Transverse instability in nonparaxial systems with four-wave mixing

We present a two-dimensional coupled nonlinear Schrödinger-like system with spatial diffractions, degree of birefringence, and four-wave mixing. This system describes two physical contexts: optical pulse propagation beyond the paraxial approximation in a weakly birefringence waveguide and light propagation near exciton-polariton resonance in semiconductor superlattice materials. We find that such systems naturally support different types of diffraction profiles, including spherical, ellipsoidal, and hyperbolic structures. We then study the transverse instability of the two-dimensional system caused by an infinitesimal perturbation-induced continuous-wave solution. Also, we find out how various physical parameters, such as nonparaxiality, degree of birefringence, power, and four-wave mixing, affect the modulational instability (MI) process, in particular. We explore the existence of bright solitary wave solutions for the proposed system as the influence of MI is closely related to the latter in a nutshell.

Challenges in describing the conformation and dynamics of proteins with ambiguous behavior

Traditionally, our understanding of how proteins operate and how evolution shapes them is based on two main data sources: the overall protein fold and the protein amino acid sequence. However, a significant part of the proteome shows highly dynamic and/or structurally ambiguous behavior, which cannot be correctly represented by the traditional fixed set of static coordinates. Representing such protein behaviors remains challenging and necessarily involves a complex interpretation of conformational states, including probabilistic descriptions. Relating protein dynamics and multiple conformations to their function as well as their physiological context (e.g., post-translational modifications and subcellular localization), therefore, remains elusive for much of the proteome, with studies to investigate the effect of protein dynamics relying heavily on computational models. We here investigate the possibility of delineating three classes of protein conformational behavior: order, disorder, and ambiguity. These definitions are explored based on three different datasets, using interpretable machine learning from a set of features, from AlphaFold2 to sequence-based predictions, to understand the overlap and differences between these datasets. This forms the basis for a discussion on the current limitations in describing the behavior of dynamic and ambiguous proteins.

Panoramic Perspective on Human Phosphosites

Protein phosphorylation is the most common reversible post-translational modification of proteins and is key in the regulation of many cellular processes. Due to this importance, phosphorylation is extensively studied, resulting in the availability of a large amount of mass spectrometry-based phospho-proteomics data. Here, we leverage the information in these large-scale phospho-proteomics data sets, as contained in Scop3P, to analyze and characterize proteome-wide protein phosphorylation sites (P-sites). First, we set out to differentiate correctly observed P-sites from false-positive sites using five complementary site properties. We then describe the context of these P-sites in terms of the protein structure, solvent accessibility, structural transitions and disorder, and biophysical properties. We also investigate the relative prevalence of disease-linked mutations on and around P-sites. Moreover, we assess the structural dynamics of P-sites in their phosphorylated and unphosphorylated states. As a result, we show how large-scale reprocessing of available proteomics experiments can enable a more reliable view on proteome-wide P-sites. Furthermore, adding the structural context of proteins around P-sites helps uncover possible conformational switches upon phosphorylation. Moreover, by placing sites in different biophysical contexts, we show the differential preference in protein dynamics at phosphorylated sites when compared to the nonphosphorylated counterparts.

PDBe-KB: collaboratively defining the biological context of structural data

The Protein Data Bank in Europe - Knowledge Base (PDBe-KB, https://pdbe-kb.org) is an open collaboration between world-leading specialist data resources contributing functional and biophysical annotations derived from or relevant to the Protein Data Bank (PDB). The goal of PDBe-KB is to place macromolecular structure data in their biological context by developing standardised data exchange formats and integrating functional annotations from the contributing partner resources into a knowledge graph that can provide valuable biological insights. Since we described PDBe-KB in 2019, there have been significant improvements in the variety of available annotation data sets and user functionality. Here, we provide an overview of the consortium, highlighting the addition of annotations such as predicted covalent binders, phosphorylation sites, effects of mutations on the protein structure and energetic local frustration. In addition, we describe a library of reusable web-based visualisation components and introduce new features such as a bulk download data service and a novel superposition service that generates clusters of superposed protein chains weekly for the whole PDB archive.

