RESUMO
Protein structures are essential to understanding cellular processes in molecular detail. While advances in artificial intelligence revealed the tertiary structure of proteins at scale, their quaternary structure remains mostly unknown. We devise a scalable strategy based on AlphaFold2 to predict homo-oligomeric assemblies across four proteomes spanning the tree of life. Our results suggest that approximately 45% of an archaeal proteome and a bacterial proteome and 20% of two eukaryotic proteomes form homomers. Our predictions accurately capture protein homo-oligomerization, recapitulate megadalton complexes, and unveil hundreds of homo-oligomer types, including three confirmed experimentally by structure determination. Integrating these datasets with omics information suggests that a majority of known protein complexes are symmetric. Finally, these datasets provide a structural context for interpreting disease mutations and reveal coiled-coil regions as major enablers of quaternary structure evolution in human. Our strategy is applicable to any organism and provides a comprehensive view of homo-oligomerization in proteomes.
Assuntos
Inteligência Artificial , Proteínas , Proteoma , Humanos , Proteínas/química , Proteínas/genética , Archaea/química , Archaea/genética , Eucariotos/química , Eucariotos/genética , Bactérias/química , Bactérias/genéticaRESUMO
The supercoiling of bacterial and archaeal flagellar filaments is required for motility. Archaeal flagellar filaments have no homology to their bacterial counterparts and are instead homologs of bacterial type IV pili. How these prokaryotic flagellar filaments, each composed of thousands of copies of identical subunits, can form stable supercoils under torsional stress is a fascinating puzzle for which structural insights have been elusive. Advances in cryoelectron microscopy (cryo-EM) make it now possible to directly visualize the basis for supercoiling, and here, we show the atomic structures of supercoiled bacterial and archaeal flagellar filaments. For the bacterial flagellar filament, we identify 11 distinct protofilament conformations with three broad classes of inter-protomer interface. For the archaeal flagellar filament, 10 protofilaments form a supercoil geometry supported by 10 distinct conformations, with one inter-protomer discontinuity creating a seam inside of the curve. Our results suggest that convergent evolution has yielded stable superhelical geometries that enable microbial locomotion.
Assuntos
Flagelos , Flagelina , Archaea , Bactérias , Microscopia Crioeletrônica , Fímbrias Bacterianas/química , Subunidades Proteicas/análiseRESUMO
Neural circuit assembly features simultaneous targeting of numerous neuronal processes from constituent neuron types, yet the dynamics is poorly understood. Here, we use the Drosophila olfactory circuit to investigate dynamic cellular processes by which olfactory receptor neurons (ORNs) target axons precisely to specific glomeruli in the ipsi- and contralateral antennal lobes. Time-lapse imaging of individual axons from 30 ORN types revealed a rich diversity in extension speed, innervation timing, and ipsilateral branch locations and identified that ipsilateral targeting occurs via stabilization of transient interstitial branches. Fast imaging using adaptive optics-corrected lattice light-sheet microscopy showed that upon approaching target, many ORN types exhibiting "exploring branches" consisted of parallel microtubule-based terminal branches emanating from an F-actin-rich hub. Antennal nerve ablations uncovered essential roles for bilateral axons in contralateral target selection and for ORN axons to facilitate dendritic refinement of postsynaptic partner neurons. Altogether, these observations provide cellular bases for wiring specificity establishment.
Assuntos
Condutos Olfatórios/citologia , Condutos Olfatórios/diagnóstico por imagem , Imagem com Lapso de Tempo , Animais , Axônios/fisiologia , Células Cultivadas , Dendritos/fisiologia , Drosophila melanogaster/citologia , Drosophila melanogaster/fisiologia , Microtúbulos/metabolismo , Neurônios Receptores Olfatórios/fisiologia , Fatores de TempoRESUMO
Since their discovery, giant viruses have expanded our understanding of the principles of virology. Due to their gargantuan size and complexity, little is known about the life cycles of these viruses. To answer outstanding questions regarding giant virus infection mechanisms, we set out to determine biomolecular conditions that promote giant virus genome release. We generated four infection intermediates in Samba virus (Mimivirus genus, lineage A) as visualized by cryoelectron microscopy (cryo-EM), cryoelectron tomography (cryo-ET), and scanning electron microscopy (SEM). Each of these four intermediates reflects similar morphology to a stage that occurs in vivo. We show that these genome release stages are conserved in other mimiviruses. Finally, we identified proteins that are released from Samba and newly discovered Tupanvirus through differential mass spectrometry. Our work revealed the molecular forces that trigger infection are conserved among disparate giant viruses. This study is also the first to identify specific proteins released during the initial stages of giant virus infection.
