Reversibility of conformational switching in light-sensitive peptides

Light-activated azobenzene peptide inhibitor of the PD-1/PD-L1 interaction

Inhibiting the PD-1/PD-L1 protein-protein interaction is a key immunotherapy for cancer. Antibodies dominate the clinical space but are costly, with limited applicability and immune side effects. We developed a photo-controlled azobenzene peptide that selectively inhibits the PD-1/PD-L1 interaction when in the cis isomer only. Activity is demonstrated in in vitro and cellular assays.

MCL-1 promiscuity and the structural resilience of its binding partners

The allosteric protein MCL-1 and its natural inhibitors, the BH3-only proteins PUMA, BIM, and NOXA regulate apoptosis by interacting promiscuously within an entangled binding network. Little is known about the transient processes and dynamic conformational fluctuations that are the basis for the formation and stability of the MCL-1/BH3-only complex. In this study, we designed photoswitchable versions of MCL-1/PUMA and MCL-1/NOXA, and investigated the protein response after an ultrafast photo-perturbation with transient infrared spectroscopy. We observed partial α-helical unfolding in all cases, albeit on strongly varying timescales (1.6 ns for PUMA, 9.7 ns for the previously studied BIM, and 85 ns for NOXA). These differences are interpreted as a BH3-only-specific "structural resilience" to defy the perturbation while remaining in MCL-1's binding pocket. Thus, the presented insights could help to better understand the differences between PUMA, BIM, and NOXA, the promiscuity of MCL-1, in general, and the role of the proteins in the apoptotic network.

Interplay of molecular dynamics and radiative decay of a TADF emitter in a glass-forming liquid

We investigate the role of molecular dynamics in the luminescent properties of a prototypical thermally activated delayed fluorescence (TADF) emitter, NAI-DMAC, in solution using a combination of temperature dependent time-resolved photoluminescence and absorption spectroscopies. We use a glass forming liquid, 2-methylfuran, to introduce an abrupt change in the temperature dependent diffusion dynamics of the solvent and examine the influence this has on the emission intensity of NAI-DMAC molecules. Comparison of experiment with first principles molecular dynamics simulations reveals that the emission intensity of NAI-DMAC molecules follows the temperature-dependent self-diffusion dynamics of the solvent. A marked reduction of emission intensity is observed as the temperature decreases toward the glass transition because the rate at which NAI-DMAC molecules can access emissive molecular conformations is greatly reduced. Below the glass transition, the diffusion dynamics of the solvent changes more slowly with temperature, which causes the emission intensity to decrease more slowly as well. The combination of experiment and computation suggests a pathway by which TADF emitters may transiently access a distribution of conformational states and avoid the need for an average conformation that strikes a balance between lower singlet-triplet energy splittings versus higher emission probabilities.

Modification of proteins with azobenzene crosslinkers using reversible covalent bonds

Bis-cyanoacrylate azobenzene (BCNA) targets di-thiol peptides in the presence of mono-thiols and enables photoswitching of helical structure.

Using azobenzene photocontrol to set proteins in motion

Controlling the activity of proteins with azobenzene photoswitches is a potent tool for manipulating their biological function. With the help of light, it is possible to change binding affinities, control allostery or manipulate complex biological processes, for example. Additionally, owing to their intrinsically fast photoisomerization, azobenzene photoswitches can serve as triggers that initiate out-of-equilibrium processes. Such switching of the activity initiates a cascade of conformational events that can be accessed with time-resolved methods. In this Review, we show how the potency of azobenzene photoswitching can be combined with transient spectroscopic techniques to disclose the order of events and experimentally observe biomolecular interactions in real time. This strategy will further our understanding of how a protein can accommodate, adapt and readjust its structure to answer an incoming signal, revealing more of the dynamical character of proteins.

A stop-flow sample delivery system for transient spectroscopy

A stop-flow sample delivery system for transient spectroscopy is presented, which is, in particular, suited for laser-based instruments (quantum-cascade lasers or amplified femtosecond lasers) with excitation pulse repetition rates in the range 10-100 Hz. Two pulsing micro-valves are mounted onto a flow cuvette designed for transient IR spectroscopy, which is integrated into a flow cycle driven by a peristaltic pump. The performance of the system is demonstrated with transient IR experiments of the trans-to-cis photoisomerization of a water-soluble azobenzene derivative. The sample stands still when the micro-valves are closed and is pushed out from the probe beam focus on a 1 ms timescale when opening the micro-valves. The setup is extremely sample efficient. It needs only small sample volumes, and at the same time, it enables excitation of a large fraction of molecules in solution.

