Local and global changes in cell density induce reorganisation of 3D packing in a proliferating epithelium.

Tissue morphogenesis is intimately linked to the changes in shape and organisation of individual cells. In curved epithelia, cells can intercalate along their own apicobasal axes, adopting a shape named 'scutoid' that allows energy minimization in the tissue. Although several geometric and biophysical factors have been associated with this 3D reorganisation, the dynamic changes underlying scutoid formation in 3D epithelial packing remain poorly understood. Here, we use live imaging of the sea star embryo coupled with deep learning-based segmentation to dissect the relative contributions of cell density, tissue compaction and cell proliferation on epithelial architecture. We find that tissue compaction, which naturally occurs in the embryo, is necessary for the appearance of scutoids. Physical compression experiments identify cell density as the factor promoting scutoid formation at a global level. Finally, the comparison of the developing embryo with computational models indicates that the increase in the proportion of scutoids is directly associated with cell divisions. Our results suggest that apico-basal intercalations appearing immediately after mitosis may help accommodate the new cells within the tissue. We propose that proliferation in a compact epithelium induces 3D cell rearrangements during development.

A geometric-tension-dynamics model of epithelial convergent extension.

Convergent extension of epithelial tissue is a key motif of animal morphogenesis. On a coarse scale, cell motion resembles laminar fluid flow; yet in contrast to a fluid, epithelial cells adhere to each other and maintain the tissue layer under actively generated internal tension. To resolve this apparent paradox, we formulate a model in which tissue flow in the tension-dominated regime occurs through adiabatic remodeling of force balance in the network of adherens junctions. We propose that the slow dynamics within the manifold of force-balanced configurations is driven by positive feedback on myosin-generated cytoskeletal tension. Shifting force balance within a tension network causes active cell rearrangements (T1 transitions) resulting in net tissue deformation oriented by initial tension anisotropy. Strikingly, we find that the total extent of tissue deformation depends on the initial cellular packing order. T1s degrade this order so that tissue flow is self-limiting. We explain these findings by showing that coordination of T1s depends on coherence in local tension configurations, quantified by a geometric order parameter in tension space. Our model reproduces the salient tissue- and cell-scale features of germ band elongation during Drosophila gastrulation, in particular the slowdown of tissue flow after approximately twofold elongation concomitant with a loss of order in tension configurations. This suggests local cell geometry contains morphogenetic information and yields experimentally testable predictions. Defining biologically controlled active tension dynamics on the manifold of force-balanced states may provide a general approach to the description of morphogenetic flow.

Morphological transformations of vesicles with confined flexible filaments.

A fundamental understanding of cell shaping with confined flexible filaments, including microtubules, actin filaments, and engineered nanotubes, has been limited by the complex interplay between the cell membrane and encapsulated filaments. Here, combining theoretical modeling and molecular dynamics simulations, we investigate the packing of an open or closed filament inside a vesicle. Depending on the relative stiffness and size of the filament to the vesicle as well as the osmotic pressure, the vesicle could evolve from an axisymmetric configuration to a general configuration with a maximum of three reflection planes, and the filament could bend in or out of plane or even coil up. A plethora of system morphologies are determined. Morphological phase diagrams predicting conditions of shape and symmetry transitions are established. Organization of actin filaments or bundles, microtubules, and nanotube rings inside vesicles, liposomes, or cells are discussed. Our results provide a theoretical basis to understand cell shaping and cellular stability and to help guide the development and design of artificial cells and biohybrid microrobots.

On Viazovska's modular form inequalities.

Viazovska proved that the [Formula: see text] lattice sphere packing is the densest sphere packing in [Formula: see text] dimensions. Her proof relies on two inequalities between functions defined in terms of modular and quasimodular forms. We give a direct proof of these inequalities that does not rely on computer calculations.

Fossil leaves reveal drivers of herbivore functional diversity during the Cenozoic.

Herbivorous arthropods are the most diverse group of multicellular organisms on Earth. The most discussed drivers of their inordinate taxonomic and functional diversity are high niche availability associated with the diversity of host plants and dense niche packing due to host partitioning among herbivores. However, the relative contributions of these two factors to dynamics in the diversity of herbivores throughout Earth's history remain unresolved. Using fossil data on herbivore-induced leaf damage from across the Cenozoic, we infer quantitative bipartite interaction networks between plants and functional feeding types of herbivores. We fit a general model of diversity to these interaction networks and discover that host partitioning among functional groups of herbivores contributed twice as much to herbivore functional diversity as host diversity. These findings indicate that niche packing primarily shaped the dynamics in the functional diversity of herbivores during the past 66 my. Our study highlights how the fossil record can be used to test fundamental theories of biodiversity and represents a benchmark for assessing the drivers of herbivore functional diversity in modern ecosystems.

