Profiling the interactome of oligonucleotide drugs by proximity biotinylation

Drug-ID is a novel method applying proximity biotinylation to identify drug-protein interactions inside living cells. The covalent conjugation of a drug with a biotin ligase enables targeted biotinylation and identification of the drug-bound proteome. We established Drug-ID for two small-molecule drugs, JQ1 and SAHA, and applied it for RNaseH-recruiting antisense oligonucleotides (ASOs). Drug-ID profiles the drug-protein interactome de novo under native conditions, directly inside living cells and at pharmacologically effective drug concentrations. It requires minimal amounts of cell material and might even become applicable in vivo. We studied the dose-dependent aggregation of ASOs and the effect of different wing chemistries (locked nucleic acid, 2'-methoxyethyl and 2'-Fluoro) and ASO lengths on the interactome. Finally, we demonstrate the detection of stress-induced, intracellular interactome changes (actinomycin D treatment) with an in situ variant of the approach, which uses a recombinant biotin ligase and does not require genetic manipulation of the target cell.

Bifurcation of Excited-State Population Leads to Anti-Kasha Luminescence in a Disulfide-Decorated Organometallic Rhenium Photosensitizer

We report a rhenium diimine photosensitizer equipped with a peripheral disulfide unit on one of the bipyridine ligands, [Re(CO)3(bpy)(S-Sbpy4,4)]+ (1+, bpy = 2,2'-bipyridine, S-Sbpy4,4 = [1,2]dithiino[3,4-c:6,5-c']dipyridine), showing anti-Kasha luminescence. Steady-state and ultrafast time-resolved spectroscopies complemented by nonadiabatic dynamics simulations are used to disclose its excited-state dynamics. The calculations show that after intersystem crossing the complex evolves to two different triplet minima: a (S-Sbpy4,4)-ligand-centered excited state (3LC) lying at lower energy and a metal-to-(bpy)-ligand charge transfer (3MLCT) state at higher energy, with relative yields of 90% and 10%, respectively. The 3LC state involves local excitation of the disulfide group into the antibonding σ* orbital, leading to significant elongation of the S-S bond. Intriguingly, it is the higher-lying 3MLCT state, which is assigned to display luminescence with a lifetime of 270 ns: a signature of anti-Kasha behavior. This assignment is consistent with an energy barrier ≥ 0.6 eV or negligible electronic coupling, preventing reaction toward the 3LC state after the population is trapped in the 3MLCT state. This study represents a striking example on how elusive excited-state dynamics of transition-metal photosensitizers can be deciphered by synergistic experiments and state-of-the-art calculations. Disulfide functionalization lays the foundation of a new design strategy toward harnessing excess energy in a system for possible bimolecular electron or energy transfer reactivity.

Synthesis of Nε-acetyl-L-homolysine by the Lossen rearrangement and its application for probing deacetylases and binding modules of acetyl-lysine

Lysine acetylation is a posttranslational protein modification mediating protein-protein interactions by recruitment of bromodomains. Investigations of bromodomains have focused so far on the sequence context of the modification site and acyl-modifications installed at lysine side chains. In contrast, there is only little information about the impact of the lysine residue that carries the modification on bromodomain binding. Here, we report a synthesis strategy for L-acetyl-homolysine from L-2-aminosuberic acid by the Lossen rearrangement. Peptide probes containing acetylated homolysine, lysine, and ornithine were generated and used for probing the binding preferences of four bromodomains from three different families. Tested bromodomains showed distinct binding patterns, and one of them bound acetylated homolysine with similar efficiency as the native substrate containing acetyl-lysine. Deacetylation assays with a bacterial sirtuin showed a strong preference for acetylated lysine, despite a broad specificity for N-acyl modifications.

Proteome-wide lysine acetylation profiling to investigate the involvement of histone deacetylase HDA5 in the salt stress response of Arabidopsis leaves

Post-translational modifications (PTMs) of proteins play important roles in the acclimation of plants to environmental stress. Lysine acetylation is a dynamic and reversible PTM, which can be removed by histone deacetylases. Here we investigated the role of lysine acetylation in the response of Arabidopsis leaves to 1 week of salt stress. A quantitative mass spectrometry analysis revealed an increase in lysine acetylation of several proteins from cytosol and plastids, which was accompanied by altered histone deacetylase activities in the salt-treated leaves. While activities of HDA14 and HDA15 were decreased upon salt stress, HDA5 showed a mild and HDA19 a strong increase in activity. Since HDA5 is a cytosolic-nuclear enzyme from the class II histone deacetylase family with yet unknown protein substrates, we performed a lysine acetylome analysis on hda5 mutants and characterized its substrate proteins. Next to histone H2B, the salt stress-responsive transcription factor GT2L and the dehydration-related protein ERD7 were identified as HDA5 substrates. In addition, in protein-protein interaction studies, HDA18 was discovered, among other interacting proteins, to work in a complex together with HDA5. Altogether, this study revealed the substrate proteins of HDA5 and identified new lysine acetylation sites which are hyperacetylated upon salt stress. The identification of specific histone deacetylase substrate proteins, apart from histones, will be important to unravel the acclimation response of Arabidopsis to salt stress and their role in plant physiology.

Synthesis, Biochemical Characterization, and Genetic Encoding of a 1,2,4-Triazole Amino Acid as an Acetyllysine Mimic for Bromodomains of the BET Family

Lysine acetylation is a charge-neutralizing post-translational modification of proteins bound by bromodomains (Brds). A 1,2,4-triazole amino acid (ApmTri) was established as acetyllysine (Kac) mimic recruiting Brds of the BET family in contrast to glutamine commonly used for simulating this modification. Optimization of triazole substituents and side chain spacing allowed BET Brd recruitment to ApmTri-containing peptides with affinities similar to native substrates. Crystal structures of ApmTri-containing peptides in complex with two BET Brds revealed the binding mode which mirrored that of Kac ligands. ApmTri was genetically encoded and recombinant ApmTri-containing proteins co-enriched BRD3(2) from cellular lysates. This interaction was blocked by BET inhibitor JQ1. With genetically encoded ApmTri, biochemistry is now provided with a stable Kac mimic reflecting charge neutralization and Brd recruitment, allowing new investigations into BET proteins in vitro and in vivo.

