Polyreactive Broadly Neutralizing B cells Are Selected to Provide Defense against Pandemic Threat Influenza Viruses.

Polyreactivity is the ability of a single antibody to bind to multiple molecularly distinct antigens and is a common feature of antibodies induced upon pathogen exposure. However, little is known about the role of polyreactivity during anti-influenza virus antibody responses. By analyzing more than 500 monoclonal antibodies (mAbs) derived from B cells induced by numerous influenza virus vaccines and infections, we found mAbs targeting conserved neutralizing influenza virus hemagglutinin epitopes were polyreactive. Polyreactive mAbs were preferentially induced by novel viral exposures due to their broad viral binding breadth. Polyreactivity augmented mAb viral binding strength by increasing antibody flexibility, allowing for adaption to imperfectly conserved epitopes. Lastly, we found affinity-matured polyreactive B cells were typically derived from germline polyreactive B cells that were preferentially selected to participate in B cell responses over time. Together, our data reveal that polyreactivity is a beneficial feature of antibodies targeting conserved epitopes.

Broadly neutralizing antibodies target a haemagglutinin anchor epitope.

Broadly neutralizing antibodies that target epitopes of haemagglutinin on the influenza virus have the potential to provide near universal protection against influenza virus infection1. However, viral mutants that escape broadly neutralizing antibodies have been reported2,3. The identification of broadly neutralizing antibody classes that can neutralize viral escape mutants is critical for universal influenza virus vaccine design. Here we report a distinct class of broadly neutralizing antibodies that target a discrete membrane-proximal anchor epitope of the haemagglutinin stalk domain. Anchor epitope-targeting antibodies are broadly neutralizing across H1 viruses and can cross-react with H2 and H5 viruses that are a pandemic threat. Antibodies that target this anchor epitope utilize a highly restricted repertoire, which encodes two public binding motifs that make extensive contacts with conserved residues in the fusion peptide. Moreover, anchor epitope-targeting B cells are common in the human memory B cell repertoire and were recalled in humans by an oil-in-water adjuvanted chimeric haemagglutinin vaccine4,5, which is a potential universal influenza virus vaccine. To maximize protection against seasonal and pandemic influenza viruses, vaccines should aim to boost this previously untapped source of broadly neutralizing antibodies that are widespread in the human memory B cell pool.

Germline de novo variant F747S extends the phenotypic spectrum of CACNA1D Ca2+ channelopathies.

Germline gain-of-function missense variants in the pore-forming Cav1.3 α1-subunit (CACNA1D gene) confer high risk for a severe neurodevelopmental disorder with or without endocrine symptoms. Here, we report a 4-week-old new-born with the novel de novo missense variant F747S with a so far not described prominent jittering phenotype in addition to symptoms previously reported for CACNA1D mutations including developmental delay, elevated aldosterone level and transient hypoglycemia. We confirmed the pathogenicity of this variant in whole-cell patch-clamp experiments with wild-type and F747S mutant channels heterologously expressed together with α2δ1 and cytosolic ß3 or membrane-bound ß2a subunits. Mutation F747S caused the quantitatively largest shift in the voltage dependence of activation (-28 mV) reported so far for CACNA1D germline mutations. It also shifted inactivation to more negative voltages, slowed the time course of current inactivation and slowed current deactivation upon repolarization with both co-expressed ß-subunits. In silico modelling and molecular docking, simulations revealed that this gain-of-function phenotype can be explained by formation of a novel inter-domain hydrogen bond between mutant residues S747 (IIS6) with N1145 (IIIS6) stabilizing selectively the activated open channel state. F747S displayed 2-6-fold increased sensitivity for the L-type Ca2+ channel blocker isradipine compared to wild type. Our data confirm the pathogenicity of the F747S variant with very strong gain-of-function gating changes, which may contribute to the novel jittering phenotype. Increased sensitivity for isradipine suggests this drug for potential symptomatic off-label treatment for carriers of this mutation.

