Local dynamics of DNA probed with optical absorption spectroscopy of bound ethidium bromide.

We have studied the local dynamics of calf thymus double-helical DNA by means of an "optical labeling" technique. The study has been performed by measuring the visible absorption band of the cationic dye ethidium bromide, both free in solution and bound to DNA, in the temperature interval 360-30 K and in two different solvent conditions. The temperature dependence of the absorption line shape has been analyzed within the framework of the vibronic coupling theory, to extract information on the dynamic properties of the system; comparison of the thermal behavior of the absorption band of free and DNA-bound ethidium bromide gave information on the local dynamics of the double helix in the proximity of the chromophore. For the dye free in solution, large spectral heterogeneity and coupling to a "bath" of low-frequency (soft) modes is observed; moreover, anharmonic motions become evident at suitably high temperatures. The average frequency of the soft modes and the amplitude of anharmonic motions depend upon solvent composition. For the DNA-bound dye, at low temperatures, heterogeneity is decreased, the average frequency of the soft modes is increased, and anharmonic motions are hindered. However, a new dynamic regime characterized by a large increase in anharmonic motions is observed at temperatures higher than approximately 280 K. The DNA double helix therefore appears to provide, at low temperatures, a rather rigid environment for the bound chromophore, in which conformational heterogeneity is reduced and low-frequency motions (both harmonic vibrations and anharmonic contributions) are hindered. The system becomes anharmonic at approximately 180 K; however, above approximately 280 K, anharmonicity starts to increase much more rapidly than for the dye free in solution; this can be attributed to the onset of wobbling of the dye in its intercalation site, which is likely connected with the onset of (functionally relevant) DNA motions, involving local opening/unwinding of the double helix. As shown by parallel measurements of the melting curves, these motions precede the melting of the double helix and depend upon solvent composition much more than does the melting itself.     

Heme structural perturbation of PEG-modified horseradish peroxidase C in aromatic organic solvents probed by optical absorption and resonance Raman dispersion spectroscopy

The heme structure perturbation of poly(ethylene glycol)-modified horseradish peroxidase (HRP-PEG) dissolved in benzene and toluene has been probed by resonance Raman dispersion spectroscopy. Analysis of the depolarization ratio dispersion of several Raman bands revealed an increase of rhombic B(1g) distortion with respect to native HRP in water. This finding strongly supports the notion that a solvent molecule has moved into the heme pocket where it stays in close proximity to one of the heme's pyrrole rings. The interactions between the solvent molecule, the heme, and the heme cavity slightly stabilize the hexacoordinate high spin state without eliminating the pentacoordinate quantum mixed spin state that is dominant in the resting enzyme. On the contrary, the model substrate benzohydroxamic acid strongly favors the hexacoordinate quantum mixed spin state and induces a B(2g)-type distortion owing to its position close to one of the heme methine bridges. These results strongly suggest that substrate binding must have an influence on the heme geometry of HRP and that the heme structure of the enzyme-substrate complex (as opposed to the resting state) must be the key to understanding the chemical reactivity of HRP.     

Structural and dynamic properties of the heme pocket in myoglobin probed by optical spectroscopy

We report the optical absorption spectra of sperm whale deoxy-, oxy-, and carbonmonoxymyoglobin in the temperature range 300–20 K and in 65% glycerol or ethylene glycol–water mixtures. By lowering the temperature, all bands exhibit half-width narrowing and peak frequency shift; moreover, the near-ir bands of deoxymyoglobin show a marked increase of the integrated intensities. Opposed to what has already been reported for human hemoglobin, the temperature dependence of the first moment of the investigated bands does not follow the behavior predicted by the harmonic Franck–Condon approximation and is sizably affected by the solvent composition; this solvent effect is larger in liganded than in nonliganded myoglobin. However, for all the observed bands the behavior of the second moment can be quite well rationalized in terms of the harmonic Franck–Condon approximation and is not dependent on solvent composition. On the basis of these data we put forward some suggestions concerning the structural and dynamic properties of the heme pocket in myoglobin and their dependence upon solvent composition. We also discuss the different behaviors of myoglobin and hemoglobin in terms of the different heme pocket structures and deformabilities of the two proteins.     