Cereblon neo-substrate binding mimics the recognition of the cyclic imide degron

In targeted protein degradation, immunomodulatory drugs (IMiDs) or cereblon (CRBN) E3 ligase modulatory drugs (CELMoDs) recruit neo-substrate proteins to the E3 ubiquitin ligase receptor CRBN for ubiquitination and subsequent proteasomal degradation. While the structural basis of this mechanism is generally understood, we have only recently described the recognition mode of the natural CRBN degron. In this communication, we reveal that the IMiD- or CELMoD-mediated binding of neo-substrates closely mimics the recognition of natural degrons. In crystal structures, we identify a conserved binding mode for natural degron peptides with an elaborate hydrogen bonding network involving the backbone of each of the six C-terminal degron residues, without the involvement of side chains. In a structural comparison, we show that neo-substrates recruited by IMiDs or CELMoDs emulate every single hydrogen bond of this network and thereby explain the origins of the largely sequence-independent recognition of neo-substrates. Our results imply that the V388I substitution in CRBN does not impair natural degron recognition and complete the structural basis for the rational design of CRBN effectors.

Superconducting single-photon detectors in the mid-infrared for physical chemistry and spectroscopy

Applications of vibrational spectroscopy throughout the field of physical chemistry are limited by detectors with poor temporal resolution, low detection efficiency, and high background levels. Up to now, the field has relied upon detectors based on semiconducting materials with small bandgaps, which unavoidably leads to a compromise between good spectral response and noise at long wavelengths. However, a revolution in mid-infrared light detection is underway based on the interactions of photons with superconducting materials, which function under fundamentally different operating principles. Superconducting detectors were first used to detect light at shorter wavelengths. However, recent developments in their sensitivity toward mid-infrared wavelengths up to 10 μm provide new opportunities for applications in molecular science, such as infrared emission experiments, exoplanet spectroscopy and single molecule microscopy. In this tutorial review, we provide background information needed for the non-expert in superconducting light detection to apply these devices in the field of mid-infrared molecular spectroscopy. We present and compare the detection mechanisms and current developments of three types of superconducting detectors: superconducting nanowire single-photon detectors (SNSPDs), transition edge sensors (TESs), and microwave kinetic inductance detectors (MKIDs). We also highlight existing applications of SNSPDs for laser-induced infrared fluorescence experiments and discuss their potential for other molecular spectroscopy applications. Ultimately, superconducting infrared detectors have the potential to approach the sensitivity and characteristics of established single-photon detectors operating in the UV/Vis region, which have existed for almost a century and become an indispensable tool within the field of physical chemistry.

Luminescent Iridium Complexes with a Sulfurated Bipyridine Ligand: PCET Thermochemistry of the Disulfide Unit and Photophysical Properties

Molecular systems combining light harvesting and charge storage are receiving great attention in the context of, for example, artificial photosynthesis and solar fuel generation. As part of ongoing efforts to develop new concepts for photoinduced proton-coupled electron transfer (PCET) reactivities, we report a cyclometallated iridium(III) complex [Ir(ppy)₂(^S-Sbpy)](PF₆) ([1]PF₆) equipped with our previously developed sulfurated bipyridine ligand ^S-Sbpy. A new one-step synthetic protocol for ^S-Sbpy is developed, starting from commercially available 2,2'-bipyridine, which significantly facilitates the use of this ligand. [1]⁺ features a two-electron reduction with potential inversion (|E₁| > |E₂|) at moderate potentials (E₁ = -1.12, E₂ = -1.11 V versus. Fc^+/0 at 253 K), leading to a dithiolate species [1]^-. Protonation with weak acids allows for determination of pK_a = 23.5 in MeCN for the S-H···S^- unit of [1H]. The driving forces for both the H atom and the hydride transfer are calculated to be ∼60 kcal mol^-1 and verified experimentally by reaction with a suitable H atom and a hydride acceptor, demonstrating the ability of [1]⁺ to serve as a versatile PCET reagent, albeit with limited thermal stability. In MeCN solution, an orange emission for [1]PF₆ from a triplet-excited state was found. Density functional calculations and ultrafast absorption spectroscopy are used to give insight into the excited-state dynamics of the complex and suggest a significantly stretched S-S bond for the lowest triplet-state T₁. The structural responsiveness of the disulfide unit is proposed to open an effective relaxation channel toward the ground state, explaining the unexpectedly short lifetime of [1]⁺. These insights as well as the quantitative ground-state thermochemistry data provide valuable information for the use of ^S-Sbpy-functionalized complexes and their disulfide-/dithiol-directed PCET reactivity.

Quantum effects in thermal reaction rates at metal surfaces

There is wide interest in developing accurate theories for predicting rates of chemical reactions that occur at metal surfaces, especially for applications in industrial catalysis. Conventional methods contain many approximations that lack experimental validation. In practice, there are few reactions where sufficiently accurate experimental data exist to even allow meaningful comparisons to theory. Here, we present experimentally derived thermal rate constants for hydrogen atom recombination on platinum single-crystal surfaces, which are accurate enough to test established theoretical approximations. A quantum rate model is also presented, making possible a direct evaluation of the accuracy of commonly used approximations to adsorbate entropy. We find that neglecting the wave nature of adsorbed hydrogen atoms and their electronic spin degeneracy leads to a 10× to 1000× overestimation of the rate constant for temperatures relevant to heterogeneous catalysis. These quantum effects are also found to be important for nanoparticle catalysts.

