Condensed-phase isomerization through tunnelling gateways.

Quantum mechanical tunnelling describes transmission of matter waves through a barrier with height larger than the energy of the wave1. Tunnelling becomes important when the de Broglie wavelength of the particle exceeds the barrier thickness; because wavelength increases with decreasing mass, lighter particles tunnel more efficiently than heavier ones. However, there exist examples in condensed-phase chemistry where increasing mass leads to increased tunnelling rates2. In contrast to the textbook approach, which considers transitions between continuum states, condensed-phase reactions involve transitions between bound states of reactants and products. Here this conceptual distinction is highlighted by experimental measurements of isotopologue-specific tunnelling rates for CO rotational isomerization at an NaCl surface3,4, showing nonmonotonic mass dependence. A quantum rate theory of isomerization is developed wherein transitions between sub-barrier reactant and product states occur through interaction with the environment. Tunnelling is fastest for specific pairs of states (gateways), the quantum mechanical details of which lead to enhanced cross-barrier coupling; the energies of these gateways arise nonsystematically, giving an erratic mass dependence. Gateways also accelerate ground-state isomerization, acting as leaky holes through the reaction barrier. This simple model provides a way to account for tunnelling in condensed-phase chemistry, and indicates that heavy-atom tunnelling may be more important than typically assumed.

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 transfer1-3 (FRET) are critical to the operation of biological light-harvesting systems4, and are used in various artificial systems made of synthetic dyes5, polymers6 or nanodots7,8. 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 reactions10-16, 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.

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.

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.

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.

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.

Velocity-resolved kinetics of site-specific carbon monoxide oxidation on platinum surfaces.

Catalysts are widely used to increase reaction rates. They function by stabilizing the transition state of the reaction at their active site, where the atomic arrangement ensures favourable interactions 1 . However, mechanistic understanding is often limited when catalysts possess multiple active sites-such as sites associated with either the step edges or the close-packed terraces of inorganic nanoparticles2-4-with distinct activities that cannot be measured simultaneously. An example is the oxidation of carbon monoxide over platinum surfaces, one of the oldest and best studied heterogeneous reactions. In 1824, this reaction was recognized to be crucial for the function of the Davy safety lamp, and today it is used to optimize combustion, hydrogen production and fuel-cell operation5,6. The carbon dioxide products are formed in a bimodal kinetic energy distribution7-13; however, despite extensive study 5 , it remains unclear whether this reflects the involvement of more than one reaction mechanism occurring at multiple active sites12,13. Here we show that the reaction rates at different active sites can be measured simultaneously, using molecular beams to controllably introduce reactants and slice ion imaging14,15 to map the velocity vectors of the product molecules, which reflect the symmetry and the orientation of the active site 16 . We use this velocity-resolved kinetics approach to map the oxidation rates of carbon monoxide at step edges and terrace sites on platinum surfaces, and find that the reaction proceeds through two distinct channels11-13: it is dominated at low temperatures by the more active step sites, and at high temperatures by the more abundant terrace sites. We expect our approach to be applicable to a wide range of heterogeneous reactions and to provide improved mechanistic understanding of the contribution of different active sites, which should be useful in the design of improved catalysts.

Modulations of DNA Contacts by Linker Histones and Post-translational Modifications Determine the Mobility and Modifiability of Nucleosomal H3 Tails.

Post-translational histone modifications and linker histone incorporation regulate chromatin structure and genome activity. How these systems interface on a molecular level is unclear. Using biochemistry and NMR spectroscopy, we deduced mechanistic insights into the modification behavior of N-terminal histone H3 tails in different nucleosomal contexts. We find that linker histones generally inhibit modifications of different H3 sites and reduce H3 tail dynamics in nucleosomes. These effects are caused by modulations of electrostatic interactions of H3 tails with linker DNA and largely depend on the C-terminal domains of linker histones. In agreement, linker histone occupancy and H3 tail modifications segregate on a genome-wide level. Charge-modulating modifications such as phosphorylation and acetylation weaken transient H3 tail-linker DNA interactions, increase H3 tail dynamics, and, concomitantly, enhance general modifiability. We propose that alterations of H3 tail-linker DNA interactions by linker histones and charge-modulating modifications execute basal control mechanisms of chromatin function.

