Fluorescence polarization analysis for revealing molecular mechanism of nucleotide-dependent phospholipid membrane binding of MinD adenosine 5'-triphosphate, adenosine triphosphatase.

Membrane binding of Walker type adenosine 5'-triphosphate, adenosine triphosphatase (ATPase), MinD, is a key step in regulating the site of cell division in Escherichia coli. Two lysine residues (K11, K16) in the Walker A motif of MinD have been suggested to be essential for both membrane binding and ATPase activity, but the relationship between the membrane binding of MinD and its ATPase activity is still unclear. To reveal the role of K11 and K16 in MinD membrane interaction and ATP-binding, we compared the functionality of wild-type MinD (WT) and two MinD mutants that lack ATPase activity, where alanine was substituted for lysine at positions 11 and 16 (K11A, K16A), using liposomes and fluorescent-labeled ATP. The ATP dissociation constant (K(d)) of wild-type MinD was 4.9 µM. Unexpectedly, the K(d) values of the two lysine mutants were almost the same as that of wild type, indicating that ATP can bind to MinD mutants, even though these mutants showed no ATPase activity and membrane binding ability. Our results presumed that K11 and K16 residues might play an important role in dimmer formation of MinD, but not ATP binding step, for recruiting to membrane.

Direct monitoring of interaction between Escherichia coli proteins, MinC and monomeric FtsZ, in solution.

MinC plays an important role in regulation of the cell division site in Escherichia coli. Previous studies using sedimentation and electron microscopic methods suggested that MinC interacts with the FtsZ polymer and inhibits further FtsZ polymerization. However, it is difficult to clarify details regarding specific molecular interactions by such static analytic methods. In this study, a fluorescence resonance energy transfer (FRET) method was developed to directly observe the interaction between Cy3-labeled MinC and Cy5-labeled FtsZ in solution. FRET analysis indicated that MinC interacts with monomeric rather than polymeric FtsZ in solution. This suggests that interactions between monomeric FtsZ and MinC are important for controlling of FtsZ polymerization by MinC.

Reduction of plastocyanin by tyrosine-containing oligopeptides.

Oxidized plastocyanin (PC) was reduced with TyrTyrTyr and LysLysLysLysTyrTyrTyr (KKKKYYY) oligopeptides at neutral pH. The TyrTyrTyr site of the peptides provided an electron to the copper active site of PC, whereas the tetralysine site of KKKKYYY functioned as the recognition site for the negative patch of PC. The reciprocal initial rate constant (1/k(int)) increased linearly with the reciprocal TyrTyrTyr concentration and proton concentration, although the electron transfer rate decreased gradually with time. The results showed that PC was reduced by the deprotonated species of TyrTyrTyr. A linear increase of log k(int) with increase in the ionic strength was observed due to decrease in the electrostatic repulsion between negatively charged PC and deprotonated (TyrTyrTyr)(-). PC was reduced faster by an addition of KKKKYYY to the PC-TyrTyrTyr solution, although KKKKYYY could not reduce PC without TyrTyrTyr. The ESI-LCMS spectrum of the products from the reaction between PC and TyrTyrTyr showed molecular ion peaks at m/z 1015.7 and 1037.7, which suggested formation of a dimerized peptide that may be produced from the reaction of a tyrosyl radical. The results indicate that PC and the tyrosine-containing oligopeptides form an equilibrium, PC(ox)/(oligopeptide)(-)-->/<--PC(red)/(oligopeptide)(*). The equilibrium is usually shifted to the left, but could shift to the right when the produced oligopeptide radical reacts with unreacted peptides. For the reaction of PC with KKKKYYY in the absence of TyrTyrTyr, the produced KKKK(YYY)(*) radical peptide could not react with other KKKKYYY peptides, since they were positively charged. In the presence of both KKKKYYY and TyrTyrTyr, PC may interact effectively with KKKKYYY through its tetralysine site and receive an electron from its TyrTyrTyr site, where the produced KKKK(YYY)(*) may interact with TyrTyrTyr peptides.

Masking mechanisms of bitter taste of drugs studied with ion selective electrodes.