Zero-Point-Energy Driven Isotopic Exchange of the [H3O]- anion Probed by Mid-Infrared Action Spectroscopy.

We present the first observation of vibrational transitions in the [H3O]- anion, an intermediate in the anion-molecule reaction of water, H2O, and hydride, H-, using a laser-induced isotopic H/D exchange reaction action spectroscopy scheme applied to anions. The observed bands are assigned as the fundamental and first overtone of the H2O-H- vibrational stretching mode, based on anharmonic calculations within the vibrational perturbation theory and vibrational configuration interaction. Although the D2O·D- species has the lowest energy, our experiments confirm the D2O·H- isotope to be a sink of the H/D exchange reaction. Ab initio calculations corroborate that the formation of D2O·H- is favored, as the zero-point-energy difference is larger between D2 and H2 than between D2O·H- and D2O·D-.

CDR L3 Loop Rearrangement Switches Multispecific SPE-7 IgE Antibody From Hapten to Protein Binding.

The monoclonal IgE antibody SPE-7 was originally raised against a 2,4-dinitrophenyl (DNP) target. Through its ability to adopt multiple conformations, the antibody is capable of binding to a diverse range of small haptens and large proteins. The present study examines a dataset of experimentally determined crystal structures of the SPE-7 antibody to gain insight into the mechanisms that contribute to its multispecificity. With the emergence of more and more therapeutic antibodies against a huge repertoire of different targets, our research could be of great interest for future drug development. We are able to discriminate between the different paratope-binding states in the conformational ensembles obtained by enhanced sampling molecular dynamics simulations, and to calculate their transition timescales and state probabilities. Furthermore, we describe the key residues responsible for discriminating between the different binding capacities and identify a tryptophan in a central position of the CDR L3 loop as the residue of greatest interest. The overall dynamics of the paratope appear to be mainly influenced by the CDR L3 and CDR L1 loops.

Solving the Puzzle of the Carbonic Acid Vibrational Spectrum - an Anharmonic Story.

Against the general belief that carbonic acid is too unstable for synthesis, it was possible to synthesize the solid[1,2] as well as gas-phase carbonic acid.[3] It was suggested that solid carbonic acid might exist in Earth's upper troposphere and in the harsh environments of other solar bodies,[4] where it undergoes a cycle of synthesis, decomposition, and dimerization.[5] To provide spectroscopic data for probing the existence of extraterrestrial carbonic acid,[2,6] matrix-isolation infrared (MI-IR) spectroscopy has shown to be essential.[3,4,6-8] However, early assignments within the harmonic approximation using scaling factors impeded a full interpretation of the rather complex MI-IR spectrum of H2CO3. Recently, carbonic acid was detected in the Galactic center molecular cloud,[9] triggering new interest in the anharmonic spectrum.[10] In this regard, we substantially reassign our argon MI-IR spectra based on accurate anharmonic calculations. We calculate a four-mode potential energy surface (PES) at the explicitly correlated coupled-cluster theory using up to triple-zeta basis sets, i. e., CCSD(T)-F12/cc-pVTZ-F12. On this PES, we perform vibrational self-consistent field and configuration interaction (VSCF/VCI) calculations to obtain accurate vibrational transition frequencies and resonance analysis of the fundamentals, first overtones, and combination bands. In total, 12 new bands can be assigned, extending the spectral data for carbonic acid and thus simplifying detection in more complex environments. Furthermore, we clarify disputed assignments between the cc- and ct-conformer.

Determining internal coordinate sets for optimal representation of molecular vibration.

