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Compared with batch and vapor diffusion methods, counter diffusion can generate larger and higher‐quality protein crystals yielding improved diffraction data and higher‐resolution structures. Typically, counter‐diffusion experiments are conducted in elongated chambers, such as glass capillaries, and the crystals are either directly measured in the capillary or extracted and mounted at the X‐ray beamline. Despite the advantages of counter‐diffusion protein crystallization, there are few fixed‐target devices that utilize counter diffusion for crystallization. In this article, different designs of user‐friendly counter‐diffusion chambers are presented which can be used to grow large protein crystals in a 2D polymer microfluidic fixed‐target chip. Methods for rapid chip fabrication using commercially available thin‐film materials such as Mylar, propylene and Kapton are also detailed. Rules of thumb are provided to tune the nucleation and crystal growth to meet users' needs while minimizing sample consumption. These designs provide a reliable approach to forming large crystals and maintaining their hydration for weeks and even months. This allows ample time to grow, select and preserve the best crystal batches before X‐ray beam time. Importantly, the fixed‐target microfluidic chip has a low background scatter and can be directly used at beamlines without any crystal handling, enabling crystal quality to be preserved. The approach is demonstrated with serial diffraction of photoactive yellow protein, yielding 1.32 Å resolution at room temperature. Fabrication of this standard microfluidic chip with commercially available thin films greatly simplifies fabrication and provides enhanced stability under vacuum. These advances will further broaden microfluidic fixed‐target utilization by crystallographers. [ABSTRACT FROM AUTHOR]

Another way to access interfacial dynamics is to study vibrational transitions localized at an interface as reported by Lee I et al. i ,[11] who use the ester carbonyl of model lipids in bilayers in conjunction with MD simulations to characterize hydration structural dynamics. Yang I et al. i [22] have investigated an energetic material, cyclotetramethylene tetranitramine (HMX), using ultrafast transient absorption and 2D-IR spectroscopy of the nitro stretch as a probe, revealing structural dynamics as well as vibrational energy transfer. Solowan I et al. i [4] study azulene using action-based 2D spectroscopy in both the liquid and gas phases, finding differences in the energetics and the rates of conical intersection (CI) and internal conversion in the two conditions. The amide I mode of peptides and proteins offers a powerful means of accessing protein structural dynamics, and the contribution from Tan I et al. i [12] shows how the vibrational anharmonicity is a sensitive probe of protein-water coupling. [Extracted from the article]

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. The data show that a commonly thought stable transient photocycle intermediate is actually formed after a sequence of several smaller structural changes. We provide residue-specific spectroscopic evidence that protonation of the chromophore on a few hundreds of microseconds timescale is delayed with respect to deprotonation of the nearby E46 residue. That implies that the direct proton donor is not E46 but most likely a water molecule. Such details may assist the ongoing photocycle and protein folding simulation efforts on the complex and wide time-spanning photocycle of the model system PYP. [ABSTRACT FROM AUTHOR]

Photoactive yellow protein (PYP) is a signaling protein whose internal p-coumaric acid chromophore undergoes reversible, light-induced trans-to-cis isomerization, which triggers a sequence of structural changes that ultimately lead to a signaling state. Since its discovery nearly 40 years ago, PYP has attracted much interest and has become one of the most extensively studied proteins found in nature. The method of time-resolved crystallography, pioneered by Keith Moffat, has successfully characterized intermediates in the PYP photocycle at near atomic resolution over 12 decades of time down to the sub-picosecond time scale, allowing one to stitch together a movie and literally watch a protein as it functions. But how close to reality is this movie? To address this question, results from numerous complementary time-resolved techniques including x-ray crystallography, x-ray scattering, and spectroscopy are discussed. Emerging from spectroscopic studies is a general consensus that three time constants are required to model the excited state relaxation, with a highly strained ground-state cis intermediate formed in less than 2.4 ps. Persistent strain drives the sequence of structural transitions that ultimately produce the signaling state. Crystal packing forces produce a restoring force that slows somewhat the rates of interconversion between the intermediates. Moreover, the solvent composition surrounding PYP can influence the number and structures of intermediates as well as the rates at which they interconvert. When chloride is present, the PYP photocycle in a crystal closely tracks that in solution, which suggests the epic movie of the PYP photocycle is indeed based in reality. [ABSTRACT FROM AUTHOR]

Time-resolved crystallography (TRX) is a method designed to investigate functional motions of biological macromolecules on all time scales. Originally a synchrotron-based method, TRX is enabled by the development of TR Laue crystallography (TRLX). TR serial crystallography (TR-SX) is an extension of TRLX. As the foundations of TRLX were evolving from the late 1980s to the turn of the millennium, TR-SX has been inspired by the development of Free Electron Lasers for hard X-rays. Extremely intense, ultrashort x-ray pulses could probe micro and nanocrystals, but at the same time, they inflicted radiation damage that necessitated the replacement by a new crystal. Consequently, a large number of microcrystals are exposed to X-rays one by one in a serial fashion. With TR-SX methods, one of the largest obstacles of previous approaches, namely, the unsurmountable challenges associated with the investigation of non-cyclic (irreversible) reactions, can be overcome. This article describes successes and transformative contributions to the TRX field by Keith Moffat and his collaborators, highlighting two major projects on protein photoreceptors initiated in the Moffat lab at the turn of the millennium. [ABSTRACT FROM AUTHOR]

This article offers insights into PAS domains, which are sensor domains found in various signaling proteins and play a crucial role in signal transduction pathways. It discusses the origins and evolution of PAS domains across different organisms, highlighting their potential as drug targets for various diseases, including cancer.

