The slow photo-induced CO release of -phthaloylglycine.

Carboxylic acids and carboxylates may release CO upon oxidation. The oxidation can be conducted electrochemically as in the Kolbe synthesis or by a suitable oxidant. In -phthaloylglycine (PG), the photo-excited phthalimide chromophore acts as an oxidant.

Time-Resolved Ion Mobility Mass Spectrometry to Solve Conformational Changes in a Cryptochrome.

Many biological mechanisms rely on the precise control of conformational changes in proteins. Understanding such dynamic processes requires methods for determining structures and their temporal evolution. In this study, we introduce a novel approach to time-resolved ion mobility mass spectrometry.

Iminothioindoxyl Donors with Exceptionally High Cross Section for Protein Vibrational Energy Transfer.

Various protein functions are related to vibrational energy transfer (VET) as an important mechanism. The underlying transfer pathways can be experimentally followed by ultrafast Vis-pump/IR-probe spectroscopy with a donor-sensor pair of non-canonical amino acids (ncAAs) incorporated in a protein. However, so far only one donor ncAA, azulenylalanine (AzAla), exists, which suffers from a comparably low Vis extinction coefficient.

Choose your leaving group: selective photodeprotection in a mixture of HP-caged compounds by VIPER excitation.

Photocages are light-triggerable molecular moieties that can locally release a pre-determined leaving group (LG). Finding a suitable photocage for a particular application may be challenging, as the choice may be limited by for instance the optical or physicochemical properties of the system. Using more than one photocage to release different LGs in a reaction mixture may even be more difficult.

Vibrationally resolved two-photon electronic spectra including vibrational pre-excitation: Theory and application to VIPER spectroscopy with two-photon excitation.

Following up on our previous work on vibrationally resolved electronic absorption spectra including the effect of vibrational pre-excitation [von Cosel et al., J. Chem.

A Triplet Label Extends Two-Dimensional Infrared Spectroscopy from Pico- to Microseconds.

In conventional two-dimensional infrared (2D-IR) spectroscopy, the inherently short vibrational lifetimes limit the time window to observe molecular dynamics typically to tens of picoseconds. The rather complex dynamics of organized molecular systems (e.g.

Femtosecond-to-millisecond mid-IR spectroscopy of photoactive yellow protein uncovers structural micro-transitions of the chromophore's protonation mechanism.

Protein structural dynamics can span many orders of magnitude in time. Photoactive yellow protein's (PYP) reversible photocycle encompasses picosecond isomerization of the light-absorbing chromophore as well as large scale protein backbone motions occurring on a millisecond timescale. Femtosecond-to-millisecond time-resolved mid-infrared spectroscopy is employed here to uncover structural details of photocycle intermediates up to chromophore protonation and the first structural changes leading to the formation of the partially unfolded signaling state pB.

Versatile Vibrational Energy Sensors for Proteins.

Vibrational energy transfer (VET) is emerging as key mechanism for protein functions, possibly playing an important role for energy dissipation, allosteric regulation, and enzyme catalysis. A deep understanding of VET is required to elucidate its role in such processes. Ultrafast VIS-pump/IR-probe spectroscopy can detect pathways of VET in proteins.

Ultrafast Photoconversion Dynamics of the Knotless Phytochrome Cph2.

The family of phytochrome photoreceptors contains proteins with different domain architectures and spectral properties. Knotless phytochromes are one of the three main subgroups classified by their distinct lack of the PAS domain in their photosensory core module, which is in contrast to the canonical PAS-GAF-PHY array. Despite intensive research on the ultrafast photodynamics of phytochromes, little is known about the primary kinetics in knotless phytochromes.

Temperature-Dependent Low-Frequency Modes in the Active Site of Bovine Carbonic Anhydrase II Probed by 2D-IR Spectroscopy.

Enzyme catalysis achieves tremendous rate accelerations. Enzyme reaction centers provide a constraint geometry that preferentially binds an activated form of the substrate and thus lowers the energy barrier. However, this transition state picture neglects the flexibility of proteins and its role in enzymatic catalysis.

Through bonds or contacts? Mapping protein vibrational energy transfer using non-canonical amino acids.

Vibrational energy transfer (VET) is essential for protein function. It is responsible for efficient energy dissipation in reaction sites, and has been linked to pathways of allosteric communication. While it is understood that VET occurs via backbone as well as via non-covalent contacts, little is known about the competition of these two transport channels, which determines the VET pathways.

Lessons from combined experimental and theoretical examination of the FTIR and 2D-IR spectroelectrochemistry of the amide I region of cytochrome c.

Amide I difference spectroscopy is widely used to investigate protein function and structure changes. In this article, we show that the common approach of assigning features in amide I difference signals to distinct secondary structure elements in many cases may not be justified. Evidence comes from Fourier transform infrared (FTIR) and 2D-IR spectroelectrochemistry of the protein cytochrome c in the amide I range, in combination with computational spectroscopy based on molecular dynamics (MD) simulations.

Local dynamics of the photo-switchable protein PYP in ground and signalling state probed by 2D-IR spectroscopy of -SCN labels.