Interaction between external medium and haem pocket in myoglobin probed by low-temperature optical spectroscopy

The visible absorption spectra of carbonmonoxymyoglobin in the temperature range 300 to 20 K are reported and compared with the analogous spectra of carbonomonoxyhaemoglobin. The temperature dependence of the zeroth, first and second moment of the observed bands is analysed to obtain information on the local dynamics in the proximity of the haem. Contrary to haemoglobin, the first moment of the observed bands in myoglobin is markedly affected by the solvent composition and its value saturates at temperatures at which the solvent undergoes the glass transition. These data indicate that solvent properties influence the haem pocket stereodynamics in myoglobin; moreover, the different behaviour between myoglobin and haemoglobin suggests that the process should involve the surfaces that are buried in the haemoglobin tetramer and exposed to the solvent in myoglobin, and/or the different protein compressibility.     

Protein folding transition states probed by loop extension

We propose a new way to characterize protein folding transition states by (1) insertion of one or more residues into an unstructured protein loop, (2) measurement of the effect on protein folding kinetics and thermodynamics, and (3) analysis of the results in terms of a rate-equilibrium free energy relationship, alpha(Loop). alpha(Loop) reports on the fraction of molecules that form the perturbed loop in the transition state. Interpretation of the changes in equilibrium free energy using standard polymer theory can help detect residual structure in the unfolded state. We illustrate our approach with data for the model proteins CI2 and the alpha spectrin SH3 domain.     

Pressure effects on the proximal heme pocket in myoglobin probed by Raman and near-infrared absorption spectroscopy.

The influence of high pressure on the heme protein conformation of myoglobin in different ligation states is studied using Raman spectroscopy over the temperature range from 30 to 295 K. Photostationary experiments monitoring the oxidation state marker bands demonstrate the change of rebinding rate with pressure. While frequency changes of vibrational modes associated with rigid bonds of the porphyrin ring are <1 cm(-1), we investigate a significant shift of the iron-histidine mode to higher frequency with increasing pressure (approximately 3 cm(-1) for deltaP = 190 MPa in Mb). The observed frequency shift is interpreted structurally as a conformational change affecting the tilt angle between the heme plane and the proximal histidine and the out-of-plane iron position. Independent evidence for iron motion comes from measurements of the redshift of band III in the near-infrared with pressure. This suggests that at high pressure the proximal heme pocket and the protein are altered toward the bound state conformation, which contributes to the rate increase for CO binding. Raman spectra of Mb and photodissociated MbCO measured at low temperature and variable pressure further support changes in protein conformation and are consistent with glasslike properties of myoglobin below 160 K.     

Cytochrome C in a dry trehalose matrix: structural and dynamical effects probed by x-ray absorption spectroscopy

We report on the structure and dynamics of the Fe ligand cluster of reduced horse heart cytochrome c in solution, in a dried polyvinyl alcohol (PVA) film, and in two trehalose matrices characterized by different contents of residual water. The effect of the solvent/matrix environment was studied at room temperature using Fe K-edge x-ray absorption fine structure (XAFS) spectroscopy. XAFS data were analyzed by combining ab initio simulations and multi-parameter fitting in an attempt to disentangle structural from disorder parameters. Essentially the same structural and disorder parameters account adequately for the XAFS spectra measured in solution, both in the absence and in the presence of glycerol, and in the PVA film, showing that this polymer interacts weakly with the embedded protein. Instead, incorporation in trehalose leads to severe structural changes, more prominent in the more dried matrix, consisting of 1), an increase up to 0.2 A of the distance between Fe and the imidazole N atom of the coordinating histidine residue and 2), an elongation up to 0.16 A of the distance between Fe and the fourth-shell C atoms of the heme pyrrolic units. These structural distortions are accompanied by a substantial decrease of the relative mean-square displacements of the first ligands. In the extensively dried trehalose matrix, extremely low values of the Debye Waller factors are obtained for the pyrrolic and for the imidazole N atoms. This finding is interpreted as reflecting a drastic hindering in the relative motions of the Fe ligand cluster atoms and an impressive decrease in the static disorder of the local Fe structure. It appears, therefore, that the dried trehalose matrix dramatically perturbs the energy landscape of cytochrome c, giving rise, at the level of local structure, to well-resolved structural distortions and restricting the ensemble of accessible conformational substates.     