Arising from the harmonic approximation in solving the vibrational Schrödinger equation, normal modes dissect molecular vibrations into distinct degrees of freedom. Normal modes are widely used as they give rise to descriptive vibrational notations and are convenient for expanding anharmonic potential energy surfaces as an alternative to higher-order Taylor series representations. Usually, normal modes are expressed in Cartesian coordinates, which bears drawbacks that can be overcome by switching to internal coordinates. Considering vibrational notations, normal modes with delocalized characters are difficult to denote, but internal coordinates offer a route to clearer notations. Based on the Hessian, normal mode decomposition schemes for a given set of internal coordinates can describe a normal mode by its contributions from internal coordinates. However, choosing a set of internal coordinates is not straightforward. While the Hessian provides unique sets of normal modes, various internal coordinate sets are possible for a given system. In the present work, we employ a normal mode decomposition scheme to choose an optimal set. Therefore, we screen reasonable sets based on topology and symmetry considerations and rely on a metric that minimizes coupling between internal coordinates. Ultimately, the Nomodeco toolkit presented here generates internal coordinate sets to find an optimal set for representing molecular vibrations. The resulting contribution tables can be used to clarify vibrational notations. We test our scheme on small to mid-sized molecules, showing how the space of definable internal coordinate sets can significantly be reduced.

Evolution in pecunia.

The paper models evolution in pecunia-in the realm of finance. Financial markets are explored as evolving biological systems. Diverse investment strategies compete for the market capital invested in long-lived dividend-paying assets. Some strategies survive and some become extinct. The basis of our paper is that dividends are not exogenous but increase with the wealth invested in an asset, as is the case in a production economy. This might create a positive feedback loop in which more investment in some asset leads to higher dividends which in turn lead to higher investments. Nevertheless, we are able to identify a unique evolutionary stable investment strategy. The problem is studied in a framework combining stochastic dynamics and evolutionary game theory. The model proposed employs only objectively observable market data, in contrast with traditional settings relying upon unobservable investors' characteristics (utilities and beliefs). Our method is analytical and based on mathematical reasoning. A numerical illustration of the main result is provided.

Energy penalties enhance flexible receptor docking in a model cavity.

Protein flexibility remains a major challenge in library docking because of difficulties in sampling conformational ensembles with accurate probabilities. Here, we use the model cavity site of T4 lysozyme L99A to test flexible receptor docking with energy penalties from molecular dynamics (MD) simulations. Crystallography with larger and smaller ligands indicates that this cavity can adopt three major conformations: open, intermediate, and closed. Since smaller ligands typically bind better to the cavity site, we anticipate an energy penalty for the cavity opening. To estimate its magnitude, we calculate conformational preferences from MD simulations. We find that including a penalty term is essential for retrospective ligand enrichment; otherwise, high-energy states dominate the docking. We then prospectively docked a library of over 900,000 compounds for new molecules binding to each conformational state. Absent a penalty term, the open conformation dominated the docking results; inclusion of this term led to a balanced sampling of ligands against each state. High ranked molecules were experimentally tested by Tm upshift and X-ray crystallography. From 33 selected molecules, we identified 18 ligands and determined 13 crystal structures. Most interesting were those bound to the open cavity, where the buried site opens to bulk solvent. Here, highly unusual ligands for this cavity had been predicted, including large ligands with polar tails; these were confirmed both by binding and by crystallography. In docking, incorporating protein flexibility with thermodynamic weightings may thus access new ligand chemotypes. The MD approach to accessing and, crucially, weighting such alternative states may find general applicability.

Quality of life after brain injury-overall scale, Japanese version: assessment of reliability and validity.

