Ultrafast Backbone Protonation in Channelrhodopsin-1 Captured by Polarization Resolved Fs Vis-pump-IR-Probe Spectroscopy and Computational Methods

Multiscale QM/MM modelling of catalytic systems with ChemShell

Hybrid quantum mechanical/molecular mechanical (QM/MM) methods are a powerful computational tool for the investigation of all forms of catalysis, as they allow for an accurate description of reactions occurring at catalytic sites in the context of a complicated electrostatic environment. The scriptable computational chemistry environment ChemShell is a leading software package for QM/MM calculations, providing a flexible, high performance framework for modelling both biomolecular and materials catalysis. We present an overview of recent applications of ChemShell to problems in catalysis and review new functionality introduced into the redeveloped Python-based version of ChemShell to support catalytic modelling. These include a fully guided workflow for biomolecular QM/MM modelling, starting from an experimental structure, a periodic QM/MM embedding scheme to support modelling of metallic materials, and a comprehensive set of tutorials for biomolecular and materials modelling.

Ultrafast protein response in the Pfr state of Cph1 phytochrome

Photoisomerization is a fundamental process in several classes of photoreceptors. Phytochromes sense red and far-red light in their Pr and Pfr states, respectively. Upon light absorption, these states react via individual photoreactions to the other state. Cph1 phytochrome shows a photoisomerization of its phycocyanobilin (PCB) chromophore in the Pfr state with a time constant of 0.7 ps. The dynamics of the PCB chromophore has been described, but whether or not the apoprotein exhibits an ultrafast response too, is not known. Here, we compare the photoreaction of ¹³C/¹⁵N labeled apoprotein with unlabeled apoprotein to unravel ultrafast apoprotein dynamics in Cph1. In the spectral range from 1750 to 1620 cm^-1 we assigned several signals due to ultrafast apoprotein dynamics. A bleaching signal at 1724 cm^-1 is tentatively assigned to deprotonation of a carboxylic acid, probably Asp207, and signals around 1670 cm^-1 are assigned to amide I vibrations of the capping helix close to the chromophore. These signals remain after photoisomerization. The apoprotein dynamics appear upon photoexcitation or concomitant with chromophore isomerization. Thus, apoprotein dynamics occur prior to and after photoisomerization on an ultrafast time-scale. We discuss the origin of the ultrafast apoprotein response with the 'Coulomb hammer' mechanism, i.e. an impulsive change of electric field and Coulombic force around the chromophore upon excitation.

Time-resolved photoacoustics of channelrhodopsins: early energetics and light-driven volume changes

In biological photoreceptors, the energy stored in early transient species is a key feature to drive the photocycle or a chain of reactions. Time-resolved photoacoustics (PA) can explore the energy landscape of transient species formed within few ns after photoexcitation, as well as volumetric changes (ΔV) of these intermediates with respect to the parental state. In this work, PA identified these important parameters for several channelrhodopsins, namely CaChR1 from Chlamydomonas augustae and CrChR2 from Chlamydomonas reinhardtii and various variants. PA has access to the sub-ns formation of the early photoproduct P1 and to its relaxation, provided that this latter process occurs within a few μs. We found that ΔVP1 for CaChR1 is ca. 12 mL/mol, while it is much smaller for CrChR2 (4.7 mL/mol) and for H. salinarum bacteriorhodopsin (HsBR, ΔVK = 2.8 mL/mol). PA experiments on variants strongly indicate that part of this large ΔVP1 value for CaChR1 is caused by the protonation dynamics of the Schiff base counterion complex involving E169 and D299. PA data further show that the energy level of P1 is higher in CrChR2 (ca. 96 kJ/mol) than in CaChr1 (ca. 46 kJ/mol), comparable to the energy level of the K state of HsBR (60 kJ/mol). Instrumental to gain these molecular values from the raw PA data was the estimation of the quantum yield (Φ) for P1 formation via transient spectroscopy; for both channelrhodopsins, ΦP2 was evaluated as ca. 0.4.