Investigating peptide-Coenzyme A-conjugates as chemical probes for proteomic profiling of N-terminal and lysine acetyltransferases

Acetyl groups are transferred from acetyl‐coenzyme A (Ac‐CoA) to protein N‐termini and lysine side chains by N‐terminal acetyltransferases (NATs) and lysine acetyltransferases (KATs), respectively. Building on lysine‐CoA conjugates as KAT probes, we have synthesized peptide probes with CoA conjugated to N‐terminal alanine (α‐Ala‐CoA), proline (α‐Pro‐CoA) or tri‐glutamic acid (α‐3Glu‐CoA) units for interactome profiling of NAT complexes. The α‐Ala‐CoA probe enriched the majority of NAT catalytic and auxiliary subunits, while a lysine CoA‐conjugate bound only a subset of endogenous KATs. Interactome profiling with the α‐Pro‐CoA probe showed reduced NAT recruitment in favor of metabolic CoA binding proteins and α‐3Glu‐CoA steered the interactome towards NAA80 and NatB. These findings agreed with the inherent substrate specificities of the target proteins and showed that N‐terminal CoA‐conjugated peptides are versatile probes for NAT complex profiling in lysates of physiological and pathological backgrounds.

Spin-Forbidden Carbon-Carbon Bond Formation in Vibrationally Excited α-CO

Fourier transform infrared spectroscopy of laser-irradiated cryogenic crystals shows that vibrational excitation of CO leads to the production of equal amounts of CO₂ and C₃O₂. The reaction mechanism is explored using electronic structure calculations, demonstrating that the lowest-energy pathway involves a spin-forbidden reaction of (CO)₂ yielding C(³P) + CO₂. C(³P) then undergoes barrierless recombination with two other CO molecules forming C₃O₂. Calculated intersystem crossing rates support the spin-forbidden mechanism, showing subpicosecond spin-flipping time scales for a (CO)₂ geometry that is energetically consistent with states accessed through vibrational energy pooling. This spin-flip occurs with an estimated ∼4% efficiency; on the singlet surface, (CO)₂ reconverts back to CO monomers, releasing heat which induces CO desorption. The discovery that vibrational excitation of condensed-phase CO leads to spin-forbidden C–C bond formation may be important to the development of accurate models of interstellar chemistry.

Detecting chirality in mixtures using nanosecond photoelectron circular dichroism

We report chirality detection of structural isomers in a gas phase mixture using nanosecond photoelectron circular dichroism (PECD). Combining pulsed molecular beams with high-resolution resonance enhanced multi-photon ionization (REMPI) allows specific isolated transitions belonging to distinct components in the mixture to be targeted.

DRP1 interacts directly with BAX to induce its activation and apoptosis

The apoptotic executioner protein BAX and the dynamin‐like protein DRP1 co‐localize at mitochondria during apoptosis to mediate mitochondrial permeabilization and fragmentation. However, the molecular basis and functional consequences of this interplay remain unknown. Here, we show that BAX and DRP1 physically interact, and that this interaction is enhanced during apoptosis. Complex formation between BAX and DRP1 occurs exclusively in the membrane environment and requires the BAX N‐terminal region, but also involves several other BAX surfaces. Furthermore, the association between BAX and DRP1 enhances the membrane activity of both proteins. Forced dimerization of BAX and DRP1 triggers their activation and translocation to mitochondria, where they induce mitochondrial remodeling and permeabilization to cause apoptosis even in the absence of apoptotic triggers. Based on this, we propose that DRP1 can promote apoptosis by acting as noncanonical direct activator of BAX through physical contacts with its N‐terminal region.

Photoinduced host-to-guest electron transfer in a self-assembled coordination cage

Light–powered host–guest charge transfer (HGCT) is shown for a coordination cage based on electron-rich phenothiazines, containing an anthraquinone acceptor as guest. Transient absorption spectroscopy and spectroelectrochemistry data is presented.

Sortase-Mediated Multi-Fragment Assemblies by Ligation Site Switching

Sortase‐mediated ligation (SML) is a powerful tool of protein chemistry allowing the ligation of peptides containing LPxTG sorting motifs and N‐terminal glycine nucleophiles. The installation of a sorting motif into the product prohibits the assembly of multiple fragments by SML. Here we report multi‐fragment SML based on switchable sortase substrates. Substitution of the Leu residue by disulfide‐containing Cys(StBu) results in active sorting motifs, which are inactivatable by reduction. In combination with a photo‐protected N‐Gly nucleophile, multi‐fragment SML is enabled by repetitive cycles of SML and ligation site switching. The feasibility of this approach was demonstrated by a proof‐of‐concept four‐fragment ligation, the assembly of peptide probes for bivalent chromatin binding proteins and oligomerization of peptide antigens. Biochemical and immuno‐assays demonstrated functionality of these probes rendering them promising tools for immunology and chromatin biochemistry.

Kinetics of NH3 Desorption and Diffusion on Pt: Implications for the Ostwald Process

We report accurate time-resolved measurements of NH₃ desorption from Pt(111) and Pt(332) and use these results to determine elementary rate constants for desorption from steps, from (111) terrace sites and for diffusion on (111) terraces. Modeling the extracted rate constants with transition state theory, we find that conventional models for partition functions, which rely on uncoupled degrees of freedom (DOFs), are not able to reproduce the experimental observations. The results can be reproduced using a more sophisticated partition function, which couples DOFs that are most sensitive to NH₃ translation parallel to the surface; this approach yields accurate values for the NH₃ binding energy to Pt(111) (1.13 ± 0.02 eV) and the diffusion barrier (0.71 ± 0.04 eV). In addition, we determine NH₃'s binding energy preference for steps over terraces on Pt (0.23 ± 0.03 eV). The ratio of the diffusion barrier to desorption energy is ∼0.65, in violation of the so-called 12% rule. Using our derived diffusion/desorption rates, we explain why established rate models of the Ostwald process incorrectly predict low selectivity and yields of NO under typical reactor operating conditions. Our results suggest that mean-field kinetics models have limited applicability for modeling the Ostwald process.