The masking mechanisms of the bitter taste of propantheline bromide (PB) and oxyphenonium (OB) bromide by native and modified cyclodextrins, saccharides, surfactants, organic acids, nonionic and anionic polymers, and other compounds were investigated with ion selective electrodes. The intensity of the bitter taste for a mixed solution of cyclodextrin with PB or OB was quantitatively explained from the observed electromotive force with the following assumptions: the complex and the masking agent do not have any tastes and the bitter taste is independent of other tastes. Sodium dodecyl sulfate reduced the bitter taste remarkably, and this reduction was also explicable on the basis of the same mechanism. Sodium taurodeoxycholate enhanced the bitter taste, because of its strong bitterness, although it formed 1 : 1 complexes with PB and OB. The masking mechanism of saccharides was ascribed to overcoming the weak bitterness of the drug by the strong sweetness. Lambda-carrageenan suppressed the bitter taste remarkably. This suppression was ascribed to the binding of PB and OB to lambda-carrageenan, the effect of the solution viscosity on the bitter taste, and the covering of the bitter taste receptor by lambda-carrageenan. It was suggested that the moderate masking by other polymers was attributable to the effect of the solution viscosity or the receptor covering. Native and modified beta-cyclodextrins, sodium dodecyl sulfate, lambda-carrageenan, Tween 20, and sodium carboxymethyl cellulose are good masking agents for the bitter tastes of PB and OB. The drug ion selective electrode is a useful tool for understanding of the masking mechanism of the bitter taste, screening of masking agents, and estimation of appropriate concentrations of the masking agents.

Conformational changes during apoplastocyanin folding observed by photocleavable modification and transient grating.

A new method to investigate the initial protein folding dynamics is developed based on a pulsed laser light triggering method and a unique transient grating method. The side chain of the cysteine residue of apoplastocyanin (apoPC) was site-specifically modified with a 4,5-dimethoxy-2-nitrobenzyl derivative, where the CD and 2D NMR spectra showed that the modified apoPC was unfolded. The substituent was cleaved with a rate of about 400 ns by photoirradiation, which was monitored by the disappearance of the absorption band at 355 nm and the increase in the transient grating signal. After a sufficient time from the photocleavage reaction, the CD and NMR spectra showed that the native beta-sheet structure was recovered. Protein folding dynamics was monitored in the time domain with the transient grating method from a viewpoint of the molecular volume change and the diffusion coefficient, both of which reflect the global structural change, including the protein-water interaction. The observed volume decrease of apoPC with a time scale of 270 micros is ascribed to the initial hydrophobic collapse. The increase in the diffusion coefficient (23 ms) is considered to indicate a change from an intermolecular to an intramolecular hydrogen bonding network. The initial folding process of apoPC is discussed based on these observations.

Significance of the molecular shape of iron corrphycene in a protein pocket.

The iron complex of a new type of corrphycene bearing two ethoxycarbonyl (-CO2C2H5) groups on the bipyrrole moiety was introduced into apomyoglobin. The reconstituted ferric myoglobin has a coordinating water molecule that deprotonates to hydroxide with a pK(a) value of 7.3 and exhibits 3-10-fold higher affinities for anionic ligands when compared with a counterpart myoglobin with the same substituents on the dipyrroethene moiety. In the ferrous state, the oxygen affinity of the new myoglobin was decreased to 1/410 of the native protein. The anomalies in the ligand binding, notably dependent on the side-chain location, were interpreted in terms of a characteristic core shape of corrphycene that produces the longer and shorter Fe-N(pyrrole) bonds. The spin-state equilibrium analysis of the ferric azide myoglobin containing the new iron corrphycene supported the nonequivalence of the Fe-N(pyrrole) bonds. These results demonstrate that the trapezoidal molecular shape of corrphycene exerts functional significance when the iron complex is placed in a protein pocket.

Micelle formation of bile salts and zwitterionic derivative as studied by two-dimensional NMR spectroscopy.