An end-to-end deep learning method for protein side-chain packing and inverse folding.

Protein side-chain packing (PSCP), the task of determining amino acid side-chain conformations given only backbone atom positions, has important applications to protein structure prediction, refinement, and design. Many methods have been proposed to tackle this problem, but their speed or accuracy is still unsatisfactory. To address this, we present AttnPacker, a deep learning (DL) method for directly predicting protein side-chain coordinates. Unlike existing methods, AttnPacker directly incorporates backbone 3D geometry to simultaneously compute all side-chain coordinates without delegating to a discrete rotamer library or performing expensive conformational search and sampling steps. This enables a significant increase in computational efficiency, decreasing inference time by over 100× compared to the DL-based method DLPacker and physics-based RosettaPacker. Tested on the CASP13 and CASP14 native and nonnative protein backbones, AttnPacker computes physically realistic side-chain conformations, reducing steric clashes and improving both rmsd and dihedral accuracy compared to state-of-the-art methods SCWRL4, FASPR, RosettaPacker, and DLPacker. Different from traditional PSCP approaches, AttnPacker can also codesign sequences and side chains, producing designs with subnative Rosetta energy and high in silico consistency.

Aster repulsion drives short-ranged ordering in the Drosophila syncytial blastoderm.

Biological systems are highly complex, yet notably ordered structures can emerge. During syncytial stage development of the Drosophila melanogaster embryo, nuclei synchronously divide for nine cycles within a single cell, after which most of the nuclei reach the cell cortex. The arrival of nuclei at the cortex occurs with remarkable positional order, which is important for subsequent cellularisation and morphological transformations. Yet, the mechanical principles underlying this lattice-like positional order of nuclei remain untested. Here, using quantification of nuclei position and division orientation together with embryo explants, we show that short-ranged repulsive interactions between microtubule asters ensure the regular distribution and maintenance of nuclear positions in the embryo. Such ordered nuclear positioning still occurs with the loss of actin caps and even the loss of the nuclei themselves; the asters can self-organise with similar distribution to nuclei in the wild-type embryo. The explant assay enabled us to deduce the nature of the mechanical interaction between pairs of nuclei. We used this to predict how the nuclear division axis orientation changes upon nucleus removal from the embryo cortex, which we confirmed in vivo with laser ablation. Overall, we show that short-ranged microtubule-mediated repulsive interactions between asters are important for ordering in the early Drosophila embryo and minimising positional irregularity.

On the abundance and importance of AXXXA sequence motifs in globular proteins and their involvement in CßCß interaction.

The AXXXA and GXXXG motifs are frequently observed in helices, especially in membrane proteins. The motif GXXXG is known to stabilize helix-helix association in membrane proteins via CαHO bonding. AXXXA sequence motif additionally stabilizes the folded state of proteins. We found 27,000 and 18,000 occurrences of AXXXA and GXXXG motifs in a non-redundant set of 6000 obligate homodimeric (OD) complexes. Interestingly, this is less pronounced in transient homodimers (TD) and heterodimers (HetD). On average each obligate homodimer contains four AXXXA motifs, it is 2 and 3.5 for HetD and TD, respectively. Focusing on the binding surface it is seen that 27 % of the ODs contain at least one AXXXA motif at the interface, whereas it is 17 % and 15 % for HetD and TD respectively. AXXXA predominantly stabilizes the OD quaternary structure via the side chain CßCß interactions. This interaction is energetically favorable and is found to be a major driving force for OD quaternary structure stability. Cß-Cß interactions are observed ∼6 times higher than the known CαHO interaction for helix-helix stabilization. Two additional new interactions of CßO and OO are observed at the AXXXA containing interface regions. The occurrence of the motif gets drastically reduced if any of the terminal Ala residues are replaced by Gly. Our findings show the importance of AXXXA in providing stability to the quaternary structure through specific hydrophobic interactions and the specificity of the Ala residue at motif termini. The knowledge gained can be used for designing synthetic proteins of improved stability and for designing peptide-based therapeutics.

Invariant point message passing for protein side chain packing.