Random Force in Molecular Dynamics with Electronic Friction

Originally conceived to describe thermal diffusion, the Langevin equation includes both a frictional drag and a random force, the latter representing thermal fluctuations first seen as Brownian motion. The random force is crucial for the diffusion problem as it explains why friction does not simply bring the system to a standstill. When using the Langevin equation to describe ballistic motion, the importance of the random force is less obvious and it is often omitted, for example, in theoretical treatments of hot ions and atoms interacting with metals. Here, friction results from electronic nonadiabaticity (electronic friction), and the random force arises from thermal electron-hole pairs. We show the consequences of omitting the random force in the dynamics of H-atom scattering from metals. We compare molecular dynamics simulations based on the Langevin equation to experimentally derived energy loss distributions. Despite the fact that the incidence energy is much larger than the thermal energy and the scattering time is only about 25 fs, the energy loss distribution fails to reproduce the experiment if the random force is neglected. Neglecting the random force is an even more severe approximation than freezing the positions of the metal atoms or modelling the lattice vibrations as a generalized Langevin oscillator. This behavior can be understood by considering analytic solutions to the Ornstein-Uhlenbeck process, where a ballistic particle experiencing friction decelerates under the influence of thermal fluctuations.

Cyanate Formation via Photolytic Splitting of Dinitrogen

Light-driven N₂ cleavage into molecular nitrides is an attractive strategy for synthetic nitrogen fixation. However, suitable platforms are rare. Furthermore, the development of catalytic protocols via this elementary step suffers from poor understanding of N-N photosplitting within dinitrogen complexes, as well as of the thermochemical and kinetic framework for coupled follow-up chemistry. We here present a tungsten pincer platform, which undergoes fully reversible, thermal N₂ splitting and reverse nitride coupling, allowing for experimental derivation of thermodynamic and kinetic parameters of the N-N cleavage step. Selective N-N splitting was also obtained photolytically. DFT computations allocate the productive excitations within the {WNNW} core. Transient absorption spectroscopy shows ultrafast repopulation of the electronic ground state. Comparison with ground-state kinetics and resonance Raman data support a pathway for N-N photosplitting via a nonstatistically vibrationally excited ground state that benefits from vibronically coupled structural distortion of the core. Nitride carbonylation and release are demonstrated within a full synthetic cycle for trimethylsilylcyanate formation directly from N₂ and CO.

NO Binding Energies to and Diffusion Barrier on Pd Obtained with Velocity-Resolved Kinetics

We report nitric oxide (NO) desorption rates from Pd(111) and Pd(332) surfaces measured with velocity-resolved kinetics. The desorption rates at the surface temperatures from 620 to 800 K span more than 3 orders of magnitude, and competing processes, like dissociation, are absent. Applying transition state theory (TST) to model experimental data leads to the NO binding energy E ₀ = 1.766 ± 0.024 eV and diffusion barrier D _T = 0.29 ± 0.11 eV on the (111) terrace and the stabilization energy for (110)-steps ΔE _ST = 0.060_-0.030 ^+0.015 eV. These parameters provide valuable benchmarks for theory.

Engineered Sortases in Peptide and Protein Chemistry

The transpeptidase sortase A of Staphylococcus aureus (Sa-SrtA) is a valuable tool in protein chemistry. The native enzyme anchors surface proteins containing a highly conserved LPxTG sorting motif to a terminal glycine residue of the peptidoglycan layer in Gram-positive bacteria. This reaction is exploited for sortase-mediated ligation (SML), allowing the site-specific linkage of synthetic peptides and recombinant proteins by a native peptide bond. However, the moderate catalytic efficiency and specificity of Sa-SrtA fueled the development of new biocatalysts for SML, including the screening of sortase A variants form microorganisms other than S. aureus and the directed protein evolution of the Sa-SrtA enzyme itself. Novel display platforms and screening formats were developed to isolate sortases with altered properties from mutant libraries. This yielded sortases with strongly enhanced catalytic activity and enzymes recognizing new sorting motifs as substrates. This minireview focuses on recent advances in the field of directed sortase evolution and applications of these tailor-made enzymes in biochemistry.

Excited-State Dynamics of [Ru(S-Sbpy)(bpy)2]2+ to Form Long-Lived Localized Triplet States

The novel photosensitizer [Ru(^S–Sbpy)(bpy)₂]²⁺ harbors two distinct sets of excited states in the UV/Vis region of the absorption spectrum located on either bpy or ^S–Sbpy ligands. Here, we address the question of whether following excitation into these two types of states could lead to the formation of different long-lived excited states from where energy transfer to a reactive species could occur. Femtosecond transient absorption spectroscopy identifies the formation of the final state within 80 fs for both excitation wavelengths. The recorded spectra hint at very similar dynamics following excitation toward either the parent or sulfur-decorated bpy ligands, indicating ultrafast interconversion into a unique excited-state species regardless of the initial state. Non-adiabatic surface hopping dynamics simulations show that ultrafast spin–orbit-mediated mixing of the states within less than 50 fs strongly increases the localization of the excited electron at the ^S–Sbpy ligand. Extensive structural relaxation within this sulfurated ligand is possible, via S–S bond cleavage that results in triplet state energies that are lower than those in the analogue [Ru(bpy)₃]²⁺. This structural relaxation upon localization of the charge on ^S–Sbpy is found to be the reason for the formation of a single long-lived species independent of the excitation wavelength.

We investigate selective excitation in two types of ligands present in [Ru(^S−Sbpy)(bpy)₂]²⁺. Femtosecond transient absorption spectroscopy identifies the formation of the same final state within 80 fs for both excitation wavelengths. Surface hopping simulations reveal ultrafast mixing of singlet and triplet states within less than 50 fs. Energy lowering due to S−S bond cleavage is identified as the driving factor for convergence to a single final state.