We successfully created a composite photonic structure out of porous silicon (PSi) microcavities doped by the photochromic protein, photoactive yellow protein (PYP). Massive incorporation of the protein molecules into the pores was substantiated by a 30 nm shift of the resonance dip upon functionalization, and light-induced reflectance changes of the device due to the protein photocycle were recorded. Model calculations for the photonic properties of the device were consistent with earlier results on the nonlinear optical properties of the protein, whose degree of incorporation into the PSi structure was also estimated. The successful proof-of-concept results are discussed in light of possible practical applications in the future. [ABSTRACT FROM AUTHOR]

Chiral and achiral vibrational sum-frequency generation (VSFG) spectroscopy was performed in the 1400–1700 and 2800–3800 cm−1 range to study the interfacial structure of photoactive yellow protein (PYP) adsorbed on polyethyleneimine (PEI) and poly-l-glutamic acid (PGA) surfaces. Nanometer-thick polyelectrolyte layers served as the substrate for PYP adsorption, with 6.5-pair layers providing the most homogeneous surfaces. When the topmost material was PGA, it acquired a random coil structure with a small number of β2-fibrils. Upon adsorption on oppositely charged surfaces, PYP yielded similar achiral spectra. However, the VSFG signal intensity increased for PGA surfaces with a concomitant redshift of the chiral Cα-H and N–H stretching bands, suggesting increased adsorption for PGA compared to PEI. At low wavenumbers, both the backbone and the side chains of PYP induced drastic changes to all measured chiral and achiral VSFG spectra. Decreasing ambient humidity led to the loss of tertiary structure with a re-orientation of α-helixes, evidenced by a strongly blue-shifted chiral amide I band of the β-sheet structure with a shoulder at 1654 cm−1. Our observations indicate that chiral VSFG spectroscopy is not only capable of determining the main type of secondary structure of PYP, i.e., β-scaffold, but is also sensitive to tertiary protein structure. [ABSTRACT FROM AUTHOR]

A fundamental problem in biological sciences is understanding how macromolecular machines work and how the structural changes of a molecule are connected to its function. Time-resolved techniques are vital in this regard and essential for understanding the structural dynamics of biomolecules. Timeresolved small- and wide-angle X-ray solution scattering has the capability to provide a multitude of information about the kinetics and global structural changes of molecules under their physiological conditions. However, standard protocols for such time-resolved measurements often require significant amounts of sample, which frequently render time-resolved measurements impossible. A cytometry-type sheath co-flow cell, developed at the BioCARS 14-ID beamline at the Advanced Photon Source, USA, allows time-resolved pump-probe X-ray solution scattering measurements to be conducted with sample consumption reduced by more than ten times compared with standard sample cells and protocols. The comparative capabilities of the standard and coflow experimental setups were demonstrated by studying time-resolved signals in photoactive yellow protein. [ABSTRACT FROM AUTHOR]

We report an extension of a hybrid polarizable embedding method incorporating solvent effects in the calculations of two-photon absorption (2PA) cross sections. We employ the equation-of-motion coupled-cluster singles and doubles method for excitation energies (EOM-EE-CCSD) for the quantum region and the effective fragment potential (EFP) method for the classical region. We also introduce a rigorous metric based on 2PA transition densities for assessing the domain of applicability of QM/MM (quantum mechanics/molecular mechanics) schemes for calculating 2PA cross sections. We investigate the impact of the environment on the 2PA cross sections of low-lying transitions in microhydrated clusters of para-nitroaniline, thymine, and the deprotonated anionic chromophore of photoactive yellow protein (PYPb). We assess the performance of EOM-EE-CCSD/EFP by comparing the 2PA cross sections against full QM calculations as well as against the non-polarizable QM/MM electrostatic embedding approach. We demonstrate that the performance of QM/EFP improves when few explicit solvent molecules are included in the QM subsystem. We correlate the errors in the 2PA cross sections with the errors in the key electronic properties—identified by the analysis of 2PA natural transition orbitals and 2PA transition densities—such as excitation energies, transition moments, and dipole-moment differences between the initial and final states. Finally, using aqueous PYPb, we investigate the convergence of 2PA cross sections to bulk values. [ABSTRACT FROM AUTHOR]

