A study of the structure and dynamics of complexes between polymyxin B and phosphatidylglycerol in monolayers by fluorescence

Interactions between the antibiotic polymyxin B and monolayers of dipalmitoylglycerophosphoglycerol have been reinvestigated through a study of the structure and dynamics of the complexes by means of an interface fluorimeter of our fabrication. A fluorescence technique has been developed where the use of linearly polarized incident beams gives the simultaneous determination of the orientation and the lateral diffusion rate of a fluorescent probe inserted in the film. The present investigation was carried out with 12-(9-anthroyloxy)-stearic acid, a fluorescent compound which forms non-fluorescent photodimers upon illumination. Orientation of the probe was studied by computing the ratio of the two dimerization constants KD and the ratio of the fluorescence intensities obtained with crossed linearly polarized incident lights. The lateral diffusion rate of the probe was obtained by measuring fluorescence recovery after photobleaching (photodimerization) of the probe. Control experiments, carried out with dimyristoylglycerophosphocholine, a lipid which does not interact with polymyxin B, show that the antibiotic does not significantly modify the behaviour of the probe. Both in terms of orientation and dynamics, with respect to dipalmitoylglycerophosphoglycerol, when the antibiotic is present in the subphase (1 microM, saturating conditions), data indicate that the lipid remains in a liquid-expanded state. This is true even at a high surface pressure (pi approximately equal to 37 mN X m-1), above the apparent 'transition' which can be observed at 30-35 mN X m-1 on its compression isotherm. Computation of the contribution of polymyxin B to the film expansion to the conclusion that this 'transition' would be a structural transition between two models of interaction: one, below the 'transition', where the polypeptide ring penetrates between the film-forming lipid molecules and another one, above the 'transition', were the antibiotic is adsorbed at the lipid-water interface with only its hydrocarbon chain penetrating the film.     

A hydrogen-deuterium exchange study of the amide protons of polymyxin B by nuclear-magnetic-resonance spectroscopy.

1. Proton magnetic resonance spectra at 270 MHz of polymyxin B, a cationic oligopeptide antibiotic, show the influence of the inorganic counteranion present in solution. 2. Hydrogen-deuterium exchange rates for the amide protons are of two types, depending on whether the anion is monovalent or polyvalent. Polyvalent anions catalyse the acid-catalysed reaction more than the monovalent anions. 3. The structure in solution was monitored using the proton signals of the amides, the phenylalanine aromatic protons, and the leucine methyl and gamma-CH protons in several polymyxin salts. The temperature coefficients of the chemical shifts of the N-H protons are used to identify two beta turns in the cyclic ring of polymyxin B. The variation in chemical shift of the N-H protons, the aromatic protons and the leucine protons are correlated with anionic size and electronegativity.     

Conformational structure of bombesin as studied by vibrational and circular dichroism spectroscopy

Raman and Fourier transform infrared (FTIR) spectroscopies and circular dichroism (CD) have been applied to investigate the secondary structure of bombesin in the solid state and in phosphate buffer solution (pH 3.8). At concentrations around 10⁻⁵ M, circular dichroism reveals that bombesin exists as an irregular or disordered conformation. However, the secondary structure of the peptide appears to be a mixture of disordered structure and intermolecular β-sheets in 0.01 M sodium phosphate buffer when the peptide concentrations are higher than around 6.5 mM. The tendency of bombesin to form aggregated β-sheet species seems to be originated mainly in the sequence of the residues 7–14, as supported by the Raman spectra and β-sheet propensities (P_β) of the amino-acid residues. It is the hydrophobic force of this amino-acid sequence, and not a salt bridge effect, that is the factor responsible for the formation of peptide aggregates.     

Tetraplex structure formation in the thrombin-binding DNA aptamer by metal cations measured by vibrational spectroscopy

Formation of intramolecular tetraplex structures by the thrombin-binding DNA aptamer (TBA) in the presence of K(+), Pb(2+), Ba(2+), Sr(2+) and Mn(2+) has been studied by vibrational spectroscopy. All tetraplex structures contain G-G Hoogsteen type base pairing, both C2'endo/anti and C2'endo/syn deoxyguanosine glycosidic conformations and local B like form DNA phosphate geometries. Addition of Pb(2+) ions modifies the structure by interacting at the level of the guanine carbonyl groups. The very important downshift of the guanine C6=O6 carbonyl vibration mode in the TBA spectrum induced by the addition of one Pb(2+) ion per TBA molecule is in agreement with a localization of the metal ion between both guanine quartets. FTIR melting experiments show an important stabilization of the tetraplex structure upon addition of Pb(2+) ions (DeltaT = 15 degrees C). This strong interaction of lead cations may be correlated with a change in the geometry of the cage formed by the two guanine quartets. A similar but weaker effect is observed for barium and strontium cations.     