Massively parallel interrogation of protein fragment secretability using SECRiFY reveals features influencing secretory system transit

While transcriptome- and proteome-wide technologies to assess processes in protein biogenesis are now widely available, we still lack global approaches to assay post-ribosomal biogenesis events, in particular those occurring in the eukaryotic secretory system. We here develop a method, SECRiFY, to simultaneously assess the secretability of >10⁵ protein fragments by two yeast species, S. cerevisiae and P. pastoris, using custom fragment libraries, surface display and a sequencing-based readout. Screening human proteome fragments with a median size of 50-100 amino acids, we generate datasets that enable datamining into protein features underlying secretability, revealing a striking role for intrinsic disorder and chain flexibility. The SECRiFY methodology generates sufficient amounts of annotated data for advanced machine learning methods to deduce secretability patterns. The finding that secretability is indeed a learnable feature of protein sequences provides a solid base for application-focused studies.

b2bTools: online predictions for protein biophysical features and their conservation

We provide integrated protein sequence-based predictions via https://bio2byte.be/b2btools/. The aim of our predictions is to identify the biophysical behaviour or features of proteins that are not readily captured by structural biology and/or molecular dynamics approaches. Upload of a FASTA file or text input of a sequence provides integrated predictions from DynaMine backbone and side-chain dynamics, conformational propensities, and derived EFoldMine early folding, DisoMine disorder, and Agmata β-sheet aggregation. These predictions, several of which were previously not available online, capture 'emergent' properties of proteins, i.e. the inherent biophysical propensities encoded in their sequence, rather than context-dependent behaviour (e.g. final folded state). In addition, upload of a multiple sequence alignment (MSA) in a variety of formats enables exploration of the biophysical variation observed in homologous proteins. The associated plots indicate the biophysical limits of functionally relevant protein behaviour, with unusual residues flagged by a Gaussian mixture model analysis. The prediction results are available as JSON or CSV files and directly accessible via an API. Online visualisation is available as interactive plots, with brief explanations and tutorial pages included. The server and API employ an email-free token-based system that can be used to anonymously access previously generated results.

Cov-MS: A Community-Based Template Assay for Mass-Spectrometry-Based Protein Detection in SARS-CoV-2 Patients

Rising population density and global mobility are among the reasons why pathogens such as SARS-CoV-2, the virus that causes COVID-19, spread so rapidly across the globe. The policy response to such pandemics will always have to include accurate monitoring of the spread, as this provides one of the few alternatives to total lockdown. However, COVID-19 diagnosis is currently performed almost exclusively by reverse transcription polymerase chain reaction (RT-PCR). Although this is efficient, automatable, and acceptably cheap, reliance on one type of technology comes with serious caveats, as illustrated by recurring reagent and test shortages. We therefore developed an alternative diagnostic test that detects proteolytically digested SARS-CoV-2 proteins using mass spectrometry (MS). We established the Cov-MS consortium, consisting of 15 academic laboratories and several industrial partners to increase applicability, accessibility, sensitivity, and robustness of this kind of SARS-CoV-2 detection. This, in turn, gave rise to the Cov-MS Digital Incubator that allows other laboratories to join the effort, navigate, and share their optimizations and translate the assay into their clinic. As this test relies on viral proteins instead of RNA, it provides an orthogonal and complementary approach to RT-PCR using other reagents that are relatively inexpensive and widely available, as well as orthogonally skilled personnel and different instruments. Data are available via ProteomeXchange with identifier PXD022550.