Many physical phenomena must be accounted for to accurately model solution-phase optical spectral line shapes, from the sampling of chromophore-solvent configurations to the electronic-vibrational transitions leading to vibronic fine structure. Here we thoroughly explore the role of nuclear quantum effects, direct and indirect solvent effects, and vibronic effects in the computation of the optical spectrum of the aqueously solvated anionic chromophores of green fluorescent protein and photoactive yellow protein. By analyzing the chromophore and solvent configurations, the distributions of vertical excitation energies, the absorption spectra computed within the ensemble approach, and the absorption spectra computed within the ensemble plus zero-temperature Franck-Condon approach, we show how solvent, nuclear quantum effects, and vibronic transitions alter the optical absorption spectra. We find that including nuclear quantum effects in the sampling of chromophore-solvent configurations using ab initio path integral molecular dynamics simulations leads to improved spectral shapes through three mechanisms. The three mechanisms that lead to line shape broadening and a better description of the high-energy tail are softening of heavy atom bonds in the chromophore that couple to the optically bright state, widening the distribution of vertical excitation energies from more diverse solvation environments, and redistributing spectral weight from the 0-0 vibronic transition to higher energy vibronic transitions when computing the Franck-Condon spectrum in a frozen solvent pocket. The absorption spectra computed using the combined ensemble plus zero-temperature Franck-Condon approach yield significant improvements in spectral shape and width compared to the spectra computed with the ensemble approach. Using the combined approach with configurations sampled from path integral molecular dynamics trajectories presents a significant step forward in accurately modeling the absorption spectra of aqueously solvated chromophores. [ABSTRACT FROM AUTHOR]

The article presents a study which demonstrated the need for conformational ensembles to understand function, using the enzyme ketosteroid isomerase (KSI) as an example. Topics discussed include KSI structure formation and the need for ensemble function, KSI expression and purification, and protein crystallization and x-ray data collection.

Keywords: light-regulation; non-canonical amino acids; optogenetics; photopharmacology; photoxenoprotein engineering; proteins EN light-regulation non-canonical amino acids optogenetics photopharmacology photoxenoprotein engineering proteins 573 613 41 04/12/22 20220401 NES 220401 Introduction Light plays a decisive role for most forms of life as it stimulates various essential processes in organisms. In many cases, the photoswitchable ligand is bioconjugated to a self-labeling protein tag such as the SNAP tag, which is genetically fused with either the target protein or an auxiliary protein interacting with the target protein ([174]; [83]). (B) The four main strategies of hybrid protein optogenetics including transduction of conformational changes, steric decaging of proteins or peptides, homotypic association/dissociation and heterotypic association/dissociation of heterocomplexes or split proteins. A generally applicable protocol has hitherto not been established due to the fact that each protein is individual; a strategy, which facilitates a high LRF for one protein, might not be able to attain photocontrol of another protein at all. The target proteins must further be specific for the cells that are the cause of the disease, e.g., overproduced proteins in tumor cells or proteins that solely exist in bacteria. [Extracted from the article]

Traditional macromolecular crystallography (MX) and recently spotlighted cryogenic electron microscopy (Cryo-EM) techniques have contributed greatly to the development of macromolecule structures and the related fields [[1], [3], [5], [7]]. Starting with serial femtosecond crystallography (SFX) using an X-ray free electron laser (XFEL) [[11]], the SX technique is widely applied to serial synchrotron crystallography (SSX) using synchrotron X-rays [[16]], which can aid in obtaining in-depth and accurate structural information. Kim and Nam reported experiments on serial crystallography using pink-beam X-rays in PLS-II [[25]]. 10.3390/cryst12020138 24 Nam K.H. Processing of Multicrystal Diffraction Patterns in Macromolecular Crystallography Using Serial Crystallography Programs. [Extracted from the article]

Photo‐control of affinity reagents offers a general approach for high‐resolution spatiotemporal control of diverse molecular processes. In an effort to develop general design principles for a photo‐controlled affinity reagent, we took a structure‐based approach to the design of a photoswitchable Z‐domain, among the simplest of affinity reagent scaffolds. A chimera, designated Z‐PYP, of photoactive yellow protein (PYP) and the Z‐domain, was designed based on the concept of mutually exclusive folding. NMR analysis indicated that, in the dark, the PYP domain of the chimera was folded, and the Z‐domain was unfolded. Blue light caused loss of structure in PYP and a two‐ to sixfold change in the apparent affinity of Z‐PYP for its target as determined using size exclusion chromatography, UV‐Vis based assays, and enyzme‐linked immunosorbent assay (ELISA). A thermodynamic model indicated that mutations to decrease Z‐domain folding energy would alter target affinity without loss of switching. This prediction was confirmed experimentally with a double alanine mutant in helix 3 of the Z‐domain of the chimera (Z‐PYP‐AA) showing >30‐fold lower dark‐state binding and no loss in switching. The effect of decreased dark‐state binding affinity was tested in a two‐hybrid transcriptional control format and enabled pronounced light/dark differences in yeast growth in vivo. Finally, the design was transferable to the αZ‐Taq affibody enabling tunable light‐dependent binding both in vitro and in vivo to the Z‐Taq target. This system thus provides a framework for the focused development of light switchable affibodies for a range of targets. [ABSTRACT FROM AUTHOR]

The article presents a study that explores tracking the Adenosine triphosphate (ATP)-binding response in adenylate kinase in real time. It mentions about time-resolved x-ray solution scattering (TR-XSS) to visualize structural changes in the Escherichia coli adenylate kinase (AdK) enzyme upon laser-induced activation of a protected ATP substrate.