Protein side chain packing (PSCP) is a fundamental problem in the field of protein engineering, as high-confidence and low-energy conformations of amino acid side chains are crucial for understanding (and designing) protein folding, protein-protein interactions, and protein-ligand interactions. Traditional PSCP methods (such as the Rosetta Packer) often rely on a library of discrete side chain conformations, or rotamers, and a forcefield to guide the structure to low-energy conformations. Recently, deep learning (DL) based methods (such as DLPacker, AttnPacker, and DiffPack) have demonstrated state-of-the-art predictions and speed in the PSCP task. Building off the success of geometric graph neural networks for protein modeling, we present the Protein Invariant Point Packer (PIPPack) which effectively processes local structural and sequence information to produce realistic, idealized side chain coordinates using χ $$ \chi $$ -angle distribution predictions and geometry-aware invariant point message passing (IPMP). On a test set of ∼1400 high-quality protein chains, PIPPack is highly competitive with other state-of-the-art PSCP methods in rotamer recovery and per-residue RMSD but is significantly faster.

Subatomic structure of orthorhombic thaumatin at 0.89 Å reveals that highly flexible conformations are crucial for thaumatin sweetness.

Thaumatin is a sweet-tasting protein that elicits a sweet taste at a threshold of approximately 50 nM. Structure-sweetness relationships in thaumatin suggest that the basicity of two amino acids residues, Arg82 and Lys67, are particularly responsible for sweetness. Using tetragonal crystals, our structural analysis suggested that flexible sidechain conformations of these two residues play an important role in sweetness. However, in tetragonal crystals, Arg82 is adjacent to symmetry-related residues, and its flexibility is relatively restrained by the crystal packing. To reduce and diminish these symmetry-related effects, orthorhombic crystals were prepared, and their structures were successfully determined at a resolution of 0.89 Å. Within the orthorhombic lattice, two alternative conformations were more clearly visible at Lys67 than in a tetragonal system. Interestingly, for the first time, three alternative conformations at Arg82 were only found in an orthorhombic system. These results suggest the importance of flexible conformations in sweetness determinants. Such subtle structural variations might serve to adjust the complementarity of the electrostatic potentials of sweet receptors, thereby eliciting the potent sweet taste of thaumatin.

The complex three-dimensional organization of epithelial tissues.

Understanding the cellular organization of tissues is key to developmental biology. In order to deal with this complex problem, researchers have taken advantage of reductionist approaches to reveal fundamental morphogenetic mechanisms and quantitative laws. For epithelia, their two-dimensional representation as polygonal tessellations has proved successful for understanding tissue organization. Yet, epithelial tissues bend and fold to shape organs in three dimensions. In this context, epithelial cells are too often simplified as prismatic blocks with a limited plasticity. However, there is increasing evidence that a realistic approach, even from a reductionist perspective, must include apico-basal intercalations (i.e. scutoidal cell shapes) for explaining epithelial organization convincingly. Here, we present an historical perspective about the tissue organization problem. Specifically, we analyze past and recent breakthroughs, and discuss how and why simplified, but realistic, in silico models require scutoidal features to address key morphogenetic events.

Molecular-Level Insight into Impact of Additives on Film Formation and Molecular Packing in Y6-based Organic Solar Cells.

Additive engineering is widely utilized to optimize film morphology in active layers of organic solar cells (OSCs). However, the role of additive in film formation and adjustment of film morphology remains unclear at the molecular level. Here, taking high-efficiency Y6-based OSC films as an example, this work thus employs all-atom molecular-dynamics simulations to investigate how introduction of additives with different π-conjugation degree thermodynamically and dynamically impacts nanoscale molecular packings. These results demonstrate that the van der Waals (vdW) interactions of the Y6 end groups with the studied additives are strongest. The larger the π-conjugation degree of the additive molecules, the stronger the vdW interactions between additive and Y6 molecules. Due to such vdW interactions, the π-conjugated additive molecules insert into the neighboring Y6 molecules, thus opening more space for relaxation of Y6 molecules to trigger more ordered packing. Increasing the interactions between the Y6 end groups and the additive molecules not only accelerates formation of the Y6 ordered packing, but also induces shorter Y6-intermolecular distances. This work reveals the fundamental molecular-level mechanism behind film formation and adjustment of film morphology via additive engineering, providing an insight into molecular design of additives toward optimizing morphologies of organic semiconductor films.

Trifluoromethylation Enables Compact 2D Linear Stacking and Improves the Efficiency and Stability of Q-PHJ Organic Solar Cells.