Structure study of recombinant RGD-hirudin by vibrational and circular dichroism spectroscopy

The secondary structure of a new type of recombinant RGD-hirudin, which has the activities of anti-thrombin and anti-platelet aggregation, has been studied by Fourier transform infrared spectroscopy (FT-IR), Raman spectroscopy and circular dichroism (CD) methods. The distribution of various secondary structure elements was determined using only a very small amount of sample protein. It was found that the recombinant RGD-hirudin contains about 26% extended chain, 21% beta-turn and 53% unordered structure, leaving no alpha-helix. The results showed that the regular secondary structure of recombinant RGD-hirudin is increased compared with wild-type hirudin. The RGD segment that is located at the end of a long arm of a beta-sheet is thought to play an important role in the additional function of anti-platelet aggregation. Throughout the experiments, FT-IR, Raman spectroscopy and CD generated mutually reinforcing results.     

DNA protection by aminothiols: study of the cysteamine - DNA interaction by vibrational spectroscopy

Infrared linear dichroism measurements and Roman scattering spectra show that the cysteamine molecule binds strongly to the DNA stabilizing the double helix in a B geometry conformation. The B→A conformational transition is not observed for a cysteamine/DNA ratio of one cysteamine molecule per two phosphate sites. No evidence of interaction has been found between the radioprotector and the DNA bases. A model is proposed in which the cysteamine molecule is bound by its two ends through electrostatic interaction to two consecutive phosphate groups along the same DNA strand.     

Structural study of the zinc and cadmium complexes of a type 2 plant (Quercus suber) metallothionein: insights by vibrational spectroscopy

Zn- and Cd-complexes of Quercus suber metallothionein (QsMT) were obtained by in vivo-synthesis, in order to obtain physiologically representative aggregates, and characterized by spectrometric and spectroscopic methods. The secondary structure elements and the coordination environments of the metal binding sites of the two aggregates were determined, as well as the main metal-containing species formed. The results obtained from the analysis of the Raman and IR spectra reveal that these metal-MT complexes predominantly contain beta-sheet elements (about 60%), whereas they lack alpha-helices. These structural features slightly depend on the divalent metal bound. In particular, Cd(II) binding to QsMT induces a slight increase of the beta-sheet percentage, as well as a decrease in beta-turn elements with respect to Zn(II) binding. Conversely, the in vivo capability of QsMT to inglobe metal and sulfide ions is metal-depending. Spectroscopic vibrational data also confirm the presence of sulfide ligands in the metal clusters of both Zn- and Cd-QsMT, while the participation of the spacer His residue in metal coordination was only found in Cd-QsMT, in agreement with the CD results. Overall data suggest different coordination environments for Zn(II) and Cd(II) ions in QsMT.     

Identification of medically relevant microorganisms by vibrational spectroscopy

In the recent years, vibrational spectroscopies (infrared and Raman spectroscopy) have been developed for all sorts of analyses in microbiology. Important features of these methods are the relative ease with which measurements can be performed. Furthermore, in order to obtain infrared or Raman spectra, there is only a limited amount of sample handling involved without the need for expensive chemicals, labels or dyes. Here, we review the potential application of vibrational spectroscopies for the use in medical microbiology. After describing some of the basics of the techniques, considerations on reproducibility and standardisation are presented. Finally, the use of infrared and Raman spectroscopy for the (rapid) identification of medically relevant microorganisms is discussed. It can be concluded that vibrational spectroscopies show high potential as novel methods in medical microbiology.     

Drug-excipient interactions in ketoprofen: a vibrational spectroscopy study

Ketoprofen (3-benzoyl-alpha-methylbenzeneacetic acid) is a widely used nonsteroidal anti-inflammatory drug (NSAID), always administered in the form of drug-excipient physical mixtures (PMs). The occurrence of possible interactions between ketoprofen and two commonly used excipients-lactose (LAC) and polyvinylpyrrolidone (PVP)-was evaluated, through vibrational spectroscopy techniques [both Raman and Inelastic Neutron Scattering (INS)]. Spectral evidence of drug:excipient close contacts, which were enhanced by aging, was verified for the (1:1) (w:w) (ketoprofen:PVP) and (ketoprofen:LAC) PMs, both by Raman and INS. These interactions were found to involve mainly the central carbonyl and the terminal methyl-carboxylic moieties of the ketoprofen molecule, this being reflected in particular vibrational modes, such as the methyl torsion, the out-of-plane C-OH bending, and the inter-ring C=O stretching.     