Weak protein-protein interactions as probed by NMR spectroscopy

Weak protein-protein interactions (PPIs) are fundamental to many cellular processes, such as reversible cell-cell contact, rapid enzyme turnover and transient assembly and/or reassembly of large signaling complexes. However, structural and functional characterizations of weak PPIs have been technically challenging and lagged behind those for strong PPIs. Here, we describe nuclear magnetic resonance (NMR) spectroscopy as a highly effective tool for unraveling the atomic details of weak PPIs. We highlight the recent advances of how NMR can be used to rapidly detect and structurally determine extremely weak PPIs (K(d)>10(-4)M). Coupled with functional approaches, NMR has the potential to look into a wide variety of biologically important weak PPIs at the detailed molecular level, thereby facilitating a thorough view of how proteins function in living cells.     

Protein dynamics: Mössbauer spectroscopy on deoxymyoglobin crystals

Mössbauer absorption experiments on ⁵⁷Fe of deoxygenated myoglobin crystals and on K₄⁵⁷Fe(CN)₆ dissolved in the water of metmyoglobin crystals were performed over a large temperature range. At low temperatures the mean square displacements, 〈x²〉, of the iron indicate solid-like behaviour of the whole system, whereas at higher temperatures protein-specific modes of motion contribute to 〈x²>. The protein dynamics are correlated with the mobility of the water within the protein crystals. A Brownian oscillator is used to model the protein-specific modes of motion measured at the ⁵⁷Fe nucleus. Three modes are necessary for understanding the Mössbauer spectrum. Two of them correspond to an extremely overdamped Brownian oscillator. The third mode can be understood as quasi-free diffusion. Whereas the protein molecule is frozen in conformational substates in the low temperature regime, it reaches transition states with a finite probability in the high temperature regime. The surface water mediates a possible trigger mechanism that switches on protein dynamics within a narrow temperature interval. Results from Mössbauer spectroscopy and from X-ray structure analysis are compared.     

Differences in flexibility of active sites of cytochromes P450 probed by resonance Raman and UV-Vis absorption spectroscopy.

Spectroscopic methods reveal differences in flexibility and stability of P450 forms. Among microsomal P450s, the most flexible active site has been found in the CYP3A4 enzyme as it is compressible and the heme vinyl side chains may adopt two different conformations. On the other hand, active site of this enzyme denatures quite easily upon hydrostatic pressure. The most rigid active site able to withstand the effect of high pressure has CYP1A2. The bacterial CYP102 (BM3) flavocytochrome has also a rather stable, but flexible active site. The differences between CYP3A4 and CYP1A2 active sites apparently reflect their ability to bind various substrates: whereas the CYP3A4 binds a vast variety of structures, the CYP1A2 preferentially binds planar, aromatic structures and its substrate specificity is relatively narrow.     

The citrate carrier CitS probed by single-molecule fluorescence spectroscopy

A prominent region of the Na(+)-dependent citrate carrier (CitS) from Klebsiella pneumoniae is the highly conserved loop X-XI, which contains a putative citrate binding site. To monitor potential conformational changes within this region by single-molecule fluorescence spectroscopy, the target cysteines C398 and C414 of the single-Cys mutants (CitS-sC398, CitS-sC414) were selectively labeled with the thiol-reactive fluorophores AlexaFluor 546/568 C(5) maleimide (AF(546), AF(568)). While both single-cysteine mutants were catalytically active citrate carriers, labeling with the fluorophore was only tolerated at C398. Upon citrate addition to the functional protein fluorophore conjugate CitS-sC398-AF(546), complete fluorescence quenching of the majority of molecules was observed, indicating a citrate-induced conformational change of the fluorophore-containing domain of CitS. This quenching was specific for the physiological substrate citrate and therefore most likely reflecting a conformational change in the citrate transport mechanism. Single-molecule studies with dual-labeled CitS-sC398-AF(546/568) and dual-color detection provided strong evidence for a homodimeric association of CitS.     