Cov-MS: A Community-Based Template Assay for Mass-Spectrometry-Based Protein Detection in SARS-CoV-2 Patients

Rising population density and global mobility are among the reasons why pathogens such as SARS-CoV-2, the virus that causes COVID-19, spread so rapidly across the globe. The policy response to such pandemics will always have to include accurate monitoring of the spread, as this provides one of the few alternatives to total lockdown. However, COVID-19 diagnosis is currently performed almost exclusively by reverse transcription polymerase chain reaction (RT-PCR). Although this is efficient, automatable, and acceptably cheap, reliance on one type of technology comes with serious caveats, as illustrated by recurring reagent and test shortages. We therefore developed an alternative diagnostic test that detects proteolytically digested SARS-CoV-2 proteins using mass spectrometry (MS). We established the Cov-MS consortium, consisting of 15 academic laboratories and several industrial partners to increase applicability, accessibility, sensitivity, and robustness of this kind of SARS-CoV-2 detection. This, in turn, gave rise to the Cov-MS Digital Incubator that allows other laboratories to join the effort, navigate, and share their optimizations and translate the assay into their clinic. As this test relies on viral proteins instead of RNA, it provides an orthogonal and complementary approach to RT-PCR using other reagents that are relatively inexpensive and widely available, as well as orthogonally skilled personnel and different instruments. Data are available via ProteomeXchange with identifier PXD022550.

Role of π conjugation in n-hexylphenothiazine dyes for solar cell-a density functional theory approach

The N-hexylphenothiazine-based organic sensitizers are designed for Dye Sensitized Solar Cell (DSSC). The different π spacer (thiophene and cyanovinyl) groups were substituted in third and seventh position N-hexylphenothiazine. From the structural modifications, the π spacer effect was analyzed. The optoelectronic properties of the dyes were tuned by structural modifications. The optimized geometry, highest occupied molecular orbital and lowest unoccupied molecular orbital energy level, and absorption spectra were calculated. The natural bond orbital analysis gives the net electron transfer from the donor to acceptor. The electrochemical properties and light-harvesting efficiency of the designed dye sensitizers were calculated. The π spacer increase resulted in the redshift of the absorption peak. Based on the density functional theory and time dependant density functional theory calculations, the designed dye molecules are evaluated for DSSC application.

Online biophysical predictions for SARS-CoV-2 proteins

BACKGROUND

The SARS-CoV-2 virus, the causative agent of COVID-19, consists of an assembly of proteins that determine its infectious and immunological behavior, as well as its response to therapeutics. Major structural biology efforts on these proteins have already provided essential insights into the mode of action of the virus, as well as avenues for structure-based drug design. However, not all of the SARS-CoV-2 proteins, or regions thereof, have a well-defined three-dimensional structure, and as such might exhibit ambiguous, dynamic behaviour that is not evident from static structure representations, nor from molecular dynamics simulations using these structures. MAIN: We present a website ( https://bio2byte.be/sars2/ ) that provides protein sequence-based predictions of the backbone and side-chain dynamics and conformational propensities of these proteins, as well as derived early folding, disorder, β-sheet aggregation, protein-protein interaction and epitope propensities. These predictions attempt to capture the inherent biophysical propensities encoded in the sequence, rather than context-dependent behaviour such as the final folded state. In addition, we provide the biophysical variation that is observed in homologous proteins, which gives an indication of the limits of their functionally relevant biophysical behaviour.

CONCLUSION

The https://bio2byte.be/sars2/ website provides a range of protein sequence-based predictions for 27 SARS-CoV-2 proteins, enabling researchers to form hypotheses about their possible functional modes of action.

Optimization of Benzoguanamine doped PVDF/KI/I2 Solid Polymer Electrolytes for Dye-Sensitized Solar Cell Applications.. [DOI: 10.21203/rs.3.rs-322818/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