Summary: Molecular switches alterable between two stable states by environmental stimuli, such as light and temperature, offer the potential for controlling biological functions. Here, we report a circular photoswitchable protein complex made of multiple protein molecules that can rapidly and reversibly switch with significant conformational changes. The structural and photochromic properties of photoactive yellow protein (PYP) are harnessed to construct circular oligomer PYPs (coPYPs) of desired sizes. Considering the light-induced N-terminal protrusion of monomer PYP, we expected coPYPs would expand upon irradiation, but time-resolved X-ray scattering data reveal that the late intermediate has a pronounced light-induced contraction motion. This work not only provides an approach to engineering a novel protein-based molecular switch based on circular oligomers of well-known protein units but also demonstrates the importance of characterizing the structural dynamics of designed molecular switches.

A detailed theoretical analysis, based on extensive ab initio second-order approximate coupled cluster calculations, has been performed for the S1 potential energy surface (PES) of four photoactive yellow protein (PYP) chromophore derivatives that are hydrogen bonded with two water molecules and differ merely in the carbonyl substituent. The main focus is put on contrasting the isomerization properties of these four species in the S1 excited state, related to torsion around the chromophore's single and double carbon-carbon bonds. The analysis provides evidence of the different isomerization behavior of these four chromophore complexes, which relates to the difference in their carbonyl substituents. While a stable double-bond torsion pathway exists on the S1 PES of the chromophores bearing the -O-CH3 and -NH2 substituents, this is not the case for the -S-CH3 and -CH3 substituted species. The presence of the -S-CH3 group leads to a strong instability of the chromophore with respect to the single-bond twist, whereas in the case of the -CH3 substituent a crossing of the S1 and S2 PESs occurs, which perturbs the pathway. Based on this analysis, the key factors that support the double-bond torsion have been identified. These are (i) the hydrogen bonds at the phenolic oxygen of the chromophore, (ii) the weak electron-acceptor character of the carbonyl group, and (iii) the ethylene-like pattern of the torsion in the beginning of the process. Our results suggest that the interplay between these factors determines the chromophore's isomerization in the solvent environment and in the native PYP environment. [ABSTRACT FROM AUTHOR]

A combined quantum mechanical/molecular mechanical/continuum (QM/MM/C) style second order Møller-Plesset perturbation theory (MP2) method that incorporates induced dipole polarizable force field and induced surface charge continuum solvation model is established. The Z-vector method is modified to include induced dipoles and induced surface charges to determine the MP2 response density matrix, which can be used to evaluate MP2 properties. In particular, analytic nuclear gradient is derived and implemented for this method. Using the Assisted Model Building with Energy Refinement induced dipole polarizable protein force field, the QM/MM/C style MP2 method is used to study the hydrogen bonding distances and strengths of the photoactive yellow protein chromopore in the wild type and the Glu46Gln mutant. [ABSTRACT FROM AUTHOR]

We present simulations of one and two-dimensional infrared (2DIR) and stimulated resonance Raman (SRR) spectra of the dark state (pG) and early red-shifted intermediate (pR) of photoactive yellow protein (PYP). Shifts in the amide I and Glu46 COOH stretching bands distinguish between pG and pR in the IR absorption and 2DIR spectra. The one-dimensional SRR spectra are similar to the spontaneous RR spectra. The two-dimensional SRR spectra show large changes in cross peaks involving the C=O stretch of the two species and are more sensitive to the chromophore structure than 2DIR spectra.

The article presents a study comparing the crystallographic diffraction data collected by serial femtosecond and serial synchrotron crystallography for the proteins myoglobin and fluoroacetate dehalogenase. It discusses the two protein systems exploited to evaluate the differences in quality, radiation damage as a limiting factor in achieving high-resolution structures at cryogenic temperatures, and protein expression and crystallization.

The structure of experimentally designed solar cells was optimized in terms of the photoactive layer thickness for both organic bulk heterojunction and hybrid perovskite solar cells. The photoactive layer thickness had a totally different behavior on the performance of the organic and hybrid solar cells. Analysis of the optical parameters using transfer matrix modeling within the Maxwell–Garnett effective refractive index model shows that light absorbance and exciton generation rate in the photoactive layer can be used to optimize the thickness range of the photoactive layer. Complete agreement between experimental and simulated data for solar cells with photoactive materials that have very different natures proves the validity of the proposed modeling method. The proposed simple method which is not time-consuming to implement permits to obtain a preliminary assessment of the reasonable range of layer thickness that will be needed for designing experimental samples. [ABSTRACT FROM AUTHOR]

This perspective article highlights the challenges in the theoretical description of photoreceptor proteins using multiscale modeling, as discussed at the CECAM workshop in Tel Aviv, Israel. The participants have identified grand challenges and discussed the development of new tools to address them. Recent progress in understanding representative proteins such as green fluorescent protein, photoactive yellow protein, phytochrome, and rhodopsin is presented, along with methodological developments. [ABSTRACT FROM AUTHOR]