Molecular photoswitches in aqueous environments

Molecular photoswitches enable dynamic control of processes with high spatiotemporal precision, using light as external stimulus, and hence are ideal tools for different research areas spanning from chemical biology to smart materials. Photoswitches are typically organic molecules that feature extended aromatic systems to make them responsive to (visible) light. However, this renders them inherently lipophilic, while water-solubility is of crucial importance to apply photoswitchable organic molecules in biological systems, like in the rapidly emerging field of photopharmacology. Several strategies for solubilizing organic molecules in water are known, but there are not yet clear rules for applying them to photoswitchable molecules. Importantly, rendering photoswitches water-soluble has a serious impact on both their photophysical and biological properties, which must be taken into consideration when designing new systems. Altogether, these aspects pose considerable challenges for successfully applying molecular photoswitches in aqueous systems, and in particular in biologically relevant media. In this review, we focus on fully water-soluble photoswitches, such as those used in biological environments, in both in vitro and in vivo studies. We discuss the design principles and prospects for water-soluble photoswitches to inspire and enable their future applications.

Diarylethene moiety as an enthalpy-entropy switch: photoisomerizable stapled peptides for modulating p53/MDM2 interaction

Analogs of the known inhibitor (peptide pDI) of the p53/MDM2 protein-protein interaction are reported, which are stapled by linkers bearing a photoisomerizable diarylethene moiety. The corresponding photoisomers possess significantly different affinities to the p53-interacting domain of the human MDM2. Apparent dissociation constants are in the picomolar-to-low nanomolar range for those isomers with diarylethene in the "open" configuration, but up to eight times larger for the corresponding "closed" isomers. Spectroscopic, structural, and computational studies showed that the stapling linkers of the peptides contribute to their binding. Calorimetry revealed that the binding of the "closed" isomers is mostly enthalpy-driven, whereas the "open" photoforms bind to the protein stronger due to their increased binding entropy. The results suggest that conformational dynamics of the protein-peptide complexes may explain the differences in the thermodynamic profiles of the binding.

Intrinsic Dynamics of Protein-Peptide Unbinding

The dynamics of peptide-protein binding and unbinding of a variant of the RNase S system has been investigated. To initiate the process, a photoswitchable azobenzene moiety has been covalently linked to the S-peptide, thereby switching its binding affinity to the S-protein. Transient fluorescence quenching was measured with the help of a time-resolved fluorometer, which has been specifically designed for these experiments and is based on inexpensive light-emitting diodes and laser diodes only. One mutant shows on-off behavior with no specific binding detectable in one of the states of the photoswitch. Unbinding is faster by at least 2 orders of magnitude, compared to that of other variants of the RNase S system. We conclude that unbinding is essentially barrier-less in that case, revealing the intrinsic dynamics of the unbinding event, which occurs on a time scale of a few hundred microseconds in a strongly stretched-exponential manner.

Real-time observation of ligand-induced allosteric transitions in a PDZ domain

While allostery is of paramount importance for protein regulation, the underlying dynamical process of ligand (un)binding at one site, resulting time evolution of the protein structure, and change of the binding affinity at a remote site are not well understood. Here the ligand-induced conformational transition in a widely studied model system of allostery, the PDZ2 domain, is investigated by transient infrared spectroscopy accompanied by molecular dynamics simulations. To this end, an azobenzene-derived photoswitch is linked to a peptide ligand in a way that its binding affinity to the PDZ2 domain changes upon switching, thus initiating an allosteric transition in the PDZ2 domain protein. The subsequent response of the protein, covering four decades of time, ranging from ∼1 ns to ∼μs, can be rationalized by a remodeling of its rugged free-energy landscape, with very subtle shifts in the populations of a small number of structurally well-defined states. It is proposed that structurally and dynamically driven allostery, often discussed as limiting scenarios of allosteric communication, actually go hand-in-hand, allowing the protein to adapt its free-energy landscape to incoming signals.

Photoswitchable affinity reagents: Computational design and efficient red-light switching

Photo-controlled affinity reagents seek to provide modular spatiotemporal control of bioactivity by conferring photo-switchability of function on an affinity reagent scaffold. Here we used Rosetta-based computational methods to screen for sites on the Fynomer affinity reagent structure for attachment of photoswitchable cross-linkers. Both established UV-based cross-linkers (azobenzene-iodoacetamide (IAC)) and an azonium-based efficient red light switchable cross-linker, piperazino-tetra-ortho-methoxy azobenzene (PIP), were then tested experimentally. Several sites compatible with Fynomer function were identified, including sites showing rapid (<10s) red light (633 nm) modulation of function. While a range of overall target binding affinities were observed, the degree of photo-switchability of Fynomer function was generally small (<2-fold). Computational models suggest that local flexibility limits the degree of switching seen in these designs.