Local magnetism in palladium bionanomaterials probed by muon spectroscopy

Palladium bionanomaterial was manufactured using the sulfate-reducing bacterium, Desulfovibrio desulfuricansm, to reduce soluble Pd(II) ions to cell-bound Pd(0) in the presence of hydrogen. The biomaterial was examined using a Superconducting Quantum Interference Device (SQUID) to measure bulk magnetisation and by Muon Spin Rotation Spectroscopy (μSR) which is uniquely able to probe the local magnetic environment inside the sample. Results showed behaviour attributable to interaction of muons both with palladium electrons and the nuclei of hydrogen trapped in the particles during manufacture. Electronic magnetism, also suggested by SQUID, is not characteristic of bulk palladium and is consistent with the presence of nanoparticles previously seen in electron micrographs. We show the first use of μSR as a tool to probe the internal magnetic environment of a biologically-derived nanocatalyst material.     

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.     

The allosteric transition in DnaK probed by infrared difference spectroscopy. Concerted ATP-induced rearrangement of the substrate binding domain

The biological activity of DnaK, the bacterial representative of the Hsp70 protein family, is regulated by the allosteric interaction between its nucleotide and peptide substrate binding domains. Despite the importance of the nucleotide-induced cycling of DnaK between substrate-accepting and releasing states, the heterotropic allosteric mechanism remains as yet undefined. To further characterize this mechanism, the nucleotide-induced absorbance changes in the vibrational spectrum of wild-type DnaK was characterized. To assign the conformation sensitive absorption bands, two deletion mutants (one lacking the C-terminal alpha-helical subdomain and another comprising only the N-terminal ATPase domain), and a single-point DnaK mutant (T199A) with strongly reduced ATPase activity, were investigated by time-resolved infrared difference spectroscopy combined with the use of caged-nucleotides. The results indicate that (1) ATP, but not ADP, binding promotes a conformational change in both subdomains of the peptide binding domain that can be individually resolved; (2) these conformational changes are kinetically coupled, most likely to ensure a decrease in the affinity of DnaK for peptide substrates and a concomitant displacement of the lid away from the peptide binding site that would promote efficient diffusion of the released peptide to the medium; and (3) the alpha-helical subdomain contributes to stabilize the interdomain interface against the thermal challenge and allows bidirectional transmission of the allosteric signal between the ATPase and substrate binding domains at stress temperatures (42 degrees C).     

Dynamic properties of oxy- and carbonmonoxyhemoglobin probed by optical spectroscopy in the temperature range of 300-20 K

We have studied the absorption bands of oxy- and carbonmonoxyhemoglobin in the wavelength range of 650–350 nm (visible and Soret bands) and in the temperature range of 300–20 K. The spectra in the whole temperature range have been successfully deconvoluted in terms of gaussian components. The analysis of the temperature dependence of the first and second moment of the bands enables us to compare dynamic properties of the heme group in oxy- and carbonmonoxyhemoglobin. The results of the analysis indicate that the “mean-effective” frequency of the nuclear motion coupled to the electronic transition responsible for the visible bands is higher in carbonmonoxy- than in oxyhemoglobin. The possible functional relevance of this finding is discussed.     

Excited-state dynamics of bacteriorhodopsin probed by broadband femtosecond fluorescence spectroscopy

The impact of varying excitation densities (approximately 0.3 to approximately 40 photons per molecule) on the ultrafast fluorescence dynamics of bacteriorhodopsin has been studied in a wide spectral range (630-900 nm). For low excitation densities, the fluorescence dynamics can be approximated biexponentially with time constants of <0.15 and approximately 0.45 ps. The spectrum associated with the fastest time constant peaks at 650 nm, while the 0.45 ps component is most prominent at 750 nm. Superimposed on these kinetics is a shift of the fluorescence maximum with time (dynamic Stokes shift). Higher excitation densities alter the time constants and their amplitudes. These changes are assigned to multi-photon absorptions.     