The self-association of sodium taurodeoxycholate (NaTDC) and a zwitterionic derivative of cholic acid (CHAPS) in deuterium oxide was investigated by one- and two-dimensional nuclear magnetic resonance spectroscopy (NMR) spectroscopy. Analysis of the concentration dependence of the chemical shifts of several protons suggested that NaTDC and CHAPS form nonamers and heptamers, respectively, as well as dimer. The equilibrium constants of dimerization and the micellar aggregation numbers are close to the literature values. From the intensities of intermolecular cross-peaks in the nuclear Overhauser effect spectroscopy (NOESY) and rotating frame nuclear Overhauser effect spectroscopy (ROESY) spectra of NaTDC and CHAPS micellar solutions, partial structures of their micelles were estimated. The CHAPS micelle consists mainly of the back-to-back association, similarly to taurocholate (NaTC). However, the NaTDC micelle consists of the back-to-face association, because the face of NaTDC is rather hydrophobic. Furthermore, the back of bile molecules forms a convex plane and the face forms a concave plane. The back-to-face structure of NaTDC will be stabilized by a close contact between these planes. The chemical shift changes of several protons of CHAPS and NaTC in the micellar state are close to each other, but are different from those of NaTDC. This finding is consistent with the difference in their micellar structures.

Molecular motions of alpha-cyclodextrin on a dodecyl chain studied by molecular dynamics simulations.

Motions of an alpha-cyclodextrin (alpha-CD) molecule on a dodecyl chain adopting the all-trans conformation were investigated in the presence of water by molecular dynamics simulations with CVFF force fields, where the trimethylammonium group of dodecyltrimethylammonium bromide (DTAB) is protruded outside the secondary hydroxyl rim of alpha-CD (the secondary-in structure). The alpha-CD molecule shuttled rapidly on the chain without decomplexation. This rapid motion is consistent with the NMR data. The plane formed by 6 O4 atoms of alpha-CD is most populated between the C6 and C7 atoms of DTAB. This structure is very close to that estimated by NMR. The alpha-CD molecule underwent a restricted rotation in a range of 60 degrees with regard to the plane of the dodecyl chain: this plane at the most population is middle between the two diagonal lines of the normal hexagon formed by 6 O4 atoms of alpha-CD. The published NMR data were reanalyzed in terms of the rotation angle, and a slightly better structure was obtained. The distortion of the alpha-CD cavity from the normal hexagon was decreased upon complex formation with DTAB. The deviation of the center of alpha-CD from the center of the dodecyl chain predicted by molecular dynamics simulations is consistent with the NMR data. The secondary-in structure is energetically more stable than the primary-in structure, as calculated by molecular mechanics with CVFF and Amber force fields. This result is consistent with the NMR data. Molecular dynamics simulations were also carried out for the primary-in structure. Some of the results are close to those of the secondary-in structure.

Oxygen binding to tyrosinase from streptomyces antibioticus studied by laser flash photolysis.

Tyrosinases catalyze the o-hydroxylation of monophenols (monophenolase activity) and the oxidation of o-diphenols to o-quinones (diphenolase activity) and possess a dinuclear copper active site. The O2 binding kinetics of oxytyrosinase is studied by flash-photolysis measurements, and the O2 binding rate constant (kO2) is obtained as kO2 = 13 +/- 3 muM-1 s-1. Small molecules, such as carbon monoxide and p-nitrophenol (a substrate-analogue inhibitor), are demonstrated to affect O2 binding kinetics. The activation enthalpy of the rate-limiting step of O2 binding is calculated by the temperature dependence of kO2 to be 12.8 +/- 2.6 kcal/mol.

Heme reduction by intramolecular electron transfer in cysteine mutant myoglobin under carbon monoxide atmosphere.

Human myoglobin (Mb) possesses a unique cysteine (Cys110), whereas other mammalian Mbs do not. To investigate the effect of a cysteine residue on Mb, we introduced cysteine to various sites on the surface of sperm whale Mb (K56C, V66C, K96C, K102C, A125C, and A144C) by mutation. The cysteines were inserted near the end of alpha-helices, except for V66C, where the cysteine was introduced in the middle of an alpha-helix. Reduction of the heme was observed for each mutant metMb by incubation at 37 degrees C under carbon monoxide atmosphere, which was much faster than reduction of wild-type metMb under the same condition. Heme reduction did not occur significantly under nitrogen or oxygen atmospheres. The rate constant for heme reduction increased for higher mutant Mb concentration, whereas it did not change significantly when the CO concentration was reduced from 100% CO to 50% CO with 50% O(2). The similarity in the rate constants with different CO concentrations indicates that CO stabilizes the reduced heme by coordination to the heme iron. SDS-PAGE analysis showed that mutant Mb dimers were formed by incubation under CO atmosphere but not under air. These dimers were converted back to Mb monomers by an addition of 2-mercaptoethanol, which showed formation of a Mb dimer through a disulfide bond. The rate constant decreased in general as the heme-cysteine distance was increased, although V66C Mb exhibited a very small rate constant. Since V66 is placed in the middle of an alpha-helix, steric hindrance would occur and prevent formation of a dimer when the cysteine residues of two different V66C Mb molecules interact with each other. The rate constants also decreased for K56C and A144C Mbs presumably because of the electrostatic repulsion during dimer formation, since they are relatively charged around the inserted cysteine.