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.

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.

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.

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.

Steric Hindrance of NH3 Diffusion on Pt(111) by Co-Adsorbed O-Atoms.

A detailed velocity-resolved kinetics study of NH3 thermal desorption rates from p(2 × 2) O/Pt(111) is presented. We find a large reduction in the NH3 desorption rate due to adsorption of O-atoms on Pt(111). A physical model describing the interactions between adsorbed NH3 and O-atoms explains these observations. By fitting the model to the derived desorption rate constants, we find an NH3 stabilization on p(2 × 2) O/Pt(111) of 0.147-0.014+0.023 eV compared to Pt(111) and a rotational barrier of 0.084-0.022+0.049 eV, which is not present on Pt(111). The model also quantitatively predicts the steric hindrance of NH3 diffusion on Pt(111) due to co-adsorbed O-atoms. The derived diffusion barrier of NH3 on p(2 × 2) O/Pt(111) is 1.10-0.13+0.22 eV, which is 0.39-0.14+0.22 eV higher than that on pristine Pt(111). We find that Perdew Burke Ernzerhof (PBE) and revised Perdew Burke Ernzerhof (RPBE) exchange-correlation functionals are unable to reproduce the experimentally observed NH3-O adsorbate-adsorbate interactions and NH3 binding energies at Pt(111) and p(2 × 2) O/Pt(111), which indicates the importance of dispersion interactions for both systems.

Identification and structural basis of C-terminal cyclic imides as natural degrons for cereblon.

Cereblon (CRBN) is a ubiquitously expressed E3 ligase substrate receptor and a key player in pharmaceutical targeted protein degradation. Despite substantial insight gained into its chemical ligand space that is exploited in small-molecule protein degraders, its cellular role and native mechanism of substrate recognition remained elusive so far. In this communication, we report the discovery of C-terminal aspartimide and aminoglutarimide residues as natural degron motifs that are recognized by CRBN with high specificity. These C-terminal cyclic imides are known to form in ageing proteins as a result of spontaneous chain breaks after an attack of an asparagine or glutamine side chain amide on the adjacent peptide bond, and thereby mark potentially malfunctional protein fragments. In crystal structures, we uncover that these C-terminal cyclic imides are bound in the same fashion as small-molecule CRBN modulators, and that the residues preceding the cyclic terminus contribute to the interaction with a sequence-unspecific backbone hydrogen bonding pattern with strictly conserved residues in CRBN. We postulate that C-terminal aspartimide and aminoglutarimide residues resulting from chain breaks are largely underappreciated protein damages and represent the native degrons of CRBN.

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.

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 pKa = 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.

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.

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.

Accessibility of different histone H3-binding domains of UHRF1 is allosterically regulated by phosphatidylinositol 5-phosphate.

UHRF1 is a multidomain protein crucially linking histone H3 modification states and DNA methylation. While the interaction properties of its specific domains are well characterized, little is known about the regulation of these functionalities. We show that UHRF1 exists in distinct active states, binding either unmodified H3 or the H3 lysine 9 trimethylation (H3K9me3) modification. A polybasic region (PBR) in the C terminus blocks interaction of a tandem tudor domain (TTD) with H3K9me3 by occupying an essential peptide-binding groove. In this state the plant homeodomain (PHD) mediates interaction with the extreme N terminus of the unmodified H3 tail. Binding of the phosphatidylinositol phosphate PI5P to the PBR of UHRF1 results in a conformational rearrangement of the domains, allowing the TTD to bind H3K9me3. Our results define an allosteric mechanism controlling heterochromatin association of an essential regulatory protein of epigenetic states and identify a functional role for enigmatic nuclear phosphatidylinositol phosphates.

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.