Benzoguanamine doped 0%, 10%, 20%, 30%, 40% and 50% PVDF/KI/I2 polymer electrolytes were prepared by solution casting technique. The crystallinity, surface morphology, ionic conductivity and photovoltaic performance of polymer electrolytes were analyzed. The PXRD studies have confirmed the decreased and increased crystallinity of benzoguanamine doped polymer electrolytes. The surface morphology of polymer electrolytes is discussed using SEM analysis. From the AC-impedance analysis, ionic conductivity of benzoguanamine doped 0%, 10%, 20%, 30%, 40% and 50% PVDF/KI/I2 polymer electrolytes were calculated as 5.57 × 10− 6 Scm− 1, 1.05 × 10− 5 Scm− 1, 5.95 × 10− 5 Scm− 1, 3.09 × 10− 5 Scm− 1, 1.56 × 10− 5 Scm− 1 and 1.48 × 10− 5 Scm− 1, respectively. The photovoltaic performance of benzoguanamine doped 0%, 10%, 20%, 30%, 40% and 50% PVDF/KI/I2 polymer electrolytes based DSSCs have achieved 1.5%, 1.9%, 2.8%, 2.5%, 2.3% and 2.1% power conversion efficiency, respectively.

MobiDB: intrinsically disordered proteins in 2021

The MobiDB database (URL: https://mobidb.org/) provides predictions and annotations for intrinsically disordered proteins. Here, we report recent developments implemented in MobiDB version 4, regarding the database format, with novel types of annotations and an improved update process. The new website includes a re-designed user interface, a more effective search engine and advanced API for programmatic access. The new database schema gives more flexibility for the users, as well as simplifying the maintenance and updates. In addition, the new entry page provides more visualisation tools including customizable feature viewer and graphs of the residue contact maps. MobiDB v4 annotates the binding modes of disordered proteins, whether they undergo disorder-to-order transitions or remain disordered in the bound state. In addition, disordered regions undergoing liquid-liquid phase separation or post-translational modifications are defined. The integrated information is presented in a simplified interface, which enables faster searches and allows large customized datasets to be downloaded in TSV, Fasta or JSON formats. An alternative advanced interface allows users to drill deeper into features of interest. A new statistics page provides information at database and proteome levels. The new MobiDB version presents state-of-the-art knowledge on disordered proteins and improves data accessibility for both computational and experimental users.

The influence of triphenylamine as a donor group on Zn–porphyrin for dye sensitized solar cell applications

Novel donor–π–acceptor based Zn–porphyrins (Ko-1 and Ko-2) have been designed and synthesized. Triphenylamine (TPA) was introduced instead of hydrogen in the porphyrin core. A solar cell efficiency was achieved that was almost equal to N719 dye.

The influence of π-linkers configuration on properties of 10-hexylphenoxazine donor-based sensitizer for dye-sensitized solar cell application - Theoretical approach

10-Hexylphenoxazine based dyes with A-(π)_n-D-(π)_n-A architecture is designed and investigated systematically for dye-sensitized solar cell (DSSC) application by Density Functional Theory (DFT) and Time-dependent Density Functional Theory (TD-DFT). The designed sensitizers consist of 10-Hexylphenoxazine as electron donor and cyanoacrylic acid as an acceptor, connected by the Thiophene and Cyanovinyl π-spacers configurations with symmetrical and asymmetrical form. The effect of π-spacers configurations on the electronic and optical properties of the dyes is also investigated. The optimized structure, electronic properties and absorption characteristics of A-(π)_n-D-(π)_n-A dyes were investigated. The charge separation and polarization properties are analyzed by co-planarity, natural bond orbital (NBO), dipole moment and linear polarizability studies. The free energy change of electron injection and dye regeneration of the sensitizers are also calculated. The addition of a greater number of π-spacers improves the electronic, spectroscopic, optical, and free energy properties of the designed sensitizer. The DFT studies also reveal that the position of the π-spacers plays an important role in the electronic and spectroscopic properties.