Highly reactive bis-cyclooctyne-modified diarylethene for SPAAC-mediated cross-linking

Photoisomerizable diarylethenes equipped with triple bonds are promising building blocks for constructing bistable photocontrollable systems.

Azobenzene switch with a long-lived cis-state to photocontrol the enzyme activity of a histone deacetylase-like amidohydrolase

The control of enzymes by use of an external stimulus such as light enables the temporal and spatial regulation of defined chemical reactions in a highly precise manner. In this work we investigated and characterized the reversible photocontrol of a bacterial histone deacetylase-like amidohydrolase (HDAH) from Bordetella/Alcaligenes strain FB188, which holds great potential to control deacetylation reactions of a broad spectrum of substrates in biotechnological and biomedical applications. Several HDAH variants with a single surface accessible cysteine close to the active site were developed and covalently modified by a monofunctional azobenzene-based photoswitch [4-phenylazomaleinanil (4-PAM)]. The enzymatic activity of three HDAH variants (M30C, S20C and M150C) were shown to be controlled by light. The thermal cis-to-trans relaxation of azobenzene conjugated to HDAH was up to 50-fold retarded compared to unbound 4-PAM allowing light pulse switching rather than continuing irradiation to maintain the thermodynamically less stable cis-state of covalently attached 4-PAM.

A 1H NMR assay for measuring the photostationary States of photoswitchable ligands

Incorporation of photoisomerizable chromophores into small molecule ligands represents a general approach for reversibly controlling protein function with light. Illumination at different wavelengths produces photostationary states (PSSs) consisting of different ratios of photoisomers. Thus optimal implementation of photoswitchable ligands requires knowledge of their wavelength sensitivity. Using an azobenzene-based ion channel blocker as an example, this protocol describes a (1)H NMR assay that can be used to precisely determine the isomeric content of photostationary states (PSSs) as a function of illumination wavelength. Samples of the photoswitchable ligand are dissolved in deuterated water and analyzed by UV/VIS spectroscopy to identify the range of illumination wavelengths that produce PSSs. The PSSs produced by these wavelengths are quantified using (1)H NMR spectroscopy under continuous irradiation through a monochromator-coupled fiber-optic cable. Because aromatic protons of azobenzene trans and cis isomers exhibit sufficiently different chemical shifts, their relative abundances at each PSS can be readily determined by peak integration. Constant illumination during spectrum acquisition is essential to accurately determine PSSs from molecules that thermally relax on the timescale of minutes or faster. This general protocol can be readily applied to any photoswitch that exhibits distinct (1)H NMR signals in each photoisomeric state.

Reversible photocontrol of peptide conformation with a rhodopsin-like photoswitch

Reversible photocontrol of biomolecules requires chromophores that can efficiently undergo large conformational changes upon exposure to wavelengths of light that are compatible with living systems. We designed a benzylidene-pyrroline chromophore that mimics the Schiff base of rhodopsin and can be used to introduce light-switchable intramolecular cross-links in peptides and proteins. This new class of photoswitch undergoes an ~10 Å change in end-to-end distance upon isomerization and can be used to control the conformation of a target peptide efficiently and reversibly using, alternately, violet (400 nm) and blue (446 nm) light.

Azobenzene photoswitching without ultraviolet light

Most azobenzene-based photoswitches use UV light for photoisomerization. This can limit their application in biological systems, where UV light can trigger unwanted responses, including cellular apoptosis. We have found that substitution of all four ortho positions with methoxy groups in an amidoazobenzene derivative leads to a substantial (~35 nm) red shift of the n-π* band of the trans isomer, separating it from the cis n-π* transition. This red shift makes trans-to-cis photoswitching possible using green light (530-560 nm). The cis state is thermally stable with a half-life of ~2.4 days in the dark in aqueous solution. Reverse (cis-to-trans) photoswitching can be accomplished with blue light (460 nm), so bidirectional photoswitching between thermally stable isomers is possible without using UV light at all.