Quantification of blockiness in pectins—A comparative study using vibrational spectroscopy and chemometrics

The gelling properties of pectins are related not only to the degree of esterification (DE), but also to the distribution of the ester groups. In this study, we have examined an experimentally designed series of 31 pectins originating from the same mother pectin and de-esterified using combinations of two different enzymatic mechanisms. The potential of using infrared (IR), Raman, and near infrared (NIR) spectroscopies combined with chemometrics for reliable and rapid determination of the DE and distribution patterns of methyl ester groups in a designed set of pectin powders was investigated. Quantitative calibration models using partial least squares (PLS) regression were developed and compared. The calibration models for prediction of DE obtained on extended inverse signal correction (EISC)-treated spectra of all three spectroscopic methods yielded models with cross-validated prediction errors (RMSECV) between 1.1%p and 1.6%p DE and correlation coefficients of 0.99. A calibration model predicting degree of random de-esterification (R) and block de-esterification (B) was developed for each spectroscopic method, yielding RMSECV values between 4.4 and 6.7 and correlation coefficients (r) between 0.79 and 0.92. Variable selection using interval PLS (iPLS) significantly improved the prediction of R for IR spectroscopy, yielding RMSECV of 3.5 and correlation coefficients of 0.95. All three spectroscopic methods were able to distinguish the spectral patterns of pectins with different enzyme treatments in simple classification models by principal component analysis (PCA). Extended canonical variate analysis revealed one specific signal in the Raman (1045 cm⁻¹) spectrum and one significant area (1250-1400 cm⁻¹) in the IR spectrum which are able to classify the pectin samples according to the four different enzyme treatments. In both Raman and IR spectra, the signal intensity decreased in the sequence R-B > B > B-R > R > re-methylated pectin.     

Determination of the structure of chiral molecules using ab initio vibrational circular dichroism spectroscopy

We discuss the theoretical prediction of vibrational circular dichroism (VCD) spectra using ab initio density functional theory (DFT) and the application of this methodology to the determination of the absolute configurations and conformations of chiral molecules.     

An infrared study of carbon monoxide complexes of hemocyanins. Evidence for the structure of the co-binding site from vibrational analysis

A vibrational analysis was carried out showing that the infrared experimental data of 13C and 18O carbon monoxide complexes of hemocyanin of Fager and Alben (Biochemistry 11 (1972) 4786) are consistent with a coordination of the carbon atom of CO to one of the two copper ions in the active site. This conclusion contradicts the original interpretation of Fager and Alben in which oxygen-coordination to copper was suggested. This vibrational analysis can also be applied to the study of Alben and Caughey (Biochemistry 7 (1968) 175) with 13C and 18O carbonyl hemoglobin, in which oxygen-coordination to iron was suggested. Carbonyl hemocyanins from several sources have also been studied by infrared spectroscopy. The single stretching vibration of CO bound to arthropodal (Cancer magister) hernocyanin (nu(co)) is at 2042.5 cm(-1), while nu(CO) for gastropod (Helix pomatia of the phylum Mollusca) alpha and beta hemocyanin is at 2064.5 cm(-1)and 2062.5 cm(-1), respectively. The intensities of the CO stretching bands were all around 1.5 X 10(4) M(-1) cm(-2). Calculations show that with the present attainable accuracy it is impossible to detect hydrogen bonding of exchangeable protons to small molecules bound to proteins (for example CO), by comparing its stretching frequencies in H2O and D2O buffers.     

Probing the structure of multi-stranded guanine-rich DNA complexes by Raman spectroscopy and enzymatic degradation.

The multi-stranded DNA complexes formed by the oligonucleotides d(T15G4T2G4), Tel, and d(T15G15), TG, were examined by nuclease digestion and Raman spectroscopy. Both Tel and TG can aggregate to form structures consisting of multiple, parallel-oriented DNA strands with two independent structural domains. Overall, the structures of the TG and Tel aggregates appear similar. According to the Raman data, the majority of bases are in C2'-endo/anti conformation. The interaction of guanines at the 3'-ends in both complexes stabilizes the complexes and protects them from degradation by exonuclease III. The 5'-extensions remain single-stranded and the thymines are accessible to single-strand-specific nuclease digestion. The extent of enzymatic cleavage at the junction at the 5' end of the 15 thymines implies a conformational change between this part of the molecule and the guanine-rich region. The differential enzymatic sensitivity of the complexes suggests there are variations in backbone conformations between TG and Tel aggregates. TG aggregates were more resistant to digestion by DNase I, Mung Bean nuclease, and S1 nuclease than Tel complexes. It is proposed that the lower DNase I sensitivity may be partly due to the more stable backbone exhibited by TG than Tel complexes. Structural uniformity along the guanine core of TG is suggested, as there is no indication of structural discontinuities or protected sites in the guanine-rich regions of TG aggregates. The lower extent of digestion by Mung Bean nuclease at the 3' end implies that these bases are inaccessible to the enzyme. This suggests that there is minimal fraying at the ends, which is consistent with the extreme thermal stability of the TG aggregates.     