Transporting and concentrating vibrational energy to promote isomerization

Visible-light absorption and transport of the resultant electronic excitations to a reaction centre through Förster resonance energy transfer^1-3 (FRET) are critical to the operation of biological light-harvesting systems⁴, and are used in various artificial systems made of synthetic dyes⁵, polymers⁶ or nanodots^7,8. The fundamental equations describing FRET are similar to those describing vibration-to-vibration (V-V) energy transfer⁹, and suggest that transport and localization of vibrational energy should, in principle, also be possible. Although it is known that vibrational excitation can promote reactions^10-16, transporting and concentrating vibrational energy has not yet been reported. We have recently demonstrated orientational isomerization enabled by vibrational energy pooling in a CO adsorbate layer on a NaCl(100) surface¹⁷. Here we build on that work to show that the isomerization reaction proceeds more efficiently with a thick ¹²C¹⁶O overlayer that absorbs more mid-infrared photons and transports the resultant vibrational excitations by V-V energy transfer to a ¹³C¹⁸O-NaCl interface. The vibrational energy density achieved at the interface is 30 times higher than that obtained with direct excitation of the interfacial CO. We anticipate that with careful system design, these concepts could be used to drive other chemical transformations, providing new approaches to condensed phase chemistry.

Time-Resolved Spectroscopy of Photoinduced Electron Transfer in Dinuclear and Tetranuclear Fe/Co Prussian Blue Analogues

The dynamics of the photodriven charge transfer-induced spin transition (CTIST) in two Fe/Co Prussian Blue Analogues (PBAs) are revealed by femtosecond IR and UV/vis pump-probe spectroscopy. Depending on temperature, the known tetranuclear square-type complex [Co₂Fe₂(CN)₆(tp*)₂(4,4'-dtbbpy)₄](PF₆)₂ (1) exists in two electronic states. In acetonitrile solution, at <240 K, the low temperature (LT) phase is prevalent consisting of low-spin Fe(II) and low-spin Co(III), [Fe^II_LSCo^III_LS]₂. Temperature rise is the reason behind thermally-induced CTIST toward the high temperature (HT) phase consisting of low-spin Fe(III) and high-spin Co(II), [Fe^III_LSCo^II_HS]₂, being prevalent at >300 K. Photoexcitation into the intervalence charge transfer (IVCT) band of the LT phase at 800 nm induces electron transfer in one Fe-Co edge of PBA 1 and produces a [Fe^III_LSCo^II_LS] intermediate which by spin-crossover (SCO) is stabilized within 400 fs to a long-lived (>1 ns) [Fe^III_LSCo^II_HS] species. In contrast, IVCT excitation of the HT phase at 400 nm generates a [Fe^II_LSCo^III_HS] species with a lifetime of 3.6 ps. Subsequent back-electron transfer populates the vibrationally hot ground state, which thermalizes within 8 ps. The newly synthesized dinuclear PBA, [CoFe(CN)₃(tp*)(pz*₄Lut)]ClO₄ (2), provides a benchmark of the HT phase of 1, i.e., [Fe^III_LSCo^II_HS], as verified by variable temperature magnetic susceptibility measurements and ⁵⁷Fe Mössbauer spectroscopy. The photoinduced charge transfer dynamics of PBA 2 indeed are almost identical to that of the HT phase of PBA 1 with a lifetime of the excited [Fe^II_LSCo^III_HS] species of 3.8 ps.

Measuring Transient Reaction Rates from Nonstationary Catalysts

Up to now, methods for measuring rates of reactions on catalysts required long measurement times involving signal averaging over many experiments. This imposed a requirement that the catalyst return to its original state at the end of each experiment—a complete reversibility requirement. For real catalysts, fulfilling the reversibility requirement is often impossible—catalysts under reaction conditions may change their chemical composition and structure as they become activated or while they are being poisoned through use. It is therefore desirable to develop high-speed methods where transient rates can be quickly measured while catalysts are changing. In this work, we present velocity-resolved kinetics using high-repetition-rate pulsed laser ionization and high-speed ion imaging detection. The reaction is initiated by a single molecular beam pulse incident at the surface, and the product formation rate is observed by a sequence of pulses produced by a high-repetition-rate laser. Ion imaging provides the desorbing product flux (reaction rate) as a function of reaction time for each laser pulse. We demonstrate the principle of this approach by rate measurements on two simple reactions: CO desorption from and CO oxidation on the 332 facet of Pd. This approach overcomes the time-consuming scanning of the delay between CO and laser pulses needed in past experiments and delivers a data acquisition rate that is 10–1000 times higher. We are able to record kinetic traces of CO₂ formation while a CO beam titrates oxygen atoms from an O-saturated surface. This approach also allows measurements of reaction rates under diffusion-controlled conditions.

The coverage dependence of the infrared absorption of CO adsorbed to NaCl(100)

CO adsorbed to NaCl(100) exhibits perhaps the weakest possible coupling between the adsorbate and solid. It is, therefore, an ideal system to observe the influence of adsorbate-adsorbate interactions on infrared absorption. In this work, we report polarized FTIR absorption spectra of CO/NaCl(100) as a function of coverage (0.02 ≤ θ ≤ 1 ML), where the coverage has been quantitatively determined by temperature-programmed desorption and molecular beam dosing. We extend a previous semi-empirical model designed to describe the screening of the local electric field due to dipole-dipole interactions in a CO monolayer. The extended model applies to sub-monolayer coverages and describes properly the electric field of the absorbed radiation at the vacuum-substrate interface. Fitting this model to coverage-dependent IR absorption data allows us to derive the vibrational and electronic polarizabilities [χ_v = 0.0435(14) ų, χ_e = 3.30(36) ų] and the integrated absorption cross section of 2.51(8) × 10^-17 cm/molecule for an isolated CO molecule adsorbed at the NaCl (100) surface. The determined integrated absorption cross section is substantially smaller than that of gas phase CO.

