Chromophore Protonation State Controls Photoswitching of the Fluoroprotein asFP595

Fluorescent proteins have been widely used as genetically encodable fusion tags for biological imaging. Recently, a new class of fluorescent proteins was discovered that can be reversibly light-switched between a fluorescent and a non-fluorescent state. Such proteins can not only provide nanoscale resolution in far-field fluorescence optical microscopy much below the diffraction limit, but also hold promise for other nanotechnological applications, such as optical data storage. To systematically exploit the potential of such photoswitchable proteins and to enable rational improvements to their properties requires a detailed understanding of the molecular switching mechanism, which is currently unknown. Here, we have studied the photoswitching mechanism of the reversibly switchable fluoroprotein asFP595 at the atomic level by multiconfigurational ab initio (CASSCF) calculations and QM/MM excited state molecular dynamics simulations with explicit surface hopping. Our simulations explain measured quantum yields and excited state lifetimes, and also predict the structures of the hitherto unknown intermediates and of the irreversibly fluorescent state. Further, we find that the proton distribution in the active site of the asFP595 controls the photochemical conversion pathways of the chromophore in the protein matrix. Accordingly, changes in the protonation state of the chromophore and some proximal amino acids lead to different photochemical states, which all turn out to be essential for the photoswitching mechanism. These photochemical states are (i) a neutral chromophore, which can trans-cis photoisomerize, (ii) an anionic chromophore, which rapidly undergoes radiationless decay after excitation, and (iii) a putative fluorescent zwitterionic chromophore. The overall stability of the different protonation states is controlled by the isomeric state of the chromophore. We finally propose that radiation-induced decarboxylation of the glutamic acid Glu215 blocks the proton transfer pathways that enable the deactivation of the zwitterionic chromophore and thus leads to irreversible fluorescence. We have identified the tight coupling of trans-cis isomerization and proton transfers in photoswitchable proteins to be essential for their function and propose a detailed underlying mechanism, which provides a comprehensive picture that explains the available experimental data. The structural similarity between asFP595 and other fluoroproteins of interest for imaging suggests that this coupling is a quite general mechanism for photoswitchable proteins. These insights can guide the rational design and optimization of photoswitchable proteins

Thermodynamic Driving Forces of Guest Confinement in a Photoswitchable Cage

Photoswitchable cages that confine small guest molecules inside their cavities offer a way to control the binding/unbinding process through irradiation with light of different wavelengths. However, a detailed characterization of the structural and thermodynamic consequences of photoswitching is very challenging to obtain by experiment alone. Thus, all-atom molecular dynamics (MD) simulations were carried out to gain insight into the relationship between structure and binding affinity. Binding free energies of the B12F122- guest were obtained for all photochemically accessible forms of a photoswitchable dithienylethene (DTE) based coordination cage. The MD simulations show that successive photo-induced closure of the four individual DTE ligands that form the cage gradually decreases the binding affinity. Closure of the first ligand already significantly lowers the unbinding barrier and the binding free energy, and therefore favours guest unbinding both kinetically and thermodynamically. Analysis of the different enthalpy contributions to the free energy shows that binding is enthalpically unfavourable and thus an entropy-driven process, in agreement with experimental data. Dissecting the enthalpy into the contributions from electrostatic, van der Waals, and bonded interactions in the force field shows that the unfavourable binding enthalpy is due to the bonded interactions being more favourable in the dissociated state, suggesting the presence of structural strain in the bound complex. Thus, the simulations provide microscopic explanations for the experimental findings and open a possible route towards the targeted design of switchable nanocontainers with modified binding properties

Laparoscopic mesh-augmented hiatoplasty without fundoplication as a method to treat large hiatal hernias

