N4BP1 coordinates ubiquitin-dependent crosstalk within the IκB kinase family to limit Toll-like receptor signaling and inflammation.

The ubiquitin-binding endoribonuclease N4BP1 potently suppresses cytokine production by Toll-like receptors (TLRs) that signal through the adaptor MyD88 but is inactivated via caspase-8-mediated cleavage downstream of death receptors, TLR3, or TLR4. Here, we examined the mechanism whereby N4BP1 limits inflammatory responses. In macrophages, deletion of N4BP1 prolonged activation of inflammatory gene transcription at late time points after TRIF-independent TLR activation. Optimal suppression of inflammatory cytokines by N4BP1 depended on its ability to bind polyubiquitin chains, as macrophages and mice-bearing inactivating mutations in a ubiquitin-binding motif in N4BP1 displayed increased TLR-induced cytokine production. Deletion of the noncanonical IκB kinases (ncIKKs), Tbk1 and Ikke, or their adaptor Tank phenocopied N4bp1 deficiency and enhanced macrophage responses to TLR1/2, TLR7, or TLR9 stimulation. Mechanistically, N4BP1 acted in concert with the ncIKKs to limit the duration of canonical IκB kinase (IKKα/ß) signaling. Thus, N4BP1 and the ncIKKs serve as an important checkpoint against over-exuberant innate immune responses.

Activation mechanism of PINK1.

Mutations in the protein kinase PINK1 lead to defects in mitophagy and cause autosomal recessive early onset Parkinson's disease1,2. PINK1 has many unique features that enable it to phosphorylate ubiquitin and the ubiquitin-like domain of Parkin3-9. Structural analysis of PINK1 from diverse insect species10-12 with and without ubiquitin provided snapshots of distinct structural states yet did not explain how PINK1 is activated. Here we elucidate the activation mechanism of PINK1 using crystallography and cryo-electron microscopy (cryo-EM). A crystal structure of unphosphorylated Pediculus humanus corporis (Ph; human body louse) PINK1 resolves an N-terminal helix, revealing the orientation of unphosphorylated yet active PINK1 on the mitochondria. We further provide a cryo-EM structure of a symmetric PhPINK1 dimer trapped during the process of trans-autophosphorylation, as well as a cryo-EM structure of phosphorylated PhPINK1 undergoing a conformational change to an active ubiquitin kinase state. Structures and phosphorylation studies further identify a role for regulatory PINK1 oxidation. Together, our research delineates the complete activation mechanism of PINK1, illuminates how PINK1 interacts with the mitochondrial outer membrane and reveals how PINK1 activity may be modulated by mitochondrial reactive oxygen species.

Integration of innate immune signalling by caspase-8 cleavage of N4BP1.

Mutations in the death receptor FAS1,2 or its ligand FASL3 cause autoimmune lymphoproliferative syndrome, whereas mutations in caspase-8 or its adaptor FADD-which mediate cell death downstream of FAS and FASL-cause severe immunodeficiency in addition to autoimmune lymphoproliferative syndrome4-6. Mouse models have corroborated a role for FADD-caspase-8 in promoting inflammatory responses7-12, but the mechanisms that underlie immunodeficiency remain undefined. Here we identify NEDD4-binding protein 1 (N4BP1) as a suppressor of cytokine production that is cleaved and inactivated by caspase-8. N4BP1 deletion in mice increased the production of select cytokines upon stimulation of the Toll-like receptor (TLR)1-TLR2 heterodimer (referred to herein as TLR1/2), TLR7 or TLR9, but not upon engagement of TLR3 or TLR4. N4BP1 did not suppress TLR3 or TLR4 responses in wild-type macrophages, owing to TRIF- and caspase-8-dependent cleavage of N4BP1. Notably, the impaired production of cytokines in response to TLR3 and TLR4 stimulation of caspase-8-deficient macrophages13 was largely rescued by co-deletion of N4BP1. Thus, the persistence of intact N4BP1 in caspase-8-deficient macrophages impairs their ability to mount robust cytokine responses. Tumour necrosis factor (TNF), like TLR3 or TLR4 agonists, also induced caspase-8-dependent cleavage of N4BP1, thereby licensing TRIF-independent TLRs to produce higher levels of inflammatory cytokines. Collectively, our results identify N4BP1 as a potent suppressor of cytokine responses; reveal N4BP1 cleavage by caspase-8 as a point of signal integration during inflammation; and offer an explanation for immunodeficiency caused by mutations of FADD and caspase-8.