Compared to the bulk heterojunction (BHJ) devices, the quasiplanar heterojunction (Q-PHJ) exhibits a more stable morphology and superior charge transfer performance. To achieve both high efficiency and long-term stability, it is necessary to design new materials for Q-PHJ devices. In this study, QxIC-CF3 and QxIC-CH3 are designed and synthesized for the first time. The trifluoromethylation of the central core exerts a modulatory effect on the molecular stacking pattern, leveraging the strong electrostatic potential and intermolecular interactions. Compared with QxIC-CH3, the single crystal structure reveals that QxIC-CF3 exhibits a more compact 2D linear stacking behavior. These benefits, combined with the separated electron and hole transport channels in Q-PHJ device, lead to increased charge mobility and reduced energy loss. The devices based on D18/QxIC-CF3 exhibit an efficiency of 18.1%, which is the highest power conversion efficiency (PCE) for Q-PHJ to date. Additionally, the thermodynamic stability of the active layer morphology enhances the lifespan of the aforementioned devices under illumination conditions. Specifically, the T80 is 420 h, which is nearly twice that of the renowned Y6-based BHJ device (T80 = 220 h). By combining the advantages of the trifluoromethylation and Q-PHJ device, efficient and stable organic solar cell devices can be constructed.

What is the Limit Size of 2D Conjugated Extension on Central Units of Small Molecular Acceptors in Organic Solar Cells?

2D conjugated extension on central units of small molecular acceptors (SMAs) has gained great successes in reaching the state-of-the-art organic photovoltaics. Whereas the limit size of 2D central planes and their dominant role in constructing 3D intermolecular packing networks are still elusive. Thus, by exploring a series of SMAs with gradually enlarged central planes, it is demonstrated that, at both single molecular and aggerated levels, there is an unexpected blue-shift for their film absorption but preferable reorganization energies, exciton lifetimes and binding energies with central planes enlarging, especially when comparing to their Y6 counterpart. More importantly, the significance of well-balanced molecular packing modes involving both central and end units is first disclosed through a systematic single crystal analysis, indicating that when the ratio of central planes area/end terminals area is no more than 3 likely provides a preferred 3D intermolecular packing network of SMAs. By exploring the limit size of 2D central planes, This work indicates that the structural profiles of ideal SMAs may require suitable central unit size together with proper heteroatom replacement instead of directly overextending 2D central planes to the maximum. These results will likely provide some guidelines for future better molecular design.

Balancing Flexible Side Chains on 2D Conjugated Acceptors Enables High-Performance Organic Solar Cell.

Balancing the rigid backbones and flexible side chains of light-harvesting materials is crucially important to reach optimized intermolecular packing, micromorphology, and thus photovoltaic performance of organic solar cells (OSCs). Herein, based on a distinctive CH-series acceptor platform with 2D conjugation extended backbones, a series of nonfullerene acceptors (CH-6F-Cn) are synthesized by delicately tuning the lengths of flexible side chains from n-octyl to n-amyl. A systemic investigation has revealed that the variation of the side chain's length can not only modulate intermolecular packing modes and crystallinity but also dramatically improve the micromorphology of the active layer and eventual photovoltaic parameters of OSCs. Consequently, the highest PCE of 18.73% can be achieved by OSCs employing D18:PM6:CH-6F-C8 as light-harvesting materials.

A Critical Review of Short Antimicrobial Peptides from Scorpion Venoms, Their Physicochemical Attributes, and Potential for the Development of New Drugs.

Scorpion venoms have proven to be excellent sources of antimicrobial agents. However, although many of them have been functionally characterized, they remain underutilized as pharmacological agents, despite their evident therapeutic potential. In this review, we discuss the physicochemical properties of short scorpion venom antimicrobial peptides (ssAMPs). Being generally short (13-25 aa) and amidated, their proven antimicrobial activity is generally explained by parameters such as their net charge, the hydrophobic moment, or the degree of helicity. However, for a complete understanding of their biological activities, also considering the properties of the target membranes is of great relevance. Here, with an extensive analysis of the physicochemical, structural, and thermodynamic parameters associated with these biomolecules, we propose a theoretical framework for the rational design of new antimicrobial drugs. Through a comparison of these physicochemical properties with the bioactivity of ssAMPs in pathogenic bacteria such as Staphylococcus aureus or Acinetobacter baumannii, it is evident that in addition to the net charge, the hydrophobic moment, electrostatic energy, or intrinsic flexibility are determining parameters to understand their performance. Although the correlation between these parameters is very complex, the consensus of our analysis suggests that there is a delicate balance between them and that modifying one affects the rest. Understanding the contribution of lipid composition to their bioactivities is also underestimated, which suggests that for each peptide, there is a physiological context to consider for the rational design of new drugs.