Membrane-bound or cytosolic light-sensitive proteins, playing a crucial role in energy- and signal-transduction processes of various photosynthetic microorganisms, have been optimized for sensing or harvesting light by myriads of years of evolution. Upon absorption of a photon, they undergo a usually cyclic reaction series of conformations, and the accompanying spectro-kinetic events assign robust nonlinear optical (NLO) properties for these chromoproteins. During recent years, they have attracted a considerable interest among researchers of the applied optics community as well, where finding the appropriate NLO material for a particular application is a pivotal task. Potential applications have emerged in various branches of photonics, including optical information storage and processing, higher-harmonic and white-light continuum generation, or biosensorics. In our earlier work, we also raised the possibility of using chromoproteins, such as bacteriorhodopsin (bR), as building blocks for the active elements of integrated optical (IO) circuits, where several organic and inorganic photonic materials have been considered as active components, but so far none of them has been deemed ideal for the purpose. In the current study, we investigate the linear and NLO properties of biofilms made of photoactive yellow protein (PYP) and bR. The kinetics of the photoreactions are monitored by time-resolved absorption experiments, while the refractive index of the films and its light-induced changes are measured using the Optical Waveguide Lightmode Spectroscopy (OWLS) and Z-scan techniques, respectively. The nonlinear refractive index and the refractive index change of both protein films were determined in the green spectral range in a wide range of intensities and at various laser repetition rates. The nonlinear refractive index and refractive index change of PYP were compared to those of bR, with respect to photonics applications. Our results imply that the NLO properties of these proteins make them promising candidates for utilization in applied photonics, and they should be considered as valid alternatives for active components of IO circuits.

PYP-phytochrome related (Ppr) protein contains the two light sensor domains, photoactive yellow protein (PYP) and bacteriophytochrome (Bph), which mainly absorb blue and red light by the chromophores of p-coumaric acid (pCA) and biliverdin (BV), respectively. As a result, Ppr has the ability to photoactivate both domains together or separately. We investigated the photoreaction of each photosensor domain under different light irradiation conditions and clarified the inter-dependency between these domains. Within the first 10 s of blue light illumination, Ppr (Holo-Holo-Ppr) accompanied by both pCA and BV demonstrated spectrum changes reflecting PYPL accumulation, which can also be observed in Ppr containing only pCA (Holo-Apo-Ppr), and a fragment of Ppr lacking the C-terminal Bph domain. Although Holo-Apo-Ppr showed PYPL as a major photoproduct under blue light, as seen in the Bph-truncated Ppr, the equilibrium in the Holo-Holo-Ppr was shifted from PYPL to PYPM as the reaction progresses under blue light. Concomitantly, the spectrum of Bph exhibited subtle but distinguishable alteration. Together with the fact, it can be proposed that Bph with BV influences the photoreaction of PYP in Ppr, and vice versa. SAXS measurements revealed substantial tertiary structure changes in Holo-Holo-Ppr under continuous blue light irradiation within the first 5 min time domain. Interestingly, the changes in tertiary structure were partially suppressed by photoactivation of the Bph domain. These observations indicate that the photoreactions of the PYP and Bph domains are coupled with each other, and that the interplay realizes the structural switch, which might be involved in downstream signal transduction.

A combined quantum mechanical/molecular mechanical/continuum (QM/MMpol/C) style method is developed for time-dependent density functional theory (TDDFT, including long-range corrected TDDFT) method, induced dipole polarizable force field, and induced surface charge continuum model. Induced dipoles and induced charges are included in the TDDFT equations to solve for the transition energies, relaxed density, and transition density. Analytic gradient is derived and implemented for geometry optimization and molecular dynamics simulation. QM/MMpol/C style DFT and TDDFT methods are used to study the hydrogen bonding of the photoactive yellow protein chromopore in ground state and excited state. [ABSTRACT FROM AUTHOR]

Membrane-bound or cytosolic light-sensitive proteins, playing a crucial role in energy- and signal-transduction processes of various photosynthetic microorganisms, have been optimized for sensing or harvesting light by myriads of years of evolution. Upon absorption of a photon, they undergo a usually cyclic reaction series of conformations, and the accompanying spectro-kinetic events assign robust nonlinear optical (NLO) properties for these chromoproteins. During recent years, they have attracted a considerable interest among researchers of the applied optics community as well, where finding the appropriate NLO material for a particular application is a pivotal task. Potential applications have emerged in various branches of photonics, including optical information storage and processing, higher-harmonic and white-light continuum generation, or biosensorics. In our earlier work, we also raised the possibility of using chromoproteins, such as bacteriorhodopsin (bR), as building blocks for the active elements of integrated optical (IO) circuits, where several organic and inorganic photonic materials have been considered as active components, but so far none of them has been deemed ideal for the purpose. In the current study, we investigate the linear and NLO properties of biofilms made of photoactive yellow protein (PYP) and bR. The kinetics of the photoreactions are monitored by time-resolved absorption experiments, while the refractive index of the films and its light-induced changes are measured using the Optical Waveguide Lightmode Spectroscopy (OWLS) and Z-scan techniques, respectively. The nonlinear refractive index and the refractive index change of both protein films were determined in the green spectral range in a wide range of intensities and at various laser repetition rates. The nonlinear refractive index and refractive index change of PYP were compared to those of bR, with respect to photonics applications. Our results imply that the NLO properties of these proteins make them promising candidates for utilization in applied photonics, and they should be considered as valid alternatives for active components of IO circuits. [ABSTRACT FROM AUTHOR]

