fluorescence of this complex and of metmyoglobin within the pH range of 3.5-13 was studied. It was shown that an increase in pH from 5.3 to 10.8 does not influence the fluorescence of PPIX in the complex and causes no essential changes in the fluorescence of Trp residues, which occur at more acidic and, correspondingly, alkaline pH values simultaneously with the protein denaturation. This is accompanied by a sharp increase in the quantum yield of tryptophan fluorescence due to dissociation of PPIX from the complex. Similar changes are observed in metMb at pH less than 4.3 and greater than 12 which is concomitant with absorption changes in the Soret band, thus indicating a higher stability of metMb towards the acid and alkaline denaturation as compared to the complex. In both cases, a slight alteration in the shape of the tryptophan fluorescence spectrum is observed, which precedes alkaline denaturation of the Mb molecule and is probably due to changes in the conformation of the N-terminal region caused by the break of the salt bridges stabilizing the native structure of the protein.