This study analyzed the linguistic and psychometric validation of the Japanese version of the Quality of Life after Brain Injury-Overall Scale (QOLIBRI-OS) consisting of six items which cover several TBI-relevant domains. We hypothesized that the Japanese version has good reliability, convergent validity, and divergent validity, compared with its long version, the 37-item QOLIBRI. The QOLIBRI-OS Japanese version was forward and back-translated from the English version. In total, 129 individuals participated in this study after experiencing a traumatic brain injury and attending clinics, rehabilitation centers, and support centers in Japan. The structure of the QOLIBRI-OS was investigated by confirmatory factor analyses and compared with the QOLIBRI. Only one factor was extracted, and a model with one underlying factor had a good fit. The QOLIBRI-OS showed good-to-excellent internal consistency and test-retest reliability. The QOLIBRI-OS was positively correlated with the QOLIBRI, Short Form Health Survey-36 version 2, and Glasgow Outcome Scale Extended, and negatively correlated with the Hospital Anxiety and Depression Scale. The results suggest that the QOLIBRI-OS Japanese version is a reliable and valid tool for assessing disease-specific health-related QOL in individuals after traumatic brain injury in Japan.

Emotion processes in social and political contexts: the case of affective polarisation.

Democratic societies have to face the challenge of increasing affective polarisation - a strong, emotionally fuelled, opposition between adherents of different political parties, or conflicting views and attitudes in different social groups. Social and psychological sciences can contribute to a better understanding of this phenomenon and the special role of emotion theory and research in this respect. In their invited contribution, Bakker and Lelkes note the lack of conceptual precision of the term affective and invite emotion scientists to fill this notion with a theoretical structure that encourages systematic research across different problem areas and cultures. Two invited comments on this article support this initiative but favour an approach that privileges discrete emotions. In his comment, Von Scheve argues that intentionality and the associated action tendencies are essential to understand the emotional basis of polarisation. Halperin et al., based on a conceptual analysis and their own empirical research, they highlight the multi-faceted emotion of disappointment, covering both negative and positive aspects, as the most promising candidate. Finally, I consider the potential role of mixed or blended emotions as well as the potential contributions of appraisal theory, especially with respect to appraisal bias and ensuing emotion dispositions and action tendencies.

Emotional expressivity in singing. Assessing physiological and acoustic indicators of two opera singers' voice characteristics.

In an earlier study, we analyzed how audio signals obtained from three professional opera singers varied when they sang one octave wide eight-tone scales in ten different emotional colors. The results showed systematic variations in voice source and long-term-average spectrum (LTAS) parameters associated with major emotion "families". For two of the singers, subglottal pressure (PSub) also was recorded, thus allowing analysis of an additional main physiological voice control parameter, glottal resistance (defined as the ratio between PSub and glottal flow), and related to glottal adduction. In the present study, we analyze voice source and LTAS parameters derived from the audio signal and their correlation with Psub and glottal resistance. The measured parameters showed a systematic relationship with the four emotion families observed in our previous study. They also varied systematically with values of the ten emotions along the valence, power, and arousal dimensions; valence showed a significant correlation with the ratio between acoustic voice source energy and subglottal pressure, while Power varied significantly with sound level and two measures related to the spectral dominance of the lowest spectrum partial. the fundamental.

Cross-linking disulfide bonds govern solution structures of diabodies.

In the last years, antibodies have emerged as a promising new class of therapeutics, due to their combination of high specificity with long serum half-life and low risk of side-effects. Diabodies are a popular novel antibody format, consisting of two Fv domains connected with short linkers. Like IgG antibodies, they simultaneously bind two target proteins. However, they offer altered properties, given their smaller size and higher rigidity. In this study, we conducted the-to our knowledge-first molecular dynamics (MD) simulations of diabodies and find a surprisingly high conformational flexibility in the relative orientation of the two Fv domains. We observe rigidifying effects through the introduction of disulfide bonds in the Fv -Fv interface and characterize the effect of different disulfide bond locations on the conformation. Additionally, we compare VH -VL orientations and paratope dynamics between diabodies and an antigen binding fragment (Fab) of the same sequence. We find mostly consistent structures and dynamics, indicating similar antigen binding properties. The most significant differences can be found within the CDR-H2 loop dynamics. Of all CDR loops, the CDR-H2 is located closest to the artificial Fv -Fv interface. All examined diabodies show similar VH -VL orientations, Fv -Fv packing and CDR loop conformations. However, the variant with a P14C-K64C disulfide bond differs most from the Fab in our measures, including the CDR-H3 loop conformational ensemble. This suggests altered antigen binding properties and underlines the need for careful validation of the disulfide bond locations in diabodies.