PURPOSE: Laparoscopic hiatal hernia repair with additional fundoplication is a commonly recommended standard surgical treatment for symptomatic large hiatal hernias with paraesophageal involvement (PEH). However, due to the risk of persistent side effects, this method remains controversial. Laparoscopic mesh-augmented hiatoplasty without fundoplication (LMAH), which combines hiatal repair and mesh reinforcement, might therefore be an alternative. METHODS: In this retrospective study of 55 (25 male, 30 female) consecutive PEH patients, the perioperative course and symptomatic outcomes were analyzed after a mean follow-up of 72 months. RESULTS: The mean DeMeester symptom score decreased from 5.1 to 1.8 (P < 0.001) and the gas bloating value decreased from 1.2 to 0.5 (P = 0.001). The dysphagia value was 0.7 before surgery and 0.6 (P = 0.379) after surgery. The majority of the patients were able to belch and vomit (96 and 92 %, respectively). Acid-suppressive therapy on a regular basis was discontinued in 68 % of patients. In 4 % of patients, reoperation was necessary due to recurrent or persistent reflux. A mesh-related stenosis that required endoscopic dilatation occurred in 2 % of patients. CONCLUSIONS: LMAH is feasible, safe and provides an anti-reflux effect, even without fundoplication. As operation-related side effects seem to be rare, LMAH is a potential treatment option for large hiatal hernias with paraesophageal involvement

The ABC transporter MsbA adopts the wide inward-open conformation in E. coli cells

Membrane proteins are currently investigated after detergent extraction from native cellular membranes and reconstitution into artificial liposomes or nanodiscs, thereby removing them from their physiological environment. However, to truly understand the biophysical properties of membrane proteins in a physiological environment, they must be investigated within living cells. Here, we used a spin-labeled nanobody to interrogate the conformational cycle of the ABC transporter MsbA by double electron-electron resonance. Unexpectedly, the wide inward-open conformation of MsbA, commonly considered a nonphysiological state, was found to be prominently populated in Escherichia coli cells. Molecular dynamics simulations revealed that extensive lateral portal opening is essential to provide access of its large natural substrate core lipid A to the binding cavity. Our work paves the way to investigate the conformational landscape of membrane proteins in cells

Steuerung der ultraschnellen Öffnungs‐ und Schließungsdynamik eines photochromen Koordinationskäfigs durch Gastmoleküle

Photochemische Studien über supramolekulare Wirte, die kleine Gastmoleküle einkapseln können, konzentrieren sich zumeist auf drei Aspekte: Die Photoschaltung des Käfigs, um den Gast freizusetzen oder einzufangen, die Wirkung der Käfigumgebung auf den Gast und die lichtinduzierte Exzitonen- oder Ladungsübertragung innerhalb der Käfigstruktur. Hier nutzen wir ultraschnelle Spektroskopie, um zu untersuchen, wie der Gast die Photoschaltcharakteristik des Käfigs verändert. Zu diesem Zweck werden die Auswirkungen von drei unterschiedlichen Gastmolekülen auf die Ringöffnung oder den Ringschluss eines Dithienylethen (DTE)-Liganden in einem photoschaltbaren Koordinationskäfig auf DTE-Basis einander gegenübergestellt. Der Gast moduliert sowohl das Ergebnis als auch die Zeitskala der Photodynamik des Käfigs durch ein Zusammenspiel von struktureller Wechselwirkung, dem Schweratomeffekt und einer Verstärkung von Ladungstransferprozessen, die der Gast auf den photoangeregten Käfig ausübt. Der Ansatz könnte sich als nützlich erweisen, um die Anwendbarkeit von photoschaltbaren Nanocontainern und gewünschten Gastverbindungen aufeinander abzustimmen

Steering the Ultrafast Opening and Closure Dynamics of a Photochromic Coordination Cage by Guest Molecules

Photochemical studies on supramolecular hosts that can encapsulate small guest molecules commonly focus on three aspects: photoswitching the cage to release or trap the guest, the effect of the confining environment on the guest, and light-induced exciton or charge transfer within the cage structure. Here, we exploit ultrafast spectroscopy to address how the guest alters the photoswitching characteristics of the cage. For this, the impacts of three disparate guest compounds on ring-opening or ring-closure of a dithienylethene (DTE) ligand in a photoswitchable DTE-based coordination cage are juxtaposed. The guest modulates both outcome and timescale of the cage's photodynamics, by an interplay of structural strain, heavy-atom effect, and enhancement of charge-transfer processes exercised by the guest on the photo-excited cage. The approach might prove beneficial for attuning the applicability of photoswitchable nanocontainers and desired guest compounds