Understanding the connection between the motion of the nuclei in a molecule and the rearrangement of its electrons lies at the heart of chemistry. While many experimental methods have been developed to probe either the electronic or the nuclear structure on the timescale of atomic motion, very few have been able to capture both these changes in concert. Here, we use time-resolved photoelectron imaging to probe the isomerisation coordinate on the excited state of an isolated model chromophore anion of the photoactive yellow protein. By probing both the electronic structure changes as well as nuclear dynamics, we are able to uniquely measure isomerisation about a specific bond. Our results demonstrate that the photoelectron signal dispersed in time, energy and angle combined with calculations can track the evolution of both electronic and geometric structure along the adiabatic state, which in turn defines that chemical transformation. Resolving concerted nuclear and electronic motion in real-time is a primary goal in chemistry. The authors monitor nuclear and valence electronic dynamics in the excited state single-bond isomerisation of a chromophore of photoactive yellow protein, using time-resolved photoelectron imaging and electronic structure calculations. [ABSTRACT FROM AUTHOR]

Although widely used in the detection and characterization of protein–protein interactions, Y2H screening has been under-used for the engineering of new optogenetic tools or the improvement of existing tools. Here we explore the feasibility of using Y2H selection and screening to evaluate libraries of photoswitchable protein–protein interactions. We targeted the interaction between circularly permuted photoactive yellow protein (cPYP) and its binding partner binder of PYP dark-state (BoPD) by mutating a set of four surface residues of cPYP that contribute to the binding interface. A library of ~ 10,000 variants was expressed in yeast together with BoPD in a Y2H format. An initial selection for the cPYP/BoPD interaction was performed using a range of concentrations of the cPYP chromophore. As expected, the majority (> 90% of cPYP variants) no longer bound to BoPD. Replica plating was then used to evaluate the photoswitchability of the surviving clones. Photoswitchable cPYP variants with BoPD affinities equal to, or higher than, native cPYP were recovered in addition to variants with altered photocycles and binders that interacted with BoPD as apo-proteins. Y2H results reflected protein–protein interaction affinity, expression, photoswitchability, and chromophore uptake, and correlated well with results obtained both in vitro and in mammalian cells. Thus, by systematic variation of selection parameters, Y2H screens can be effectively used to generate new optogenetic tools for controlling protein–protein interactions for use in diverse settings. Unlabelled Image • A library of ~ 10,000 variants of photoactive yellow protein (PYP) was evaluated for binding to a partner protein Binder of PYP-Dark (BoPD) using a yeast two-hybrid approach. • By varying parameters of the two-hybrid selection, distinct photoswitchable behaviors were recovered including PYP variants with altered affinity, kinetics, and apo-state binding. • Phenotypes observed in yeast two-hybrid assays correlate well with results obtained in vitro and in mammalian cells. [ABSTRACT FROM AUTHOR]

Integrated optics (IO) is a field of photonics which focuses on manufacturing circuits similar to those in integrated electronics, but that work on an optical basis to establish means of faster data transfer and processing. Currently, the biggest task in IO is finding or manufacturing materials with the proper nonlinear optical characteristics to implement as active components in IO circuits. Using biological materials in IO has recently been proposed, the first material to be investigated for this purpose being the protein bacteriorhodopsin; however, since then, other proteins have also been considered, such as the photoactive yellow protein (PYP). In our current work, we directly demonstrate the all-optical switching capabilities of PYP films combined with an IO Mach–Zehnder interferometer (MZI) for the first time. By exploiting photoreactions in the reaction cycle of PYP, we also show how a combination of exciting light beams can introduce an extra degree of freedom to control the operation of the device. Based on our results, we discuss how the special advantages of PYP can be utilized in future IO applications.

The mechanism by which proteins are solvated in hydrated ionic liquids remains an open question. Herein, the photoexcitation dynamics of photoactive yellow protein dissolved in hydrated choline dihydrogen phosphate (Hy[ch][dhp]) were studied by transient absorption and transient grating spectroscopy. The photocyclic reaction of the protein in Hy[ch][dhp] was similar to that observed in the buffer solution, as confirmed by transient absorption spectroscopy. However, the structural change of the protein during the photocycle in Hy[ch][dhp] was found to be different from that observed in the buffer solution. The known change in the diffusion coefficient of the protein was apparently suppressed in high concentrations of [ch][dhp], plausibly due to stabilization of the secondary structure.