Identification and characterization of diverse OTU deubiquitinases in bacteria.

Manipulation of host ubiquitin signaling is becoming an increasingly apparent evolutionary strategy among bacterial and viral pathogens. By removing host ubiquitin signals, for example, invading pathogens can inactivate immune response pathways and evade detection. The ovarian tumor (OTU) family of deubiquitinases regulates diverse ubiquitin signals in humans. Viral pathogens have also extensively co-opted the OTU fold to subvert host signaling, but the extent to which bacteria utilize the OTU fold was unknown. We have predicted and validated a set of OTU deubiquitinases encoded by several classes of pathogenic bacteria. Biochemical assays highlight the ubiquitin and polyubiquitin linkage specificities of these bacterial deubiquitinases. By determining the ubiquitin-bound structures of two examples, we demonstrate the novel strategies that have evolved to both thread an OTU fold and recognize a ubiquitin substrate. With these new examples, we perform the first cross-kingdom structural analysis of the OTU fold that highlights commonalities among distantly related OTU deubiquitinases.

Structure of PINK1 in complex with its substrate ubiquitin.

Autosomal-recessive juvenile Parkinsonism (AR-JP) is caused by mutations in a number of PARK genes, in particular the genes encoding the E3 ubiquitin ligase Parkin (PARK2, also known as PRKN) and its upstream protein kinase PINK1 (also known as PARK6). PINK1 phosphorylates both ubiquitin and the ubiquitin-like domain of Parkin on structurally protected Ser65 residues, triggering mitophagy. Here we report a crystal structure of a nanobody-stabilized complex containing Pediculus humanus corporis (Ph)PINK1 bound to ubiquitin in the 'C-terminally retracted' (Ub-CR) conformation. The structure reveals many peculiarities of PINK1, including the architecture of the C-terminal region, and reveals how the N lobe of PINK1 binds ubiquitin via a unique insertion. The flexible Ser65 loop in the Ub-CR conformation contacts the activation segment, facilitating placement of Ser65 in a phosphate-accepting position. The structure also explains how autophosphorylation in the N lobe stabilizes structurally and functionally important insertions, and reveals the molecular basis of AR-JP-causing mutations, some of which disrupt ubiquitin binding.

An invisible ubiquitin conformation is required for efficient phosphorylation by PINK1.

The Ser/Thr protein kinase PINK1 phosphorylates the well-folded, globular protein ubiquitin (Ub) at a relatively protected site, Ser65. We previously showed that Ser65 phosphorylation results in a conformational change in which Ub adopts a dynamic equilibrium between the known, common Ub conformation and a distinct, second conformation wherein the last ß-strand is retracted to extend the Ser65 loop and shorten the C-terminal tail. We show using chemical exchange saturation transfer (CEST) nuclear magnetic resonance experiments that a similar, C-terminally retracted (Ub-CR) conformation also exists at low population in wild-type Ub. Point mutations in the moving ß5 and neighbouring ß-strands shift the Ub/Ub-CR equilibrium. This enabled functional studies of the two states, and we show that while the Ub-CR conformation is defective for conjugation, it demonstrates improved binding to PINK1 through its extended Ser65 loop, and is a superior PINK1 substrate. Together our data suggest that PINK1 utilises a lowly populated yet more suitable Ub-CR conformation of Ub for efficient phosphorylation. Our findings could be relevant for many kinases that phosphorylate residues in folded protein domains.

Cyanide Bridged Platinum-Iron Complexes as Cisplatin Prodrug Systems: Design and Computational Study.