146 Amyloid fibril polymorphism probed by advanced vibrational spectroscopy

Amyloid fibrils are associated with many neurodegenerative diseases. All known amyloids including pathogenic and nonpathogenic forms display functional and structural heterogeneity (polymorphism) which determines the level of their toxicity. Despite a significant biological and biomedical importance, the nature of the amyloid fibril polymorphism remains elusive. We utilized for the first time three most advanced vibrational techniques to probe the core, the surface, and supramolecular chirality of fibril polymorphs. A new type of folding, aggregation phenomenon, spontaneous refolding from one polymorph to another, was discovered (Kurouski, Lauro et al., 2010). Hydrogen–deuterium exchange deep UV resonance Raman spectroscopy (Oladepo, Xiong et al., 2012) combined with advanced statistical analysis (Shashilov & Lednev, 2010) allowed for structural characterization of the highly ordered cross-β core of amyloid fibrils. We reported several examples showing significant variations in the core structure for fibril polymorphs. Amyloid fibrils are generally composed of several protofibrils and may adopt variable morphologies, such as twisted ribbons or flat-like sheets. We discovered the existence of another level of amyloid polymorphism, namely, that associated with fibril supramolecular chirality. Two chiral polymorphs of insulin, which can be controllably grown by means of small pH variations, exhibit opposite signs of vibrational circular dichroism (VCD) spectra (Kurouski, Dukor et al. 2012). VCD supramolecular chirality is correlated not only by the apparent fibril handedness but also by the sense of supramolecular chirality from a deeper level of chiral organization at the protofilament level of fibril structure. A small pH change initiates spontaneous transformation of insulin fibrils from one polymorph to another. As a result, fibril supramolecular chirality overturns both accompanying morphological and structural changes (Kurouski, Dukor et al. 2012). No conventional methods could probe the fibril surface despite its significant role in the biological activity. We utilized tip-enhanced Raman spectroscopy (TERS) to characterize the surface structure of an individual fibril due to a high depth and lateral spatial resolution of the method in the nanometer range (Kurouski, Deckert-Gaudig et al. 2012). It was found that the surface is strongly heterogeneous and consists of clusters with various protein conformations and amino acid composition.     

1,2-diacyl-phosphatidylcholine flip-flop measured directly by sum-frequency vibrational spectroscopy

Sum-frequency vibrational spectroscopy (SFVS) is used to measure the intrinsic rate of lipid flip-flop for 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), and 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC) in planar-supported lipid bilayers (PSs). Asymmetric PSLBs were prepared using the Langmuir-Blodgett/Langmuir-Schaefer method by placing a perdeuterated lipid analog in one leaflet of the PSLB. SFVS was used to directly measure the asymmetric distribution of the native lipid within the membrane by measuring the decay in the CH3 v(s) intensity at 2875 cm(-1) with time and as a function of temperature. An average activation energy of 220 kJ/mol for the translocation of DMPC, DPPC, and DSPC was determined. A decrease in alkyl chain length resulted in a substantial increase in the rate of flip-flop manifested as an increase in the Arrhenius preexponential factor. The effect of lipid labeling was investigated by measuring the exchange of 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine-n,n-Dimethyl-n-(2',2',6',6'-tetramethyl-4'-piperidyl) (TEMPO-DPPC). The rate of TEMPO-DPPC flip-flop was an order-of-magnitude slower compared to DPPC. An activation energy of 79 kJ/mol was measured which is comparable to that previously measured by electron spin resonance. The results of this study illustrate how SFVS can be used to directly measure lipid flip-flop without the need for a fluorescent or spin-labeled lipid probe, which can significantly alter the rate of lipid translocation.     

Torsional vibrational modes of tryptophan studied by terahertz time-domain spectroscopy

The low-frequency torsional modes, index of refraction, and absorption of a tryptophan film and pressed powders from 0.2 to 2.0 THz (6.6-66 cm(-1)) were measured by terahertz time-domain spectroscopy at room temperature. It was found that there were two dominated torsional vibrational modes at around 1.435 and 1.842 THz. The associated relaxation lifetimes ( approximately 1 ps) for these modes of the tryptophan molecule were measured. Using a density-functional calculation, the origins of the observed torsional vibrations were assigned to the chain and ring of the tryptophan molecule.