Non-valence states in neutral molecules (Rydberg states) have well-established roles and importance in photochemistry, however, considerably less is known about the role of non-valence states in photo-induced processes in anions. Here, femtosecond time-resolved photoelectron imaging is used to show that photoexcitation of the S1(ππ*) state of the methyl ester of deprotonated para-coumaric acid – a model chromophore for photoactive yellow protein (PYP) – leads to a bifurcation of the excited state wavepacket. One part remains on the S1(ππ*) state forming a twisted intermediate, whilst a second part leads to the formation of a non-valence (dipole-bound) state. Both populations eventually decay independently by vibrational autodetachment. Valence-to-non-valence internal conversion has hitherto not been observed in the intramolecular photophysics of an isolated anion, raising questions into how common such processes might be, given that many anionic chromophores have bright valence states near the detachment threshold. Photoactive biomolecules rely on chromophores whose photochemistry depends on the environment. Here, the excited state dynamics of a model for the anionic biochromophore in photoactive yellow protein is investigated by time-resolved photoelectron spectroscopy showing involvement of a non-valence state, and lack of E-Z isomerisation in the gas phase. [ABSTRACT FROM AUTHOR]

Labelling technologies developed over the past few years have changed the way of looking at biomolecules and have made a considerable contribution to our understanding of the functions and regulation of dynamic biological processes. One of the robust technologies employed to image proteins in a cellular environment is based on the use of chemical tags and their fluorescent probes, which provides flexibility in developing probes with a wide range of synthetic fluorophores. A variety of chemical tags, ranging from short amino acid sequences to small proteins, have been employed to generate protein-labelling systems. One such chemical tag is the photoactive yellow protein (PYP)-tag, which is a small bacterial protein, developed for the selective labelling and imaging of proteins. Herein, we briefly discuss the protein-labelling system developed based on PYP-tag technology, with a focus on the design strategy for PYP-tag labelling probes and their applications in protein imaging. [ABSTRACT FROM AUTHOR]

In this paper, the photocycle of the dried photoactive yellow protein film has been investigated in different humidity environments, in order to characterize its nonlinear optical properties for possible integrated optical applications. The light-induced spectral changes of the protein films were monitored by an optical multichannel analyser set-up, while the accompanying refractive index changes were measured with the optical waveguide lightmode spectroscopy method. To determine the number and kinetics of spectral intermediates in the photocycle, the absorption kinetic data were analysed by singular value decomposition and multiexponential fitting methods, whose results were used in a subsequent step of fitting a photocycle model to the data. The absorption signals of the films were found to be in strong correlation with the measured light-induced refractive index changes, whose size and kinetics imply that photoactive yellow protein may be a good alternative for utilization as an active nonlinear optical material in future integrated optical applications. [ABSTRACT FROM AUTHOR]

Based on a bacterial blue light photoreceptor, photoactive yellow protein (PYP), we have developed a photoresponsive protein module, Hpg5‐PYP, bearing five alkynyl groups as reactive sites. We constructed a yellow‐colored photoresponsive protein–polymer conjugate by using covalently bonded Hpg5‐PYP with poly(N,N‐dimethylacrylamide‐co‐2‐hydroxy‐3‐azidopropyl methacrylate) (DMA‐HAZPMA copolymer). Hpg5‐PYP retained photoreactivity towards blue‐light irradiation in the conjugate, and the conjugate showed a photoresponsive viscosity change upon irradiation with blue light at 25 °C. In contrast, a mixture of Hpg5‐PYP and DMA‐HAZPMA copolymer prepared for reference did not show any dependency of the viscosity on light irradiation, indicating the importance of crosslinking. [ABSTRACT FROM AUTHOR]

The article reports that fifth-order time-domain Raman spectroscopy of photoactive yellow protein (PYP), with the aim to visualize vibrational coupling in its excited state. The unveiled coupling suggests the importance of the low-frequency vibrational motion in the primary photoreaction of PYP highlighting the unique capability of this spectroscopic approach for studying ultrafast reaction dynamics.

The role and existence of low-barrier hydrogen bonds (LBHBs) in enzymatic and protein activity has been largely debated. An interesting case is that of the photoactive yellow protein (PYP). In this protein, two short HBs adjacent to the chromophore, p-coumaric acid (pCA), have been identified by X-ray and neutron diffraction experiments. However, there is a lack of agreement on the chemical nature of these H-bond interactions. Additionally, no consensus has been reached on the presence of LBHBs in the active site of the protein, despite various experimental and theoretical studies having been carried out to investigate this issue. In this work, we perform a computational study that combines classical and density functional theory (DFT)-based quantum mechanical/molecular mechanical (QM/MM) simulations to shed light onto this controversy. Furthermore, we aim to deepen our understanding of the chemical nature and dynamics of the protons involved in the two short hydrogen bonds that, in the dark state of PYP, connect pCA with the two binding pocket residues (E46 and Y42). Our results support the existence of a strong LBHB between pCA and E46, with the H fully delocalized and shared between both the carboxylic oxygen of E46 and the phenolic oxygen of pCA. Additionally, our findings suggest that the pCA interaction with Y42 can be suitably described as a typical short ionic H-bond of moderate strength that is fully localized on the phenolic oxygen of Y42.