Control of iron(III) spin-state in the model complexes of azide hemoprotein by porphycene, corrphycene, and hemiporphycene macrocycles.

Spin states of the iron(III) complexes of porphyrin, porphycene, hemiporphycene, and corrphycene bearing both 1-methylimidazole and azide as axial ligands were analyzed with infrared (IR) spectroscopy at 20 degrees C. The IR stretching band of coordinating azide split into two peaks around 2047 and 2017 cm(-1) reflecting an equilibrium between the high- (S = 5/2) and low- (S = 1/2) spin states. The high-spin fraction changed over a 0-90% range among the macrocycles, demonstrating that the tetrapyrrole array is essential to control the equilibrium.

Functional evaluation of heme vinyl groups in myoglobin with symmetric protoheme isomers.

We replaced protoheme-IX in native myoglobin with the symmetric protohemes-III and -XIII, in order to investigate the role of heme vinyl-globin contacts on Mb function. The UV-visible spectra and the resonance Raman spectra in the high-frequency region (containing oxidation, spin, and coordination state marker lines) of the two reconstituted Mbs were very similar. However, the signal intensity of the Soret band in the CD spectra and the resonance Raman lines for vinyl bending modes in the low-frequency region notably differed, thereby reflecting altered heme peripheral contacts. The redox potentials, formal heterogeneous electron-transfer rates, and thermal denaturation temperatures of the two reconstituted Mbs were also indistinguishable. In addition, the oxygen binding properties of the ferrous deoxy Mbs were comparable. These results demonstrate that altered heme vinyl-globin interactions only slightly affect the physical properties of Mb. It is therefore likely that the orientation of protoheme-IX about the alpha,gamma-axis in the heme pocket is not necessarily a crucial factor for oxygen binding to native Mb.

Structure and ethanol complexation of cyclic tetrasaccharide in aqueous solution studied by NMR and molecular mechanics.

The structure and ethanol complexation of a cyclic tetrasaccharide (CTS) in aqueous solution were investigated by proton NMR spectroscopy and molecular mechanics calculations. Two glucose units, A and B, of CTS are alternatively bonded by alpha-1,3 and alpha-1,6 linkages. The overlapped signals of protons A5, A6S, A6R, B3, B6S and B6R were resolved by spectral simulations to determine their chemical shifts and vicinal coupling constants. All vicinal coupling constants except for the A5-A6 spin system are consistent with the dihedral angles in the X-ray crystal structure. Each of protons A5, A6S, and A6R in the two units of A is equivalent with respect to the chemical shift. The vicinal coupling constants of (3)J(5-6S) and (3)J(5-6R) for unit A are close to the average of two rotamers that are present in crystals. The intensities of cross-peaks in the rotating frame nuclear Overhauser effect spectroscopy (ROESY) spectrum were rather well correlated with the effective distances calculated for the X-ray structure and molecular mechanics structures calculated in vacuo and water, although they are slightly better correlated with molecular mechanics structure in vacuo than with the other structures. From the changes of the chemical shifts of several CTS protons with increasing ethanol concentration, it was suggested that adsorption sites of ethanol on the plate structure of CTS are protons B2 and B4 (site B) in the concave face side and protons A1 and A2 (site A) in the convex back side. The binding constants for sites A and B are 0.0061 and 0.0176 M(-1), respectively. These binding constants are much smaller than a value of 4.1 M(-1) for the ethanol-alpha-cyclodextrin complex.

Interaction of plastocyanin with oligopeptides: effect of lysine distribution within the peptide.

