Biexcitonic fine structure of CdSe nanocrystals probed by polarization-dependent two-dimensional photon echo spectroscopy

The spectroscopy of colloidal CdSe nanocrystals is investigated using two-dimensional photon echo (2DPE) spectroscopy with copolarized and cross-polarized pulse sequences. Clearly resolved excited state absorption features are observed to beat at the frequency of the longitudinal-optical phonon, and the phase of this beating is found to be polarization-dependent. A simulation is performed using the excitonic and biexcitionic fine structure states predicted by theory, and the polarization-dependent beating allows each feature to be assigned to a particular excited state absorption pathway. Owing to their circularly polarized selection rules, the polarization-dependent 2DPE technique provides valuable insights into the spectroscopy of quantum dots. In particular, transient absorption features observed in pump-probe studies of CdSe quantum dots can now be assigned to specific fine structure transitions to the ground state biexciton.     

Folding, conformational changes, and dynamics of cytochromes C probed by NMR spectroscopy

NMR spectroscopy has become a vital tool for studies of protein conformational changes and dynamics. Oxidized Fe(III)cytochromes c are a particularly attractive target for NMR analysis because their paramagnetism (S = (1)/(2)) leads to high (1)H chemical shift dispersion, even for unfolded or otherwise disordered states. In addition, analysis of shifts induced by the hyperfine interaction reveals details of the structure of the heme and its ligands for native and nonnative protein conformational states. The use of NMR spectroscopy to investigate the folding and dynamics of paramagnetic cytochromes c is reviewed here. Studies of nonnative conformations formed by denaturation and by anomalous in vivo maturation (heme attachment) are facilitated by the paramagnetic, low-spin nature of native and nonnative forms of cytochromes c. Investigation of the dynamics of folded cytochromes c also are aided by their paramagnetism. As an example of this analysis, the expression in Escherichia coli of cytochrome c(552) from Nitrosomonas europaea is reported here, along with analysis of its unusual heme hyperfine shifts. The results are suggestive of heme axial methionine fluxion in N. europaea ferricytochrome c(552). The application of NMR spectroscopy to investigate paramagnetic cytochrome c folding and dynamics has advanced our understanding of the structure and dynamics of both native and nonnative states of heme proteins.     

Dynamical flexibility and proton transfer in the arginase active site probed by ab initio molecular dynamics

We have used ab initio molecular dynamics (AIMD) to investigate the dynamical flexibility of the bridged binuclear structural motif in the active site of arginase. Dynamical transformations play a crucial role in catalysis. We have provided direct insight into the motions of the first-shell ligands with emphasis on the chelating and bridging carboxylates. In the case of the terminal Asp234 residue we observe changes in the binding mode (carboxylate shifts). AIMD dynamics of sufficient duration has allowed us to observe proton transfer from the bridging nucleophile to the catalytically essential Asp 128 residue and to map the underlying free energy surface in terms of simple reaction coordinates, such as the oxygen-oxygen distance Ro-o and the asymmetric stretch delta. This has provided valuable insight into the nature of the last step of the catalytic cycle. In addition, constrained molecular dynamics permitted us to compare the deprotonation free energy of the bridging nucleophile in the case of native versus metal-depleted arginase.     

Redox-linked protein dynamics of cytochrome c probed by time-resolved surface enhanced infrared absorption spectroscopy

Time-resolved surface enhanced infrared absorption (SEIRA) spectroscopy is employed to analyse the dynamics of the protein structural changes coupled to the electron transfer process of immobilised cytochrome c (Cyt-c). Upon electrostatic binding of Cyt-c to Au electrodes coated with self-assembled monolayers (SAMs) of carboxyl-terminated thiols, cyclic voltammetric measurements demonstrate a reversible redox process with a redox potential that is similar to that of Cyt-c in solution, and a non-exponential distance-dependence of the electron transfer rate as observed previously (D. H. Murgida and P. Hildebrandt, Chem. Soc. Rev. 2008, 37, 937). On the basis of characteristic redox-state-sensitive amide I bands, the protein structural changes triggered by the electron transfer are monitored by rapid scan and step scan SEIRA spectroscopy in combination with the potential jump technique. Whereas the temporal evolution of the conjugate bands at 1693 and 1673 cm(-1) displays the same rate constants as electron transfer, the time-dependent changes of the 1660-cm(-1) band are slower by about a factor of 2. The study demonstrates that time-resolved SEIRA spectroscopy provides further information about the dynamics and mechanism of interfacial processes of redox proteins, thereby complementing the results obtained from other surface-sensitive techniques. In comparison with previous surface enhanced resonance Raman spectroscopic findings, the present results are discussed in terms of the local electric field strengths at the Au/SAM/Cyt-c interface.     