Vibrational Predissociation Spectra of C2 N- and C3 N- : Bending and Stretching Vibrations.

We present infrared predissociation spectra of C2 N- (H2 ) and C 3 N- (H2 ) in the 300-1850 cm-1 range. Measurements were performed using the FELion cryogenic ion trap end user station at the Free Electron Lasers for Infrared eXperiments (FELIX) laboratory. For C2 N- (H2 ), we detected the CCN bending and CC-N stretching vibrations. For the C3 N- (H2 ) system, we detected the CCN bending, the CC-CN stretching, and multiple overtones and/or combination bands. The assignment and interpretation of the presented experimental spectra is validated by calculations of anharmonic spectra within the vibrational configuration interaction (VCI) approach, based on potential energy surfaces calculated at explicitly correlated coupled cluster theory (CCSD(T)-F12/cc-pVTZ-F12). The H2 tag acts as an innocent spectator, not significantly affecting the C2,3 N- bending and stretching mode positions. The recorded infrared predissociation spectra can thus be used as a proxy for the vibrational spectra of the bare anions.

Addressing Challenges of Macrocyclic Conformational Sampling in Polar and Apolar Solvents: Lessons for Chameleonicity.

We evaluated a workflow to reliably sample the conformational space of a set of 47 peptidic macrocycles. Starting from SMILES strings, we use accelerated molecular dynamics simulations to overcome high energy barriers, in particular, the cis-trans isomerization of peptide bonds. We find that our approach performs very well in polar solvents like water and dimethyl sulfoxide. Interestingly, the protonation state of a secondary amine in the ring only slightly influences the conformational ensembles of our test systems. For several of the macrocycles, determining the conformational distribution in chloroform turns out to be considerably more challenging. Especially, the choice of partial charges crucially influences the ensembles in chloroform. We address these challenges by modifying initial structures and the choice of partial charges. Our results suggest that special care has to be taken to understand the configurational distribution in apolar solvents, which is a key step toward a reliable prediction of membrane permeation of macrocycles and their chameleonic properties.

PEP-Patch: Electrostatics in Protein-Protein Recognition, Specificity, and Antibody Developability.

The electrostatic properties of proteins arise from the number and distribution of polar and charged residues. Electrostatic interactions in proteins play a critical role in numerous processes such as molecular recognition, protein solubility, viscosity, and antibody developability. Thus, characterizing and quantifying electrostatic properties of a protein are prerequisites for understanding these processes. Here, we present PEP-Patch, a tool to visualize and quantify the electrostatic potential on the protein surface in terms of surface patches, denoting separated areas of the surface with a common physical property. We highlight its applicability to elucidate protease substrate specificity and antibody-antigen recognition and predict heparin column retention times of antibodies as an indicator of pharmacokinetics.

Structural mechanism of Fab domain dissociation as a measure of interface stability.

Therapeutic antibodies should not only recognize antigens specifically, but also need to be free from developability issues, such as poor stability. Thus, the mechanistic understanding and characterization of stability are critical determinants for rational antibody design. In this study, we use molecular dynamics simulations to investigate the melting process of 16 antigen binding fragments (Fabs). We describe the Fab dissociation mechanisms, showing a separation in the VH-VL and in the CH1-CL domains. We found that the depths of the minima in the free energy curve, corresponding to the bound states, correlate with the experimentally determined melting temperatures. Additionally, we provide a detailed structural description of the dissociation mechanism and identify key interactions in the CDR loops and in the CH1-CL interface that contribute to stabilization. The dissociation of the VH-VL or CH1-CL domains can be represented by conformational changes in the bend angles between the domains. Our findings elucidate the melting process of antigen binding fragments and highlight critical residues in both the variable and constant domains, which are also strongly germline dependent. Thus, our proposed mechanisms have broad implications in the development and design of new and more stable antigen binding fragments.