The Arabidopsis Nα -acetyltransferase NAA60 locates to the plasma membrane and is vital for the high salt stress response

In humans and plants, N-terminal acetylation plays a central role in protein homeostasis, affects 80% of proteins in the cytoplasm and is catalyzed by five ribosome-associated N-acetyltransferases (NatA-E). Humans also possess a Golgi-associated NatF (HsNAA60) that is essential for Golgi integrity. Remarkably, NAA60 is absent in fungi and has not been identified in plants. Here we identify and characterize the first plasma membrane-anchored post-translationally acting N-acetyltransferase AtNAA60 in the reference plant Arabidopsis thaliana by the combined application of reverse genetics, global proteomics, live-cell imaging, microscale thermophoresis, circular dichroism spectroscopy, nano-differential scanning fluorometry, intrinsic tryptophan fluorescence and X-ray crystallography. We demonstrate that AtNAA60, like HsNAA60, is membrane-localized in vivo by an α-helical membrane anchor at its C-terminus, but in contrast to HsNAA60, AtNAA60 localizes to the plasma membrane. The AtNAA60 crystal structure provides insights into substrate-binding, the broad substrate specificity and the catalytic mechanism probed by structure-based mutagenesis. Characterization of the NAA60 loss-of-function mutants (naa60-1 and naa60-2) uncovers a plasma membrane-localized substrate of AtNAA60 and the importance of NAA60 during high salt stress. Our findings provide evidence for the plant-specific evolution of a plasma membrane-anchored N-acetyltransferase that is vital for adaptation to stress.

Following the microscopic pathway to adsorption through chemisorption and physisorption wells

Adsorption involves molecules colliding at the surface of a solid and losing their incidence energy by traversing a dynamical pathway to equilibrium. The interactions responsible for energy loss generally include both chemical bond formation (chemisorption) and nonbonding interactions (physisorption). In this work, we present experiments that revealed a quantitative energy landscape and the microscopic pathways underlying a molecule’s equilibration with a surface in a prototypical system: CO adsorption on Au(111). Although the minimum energy state was physisorbed, initial capture of the gas-phase molecule, dosed with an energetic molecular beam, was into a metastable chemisorption state. Subsequent thermal decay of the chemisorbed state led molecules to the physisorption minimum. We found, through detailed balance, that thermal adsorption into both binding states was important at all temperatures.

Examining histone modification crosstalk using immobilized libraries established from ligation-ready nucleosomes

Chromatin signaling relies on a plethora of posttranslational modifications (PTM) of the histone proteins which package the long DNA molecules of our cells in reoccurring units of nucleosomes. Determining the biological function and molecular working mechanisms of different patterns of histone PTMs requires access to various chromatin substrates of defined modification status. Traditionally, these are achieved by individual reconstitution of single nucleosomes or arrays of nucleosomes in conjunction with modified histones produced by means of chemical biology. Here, we report an alternative strategy for establishing a library of differentially modified nucleosomes that bypasses the need for many individual syntheses, purification and assembly reactions by installing modified histone tails on ligation-ready, immobilized nucleosomes reconstituted in a single batch. Using the ligation-ready nucleosome strategy with sortase-mediated ligation for histone H3 and intein splicing for histone H2A, we generated libraries of up to 280 individually modified nucleosomes in 96-well plate format. Screening these libraries for the effects of patterns of PTMs onto the recruitment of a well-known chromatin factor, HP1 revealed a previously unknown long-range cross-talk between two modifications. H3S28 phosphorylation enhances recruitment of the HP1 protein to the H3K9 methylated H3-tail only in nucleosomal context. Detailed structural analysis by NMR measurements implies negative charges at position 28 to increase nucleosomal H3-tail dynamics and flexibility. Our work shows that ligation-ready nucleosomes enable unprecedented access to the ample space and complexity of histone modification patterns for the discovery and dissection of chromatin regulatory principles.

280 different patterns of histone modifications were installed in preassembled nucleosomes using PTS and SML enabling screening of readout crosstalk.

Dual lysine and N-terminal acetyltransferases reveal the complexity underpinning protein acetylation

Protein acetylation is a highly frequent protein modification. However, comparatively little is known about its enzymatic machinery. N-α-acetylation (NTA) and ε-lysine acetylation (KA) are known to be catalyzed by distinct families of enzymes (NATs and KATs, respectively), although the possibility that the same GCN5-related N-acetyltransferase (GNAT) can perform both functions has been debated. Here, we discovered a new family of plastid-localized GNATs, which possess a dual specificity. All characterized GNAT family members display a number of unique features. Quantitative mass spectrometry analyses revealed that these enzymes exhibit both distinct KA and relaxed NTA specificities. Furthermore, inactivation of GNAT2 leads to significant NTA or KA decreases of several plastid proteins, while proteins of other compartments were unaffected. The data indicate that these enzymes have specific protein targets and likely display partly redundant selectivity, increasing the robustness of the acetylation process in vivo. In summary, this study revealed a new layer of complexity in the machinery controlling this prevalent modification and suggests that other eukaryotic GNATs may also possess these previously underappreciated broader enzymatic activities.