Determination of membrane protein structure and dynamics by magic-angle-spinning solid-state NMR spectroscopy

It is shown that molecular structure and dynamics of a uniformly labeled membrane protein can be studied under magic-angle-spinning conditions. For this purpose, dipolar recoupling experiments are combined with novel through-bond correlation schemes that probe mobile protein segments. These NMR schemes are demonstrated on a uniformly [13C,15N] variant of the 52-residue polypeptide phospholamban. When reconstituted in lipid bilayers, the NMR data are consistent with an alpha-helical trans-membrane segment and a cytoplasmic domain that exhibits a high degree of structural disorder.     

Vanadate complex spectroscopy at the RNase A active site

Knowledge of the ionicity of the phosphorane intermediate is important to the analysis of the microscopic mechanism of the hydrolysis of the phosphate ester bond by ribonuclease A (RNase A). Five-coordinate uridine vanadate, an analog of the phosphorane, binds to RNase A as the monoanion. The absorption spectra of the vanadate is a probe of the electronic structure of the active site. An in vacuo theoretical model of H₄VO₅⁻ is calculated to have transitions only in the far ultraviolet (UV). However, H₂VO₅C₂H₄⁻ has one in the near UV as well as others further into the UV. The transition energy of the monoanion calculated in the field of the protein active site with effective fragment potentials shifts modestly to the red. Broad monoanion absorptions are predicted which would overlap an observed incomplete very broad absorption attributed to the complex of uridine vanadate with RNase A. The absorption bands of neutral ethylene glycol vanadate are predicted to be further to the red but also overlap the experimental absorption. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 69: 11–19, 1998     

Ring current effects in the active site of medium-chain Acyl-CoA dehydrogenase revealed by NMR spectroscopy

Medium-chain acyl-CoA dehydrogenase (MCAD) catalyzes the flavin-dependent oxidation of fatty acyl-CoAs to the corresponding trans-2-enoyl-CoAs. The interaction of hexadienoyl-CoA (HD-CoA), a product analogue, with recombinant pig MCAD (pMCAD) has been studied using (13)C NMR and (1)H-(13)C HSQC spectroscopy. Upon binding to oxidized pMCAD, the chemical shifts of the C1, C2, and C3 HD carbons are shifted upfield by 12.8, 2.1, and 13.8 ppm, respectively. In addition, the (1)H chemical shift of the C3-H is also shifted upfield by 1.31 ppm while the chemical shift of the C4 HD-CoA carbon is unchanged upon binding. These changes in chemical shift are unexpected given the results of previous Raman studies which revealed that the C3=C2-C1=O HD enone fragment is polarized upon binding to MCAD such that the electron density at the C3 and C1 carbons is reduced, not increased (Pellet et al. Biochemistry 2000, 39, 13982-13992). To investigate the apparent discrepancy between the NMR and Raman data for HD-CoA bound to MCAD, (13)C NMR spectra have been obtained for HD-CoA bound to enoyl-CoA hydratase, an enzyme system that has also previously been studied using Raman spectroscopy. Significantly, binding to enoyl-CoA hydratase causes the chemical shifts of the C1 and C3 HD carbons to move downfield by 4.8 and 5.6 ppm, respectively, while the C2 resonance moves upfield by 2.2 ppm, in close agreement with the alterations in electron density at these carbons predicted from Raman spectroscopy (Bell, A. F.; Wu, J.; Feng, Y.; Tonge, P. J. Biochemistry 2001, 40, 1725-33). The large increase in shielding experienced by the C1 and C3 HD carbons in the HD-CoA/MCAD complex is proposed to arise from the ring current field from the isoalloxazine portion of the flavin cofactor. The flavin ring current, which is only present when the enzyme is placed in an external magnetic field, also explains the differences in (13)C NMR chemical shifts for acetoacetyl-CoA when bound as an enolate to MCAD and enoyl-CoA hydratase and is used to rationalize the observation that the line widths of the C1 and C3 resonances are narrower when the ligands are bound to MCAD than when they are free in the protein solution.     