Photoactive yellow protein (PYP) has a characteristic hydrogen bond (H bond) between p-coumaric acid chromophore and Glu46, whose OH bond length has been observed to be 1.21 Å by the neutron diffraction technique [Proc. Natl. Acad. Sci. 106, 440–4]. Although it has been expected that such a drastic elongation of the OH bond could be caused by the quantum effect of the hydrogen nucleus, previous theoretical computations including the nuclear quantum effect have so far underestimated the bond length by more than 0.07 Å. To elucidate the origin of the difference, we performed a vibrational analysis of the H bond on potential energy curve with O…O distance of 2.47 Å on the equilibrium structure, and that with O…O distance of 2.56 Å on the experimental crystal structure. While the vibrationally averaged OH bond length for equilibrium structure was underestimated, the corresponding value for crystal structure was in reasonable agreement with the corresponding experimental values. The elongation of the O…O distance by the quantum mechanical or thermal fluctuation would be indispensable for the formation of a low-barrier hydrogen bond in PYP.

Photoactive proteins that efficiently and selectively transfer light energy into a physical response are ubiquitous in nature. The small molecule chromophores that lie at the heart of these processes often exist as closed-shell anions following deprotonation in proton-transfer reactions. This review highlights the important role that anion photoelectron spectroscopy, combined with computational chemistry calculations, is playing in improving our understanding of the electronic structure and relaxation dynamics of these protein chromophores. We discuss key aspects of anion photoelectron spectroscopy. We then review recent anion photoelectron spectroscopy studies of the deprotonated chromophore anions found in green fluorescent protein (GFP), photoactive yellow protein (PYP) and the deprotonated luciferin anion found in the luciferase enzyme. [ABSTRACT FROM AUTHOR]

Normal mode analysis provides a powerful tool in biophysical computations. Particularly, we shed light on its application to protein properties because they directly lead to biological functions. As a result of normal mode analysis, the protein motion is represented as a linear combination of mutually independent normal mode vectors. It has been widely accepted that the large amplitude motions throughout the entire protein molecule can be well described with a few low-frequency normal modes. Furthermore, it is possible to represent the effect of external perturbations, e.g., ligand binding, hydrostatic pressure, as the shifts of normal mode variables. Making use of this advantage, we are able to explore mechanical properties of proteins such as Young’s modulus and compressibility. Within thermally fluctuating protein molecules under physiological conditions, tightly packed amino acid residues interact with each other through heat and energy exchanges. Since the structure and dynamics of protein molecules are highly anisotropic, the flow of energy and heat should also be anisotropic. Based on the harmonic approximation of the heat current operator, it is possible to analyze the communication map of a protein molecule. By using this method, the energy transfer pathways of photoactive yellow protein were calculated. It turned out that these pathways are similar to those obtained via the Green-Kubo formalism with equilibrium molecular dynamics simulations, indicating that normal mode analysis captures the intrinsic nature of the transport properties of proteins. [ABSTRACT FROM AUTHOR]

Molecular and supramolecular‐based systems and materials that can perform predetermined functions in response to light stimulation have been extensively studied in the past three decades. Their investigation continues to be a highly stimulating topic of chemical research, not only because of the inherent scientific value related to a bottom‐up approach to functional nanostructures, but also for the prospective applications in diverse fields of technology and medicine. Light is an important tool in this context, as it can be conveniently used both for supplying energy to the system and for probing its states and transformations. In this microreview we recall some basic aspects of light‐induced processes in (supra)molecular assemblies, and discuss their exploitation to implement novel functionalities with nanostructured devices, machines and materials. To this aim we illustrate a few examples from our own recent work, which are meant to illustrate the trends of current research in the field. A bright future: the combination of the concepts and tools of photophysics and photochemistry with appropriately designed molecular and supramolecular systems can lead to the realization of nanoscale devices, machines and materials that can execute sophisticated functions in response to light stimulation. [ABSTRACT FROM AUTHOR]

Abstract The direct conversion of sunlight into chemical energy via photosynthesis is a unique capability of plants and some bacterial species. Aimed at mimicking this energy conversion process, the combination of inorganic substrates and organic photoactive proteins into an artificial biohybrid system is of a great interest for artificial bio-photovoltaic applications. It also allows to better understand charge transfer processes involved in the photosynthetic chain. In this work, single layer graphene (SLG) and multilayer graphene (MLG) electrodes are used as a platform for the immobilization of reaction centers (RCs) from purple bacteria Rhodobacter sphaeroides , a protein complex responsible for the generation of photo-excited charges. Electrochemical experiments with graphene electrodes and redox molecules reveal fundamental differences in the charge transfer processes for SLG and MLG films. We demonstrate that both graphene-based materials enable the immobilization of RCs without loss of functionality, attested by a photocurrent generation under illumination with IR-light at a wavelength of 870 nm. Furthermore, we report on the dependence of the generated photocurrent on the applied bias voltage, as well as on the presence of charge mediators in the surrounding electrolyte. This work demonstrates that SLG and MLG are a suitable platform for RC immobilization and subsequent photocurrent generation, suggesting a promising potential for graphene-based materials in bio-photovoltaics. Graphical abstract Unlabelled Image Highlights • Charge transfer processes of single and multilayer graphene electrodes • Immobilization of bacterial reaction centers on graphene electrodes • Comparison of photovoltaic performance of reaction centers on single and multilayer graphene electrodes [ABSTRACT FROM AUTHOR]