Large-scale ordering of nanoparticles using viscoelastic shear processing

This is the author accepted manuscript. It is currently under an indefinite embargo pending publication by Nature Publishing Group.Despite the availability of elaborate varieties of nanoparticles, their assembly into regular superstructures and photonic materials remains challenging. Here we show how flexible films of stacked polymer nanoparticles can be directly assembled in a roll-to-roll process using a bending-induced oscillatory shear (BIOS) technique. For sub-micron spherical nanoparticles, this gives elastomeric photonic crystals termed polymer opals showing extremely strong structural colour. With oscillatory strain amplitudes of 300%, crystallisation initiates at the wall and develops quickly across the bulk within only 5 oscillations yielding sharp intense reflectance peaks of tunable colour. The resulting structure of randomly stacked hexagonal close-packed layers parallel to the shear plane, is improved by shearing bidirectionally, alternating between two in-plane directions. Our theoretical framework indicates how the reduction in shear viscosity with increasing order of each layer accounts for these results, even when diffusion is totally absent. This general principle of shear ordering in viscoelastic media opens the way to manufacturable photonics materials, and forms a generic tool for ordering nanoparticles.We acknowledge EPSRC grants EP/G060649/1, EP/H027130/1, EP/E040241, EP/L027151/1 and EU ERC grants LINASS 320503 and FP7 291522-3DIMAGE

Novel insights into host-fungal pathogen interactions derived from live-cell imaging

Acknowledgments The authors acknowledge funding from the Wellcome Trust (080088, 086827, 075470 and 099215) including a Wellcome Trust Strategic Award for Medical Mycology and Fungal Immunology 097377 and FP7-2007–2013 grant agreement HEALTH-F2-2010-260338–ALLFUN to NARG.Peer reviewedPublisher PD

Polarizable Water Model for the Coarse-Grained MARTINI Force Field

Coarse-grained (CG) simulations have become an essential tool to study a large variety of biomolecular processes, exploring temporal and spatial scales inaccessible to traditional models of atomistic resolution. One of the major simplifications of CG models is the representation of the solvent, which is either implicit or modeled explicitly as a van der Waals particle. The effect of polarization, and thus a proper screening of interactions depending on the local environment, is absent. Given the important role of water as a ubiquitous solvent in biological systems, its treatment is crucial to the properties derived from simulation studies. Here, we parameterize a polarizable coarse-grained water model to be used in combination with the CG MARTINI force field. Using a three-bead model to represent four water molecules, we show that the orientational polarizability of real water can be effectively accounted for. This has the consequence that the dielectric screening of bulk water is reproduced. At the same time, we parameterized our new water model such that bulk water density and oil/water partitioning data remain at the same level of accuracy as for the standard MARTINI force field. We apply the new model to two cases for which current CG force fields are inadequate. First, we address the transport of ions across a lipid membrane. The computed potential of mean force shows that the ions now naturally feel the change in dielectric medium when moving from the high dielectric aqueous phase toward the low dielectric membrane interior. In the second application we consider the electroporation process of both an oil slab and a lipid bilayer. The electrostatic field drives the formation of water filled pores in both cases, following a similar mechanism as seen with atomistically detailed models

Machine learning algorithms performed no better than regression models for prognostication in traumatic brain injury

Objective: We aimed to explore the added value of common machine learning (ML) algorithms for prediction of outcome for moderate and severe traumatic brain injury. Study Design and Setting: We performed logistic regression (LR), lasso regression, and ridge regression with key baseline predictors in the IMPACT-II database (15 studies, n = 11,022). ML algorithms included support vector machines, random forests, gradient boosting machines, and artificial neural networks and were trained using the same predictors. To assess generalizability of predictions, we performed internal, internal-external, and external validation on the recent CENTER-TBI study (patients with Glasgow Coma Scale <13, n = 1,554). Both calibration (calibration slope/intercept) and discrimination (area under the curve) was quantified. Results: In the IMPACT-II database, 3,332/11,022 (30%) died and 5,233(48%) had unfavorable outcome (Glasgow Outcome Scale less than 4). In the CENTER-TBI study, 348/1,554(29%) died and 651(54%) had unfavorable outcome. Discrimination and calibration varied widely between the studies and less so between the studied algorithms. The mean area under the curve was 0.82 for mortality and 0.77 for unfavorable outcomes in the CENTER-TBI study. Conclusion: ML algorithms may not outperform traditional regression approaches in a low-dimensional setting for outcome prediction after moderate or severe traumatic brain injury. Similar to regression-based prediction models, ML algorithms should be rigorously validated to ensure applicability to new populations