Bis-azobenzene crosslinkers for photocontrol of peptide structure

Crosslinkers that undergo large changes in length upon photoisomerization can produce large conformational changes, and thereby functional changes, in biomolecules. We have designed and synthesized extended and rigid bis-azobenzene crosslinkers: 4,4'-bis(4-(2-chloroacetamido)phenyl)diazenylbiphenyl (BPDB) and the water-soluble sulfonated analogue 4,4'-bis(4-(2-chloroacetamido)phenyl)diazenylbiphenyl-2,2'-disulfonate (BPDBS). These photoswitches can produce end-to-end distance changes of a minimum of ≈5 Å and a maximum of ≈23 Å upon trans/cis isomerization. They have high absorption coefficients (45-60 000 M(-1)  cm(-1) ) and can produce up to ≈80 % cis isomers under favorable conditions. The photoswitching behavior of BPDBS-crosslinked peptides was found to be highly dependent on the crosslinker attachment site. Upon UV irradiation (365 nm), significant decreases in α-helix content were observed for peptides that were crosslinked with BPDBS through Cys residues at i,i+19, and i,i+21 positions. In contrast, large increases in α-helix content were exhibited by i,i+11 crosslinked peptides. BPDBS thus constitutes a particularly bright and effective photoswitch for biomolecule photocontrol.

Azobenzene photoswitches for biomolecules

The photoisomerization of azobenzene has been known for almost 75 years but only recently has this process been widely applied to biological systems. The central challenge of how to productively couple the isomerization process to a large functional change in a biomolecule has been met in a number of instances and it appears that effective photocontrol of a large variety of biomolecules may be possible. This critical review summarizes key properties of azobenzene that enable its use as a photoswitch in biological systems and describes strategies for using azobenzene photoswitches to drive functional changes in peptides, proteins, nucleic acids, lipids, and carbohydrates (192 references).

A light-gated, potassium-selective glutamate receptor for the optical inhibition of neuronal firing

Genetically targeted light-activated ion channels and pumps make it possible to determine the role of specific neurons in neuronal circuits, information processing and behavior. Here, we describe the development of a K⁺-selective ionotropic glutamate receptor that reversibly inhibits neuronal activity in response to light in dissociated neurons and brain slice and reversibly suppresses behavior in zebrafish. The receptor is a chimera of the pore region of a K⁺-selective bacterial glutamate receptor and the ligand binding domain of the light-gated mammalian kainate receptor (iGluR6/GluK2). This hyperpolarizing light-gated channel, HyLighter, is turned on by a brief light pulse at one wavelength and turned off by a pulse at a second wavelength. The control is obtained at moderate intensity. After optical activation, the photo-current and optical silencing of activity persist in the dark for extended periods. The low light requirement and bi-stability of HyLighter represent advantages for the dissection of neural circuitry.

Controlling the enzymatic activity of a restriction enzyme by light

For many applications it would be desirable to be able to control the activity of proteins by using an external signal. In the present study, we have explored the possibility of modulating the activity of a restriction enzyme with light. By cross-linking two suitably located cysteine residues with a bifunctional azobenzene derivative, which can adopt a cis- or trans-configuration when illuminated by UV or blue light, respectively, enzymatic activity can be controlled in a reversible manner. To determine which residues when cross-linked show the largest "photoswitch effect," i.e., difference in activity when illuminated with UV vs. blue light, > 30 variants of a single-chain version of the restriction endonuclease PvuII were produced, modified with azobenzene, and tested for DNA cleavage activity. In general, introducing single cross-links in the enzyme leads to only small effects, whereas with multiple cross-links and additional mutations larger effects are observed. Some of the modified variants, which carry the cross-links close to the catalytic center, can be modulated in their DNA cleavage activity by a factor of up to 16 by illumination with UV (azobenzene in cis) and blue light (azobenzene in trans), respectively. The change in activity is achieved in seconds, is fully reversible, and, in the case analyzed, is due to a change in V(max) rather than K(m).

Useful spectrokinetic methods for the investigation of photochromic and thermo-photochromic spiropyrans

This review reports on the main results of a set of kinetic elucidation methods developed by our team over the last few years. Formalisms, procedures and examples to solve all possible AB photochromic and thermophotochromic kinetics are presented. Also, discussions of the operating conditions, the continuous irradiation experiment, the spectrokinetic methods testing with numerical integration methods, and the identifiability/distinguishability problems, are included.

Two-dimensional infrared spectroscopy of photoswitchable peptides

We present a detailed discussion of the complimentary fields of the application of two-dimensional infrared (2D-IR) spectroscopy in comparison with two-dimensional nuclear magnetic resonance (2D-NMR) spectroscopy. Transient 2D-IR (T2D-IR) spectroscopy of nonequilibrium ensembles is probably one of the most promising strengths of 2D-IR spectroscopy, as the possibilities of 2D-NMR spectroscopy are limited in this regime. T2D-IR spectroscopy uniquely combines ultrafast time resolution with microscopic structural resolution. In this article we summarize our recent efforts to investigate the ultrafast structural dynamics of small peptides, such as the unfolding of peptide secondary structure motifs. The work requires two ingredients: 2D-IR spectroscopy and the possibility of triggering a structural transition of a peptide on an ultrafast timescale using embedded or intrinsic photoswitches. Several photoswitches have been tested, and we discuss our progress in merging these two pathways of research.