Exploring the light-induced dynamics in solvated metallogrid complexes with femtosecond pulses across the electromagnetic spectrum

Oligonuclear complexes of d⁴-d⁷ transition metal ion centers that undergo spin-switching have long been developed for their practical role in molecular electronics. Recently, they also have appeared as promising photochemical reactants demonstrating improved stability. However, the lack of knowledge about their photophysical properties in the solution phase compared to mononuclear complexes is currently hampering their inclusion into advanced light-driven reactions. In the present study, the ultrafast photoinduced dynamics in a solvated [2 × 2] iron(II) metallogrid complex are characterized by combining measurements with transient optical-infrared absorption and x-ray emission spectroscopy on the femtosecond time scale. The analysis is supported by density functional theory calculations. The photocycle can be described in terms of intra-site transitions, where the Fe^II centers in the low-spin state are independently photoexcited. The Franck-Condon state decays via the formation of a vibrationally hot high-spin (HS) state that displays coherent behavior within a few picoseconds and thermalizes within tens of picoseconds to yield a metastable HS state living for several hundreds of nanoseconds. Systematic comparison with the closely related mononuclear complex [Fe(terpy)₂]²⁺ reveals that nuclearity has a profound impact on the photoinduced dynamics. More generally, this work provides guidelines for expanding the integration of oligonuclear complexes into new photoconversion schemes that may be triggered by ultrafast spin-switching.

Asymmetric Disulfanylbenzamides as Irreversible and Selective Inhibitors of Staphylococcus aureus Sortase A

Staphylococcus aureus is one of the most frequent causes of nosocomial and community-acquired infections, with drug-resistant strains being responsible for tens of thousands of deaths per year. S. aureus sortase A inhibitors are designed to interfere with virulence determinants. We have identified disulfanylbenzamides as a new class of potent inhibitors against sortase A that act by covalent modification of the active-site cysteine. A broad series of derivatives were synthesized to derive structure-activity relationships (SAR). In vitro and in silico methods allowed the experimentally observed binding affinities and selectivities to be rationalized. The most active compounds were found to have single-digit micromolar Ki values and caused up to a 66 % reduction of S. aureus fibrinogen attachment at an effective inhibitor concentration of 10 μM. This new molecule class exhibited minimal cytotoxicity, low bacterial growth inhibition and impaired sortase-mediated adherence of S. aureus cells.

Revealing Hot and Long-Lived Metastable Spin States in the Photoinduced Switching of Solvated Metallogrid Complexes with Femtosecond Optical and X-ray Spectroscopies

An atomistic understanding of the photoinduced spin-state switching (PSS) within polynuclear systems of d⁴-d⁷ transition metal ion complexes is required for their rational integration into light-driven reactions of chemical and biological interest. However, in contrast to mononuclear systems, the multidimensional dynamics of the PSS in solvated molecular arrays have not yet been elucidated due to the expected complications associated with the connectivity between the metal centers and the strong interactions with the surroundings. In this work, the PSS in a solvated triiron(II) metallogrid complex is characterized using transient optical absorption and X-ray emission spectroscopies on the femtosecond time scale. The complementary measurements reveal the photoinduced creation of energy-rich (hot) and long-lived quintet states, whose dynamics differ critically from their mononuclear congeners. This finding opens major prospects for developing novel schemes in solution-phase spin chemistry that are driven by the dynamic PSS process in compact oligometallic arrays.

Observation of an isomerizing double-well quantum system in the condensed phase

Molecular isomerization fundamentally involves quantum states bound within a potential energy function with multiple minima. For isolated gas-phase molecules, eigenstates well above the isomerization saddle points have been characterized. However, to observe the quantum nature of isomerization, systems in which transitions between the eigenstates occur-such as condensed-phase systems-must be studied. Efforts to resolve quantum states with spectroscopic tools are typically unsuccessful for such systems. An exception is CO adsorbed on NaCl(100), which is bound with the well-known OC-Na⁺ structure. We observe an unexpected upside-down isomer (CO-Na⁺) produced by infrared laser excitation and obtain well-resolved infrared fluorescence spectra from highly energetic vibrational states of both orientational isomers. This distinctive condensed-phase system is ideally suited to spectroscopic investigations of the quantum nature of isomerization.

Vibrational Relaxation Lifetime of a Physisorbed Molecule at a Metal Surface

Previous measurements of vibrational relaxation lifetimes for molecules adsorbed at metal surfaces yielded values of 1-3 ps; however, only chemisorbed molecules have been studied. We report the first measurements of the vibrational relaxation lifetime of a molecule physisorbed to a metal surface. For CO(v=1) adsorbed on Au(111) at 35 K the vibrational lifetime of the excited stretching mode is 49±3  ps. The long lifetime seen here is likely to be a general feature of physisorption, which involves weaker electronic coupling between the adsorbate and the solid due to bonding at larger distances.

Peptide-Based 2-Aminophenylamide Probes for Targeting Endogenous Class I Histone Deacetylase Complexes

Lysine deacetylases or histone deacetylases (HDACs) remove acetylation markers from numerous cellular proteins, thereby regulating their function and activity. Recently established peptide probes containing the HDAC‐trapping amino acid α‐aminosuberic acid ω‐hydroxamate (AsuHd) have been used to investigate the compositions of HDAC complexes in a site‐specific manner. Here we report the new HDAC‐trapping amino acid 2‐amino‐8‐[(2‐aminophenyl)amino]‐8‐oxooctanoic acid (AsuApa) and the utility of AsuApa‐containing probes for HDAC complex profiling on a proteome‐wide scale. Unlike AsuHd‐containing probes, AsuApa enriched only HDACs 1, 2, and 3 efficiently and was the most potent probe tested for capturing the last of these. These findings indicate that the inherent specificity of reported small‐molecule pimelic diphenylamide HDAC inhibitors is preserved in AsuApa and that this HDAC‐trapping amino acid represents a potent tool for investigating class I HDAC complexes.

The Sommerfeld ground-wave limit for a molecule adsorbed at a surface

Using a mid-infrared emission spectrometer based on a superconducting nanowire single-photon detector, we observed the dynamics of vibrational energy pooling of carbon monoxide (CO) adsorbed at the surface of a sodium chloride (NaCl) crystal. After exciting a majority of the CO molecules to their first vibrationally excited state (v = 1), we observed infrared emission from states up to v = 27. Kinetic Monte Carlo simulations showed that vibrational energy collects in a few CO molecules at the expense of those up to eight lattice sites away by selective excitation of NaCl’s transverse phonons. The vibrating CO molecules behave like classical oscillating dipoles, losing their energy to NaCl lattice vibrations via the electromagnetic near-field. This is analogous to Sommerfeld’s description of radio transmission along Earth’s surface by ground waves.