We synthesized and purified four oligopeptides containing four lysines (KKKK, GKKGGKK, KKGGGKK, and KGKGKGK) as models for the plastocyanin (PC) interacting site of cytochrome f. These peptides competitively inhibited electron transfer between cytochrome c and PC. The inhibitory effect increased as the peptide concentrations were increased. The association constants between PC and the peptides did not differ significantly (3500-5100 M(-1)), although the association constant of PC-KGKGKGK was a little larger than the constants between PC and other peptides. Changes in the absorption spectrum of PC were observed when the peptides were added to the PC solution: peaks and troughs were detected at about 460 and 630 nm and at about 560 and 700 nm, respectively, in the difference absorption spectra between the spectra with and without peptides. These changes were attributed to the structural change at the copper site of PC by interaction with the peptides. The structural change was most significant when tetralysine was used. These results show that binding of the oligopeptide to PC is slightly more efficient when lysines are distributed uniformly within the peptide, whereas the structural change of PC becomes larger when the lysines are close to each other within the peptide.

Solution structures of 1:1 complexes of oxyphenonium bromide with beta- and gamma-cyclodextrins.

The solution structures of complexes of oxyphenonium bromide (OB) with beta- and gamma-cyclodextrins (beta- and gamma-CDs, respectively) in deuterium oxide have been investigated by 500 MHz proton NMR spectroscopy and molecular mechanics calculations. The chemical shifts induced by complex formation provide the 1:1 binding constants and the chemical shift variations, DeltadeltaOB-CD, with complexation for the protons of OB and the CDs. The observed binding constants are very close to those obtained by other methods and are in the following order: beta-CD > gamma-CD > alpha-CD. Initial structures of the complexes are constructed on the basis of the ROESY spectra and the DeltadeltaOB-CD values and are optimized by molecular mechanics calculations. The intermolecular distances between the protons of OB and CD calculated for these structures are well-correlated with the observed ROESY intensities. The cyclohexyl group of OB penetrates deeply into a beta-CD cavity, and the phenyl group is close to the wide rim of the cavity. The phenyl and cyclohexyl groups of OB are both incorporated into a gamma-CD cavity. Furthermore, these structures of the complexes are consistent with the suppression of bitter taste and basic hydrolysis of OB by CDs and the polarity of binding sites of OB.

Iron hemiporphycene as a functional prosthetic group for myoglobin.

The iron complex of hemiporphycene, a molecular hybrid of porphyrin with porphycene, was incorporated into the apomyoglobin pocket to examine ligand binding ability of the iron atom in the novel porphyrinoid. Apomyoglobin was successfully coupled with a stoichiometric amount of ferric hemiporphycene to afford the reconstituted myoglobin equipped with the iron coordination structure of native protein. Cyanide, imidazole, and fluoride coordinated to the ferric protein with affinities comparable with those for native myoglobin. The ferrous myoglobin was functionally active to bind O(2) and CO reversibly at pH 7.4 and 20 degrees C. The O(2) affinity is 12-fold higher than that of native myoglobin while the CO affinity is slightly lower, suggesting decreased discrimination between O(2) and CO in the heme pocket. The functional anomaly was interpreted to reflect increased sigma-bonding character in the Fe(II)-O(2) bond. In contrast with 6-coordinate native NO protein, the NO myoglobin containing ferrous hemiporphycene is in a mixed 5- and 6-coordinate state. This observation suggests that the in-plane configuration of the iron atom in hemiporphycene is destabilized by NO. Influence of the core deformation was also detected with both the infrared absorption for the ferrous CO derivative and electron paramagnetic resonance for ferric imidazole complex. Anomalies in the ferric and ferrous derivatives were ascribed to the modified iron-N(pyrrole) interactions in the asymmetric metallo core of hemiporphycene.

Molecular structures of five-coordinated halide ligated iron(III) porphyrin, porphycene, and corrphycene complexes.

Molecular structures of 12 porphyrin analogues, Fe(III)(EtioP)X(1(a)-1(d)), Fe(III)(EtioCn)X(2(a)-2(d)), and Fe(III)(Etio-Pc)X(3(a)-3(d)), where X = F (a), Cl (b), Br (c), and I (d), are determined on the basis of X-ray crystallography. Combined analyses using Mössbauer, (1)H NMR, and EPR spectroscopy as well as SQUID magnetometry have revealed that 3(d) exhibits a quite pure S = 3/2 spin state with a small amount of an S = 5/2 spin admixture. In contrast, all the other complexes show the S = 5/2 spin state with a small amount of the S = 3/2 spin admixture. The structural and spectroscopic data indicate a strong correlation between the spin states of the complexes and the core geometries such as Fe-N bond lengths, cavity areas, and DeltaFe values.