Growth, Hirshfeld surfaces, spectral, quantum chemical calculations, photoconductivity and chemical etching analyses of nonlinear optical p-toluidine p-toluenesulfonate single crystal

A single crystal of p-toluidine p-toluenesulfonate (PTPT) has been grown by slow evaporation solution technique (SEST) at room temperature. Single crystal X-ray analysis confirms that grown crystal belongs to the monoclinic structure with space group P2₁. Intermolecular interactions and fingerprint plots of PTPT molecules are executed by Hirshfeld surface analysis. It was found that H···H (44.2%) contacts have maximum intermolecular interactions contributions in the total Hirshfeld surface area. The characteristic absorption band occurs at below 290 nm. The functional groups were identified using FTIR and FT-Raman analyses and compared with theoretical values. The title molecule contains fourteen CH bonds and three OH bonds. The calculated HOMO and LUMO energy values are -6.125 eV and -1.157 eV, respectively. The chemical potential (μ) and electronegativity (χ) values are estimated to be -3.4938 eV and 3.4938 eV, respectively. The strongest negative hyperconjugation occurs due to the charge transfer from the occupied orbital (σ) to the unoccupied orbital (π*) which is calculated for the σ(N20-C21) → π*(N20-O18). The green and red lines in the total density of states (TDOS) spectrum indicate the occupied orbital and virtual orbital levels, respectively. Photoconductivity studies have been done for the grown crystal. It is observed that the dark current is greater than photocurrent. It shows negative photoconductivity nature of PTPT crystal. The etching analysis was executed on (001) plane of PTPT crystal. It has rectangular shape etch pits patterns.

Donor functionalized quinoline based organic sensitizers for dye sensitized solar cell (DSSC) applications: DFT and TD-DFT investigations

The influence of different donor groups in quinoline based novel sensitizers for dye sensitized solar cell (DSSC) applications is analyzed by using density functional theory (DFT) and time dependent density functional theory (TD-DFT). Quinoline and donor functionalized quinoline based novel organic sensitizers have been designed with different π-spacers for DSSC applications. The ground state molecular structure of novel organic sensitizers is fully optimized by DFT calculation in both gas and chloroform phases. Electronic absorption characteristics are predicted by the TD-DFT calculation in both gas and chloroform phases. The polarizable continuum model is used for solvent phase optimization. The net electron transfer from the donor to acceptor is calculated from natural bond orbital (NBO) analysis. The injection energy and dye regeneration energy values are also calculated. Different donor groups are substituted in quinoline, and these substituted quinoline donors are used as the donor group. Cyanovinyl and thiophene groups act as π-spacers and cyanoacrylic acid acts as an acceptor. DFT and TD-DFT studies of the quinoline and donor functionalized quinoline sensitizers show that the coumarin based and N-hexyltetrahydroquinoline donors are more efficient for DSSC application.

More than the "Killer Trait": Infection with the Bacterial Endosymbiont Caedibacter taeniospiralis Causes Transcriptomic Modulation in Paramecium Host

Endosymbiosis is a widespread phenomenon and hosts of bacterial endosymbionts can be found all-over the eukaryotic tree of life. Likely, this evolutionary success is connected to the altered phenotype arising from a symbiotic association. The potential variety of symbiont’s contributions to new characteristics or abilities of host organisms are largely unstudied. Addressing this aspect, we focused on an obligate bacterial endosymbiont that confers an intraspecific killer phenotype to its host. The symbiosis between Paramecium tetraurelia and Caedibacter taeniospiralis, living in the host’s cytoplasm, enables the infected paramecia to release Caedibacter symbionts, which can simultaneously produce a peculiar protein structure and a toxin. The ingestion of bacteria that harbor both components leads to the death of symbiont-free congeners. Thus, the symbiosis provides Caedibacter-infected cells a competitive advantage, the “killer trait.” We characterized the adaptive gene expression patterns in symbiont-harboring Paramecium as a second symbiosis-derived aspect next to the killer phenotype. Comparative transcriptomics of infected P. tetraurelia and genetically identical symbiont-free cells confirmed altered gene expression in the symbiont-bearing line. Our results show up-regulation of specific metabolic and heat shock genes whereas down-regulated genes were involved in signaling pathways and cell cycle regulation. Functional analyses to validate the transcriptomics results demonstrated that the symbiont increases host density hence providing a fitness advantage. Comparative transcriptomics shows gene expression modulation of a ciliate caused by its bacterial endosymbiont thus revealing new adaptive advantages of the symbiosis. Caedibacter taeniospiralis apparently increases its host fitness via manipulation of metabolic pathways and cell cycle control.