Incorporation of minimally perturbative vibrational probes into proteins allows combination of the femtosecond time resolution of two dimensional infrared (2D-IR) spectroscopy with a spatial resolution on the level of single side chains. Here, we apply the thiocyanate (-SCN) label introduced by the cyanylation of cysteine to probe local dynamics in the photo-switchable protein PYP. We incorporated the -SCN label into five positions of the protein structure including PYP's core region, its solvent exposed surface and the chromophore-binding pocket.

Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction.

Vibrational spectroscopy is an essential tool in chemical analyses, biological assays, and studies of functional materials. Over the past decade, various coherent nonlinear vibrational spectroscopic techniques have been developed and enabled researchers to study time-correlations of the fluctuating frequencies that are directly related to solute-solvent dynamics, dynamical changes in molecular conformations and local electrostatic environments, chemical and biochemical reactions, protein structural dynamics and functions, characteristic processes of functional materials, and so on. In order to gain incisive and quantitative information on the local electrostatic environment, molecular conformation, protein structure and interprotein contacts, ligand binding kinetics, and electric and optical properties of functional materials, a variety of vibrational probes have been developed and site-specifically incorporated into molecular, biological, and material systems for time-resolved vibrational spectroscopic investigation.

Exploring the 2D-IR repertoire of the -SCN label to study site-resolved dynamics and solvation in the calcium sensor protein calmodulin.

The calcium sensor protein calmodulin is ubiquitous among eukaryotes. It translates intracellular Ca2+ influx (by a decrease of conformational flexibility) into increased target recognition affinity. Here we demonstrate that by using the IR reporter -SCN in combination with 2D-IR spectroscopy, global structure changes and local dynamics, degree of solvent exposure and protein-ligand interaction can be characterised in great detail.

Vibrational Lifetime of the SCN Protein Label in HO and DO Reports Site-Specific Solvation and Structure Changes During PYP's Photocycle.

The application of vibrational labels such as thiocyanate  (-S-C≡N) for studying protein structure and dynamics is thriving. Absorption spectroscopy is usually employed to obtain wavenumber and line shape of the label. An observable of great significance might be the vibrational lifetime, which can be obtained by pump probe or 2D-IR spectroscopy.

Following local light-induced structure changes and dynamics of the photoreceptor PYP with the thiocyanate IR label.

Photoactive Yellow Protein (PYP) is a bacterial blue light receptor that enters a photocycle after excitation. The intermediate states are formed on time scales ranging from femtoseconds up to hundreds of milliseconds, after which the signaling state with a lifetime of about 1 s is reached. To investigate structural changes and dynamics, we incorporated the SCN IR label at distinct positions of the photoreceptor via cysteine mutation and cyanylation.

Site-Resolved Observation of Vibrational Energy Transfer Using a Genetically Encoded Ultrafast Heater.

Allosteric information transfer in proteins has been linked to distinct vibrational energy transfer (VET) pathways in a number of theoretical studies. Experimental evidence for such pathways, however, is sparse because site-selective injection of vibrational energy into a protein, that is, localized heating, is required for their investigation. Here, we solved this problem by the site-specific incorporation of the non-canonical amino acid β-(1-azulenyl)-l-alanine (AzAla) through genetic code expansion.

Controlling Photochemistry via Isotopomers and IR Pre-excitation.

It is a photochemist's dream to be able to photoinduce a reaction of a specific molecular species in an ensemble of similar but not identical ones. The problem is that similar molecules often exhibit nearly identical UV-Vis absorption spectra, making them difficult or impossible to distinguish or to select spectroscopically. The ultrafast VIPER (VIbrationally Promoted Electronic Resonance) pulse sequence allows to pick a single species for electronic excitation based on its infrared spectrum.

Impact of Azidohomoalanine Incorporation on Protein Structure and Ligand Binding.

The impact of the incorporation of a non-natural amino acid (NNAA) on protein structure, dynamics, and ligand binding has not been studied rigorously so far. NNAAs are regularly used to modify proteins post-translationally in vivo and in vitro through click chemistry. Herein, structural characterisation of the impact of the incorporation of azidohomoalanine (AZH) into the model protein domain PDZ3 is examined by means of NMR spectroscopy and X-ray crystallography.

Ultrafast Light-Driven Substrate Expulsion from the Active Site of a Photoswitchable Catalyst.

The photoswitchable piperidine general base catalyst is a prototype structure for light control of catalysis. Its azobenzene moiety moves sterically shielding groups to either protect or expose the active site, thereby changing the basicity and hydrogen-bonding affinity of the compound. The reversible switching dynamics of the catalyst is probed in the infrared spectral range by monitoring hydrogen bond (HB) formation between its active site and methanol (MeOH) as HB donor.

Correction: Vibrational dynamics and solvatochromism of the label SCN in various solvents and hemoglobin by time dependent IR and 2D-IR spectroscopy.

Correction for 'Vibrational dynamics and solvatochromism of the label SCN in various solvents and hemoglobin by time dependent IR and 2D-IR spectroscopy' by Luuk J. G. W.