Cobalt spectroscopy and the structure of the active site of carbonic anhydrase

Theoretical models of divalent cobalt bound to the active site of the enzyme, carbonic anhydrase, are constructed to study the effect of the first-shell geometry and coordination number on the experimentally observed visible spectra. Favorable comparisons of the ab initio calculations of the hexa-aquo complex of Co(II) with experimental results provides a test of the method. The d–d spectra variation with pH in the enzyme is found to be determined by the first-shell complex geometry as obtained from energy optimization. The low pH complex is predicted to be predominantly five-coordinate with two waters in the first-shell, whereas the high pH complex is predominantly four-coordinate. Equilibria between the four- and five-coordinate structures at low pH is not indicated by the calculation.     

Heterogeneous dynamics and dynamic heterogeneities at the glass transition probed with single molecule spectroscopy

We studied the temperature dependence of the structural relaxation in poly(vinyl acetate) near the glass transition temperature with single molecule spectroscopy from Tg-1 K to Tg+12 K. The temperature dependence of the observed relaxation times matches results from bulk experiments; the observed relaxation times are, however, 80-fold slower than those from bulk experiments at the same temperature. We attribute this factor to the size of the probe molecule. The individual relaxation times of the single molecule environments are distributed normally on a logarithmic time scale, confirming that the dynamics in poly(vinyl acetate) is heterogeneous. The width of the distribution of individual relaxation times is essentially independent of temperature. The observed full width at half maximum (FWHM) on a logarithmic time axis is approximately 0.7, corresponding to a factor of about 5-fold, significantly narrower than the dielectric spectrum of the same material with a FWHM of about 2.0 on a logarithmic time axis, corresponding to a factor of about 100-fold. We explain this narrow width as the effect of temporal averaging of single molecule fluorescence signals over numerous environments due to a limited lifetime of the probed heterogeneities, indicating that heterogeneities are dynamic. We determine a loose upper limit for the ratio of the structural relaxation time to the lifetime of the heterogeneities (the rate memory parameter) of Q<80 for the range of investigated temperatures.     

Analysing and understanding the active site by IR spectroscopy

IR spectroscopy is a technique particularly adapted for understanding the mechanism of catalytic reactions, being able to probe the surface mechanisms at the molecular level. In this critical review the main advances in the field are presented, both under the aspects of the in situ and operando approaches. A broad view of the most authoritative literature of the domain is given, based largely on the experience built up at the LCS laboratory in the last decades. After having presented the general methodology to observe a potential active site directly or by probe molecule adsorption, several examples illustrate the qualitative and quantitative analysis of the physical-chemical properties of the surface entities. The last part of the review is dedicated to the discrimination of the role of the active site and its links with the catalytic steps; the hot problem of the reaction intermediates and their visibility via spectroscopic techniques is critically addressed (138 references).     

H-bond refinement for electron transfer membrane-bound protein–protein complexes: Cytochrome c oxidase and cytochrome c552

In this study we propose a protocol to evaluate membrane-bound cytochrome c oxidase–cytochrome c552 docking candidates. An initial rigid docking algorithm generates docking poses of the cytochrome c oxidase–cytochrome c552, candidates are then aggregated into a 512-DPPC membrane model and solvated in explicit solvent. Molecular dynamic simulations are performed to induce conformational changes to membrane-bound protein complexes. Lastly each protein–protein complex is optimized in terms of its hydrogen bond network, evaluated energetically and ranked. The protocol is directly applicable to other membrane-protein complexes, such as protein–ligand systems.     

Solute-solvent complex kinetics and thermodynamics probed by 2D-IR vibrational echo chemical exchange spectroscopy

The formation and dissociation kinetics of a series of triethylsilanol/solvent weakly hydrogen bonding complexes with enthalpies of formation ranging from -1.4 to -3.3 kcal/mol are measured with ultrafast two-dimensional infrared (2D IR) chemical exchange spectroscopy in liquid solutions at room temperature. The correlation between the complex enthalpies of formation and dissociation rate constants can be expressed with an equation similar to the Arrhenius equation. The experimental results are in accord with previous observations on eight phenol/solvent complexes with enthalpies of formation from -0.6 to -2.5 kcal/mol. It was found that the inverse of the solute-solvent complex dissociation rate constant is linearly related to exp(-DeltaH0/RT) where DeltaH0 is the complex enthalpy of formation. It is shown here, that the triethylsilanol-solvent complexes obey the same relationship with the identical proportionality constant, that is, all 13 points, five silanol complexes and eight phenol complexes, fall on the same line. In addition, features of 2D IR chemical exchange spectra at long reaction times (spectral diffusion complete) are explicated using the triethylsilanol systems. It is shown that the off-diagonal chemical exchange peaks have shapes that are a combination (outer product) of the absorption line shapes of the species that give rise to the diagonal peaks.     