Synthesis of 3,3'-bis(sulfonato)-4,4'-bis(chloroacetamido)azobenzene and cysteine cross-linking for photo-control of protein conformation and activity

This protocol describes a procedure for the synthesis of 3,3'-bis(sulfonato)-4,4'-bis(chloroacetamido)azobenzene (BSBCA), a water-soluble, thiol-reactive, photo-switchable cross-linker. In addition, a protocol is outlined for installing the cross-linker in an intramolecular fashion onto proteins bearing two surface-exposed Cys residues. BSBCA is designed to be used as an in vitro activity switch that operates by exerting temporal and reversible photo-control over alpha-helix content within synthetic peptides and recombinant proteins. Synthesis of the cross-linker requires approximately 4.5 d, and cross-linking can be performed in 10-12 h.

Biologically active molecules with a "light switch"

Biologically active compounds which are light-responsive offer experimental possibilities which are otherwise very difficult to achieve. Since light can be manipulated very precisely, for example, with lasers and microscopes rapid jumps in concentration of the active form of molecules are possible with exact control of the area, time, and dosage. The development of such strategies started in the 1970s. This review summarizes new developments of the last five years and deals with "small molecules", proteins, and nucleic acids which can either be irreversibly activated with light (these compounds are referred to as "caged compounds") or reversibly switched between an active and an inactive state.

A nearly isosteric photosensitive amide-backbone substitution allows enzyme activity switching in ribonuclease s

psi[CS-NH]4-RNase S, a site specific modified version of RNase S obtained by thioxylation (O/S exchange) at the Ala4-Ala5- peptide bond, was used to evaluate the impact of protein backbone photoswitching on bioactivity. psi[CS-NH](4)-RNase S was yielded by recombination of the S-protein and the respective chemically synthesized thioxylated S-peptide derivative. Comparison with RNase S revealed similar thermodynamic stability of the complex and an unperturbed enzymatic activity toward cytidine 2',3'-cyclic monophosphate (cCMP). Reversible photoisomerization with a highly increased cis/trans isomer ratio of the thioxopeptide bond of psi[CS-NH](4)-RNase S in the photostationary state occurred under UV irradiation conditions (254 nm). The slow thermal reisomerization (t(1/2) = 180 s) permitted us to determine the enzymatic activity of cis psi[CS-NH](4)-RNase S by measurement of initial rates of cCMP hydrolysis. Despite thermodynamic stability of cis psi[CS-NH](4)-RNase S, its enzymatic activity is completely abolished but recovers after reisomerization. We conclude that the thioxopeptide bond modified polypeptide backbone represents a versatile probe for site-directed photoswitching of proteins.

Folding and unfolding of a photoswitchable peptide from picoseconds to microseconds

Using time-resolved IR spectroscopy, we monitored the kinetics of folding and unfolding processes of a photoswitchable 16-residue alanine-based alpha-helical peptide on a timescale from few picoseconds to almost 40 micros and over a large temperature range (279-318 K). The folding and unfolding processes were triggered by an ultrafast laser pulse that isomerized the cross linker within a few picoseconds. The main folding and unfolding times (700 ns and 150 ns, respectively, at room temperature) are in line with previous T-jump experiments obtained from similar peptides. However, both processes show complex, strongly temperature-dependent spectral kinetics that deviate clearly from a single-exponential behavior. Whereas in the unfolding experiment the ensemble starts from a well defined folded state, the starting ensemble in the folding experiment is more heterogeneous, which leads to distinctly different kinetics of the experiments, because they are sensitive to different regions of the energy surface. A qualitative agreement with the experimental data-set can be obtained by a model where the unfolded states act as a hub connected to several separated "misfolded" states with a distribution of rates. We conclude that a rather large spread of rates (k(1) : k(n) approximately 9) is needed to explain the experimentally observed stretched exponential response with stretching factor beta = 0.8 at 279 K.

Peptide-based stimuli-responsive biomaterials

This article explores recent advances in the design and engineering of materials wholly or principally constructed from peptides. We focus on materials that are able to respond to changes in their environment (pH, ionic strength, temperature, light, oxidation/reduction state, presence of small molecules or the catalytic activity of enzymes) by altering their macromolecular structure. Such peptide-based responsive biomaterials have exciting prospects for a variety of biomedical and bionanotechnology applications in drug delivery, bio-sensing and regenerative medicine.