Graphical Abstract

High-precision background correction and artifact suppression for ultrafast spectroscopy by quasi-simultaneous measurements in a split-sample cell

Alternating acquisition of background and sample spectra is often employed in conventional Fourier-transform infrared spectroscopy or ultraviolet-visible spectroscopy for accurate background subtraction. For example, for solvent background correction, typically a spectrum of a cuvette with solvent is measured and subtracted from a spectrum of a cuvette with solvent and solute. Ultrafast spectroscopies, though, come with many peculiarities that make the collection of well-matched, subtractable background and sample spectra challenging. Here, we present a demountable split-sample cell in combination with a modified Lissajous scanner to overcome these challenges. It allows for quasi-simultaneous measurements of background and sample spectra, mitigating the effects of drifts of the setup and maintaining the beam and sample geometry when swapping between background and sample measurements. The cell is moving between subsequent laser shots to refresh the excited sample volume. With less than 45 μl of solution for 150 μm optical thickness, sample usage is economical. Cell assembly is a key step and covered in an illustrated protocol.

Impact of Ultrafast Electric Field Changes on Photoreceptor Protein Dynamics

Studies on photoreceptors provide a wealth of information on cofactor and protein dynamics on the microsecond to seconds time-scale. Up to now, ultrafast dynamics addresses mainly the cofactor or chromophore, but ultrafast protein dynamics are poorly understood. Increasing evidence show that protein responses can occur even faster than the cofactor dynamics. The causal reason for the ultrafast protein response cannot be explained by the localized cofactor excitation or its excited-state decay, alone. We propose a Coulomb interaction mechanism started by a shock wave and stabilized by a dipole moment change at least partially responsible for coherent oscillations in proteins, protonation changes, water dislocations, and protein changes prior to and beyond chromophore's excited-state decay. Photoexcitation changes the electron density distribution of the chromophore within a few femtoseconds: The Coulomb shock wave affects polar groups, hydrogen bonds, and protein bound water molecules. The process occurs on a time-scale even faster than excited-state decay of the chromophore. We discuss studies on selected photoreceptors in light of this mechanism and its impact on a detailed understanding of protein dynamics.

Novel nano network trigonal prismatic Ba2CoO4-deficient BaCoO3 for high-affinity sorption of radiolanthanide elements of biomedical applications: synthesis and sorption studies

Nano trigonal prismatic Ba₂CoO₄ with hierarchical structure and deficient BaCoO₃ with columnar structure have been prepared at low temperatures (400 [BC4] and 500 [BC5]) °C/3h using green method. X-ray diffraction (XRD) results demonstrate the presence of enriched Ba₂CoO₄ phase at 400 °C and multiphase structures: BaCoO₃, BaCoO_3-δ, and Co₃O₄ with a decrease in the amount of Ba₂CoO₄ at 500 °C. The prepared powders are characterized by a high specific surface area (SSA) values which are reflected to the mode of synthesis that leads to produce materials with massive active sites. The SSA of BC4 is higher than that of BC5 which can be correlated to the difference in the microstructure analysis of BC4 and BC5 as given from scanning electron microscope (SEM) and high-resolution transmission electron microscope (HRTEM) studies. Electron spin resonance (ESR) spectroscopy as an effective method for the characterization of vacancy-rich nanostructures indicates that the presence of oxygen vacancies is related mainly to BaCoO₃, BaCoO_3-δ, and Co₃O₄ phases while the effective oxygen vacancies is in BaCoO₃ and BaCoO_3-δ. The nanocrystalline structures of BC4 and BC5 as novel nano-adsorbents are the first time to be tested. Production of Gd radioisotopes through ^natGd(n,γ)^153,159,161Gd and carrier-free ¹⁶¹Tb through ¹⁶⁰Gd(n,γ,) ¹⁶¹Gd [Formula: see text] ¹⁶¹Tb are achieved at 2nd Egyptian nuclear research reactor (ETRR-2). Preliminary sorption study of Gd radioisotopes (represent the lanthanide elements) shows a promising material for the application in the separation and removal of lanthanide elements. The results demonstrated that the fast interaction and efficient sorption of lanthanides ions are based on the novel synthesized nanomaterial that can be considered for the upscale application in this field.