Alpha-synuclein structures probed by 5-fluorotryptophan fluorescence and 19F NMR spectroscopy

Alpha-synuclein, the main protein component of fibrillar deposits found in Parkinson's disease, is intrinsically disordered in vitro. Site-specific information on the protein conformation has been obtained by biosynthetic incorporation of an unnatural amino acid, 5-fluorotryptophan (5FW), into the recombinant protein. Using fluorescence and 19F NMR spectroscopy, we have characterized three proteins with 5FW at positions 4, 39, and 94. Steady-state emission spectra (maxima at 353 nm; quantum yields approximately 0.2) indicate that all three indole side chains are exposed to the aqueous medium. Virtually identical single-exponential excited-state decays (tau approximately 3.4 ns) were observed in all three cases. Single 19F NMR resonances were measured for W4, W39, and W94 at -49.0 +/- 0.1 ppm. Our analysis of the spectroscopic data suggests that the protein conformations are very similar in the regions near the three sites.     

Cytochrome c: Ascorbate reduction site and possible electron-transfer path

The ascorbate reduction reaction of the native and urea-perturbed forms, 0–8M urea, of horse heart ferricytochrome c is found to be a three-step process: a urea-dependent equilibrium step between a reducible and an irreducible form with a midconcentration of urea of 7.4M, a binding step with a binding constant of 5.9M^–1, and a reduction step with a urea-independent rate constant of 2.9 ± 0.3 s^–1 [J. Biol. Chem. 255 , 9666 (1980)]. The effect of adding urea, in addition to the generation of an irreducible form, is a slight lowering of the ascorbate-protein binding constant, 5.9 to 2.7M^–1, which is limited to the 0–5.5M concentration range. The thermodynamics of the ureadenaturation process also yields a three-step mechanism, N? X₁? X₂? D, with midconcentrations of urea of 2.5–3M, 6.2M, and 7.5M, respectively, where N, D, and the X_s are the native, the 9-M-urea, and the intermediate forms. The three processes are described as the loosening of the heme crevice opening, the solvent exposure of the polypeptide backbone, and the disruption of the tryptophan–porphyrin interactions, respectively [Biochemistry 19 , 199 (1980)]. The reaction of the protein with 2,3-butanedione, a group-specific reagent for the guanidinium groups and an electron donor for this protein, is inhibited in the presence of ascorbate, but only one of the two functional groups is involved [J. Biol. Chem. 255 , 11094 (1980)]. A correlation of kinetic and thermodynamic observations led to the conclusion that the ascorbate reduction of the protein is independent of the state of the heme crevice opening and of the polypeptide organized structures; instead, it is determined by the integrity of the tryptophan indole–porphyrin interactions. This information, when taken in conjunction with the selective inhibition of the reaction of the arginine side chains by ascorbate, establishes the binding site of ascrobate as one of the two arginyl side chains, and not the opening of the crevice or its vicinity. From the three-dimensional structure of the protein, and taking into consideration the variability of the protein sequence, it is suggested that Arg-38 is the ascorbate binding site, and that the electronic interaction between the indole of Trp-59 and the porphyrin moiety must constitute, at least in part, the electron-transfer path to heme iron.     

Biogels of cytochrome c : Cytochrome c peroxidase complex studied by electron paramagnetic resonance spectroscopy