The potential role of cyanide-bridged platinum-iron complexes as an anti-cancer Pt(IV) prodrug is studied. We present design principles of a dual-function prodrug that can upon reduction dissociate and release concurrently six cisplatin units and a ferricyanide anion per prodrug unit. The prodrug molecule is a unique complex of hepta metal centers consisting of a ferricyanide core with six Pt(IV) centers each bonded to the Fe(III) core through a cyano ligand. The functionality of the prodrug is addressed through density functional theory (DFT) calculations.

Mechanism of phospho-ubiquitin-induced PARKIN activation.

The E3 ubiquitin ligase PARKIN (encoded by PARK2) and the protein kinase PINK1 (encoded by PARK6) are mutated in autosomal-recessive juvenile Parkinsonism (AR-JP) and work together in the disposal of damaged mitochondria by mitophagy. PINK1 is stabilized on the outside of depolarized mitochondria and phosphorylates polyubiquitin as well as the PARKIN ubiquitin-like (Ubl) domain. These phosphorylation events lead to PARKIN recruitment to mitochondria, and activation by an unknown allosteric mechanism. Here we present the crystal structure of Pediculus humanus PARKIN in complex with Ser65-phosphorylated ubiquitin (phosphoUb), revealing the molecular basis for PARKIN recruitment and activation. The phosphoUb binding site on PARKIN comprises a conserved phosphate pocket and harbours residues mutated in patients with AR-JP. PhosphoUb binding leads to straightening of a helix in the RING1 domain, and the resulting conformational changes release the Ubl domain from the PARKIN core; this activates PARKIN. Moreover, phosphoUb-mediated Ubl release enhances Ubl phosphorylation by PINK1, leading to conformational changes within the Ubl domain and stabilization of an open, active conformation of PARKIN. We redefine the role of the Ubl domain not only as an inhibitory but also as an activating element that is restrained in inactive PARKIN and released by phosphoUb. Our work opens up new avenues to identify small-molecule PARKIN activators.

Simulating energy transfer dynamics in the Fenna-Matthews-Olson complex via the modified generalized quantum master equation.

The generalized quantum master equation (GQME) provides a general and formally exact framework for simulating the reduced dynamics of open quantum systems. The recently introduced modified approach to the GQME (M-GQME) corresponds to a specific implementation of the GQME that is geared toward simulating the dynamics of the electronic reduced density matrix in systems governed by an excitonic Hamiltonian. Such a Hamiltonian, which is often used for describing energy and charge transfer dynamics in complex molecular systems, is given in terms of diabatic electronic states that are coupled to each other and correspond to different nuclear Hamiltonians. Within the M-GQME approach, the effect of the nuclear degrees of freedom on the time evolution of the electronic density matrix is fully captured by a memory kernel superoperator, which can be obtained from short-lived (compared to the time scale of energy/charge transfer) projection-free inputs. In this paper, we test the ability of the M-GQME to predict the energy transfer dynamics within a seven-state benchmark model of the Fenna-Matthews-Olson (FMO) complex, with the short-lived projection-free inputs obtained via the Ehrenfest method. The M-GQME with Ehrenfest-based inputs is shown to yield accurate results across a wide parameter range. It is also found to dramatically outperform the direct application of the Ehrenfest method and to provide better-behaved convergence with respect to memory time in comparison to an alternative implementation of the GQME approach previously applied to the same FMO model.

A modified approach for simulating electronically nonadiabatic dynamics via the generalized quantum master equation.

We present a modified approach for simulating electronically nonadiabatic dynamics based on the Nakajima-Zwanzig generalized quantum master equation (GQME). The modified approach utilizes the fact that the Nakajima-Zwanzig formalism does not require casting the overall Hamiltonian in system-bath form, which is arguably neither natural nor convenient in the case of the Hamiltonian that governs nonadiabatic dynamics. Within the modified approach, the effect of the nuclear degrees of freedom on the time evolution of the electronic reduced density operator is fully captured by a memory kernel super-operator. A methodology for calculating the memory kernel from projection-free inputs is developed. Simulating the electronic dynamics via the modified approach, with a memory kernel obtained using exact or approximate methods, can be more cost effective and/or lead to more accurate results than direct application of those methods. The modified approach is compared to previously proposed GQME-based approaches, and its robustness and accuracy are demonstrated on a benchmark spin-boson model with a memory kernel which is calculated within the Ehrenfest method.