Linear, Planar, Orbicular, and Macrocyclic Multinuclear Zinc (Meth)acrylate Complexes.

Zinc carboxylate complexes are widely utilized as artificial models of metalloenzymes and as secondary building units of PCPs/MOFs. However, the relationship between the structure of the monodentate carboxylato ligand and the molecular arrangement of multinuclear zinc carboxylate complexes is not fully understood because of the coordination flexibility of the Zn ion and carboxylato ligands. Herein, we report the structural analysis of a series of complexes derived from zinc (meth)acrylate which has a linear infinite chain structure. The molecular structure of µ4-oxido-bridged tetranuclear complexes [Zn4(µ4-O)(OCOR)6] revealed a distorted Zn4O core. Crystallization of zinc acrylate under aqueous conditions afforded a µ3-hydroxido-containing pentanuclear complex [Zn5(µ3-OH)2(OCOR)8] as the repeating unit of an infinite sheet-like structure in the solid state. It was also obtained by the hydrolysis of the µ4-oxido-bridged tetranuclear complex. In sharp contrast, the methacrylate analog retained the methacrylato ligands under aqueous crystallization conditions to form a macrocyclic dodecanuclear complex with methacrylato as the sole ligand.

Organoboron Polymorphs with Different Molecular Packing Modes for Optical Waveguides.

Organoboron compounds offer a new strategy to design optoelectronic materials with high fluorescence efficiency. In this paper, the organoboron compound B-BNBP with double B←N bridged bipyridine bearing four fluorine atoms as core unit is facilely synthesized and exhibits a narrowband emission spectrum and a high photoluminescence quantum yield (PLQY) of 86.53 % in solution. Its polymorphic crystals were controllable prepared by different solution self-assembly methods. Two microcrystals possess different molecular packing modes, one-dimensional microstrips (1D-MSs) for H-aggregation and two-dimensional microdisks (2D-MDs) for J-aggregation, owing to abundant intermolecular interactions of four fluorine atoms sticking out conjugated plane. Their structure-property relationships were investigated by crystallographic analysis and theoretical calculation. Strong emission spectra with the full width at half maximum (FWHM) of less than 30 nm can also be observed in thin film and 2D-MDs. 1D-MSs possess thermally activated delayed fluorescence (TADF) property and exhibit superior optical waveguide performance with an optical loss of 0.061 dB/µm. This work enriches the diversity of polymorphic microcrystals and further reveals the structure-property relationship in organoboron micro/nano-crystals.

Columnar Organization of Nonalternant Fluorinated Dehydrobenzannulenes.

Two new partially fluorinated dehydrobenzannulenes have been prepared by inter- and intramolecular oxidative homocoupling of diyne precursors. These systems contain fluorinated and nonfluorinated arene rings in a non-alternant arrangement. Both macrocycles are roughly planar and organize into extended columns in the solid state. The assembly of these columns is mediated by the combination of dispersion interactions, slipped [π···π] stacking interactions of the perfluorinated rings with each other, and their association with the nonfluorinated rings in the molecules of the neighboring macrocycles. These results suggest that partial fluorination of dehydrobenzannulenes can serve as a versatile motif for their assembly into columnar superstructures.

Molecular Packing Topology and Interactions to Decipher Mechanical Compliances in Dicyano-Distyrylbenzene Derivatives.

Flexible optoelectronics is the need of the hour as the market moves toward wearable and conformable devices. Crystalline π-conjugated materials offer high performance as active materials compared to their amorphous counterpart, but they are typically brittle. This poses a significant challenge that needs to be overcome to unfold their potential in optoelectronic devices. Unveiling the molecular packing topology and identifying interaction descriptors that can accommodate strain offers essential guiding principles for developing conjugated materials as active components in flexible optoelectronics. The molecular packing and interaction topology of eight crystal systems of dicyano-distyrylbenzene derivatives are investigated. Face-to-face π-stacks in an inclined orientation relative to the bending surface can accommodate expansion and compression with minimal molecular motion from their equilibrium positions. This configuration exhibits good compliance towards mechanical strain, while a similar structure with a criss-cross arrangement capable of distributing applied strain equally in opposite directions enhances the flexibility. Molecular arrangements that cannot reversibly undergo expansion and compression exhibit brittleness. In the isometric CT crystals, the disproportionate strength of the interactions along the bending plane and orthogonal directions makes these materials sustain a moderate bending strain. These results provide an updated explanation for the elastic bending in semiconducting π-conjugated crystals.