Essential role of a conserved aspartate for the enzymatic activity of plasmanylethanolamine desaturase.

Plasmalogens are an abundant class of glycerophospholipids in the mammalian body, with special occurrence in the brain and in immune cell membranes. Plasmanylethanolamine desaturase (PEDS1) is the final enzyme of plasmalogen biosynthesis, which introduces the characteristic 1-O-alk-1'-enyl double bond. The recent sequence identification of PEDS1 as transmembrane protein 189 showed that its protein sequence is related to a special class of plant desaturases (FAD4), with whom it shares a motif of 8 conserved histidines, which are essential for the enzymatic activity. In the present work, we wanted to gain more insight into the sequence-function relationship of this enzyme and mutated to alanine additional 28 amino acid residues of murine plasmanylethanolamine desaturase including those 20 residues, which are also totally conserved-in addition to the eight-histidine-motif-among the animal PEDS1 and plant FAD4 plant desaturases. We measured the enzymatic activity by transient transfection of tagged murine PEDS1 expression clones to a PEDS1-deficient human HAP1 cell line by monitoring of labeled plasmalogens formed from supplemented 1-O-pyrenedecyl-sn-glycerol in relation to recombinant protein expression. Surprisingly, only a single mutation, namely aspartate 100, led to a total loss of PEDS1 activity. The second strongest impact on enzymatic activity had mutation of phenylalanine 118, leaving only 6% residual activity. A structural model obtained by homology modelling to available structures of stearoyl-CoA reductase predicted that this aspartate 100 residue interacts with histidine 96, and phenylalanine 118 interacts with histidine 187, both being essential histidines assumed to be involved in the coordination of the di-metal center of the enzyme.

Emotion processes and perceptual control of action choice.

This editorial introduces an invited article by Andreas Eder on a new perceptual control theory of action choice, based on the comparison of real and simulated interoceptive signals generated by action alternatives. Eder extends the cognitive action-control framework, postulating a bi-directional connection between outcomes and actions by introducing "emotional feelings", defined as valued interoceptive signals from the body. An invited commentary by Agnes Moors compares this theory with her own goal-directed theory of action control. While agreeing on the central role of a control cycle and the goal-directed nature of emotional actions, Moors disagrees on the content of the representations involved in the control cycle and the nature of the feelings involved. A second commentary by Bob Bramson and Karin Roelofs discusses the issues of the distinction between perception control vs. action control, the need for biologically plausible implementation alternatives, and potential implications for psychopathology and clinical intervention. Finally, the potential relevance of predictive coding theory and the role of appraisal processes in emotion generation with respect to their bearing on action comparison and choice are discussed.

Emotion regulation via reappraisal - mechanisms and strategies.

Emotion regulation, and in particular cognitive reappraisal. Gross has been booming in theory development and empirical research for the last two decades. A large number of publications have demonstrated the importance of these mechanisms for understanding and promoting well-being and mental health. It is thus timely for Cognition and Emotion to examine the current state of theory in this domain. The resultant invited article, authored by Uusberg, A., Ford, Uusberg, H., and Gross, aims to expand the scope of reappraisal theory by extending their recent reAppraisal model by suggesting different forms of goal commitment and situation construals. Their suggestions are commented on by Kashdan and Goodman from a purpose in life perspective, Ehring, and Woud from a clinical psychopathology perspective. In this editorial, I briefly discuss the lack of specification of the goal construct, which is central to the reappraisal model. Moreover, I point to recent evidence showing that problems may arise because of appraisal biases, in the case of individuals prone to inappropriate evaluations of situations. I suggest that future work in this domain could benefit from increased interaction between theorists and researchers working on appraisal and reappraisal processes.