Combining the mapping Hamiltonian linearized semiclassical approach with the generalized quantum master equation to simulate electronically nonadiabatic molecular dynamics.

The generalized quantum master equation (GQME) provides a powerful framework for simulating electronically nonadiabatic molecular dynamics. Within this framework, the effect of the nuclear degrees of freedom on the time evolution of the electronic reduced density matrix is fully captured by a memory kernel superoperator. In this paper, we consider two different procedures for calculating the memory kernel of the GQME from projection-free inputs obtained via the combination of the mapping Hamiltonian (MH) approach and the linearized semiclassical (LSC) approximation. The accuracy and feasibility of the two procedures are demonstrated on the spin-boson model. We find that although simulating the electronic dynamics by direct application of the two LSC-based procedures leads to qualitatively different results that become increasingly less accurate with increasing time, restricting their use to calculating the memory kernel leads to an accurate description of the electronic dynamics. Comparison with a previously proposed procedure for calculating the memory kernel via the Ehrenfest method reveals that MH/LSC methods produce memory kernels that are better behaved at long times and lead to more accurate electronic dynamics.

A novel approach for assessing effects of ship traffic on distributions and movements of seabirds.

Marine habitats are nowadays strongly affected by human activities, while for many species the consequences of these impacts are still unclear. The red-throated diver (Gavia stellata) has been reported to be sensitive to ship traffic and other anthropogenic pressures and is consequently of high conservation concern. We studied red-throated divers in the German Bight (North Sea) using satellite telemetry and digital aerial surveys with the aim of assessing effects of ship traffic on the distribution and movements of this species during the non-breeding season. Data from the automatic identification system of ships (AIS) were intersected with bird data and allowed detailed spatial and temporal analyses. During the study period, ship traffic was present throughout the main distribution area of divers. Depending on impact radius, only small areas existed in which ship traffic was present on less than 20% of the days. Ship traffic was dominated by fishing vessels and cargo ships, but also wind farm-related ships were frequently recorded. Red-throated divers were more abundant in areas with no or little concurrent ship traffic. Analysis of aerial survey data revealed strong effects of ship speed on divers: in areas with vessels sailing at high speed only a slow resettlement of the area was observed after the disturbance, while in areas with vessels sailing at medium speed the resettlement was more rapid during the observed time period of 7 hours. Data from satellite-tracking of divers suggest that large relocation distances of individuals are related to disturbance by ships which often trigger birds to take flight. Effective measures to reduce disturbance could include channeled traffic in sensitive areas, as well as speed limits for ships traveling within the protected marine area.

Outcome of non-surgical root canal treatment related to periodontitis and chronic disease medication among adults in age group of 60 years or more.

OBJECTIVE: To assess the impact of non-endodontic factors like periodontitis and chronic disease medication (CDM) mostly affecting elderly people's health on the outcome of non-surgical root canal treatment (NSRCT). BACKGROUND: An increasing number of elderly people with high prevalence of marginal periodontitis and CDM benefit from adequate endodontic therapy, if irreversible pulpitis or apical periodontitis occurs. Only few data exist about the relevance of those non-endodontic factors on healing of endodontic lesions in a population 60 years or more. MATERIAL AND METHODS: Of 177 patients aged 60 years or more with 212 NSRCTs performed between the year of 2010 and 2013, complete documentation was available for 112 teeth in 93 participants. Mean time between baseline and last follow-up was 38.93 months. The primary endodontic factors studied were the periapical index (PAI) of periapical health, quality of the root canal filling and of coronal restoration, periodontal probing depth (PPD, mm) and tooth mobility (TM, 0-3). Secondary non-endodontic factors included the presence of marginal periodontitis and CDM, in particular antidiabetics, antihypertensives and anticoagulants. Statistical analyses were performed using Chi-square test statistics and logistic regression analysis. RESULTS: Periodontitis and CDM had no effect on endodontic outcome. Chronic intake of anticoagulants showed a significant association with endodontic outcome. Root-filled teeth with preoperative periapical lesions had a significantly higher rate of endodontic failure than those without preoperative lesion. The overall success rate of NSRCT was 87.1% with 81 healed teeth. CONCLUSION: Periodontitis and CDM have no impact on the endodontic outcome of NSRCT in a population 60 years or more.