The Symmetric Tetravalent Sulfhydryl-Specific Linker NATBA Facilitates a Combinatorial "Tool Kit" Strategy for Phage Display-Based Selection of Functionalized Bicyclic Peptides

The rigid conformation of constrained bicyclic peptides provides a number of advantages over larger protein-based ligands, including better chemical stability, enhanced tissue penetration, and a wider field of possible applications. Selective chemical modification strategies are able to extend the scope of applications not only in a therapeutic manner but also for the development of novel tools for protein capturing, bioimaging, and targeted drug delivery. Herein, we report the synthesis of an adamantane-based, symmetrical, tetravalent, sulfhydryl-specific peptide linker. We have developed an in vitro two-step modification strategy that allows the generation of differently functionalized bicyclic peptides. This "tool kit" strategy was applied to cyclize and functionalize a phage-encoded peptide library bearing the sequence CX₆CX₆C. After phage display against a model target, isolated peptides show strong consensus sequences, indicating target-specific binding. The newly developed symmetric tetravalent linker opens new avenues for the combinatorial selection and functionalization of bicyclic peptide ligands with affinity to virtually any target.

Switching Between Bicyclic and Linear Peptides - The Sulfhydryl-Specific Linker TPSMB Enables Reversible Cyclization of Peptides

Phage display-selected bicyclic peptides have already shown their great potential for the development as bioactive modulators of therapeutic targets. They can provide enhanced proteolytic stability and improved membrane permeability. Molecular design of new linker molecules has led to a variety of new synthetic approaches for the generation of chemically constrained cyclic peptides. This diversity can be useful for the development of novel peptide-based therapeutic, diagnostic, and scientific tools. Herein, we introduce 1,3,5-tris((pyridin-2-yldisulfanyl)methyl)benzene (TPSMB) as a planar, trivalent, sulfhydryl-specific linker that facilitates reversible cyclization and linearization via disulfide bond formation and cleavage of bicyclic peptides of the format CXnCXnC, where X is any proteinogenic amino acid except cysteine. The rapid and highly sulfhydryl-specific reaction of TPSMB under physiological conditions is demonstrated by selecting bicyclic peptide binders against c-Jun N-terminal kinase 3 (JNK3) as a model target. While model peptides remain stably cyclized for several hours in presence of typical blood levels of glutathione in vitro, high cytosolic concentrations of glutathione linearize these peptides completely within 1 h. We propose that reversible linkers can be useful tools for several technical applications where target affinity depends on the bicyclic structure of the peptide.

Chloroplast Acetyltransferase NSI Is Required for State Transitions in Arabidopsis thaliana

The amount of light energy received by the photosynthetic reaction centers photosystem II (PSII) and photosystem I (PSI) is balanced through state transitions. Reversible phosphorylation of a light-harvesting antenna trimer (L-LHCII) orchestrates the association between L-LHCII and the photosystems, thus adjusting the amount of excitation energy received by the reaction centers. In this study, we identified the enzyme NUCLEAR SHUTTLE INTERACTING (NSI; AT1G32070) as an active lysine acetyltransferase in the chloroplasts of Arabidopsis thaliana Intriguingly, nsi knockout mutant plants were defective in state transitions, even though they had a similar LHCII phosphorylation pattern as the wild type. Accordingly, nsi plants were not able to accumulate the PSI-LHCII state transition complex, even though the LHCII docking site of PSI and the overall amounts of photosynthetic protein complexes remained unchanged. Instead, the nsi mutants showed a decreased Lys acetylation status of specific photosynthetic proteins including PSI, PSII, and LHCII subunits. Our work demonstrates that the chloroplast acetyltransferase NSI is needed for the dynamic reorganization of thylakoid protein complexes during photosynthetic state transitions.

Ultra-sensitive mid-infrared emission spectrometer with sub-ns temporal resolution

We evaluate the performance of a mid-infrared emission spectrometer operating at wavelengths between 1.5 and 6 μm based on an amorphous tungsten silicide (a-WSi) superconducting nanowire single-photon detector (SNSPD). We performed laser induced fluorescence spectroscopy of surface adsorbates with sub-monolayer sensitivity and sub-nanosecond temporal resolution. We discuss possible future improvements of the SNSPD-based infrared emission spectrometer and its potential applications in molecular science.

Ultrafast IR spectroscopy of photo-induced electron transfer in self-assembled donor-acceptor coordination cages

Photo-induced processes in self-assembled coordination cages were studied by femtosecond infrared pump-probe spectroscopy. Densely packed, interpenetrated double cages were constructed from eight bis-monodentate redoxactive ligands bound to four Pd(ii) nodes. Two types of ligands consisting of electron rich phenothiazine (PTZ) or electron deficient anthraquinone (ANQ) chromophores were used to assemble either homo-octameric or mixed-ligand cages. Upon photoexcitation the homo-octameric acceptor cage undergoes intersystem crossing to a long-lived triplet state, similar to the free acceptor ligand. Excitation of the free donor ligand leads to a fluorescent state with intramolecular charge transfer character. This fluorescence is completely quenched in the homo-octameric donor double cage due to a ligand-to-metal charge transfer followed by back electron transfer on a ps timescale. Only for the mixed-ligand cage irradiation produces a charge separated state with an oxidized PTZ radical cation and a reduced ANQ radical anion as proven by their vibrational fingerprints in the transient IR spectra. In dichloromethane the lifetime of this charge separated state extends from tens of ps to >1.5 ns which is attributed to the broad distribution of mixed-ligand cages with different stoichiometry and/or stereo configurations.