Multiple retinal isomerizations during the early phase of the bestrhodopsin photoreaction.

Bestrhodopsins constitute a class of light-regulated pentameric ion channels that consist of one or two rhodopsins in tandem fused with bestrophin ion channel domains. Here, we report on the isomerization dynamics in the rhodopsin tandem domains of Phaeocystis antarctica bestrhodopsin, which binds all-trans retinal Schiff-base (RSB) absorbing at 661 nm and, upon illumination, converts to the meta-stable P540 state with an unusual 11-cis RSB. The primary photoproduct P682 corresponds to a mixture of highly distorted 11-cis and 13-cis RSB directly formed from the excited state in 1.4 ps. P673 evolves from P682 in 500 ps and contains highly distorted 13-cis RSB, indicating that the 11-cis fraction in P682 converts to 13-cis. Next, P673 establishes an equilibrium with P595 in 1.2 µs, during which RSB converts to 11-cis and then further proceeds to P560 in 48 µs and P540 in 1.0 ms while remaining 11-cis. Hence, extensive isomeric switching occurs on the early ground state potential energy surface (PES) on the hundreds of ps to µs timescale before finally settling on a metastable 11-cis photoproduct. We propose that P682 and P673 are trapped high up on the ground-state PES after passing through either of two closely located conical intersections that result in 11-cis and 13-cis RSB. Co-rotation of C11=C12 and C13=C14 bonds results in a constricted conformational landscape that allows thermal switching between 11-cis and 13-cis species of highly strained RSB chromophores. Protein relaxation may release RSB strain, allowing it to evolve to a stable 11-cis isomeric configuration in microseconds.

Evidence of Self-Association and Conformational Change in Nisin Antimicrobial Polypeptide Solutions: A Combined Raman and Ultrasonic Relaxation Spectroscopic and Theoretical Study.

The polypeptide Nisin is characterized by antibacterial properties, making it a compound with many applications, mainly in the food industry. As a result, a deeper understanding of its behaviour, especially after its dissolution in water, is of the utmost importance. This could be possible through the study of aqueous solutions of Nisin by combining vibrational and acoustic spectroscopic techniques. The velocity and attenuation of ultrasonic waves propagating in aqueous solutions of the polypeptide Nisin were measured as a function of concentration and temperature. The computational investigation of the molecular docking between Nisin monomeric units revealed the formation of dimeric units. The main chemical changes occurring in Nisin structure in the aqueous environment were tracked using Raman spectroscopy, and special spectral markers were used to establish the underlying structural mechanism. Spectral changes evidenced the presence of the dimerization reaction between Nisin monomeric species. The UV/Vis absorption spectra were dominated by the presence of π → π* transitions in the peptide bonds attributed to secondary structural elements such as α-helix, ß-sheets and random coils. The analysis of the acoustic spectra revealed that the processes primarily responsible for the observed chemical relaxations are probably the conformational change between possible conformers of Nisin and its self-aggregation mechanism, namely, the dimerization reaction. The activation enthalpy and the enthalpy difference between the two isomeric forms were estimated to be equal to ΔH1* = 0.354 ± 0.028 kcal/mol and ΔH10 = 3.008 ± 0.367 kcal/mol, respectively. The corresponding thermodynamic parameters of the self-aggregation mechanism were found to be ΔH2* = 0.261 ± 0.004 kcal/mol and ΔH20 = 3.340 ± 0.364 kcal/mol. The effect of frequency on the excess sound absorption of Nisin solutions enabled us to estimate the rate constants of the self-aggregation mechanism and evaluate the isentropic and isothermal volume changes associated with the relaxation processes occurring in this system. The results are discussed in relation to theoretical and experimental findings.

Exploring the influence of experimental parameters on the interaction of asymmetric ω/2ω fields with water isotopologues.

Water isotopologues are doubly ionized by phase-controlled asymmetric ω/2ω laser fields, and their two-body fragmentation channels leading to pairs of OH+/H+ [channel (I)] and H2 +/O+ [channel (II)] are systematically investigated. The dependence of the ionic fragments on phase distinguishes between two dissociation channels, while a quantity that is proportional to the directionality of the ejected fragments, called asymmetry parameter (ß), is measured as a function of composite field's phase. The dependence of the two channels' asymmetry amplitude (ß0) on the experimental parameters that characterize the composite field (wavelength, anisotropic shape, and total intensity) is found to differ significantly. The channel leading to H2 + and O+ ions' ejection shows increased asymmetry compared to the other channel and is found to be dependent on excitation of overtones and combinations of vibrational modes as well as from the field's shape and intensity. The asymmetry (ß) of the channel leading to the release of a H+ and an OH+ ions is far less sensitive to the experimental parameters. Inspection of the individual OH+ peak's dependence on phase reveals information on the effect of the field's profile, which is unclear when asymmetry (ß) is inspected.

Controlling intramolecular hydrogen migration by asymmetric laser fields: the water case.

Hydrogen and deuterium intramolecular migration in water's isotopomer dications has been found to depend on the wavelength of the laser used for the excitation. This is imprinted in H2+ and D2+ fragment ions' observation in the mass spectra induced by single color fs laser irradiation with 800 nm ≤λ≤ 1570 nm. Based on these findings, experiments with ω/2ω asymmetric laser fields (1400/700 nm) have been performed. The dissociation channels of the dications exhibit different dependence on the phase between the ω and 2ω components of the field thus offering an ability for controlling the fragmentation. For the interpretation of these observations, a tunneling mechanism is invoked.

The role of CN and CO ligands in the vibrational relaxation dynamics of model compounds of the [FeFe]-hydrogenase enzyme.

The vibrational dynamics of (µ-propanedithiolate)Fe(2)(CO)(4)(CN)(2)(2-), a model compound of the active site of the [FeFe]-hydrogenase enzyme, have been examined via ultrafast 2D-IR spectroscopy. The results indicate that the vibrational coupling between the stretching modes of the CO and CN ligands is small and restricted to certain modes but the slow growth of off-diagonal peaks is assigned to population transfer processes occurring between these modes on timescales of 30-40 ps. Analysis of the dynamics in concert with anharmonic density functional theory simulations shows that the presence of CN ligands alters the vibrational relaxation dynamics of the CO modes in comparison to all-carbonyl model systems and suggests that the presence of these ligands in the enzyme may be an important feature in terms of directing the vibrational relaxation mechanism.

Femtosecond to microsecond photochemistry of a [FeFe]hydrogenase enzyme model compound.

The photochemistry and dynamics of a model compound of the active site of the [FeFe]hydrogenase enzyme system have been studied on a wide range of time scales using a unique combination of femtosecond time-resolved infrared spectroscopy, nanosecond time-resolved infrared spectroscopy, and steady-state UV-FTIR methods. Using three different solvents, heptane, acetonitrile, and cyanoheptane, we have observed the rapid formation of solvent adduct species from the first solvation shell of the solute following photolysis of a carbonyl ligand and global fitting techniques have been employed to provide new insights into the ultrafast dynamics of this process. In addition, the use of solvent mixtures has enabled the observation of competitive ligand substitution processes at the newly created coordination site on time scales of a few nanoseconds, shedding new light on the chemical behavior of these enzyme models.