The solution structure of concanavalin A probed by FT-IR spectroscopy

The secondary structural properties of various forms of concanavalin A in solution were investigated by Fourier-transform infrared spectroscopy in the Amide I region. As in the crystal, the solution structure of the native protein consists mainly of antiparallel beta-sheet. Carbohydrate binding does not produce major changes in the overall secondary structure of concanavalin A, but affects infrared bands due to loops and beta-turns. Upon demetallization, the spectrum of concanavalin A shows only a small change in the Amide I band, indicating that whereas the beta-sheet structure is conserved, the tertiary properties may be altered. There are also changes in the bands from the tyrosine residues which are compatible with local changes in structure. Confirming tertiary structural differences, the cation-depleted apoprotein is much less stable, denaturing around 63 degrees C, while the native protein denatures only at temperatures around 85 degrees C. Tetramerization proceeds without significant secondary structural change. However, aggregation of the tetramers leads to a significant decrease of the bands corresponding to beta-sheet structure, and changes in the tyrosine bands.     

Relaxation dynamics in three polypyridyl iron(II)-based complexes probed by nanosecond and sub-picosecond transient absorption spectroscopy

The results of a sub-picosecond transient absorption spectroscopy study on a mononuclear and two dinuclear low-spin iron(II) complexes is reported. The dinuclear derivatives are homonuclear (i.e. Fe–Fe) and heterodinuclear (Fe–Zn) in nature. The ligands we used were 2-pyridylmethyl-ketazine and 2-pyridylmethyl-hydrazone. Irradiation was made on the metal-to-ligand CT band occurring around 500 nm. The observed pattern of the relaxation decays is consistent with the population of the metastable ⁵T₂ ligand field state within the first 100 fs after the photon absorption from the three different chromophores. The suggested implication of triplet intermediate states was not detected. The ground state recovery was observed to occur with a time constant of 350 ps for the mononuclear complex and 1600–1800 ps for the two dinuclear complexes.     

Metallodrug-protein interaction probed by synchrotron terahertz and neutron scattering spectroscopy

This experimental work applied coherent synchrotron-radiation terahertz spectroscopy and inelastic neutron scattering to address two processes directly associated with the mode of action of metal-based anticancer agents that can severely undermine chemotherapeutic treatment: drug binding to human serum albumin, occurring during intravenous drug transport, and intracellular coordination to thiol-containing biomolecules (such as metallothioneins) associated with acquired drug resistance. Cisplatin and two dinuclear platinum (Pt)- and palladium (Pd)-polyamine agents developed by this research group, which have yielded promising results toward some types of human cancers, were investigated. Complementary synchrotron-radiation-terahertz and inelastic neutron scattering data revealed protein metalation, through S- and N-donor ligands from cysteine, methionine, and histidine residues. A clear impact of the Pt and Pd agents was evidenced, drug binding to albumin and metallothionein having been responsible for significant changes in the overall protein conformation, as well as for an increased flexibility and possible aggregation.     

Amyloid oligomer formation probed by water proton magnetic resonance spectroscopy

Formation of amyloid oligomers, the most toxic species of amyloids in degenerative diseases, is critically coupled to the interplay with surrounding water. The hydrophobic force driving the oligomerization causes water removal from interfaces, changing the surface-hydration properties. Here, we show that such effects alter the magnetic relaxation response of local water in ways that may enable oligomer detection. By using water proton magnetic resonance spectroscopy, we measured significantly longer transverse magnetic relaxation (T₂) times in mixtures of serum and amyloidogenic Aβ_1-42 peptides versus similar concentration solutions of serum and nonamyloidogenic scrambled Aβ_42-1 peptides. Immunochemistry with oligomer-specific antibodies, electron microscopy and computer simulations demonstrated that the hyperintense magnetic signal correlates with Aβ_1-42 oligomerization. Finding early biophysical markers of the oligomerization process is crucial for guiding the development of new noninvasive imaging techniques, enabling timely diagnosis of amyloid-related diseases and pharmacological intervention.