A comparative study of different methods for calculating electronic transition rates.

We present a comprehensive comparison of the following mixed quantum-classical methods for calculating electronic transition rates: (1) nonequilibrium Fermi's golden rule, (2) mixed quantum-classical Liouville method, (3) mean-field (Ehrenfest) mixed quantum-classical method, and (4) fewest switches surface-hopping method (in diabatic and adiabatic representations). The comparison is performed on the Garg-Onuchic-Ambegaokar benchmark charge-transfer model, over a broad range of temperatures and electronic coupling strengths, with different nonequilibrium initial states, in the normal and inverted regimes. Under weak to moderate electronic coupling, the nonequilibrium Fermi's golden rule rates are found to be in good agreement with the rates obtained via the mixed quantum-classical Liouville method that coincides with the fully quantum-mechanically exact results for the model system under study. Our results suggest that the nonequilibrium Fermi's golden rule can serve as an inexpensive yet accurate alternative to Ehrenfest and the fewest switches surface-hopping methods.

Mixed quantum-classical simulations of the vibrational relaxation of photolyzed carbon monoxide in a hemoprotein.

We present mixed quantum-classical simulations on relaxation and dephasing of vibrationally excited carbon monoxide within a protein environment. The methodology is based on a vibrational surface hopping approach treating the vibrational states of CO quantum mechanically, while all remaining degrees of freedom are described by means of classical molecular dynamics. The CO vibrational states form the "surfaces" for the classical trajectories of protein and solvent atoms. In return, environmentally induced non-adiabatic couplings between these states cause transitions describing the vibrational relaxation from first principles. The molecular dynamics simulation yields a detailed atomistic picture of the energy relaxation pathways, taking the molecular structure and dynamics of the protein and its solvent fully into account. Using the ultrafast photolysis of CO in the hemoprotein FixL as an example, we study the relaxation of vibrationally excited CO and evaluate the role of each of the FixL residues forming the heme pocket.

Identification of ultrafast relaxation processes as a major reason for inefficient exciton diffusion in perylene-based organic semiconductors.

The exciton diffusion length (LD) is a key parameter for the efficiency of organic optoelectronic devices. Its limitation to the nm length scale causes the need of complex bulk-heterojunction solar cells incorporating difficulties in long-term stability and reproducibility. A comprehensive model providing an atomistic understanding of processes that limit exciton trasport is therefore highly desirable and will be proposed here for perylene-based materials. Our model is based on simulations with a hybrid approach which combines high-level ab initio computations for the part of the system directly involved in the described processes with a force field to include environmental effects. The adequacy of the model is shown by detailed comparison with available experimental results. The model indicates that the short exciton diffusion lengths of α-perylene tetracarboxylicdianhydride (PTCDA) are due to ultrafast relaxation processes of the optical excitation via intermolecular motions leading to a state from which further exciton diffusion is hampered. As the efficiency of this mechanism depends strongly on molecular arrangement and environment, the model explains the strong dependence of LD on the morphology of the materials, for example, the differences between α-PTCDA and diindenoperylene. Our findings indicate how relaxation processes can be diminished in perylene-based materials. This model can be generalized to other organic compounds.

Theoretical analysis of the relaxation dynamics in perylene bisimide dimers excited by femtosecond laser pulses.

We present a model for the relaxation dynamics in perylene bisimide dimers, which is based on ab initio electronic structure and quantum dynamics calculations including effects of dissipation. The excited-state dynamics proceeds via a mixing of electronic states of local Frenkel and charge-transfer characters, which becomes effective upon a small distortion of the dimer geometry. In this way, it is possible to explain the fast depopulation of the photoexcited state, which we characterize by femtosecond transient absorption measurements. The combined theoretical and experimental analysis hints at a trapping mechanism, which involves nonadiabatic and dissipative dynamics in an excited-state vibronic manifold and provides an atomistic picture that might prove valuable for future design of photovoltaic materials.