Synthesis, crystal growth and characterization of Zn0.5Mn0.5Te single crystal grown via the Bridgman technique

Single crystal of Zn_0.5Mn_0.5Te has been grown by the vertical Bridgman method.

Synthesis, crystal growth, physio-chemical characterization and quantum chemical calculations of NLO active metal–organic crystal: dibromo(4-hydroxy-l-proline)cadmium(ii) for non-linear optical applications

Single crystals of DB4HPC, a new metal–organic complex, have been grown from saturated solution for the first time. DB4HPC crystallizes in a monoclinic crystal system with noncentrosymmetric space group P2₁ and is thermally stable up to 240 °C.

Directional growth, physicochemical and quantum chemical investigations on pyridinium 2-carboxylate: 4-nitrophenol (P2C4N) single crystal for nonlinear optical (NLO) applications

An organic nonlinear optical (NLO) single crystal of pyridinium 2-carboxylate: 4-nitrophenol (P2C4N) was grown by the Sankaranarayanan-Ramasamy (SR) method using the (1 1 −1) plane.

Synthesis, crystal growth, physicochemical properties and quantum chemical investigations of a D–π–A type organic single crystal: 2-amino-5-nitropyridinium p-phenolsulfonate (2A5NPP) for nonlinear optical (NLO) applications

Efficient organic NLO 2A5NPP single crystals have been grown by slow cooling method.

Investigation on the structural, linear/nonlinear optical and electrical characteristics of Cd- and Mn-doped polar lithium sulfate monohydrate crystals

Doped LSMH single crystals exhibited good transmittance percentage, lower birefringence, enhanced SHG efficiency and good piezoelectric response compared to undoped LSMH crystals.

Differential subcellular distribution of four phospholipase C isoforms and secretion of GPI-PLC activity

Phospholipase C (PLC) is an important enzyme of signal transduction pathways by generation of second messengers from membrane lipids. PLCs are also indicated to cleave glycosylphosphatidylinositol (GPI)-anchors of surface proteins thus releasing these into the environment. However, it remains unknown whether this enzymatic activity on the surface is due to distinct PLC isoforms in higher eukaryotes. Ciliates have, in contrast to other unicellular eukaryotes, multiple PLC isoforms as mammals do. Thus, Paramecium represents a perfect model to study subcellular distribution and potential surface activity of PLC isoforms. We have identified distinct subcellular localizations of four PLC isoforms indicating functional specialization. The association with different calcium release channels (CRCs) argues for distinct subcellular functions. They may serve as PI-PLCs in microdomains for local second messenger responses rather than free floating IP₃. In addition, all isoforms can be found on the cell surface and they are found together with GPI-cleaved surface proteins in salt/ethanol washes of cells. We can moreover show them in medium supernatants of living cells where they have access to GPI-anchored surface proteins. Among the isoforms we cannot assign GPI-PLC activity to specific PLC isoforms; rather each PLC is potentially responsible for the release of GPI-anchored proteins from the surface.

Globalization and Transnational Migration: The Malaysian State's Response to Voluntary and Forced Migration

The ability of nation-states to control the flow of transnational migrants has been affected by globalization. The imposition of strict immigration controls reflects the contradictory nature of states' responses to address economic and social problems. Despite the rhetoric of strict immigration control, Malaysia has not been able to control the flow of voluntary and forced migrants. The state's goal to attain a developed status by 2020 makes it difficult to have full authority over transnational migrants. The lack of differentiation between economic and forced migrants makes it rather difficult for the latter to seek protection from the state and the fear of deportation denies them the limited protection granted to legal economic migrants. The state's recognition of the refugee status of the Rohingyas seems to be an important step in providing security for a small number of forced migrants. While the impact of globalization might be uneven, it has certainly transformed in limited ways how the state relates to transnational migration.