Cytochrome c: cytochrome c peroxidase (Cc: CcP in 1: 1 ratio) complex was successfully encapsulated in sol-gel derived glass. The electron paramagnetic resonance (e.p.r.) and optical absorption techniques were used to characterize the coordination number, spin state, charge-transfer activity and structural orientation of Cc: CcP complex and its constituents. The sol-gel encapsulation of metalloproteins allows, for the first time, the detection of e.p.r. signals of biological systems at room temperature. CcP exhibits an e.p.r. spectrum representing the high spin and purely axial symmetry with parameters at g 6 and g 2 and an electronic absorption spectrum with a descent in spectral intensity of shoulder band at 380 nm and a blue-shifted charge-transfer band at 620 nm. Cc shows an e.p.r. spectrum characterizing a mixture of high spin (g 6 and g 2) and low spin (g _x=2.7, g _y=2.2 and g _z=1.8) components. Upon complexation, Cc:CcP pair displays a single and broad e.p.r. spectrum at g 2 and a light absorption spectrum with a red-shifted Soret band at 423 nm, a blue-shifted charge-transfer band at 620 nm and an intensified charge-transfer band at 507 nm. These results suggest that the sol-gel encapsulated Cc:CcP complex has the following chemical and physical characteristics: (a) a hexa-coordination, (b) a high-spin state, (c) an active charge-transfer (or redox) pair, and (d) the direction of the g paramagnetic center of Cc : CcP complex lies nearly parallel to that of the heme normal. The structural coordinations of the sol-gel encapsulated Cc, CcP and Cc : CcP are examined. Moreover, the possible use of biogels at the sol, gelation, and xerogel stages during gel processing to control the structural rigidity and spatial separation/orientation of the encapsulated heme proteins and to study their possible routes of long-range electron transfer reactions are also discussed.     

Static normal coordinate deformations of the heme group in mutants of ferrocytochrome c from Saccharomyces cerevisiae probed by resonance Raman spectroscopy

The function of heme proteins is, to a significant extent, influenced by the ligand field probed by the heme iron, which itself can be affected by deformations of the heme macrocycle. The exploration of this field is difficult because the heme structure obtained from X-ray crystallography is not resolved enough to unambiguously identify structural changes on the scale of 10(-2) A. However, asymmetric deformations in this order of magnitude affect the depolarization ratio of the resonance Raman lines assignable to normal vibrations of the heme group. We have measured the dispersion of the depolarization ratios of four structure sensitive Raman bands (i.e., nu4, nu11, nu21, and nu28) in yeast iso-1-ferrocytochrome c and its mutants N52V, Y67F, and N52VY67F with B- and Q-band excitation. The DPR dispersion of all bands indicates the presence of asymmetric in-plane and out-of-plane deformations. The replacement of the polar tyrosine residue at position 67 by phenylalanine significantly increases the triclinic B2g deformation, which involves a distortion of the pyrrole symmetry. We relate this deformation to changes of the electronic structure of pyrrole A, which modulates the interaction between its propionate substituents and the protein environment. This specific heme deformation is eliminated in the double mutant N52VY67F. The additional substitution of N52 by valine induces a tetragonal B1g deformation which involves asymmetric changes of the Fe-N distances and increases the rhombicity of the ligand field probed by the heme iron. This heme deformation might be caused by the elimination of the water-protein hydrogen-bonding network in the heme cavity. The single mutation N52V does not significantly perturb the heme symmetry, but a small B1g deformation is consistent with our data and the heme structure obtained from a 1 ns molecular dynamics simulation of the protein.     

Conformational dynamics at the active site of alpha-chymotrypsin and enzymatic activity

The role of dynamical flexibility at the active site of a proteolytic enzyme alpha-chymotrypsin (CHT) has been correlated with its catalytic activity. The temperature-dependent efficiency of catalysis reveals a bell-shaped feature with a peak at 37 degrees C, the typical body temperature of homeothermal animals. The overall structural integrity of the enzyme in our experimental temperature range has been confirmed from dynamic light scattering (DLS) and circular dichroism (CD) studies. We have followed the dynamical evolution at the active site of CHT with temperature using picosecond-resolved fluorescence anisotropy of anthraniloyl probe (covalently attached to the serine-195 residue) and a substrate mimic (inhibitor) proflavin. The conformational dynamics at the active site is found to have a distinct connection with the enzyme functionality. The conformational flexibility of the enzyme is also evidenced from the compressibility studies on the enzyme. The site selective fluorescence detected circular dichroism (FDCD) studies reveal that the conformational flexibility of the enzyme has an effect on the structural perturbation at the active site. We have also proposed the possible implications of the dynamics in the associated energetics.     

Fast enzyme dynamics at the active site of formate dehydrogenase

The role of femtosecond-picosecond structural dynamics of proteins in enzyme-catalyzed reactions is a hotly debated topic. We report infrared photon echo measurement of the formate dehydrogenase-NAD+-azide ternary complex. In contrast to earlier studies of protein dynamics, the data show complete spectral diffusion on the femtosecond-picosecond time scale with no static heterogeneity. This result indicates that this transition-state analogue complex completely samples the distribution of structures that determine the distribution of azide vibrational frequencies within a few picoseconds and that there are no slower motions that perturb the H-bond network at the active site.