Assuntos
Vírus Gigantes/genética , Vírus Gigantes/metabolismo , Vírus Gigantes/fisiologia , Capsídeo/metabolismo , Vírus de DNA/genética , Genoma Viral/genética , Proteômica/métodos , Montagem de Vírus/genética , Montagem de Vírus/fisiologia , Viroses/genética , Vírus/genéticaRESUMO
Polarization along an apico-basolateral axis is a hallmark of epithelial cells and is essential for their selective barrier and transporter functions, as well as for their ability to provide mechanical resiliency to organs. Loss of polarity along this axis perturbs development and is associated with a wide number of diseases. We describe three steps involved in polarization: symmetry breaking, polarity establishment, and polarity maintenance. While the proteins involved in these processes are highly conserved among epithelial tissues and species, the execution of these steps varies widely and is context dependent. We review both theoretical principles underlying these steps and recent work demonstrating how apico-basolateral polarity is established in vivo in different tissues, highlighting how developmental and physiological contexts play major roles in the execution of the epithelial polarity program.
Assuntos
Membrana Basal/metabolismo , Polaridade Celular , Células Epiteliais/citologia , Epitélio/metabolismo , Animais , Membrana Basal/citologia , Comunicação Celular , Matriz Extracelular/metabolismo , Humanos , Proteínas de Membrana/metabolismo , Transdução de SinaisRESUMO
Dozens of proteins are known to convert to the aggregated amyloid state. These include fibrils associated with systemic and neurodegenerative diseases and cancer, functional amyloid fibrils in microorganisms and animals, and many denatured proteins. Amyloid fibrils can be much more stable than other protein assemblies. In contrast to globular proteins, a single protein sequence can aggregate into several distinctly different amyloid structures, termed polymorphs, and a given polymorph can reproduce itself by seeding. Amyloid polymorphs may be the molecular basis of prion strains. Whereas the Protein Data Bank contains some 100,000 globular protein and 3,000 membrane protein structures, only a few dozen amyloid protein structures have been determined, and most of these are short segments of full amyloid-forming proteins. Regardless, these amyloid structures illuminate the architecture of the amyloid state, including its stability and its capacity for formation of polymorphs.
Assuntos
Proteínas Amiloidogênicas/química , Proteínas Priônicas/química , Agregação Patológica de Proteínas/metabolismo , Motivos de Aminoácidos , Proteínas Amiloidogênicas/genética , Proteínas Amiloidogênicas/metabolismo , Animais , Microscopia Crioeletrônica , Expressão Gênica , Humanos , Ressonância Magnética Nuclear Biomolecular , Proteínas Priônicas/genética , Proteínas Priônicas/metabolismo , Agregação Patológica de Proteínas/genética , Agregação Patológica de Proteínas/patologia , Desnaturação Proteica , Multimerização Proteica , Estabilidade Proteica , Estrutura Secundária de Proteína , Difração de Raios XRESUMO
We present an overview of symmetry breaking in early mammalian development as a continuous process from compaction to specification of the body axes. While earlier studies have focused on individual symmetry-breaking events, recent advances enable us to explore progressive symmetry breaking during early mammalian development. Although we primarily discuss embryonic development of the mouse, as it is the best-studied mammalian model system to date, we also highlight the shared and distinct aspects between different mammalian species. Finally, we discuss how insights gained from studying mammalian development can be generalized in light of self-organization principles. With this review, we hope to highlight new perspectives in studying symmetry breaking and self-organization in multicellular systems.
Assuntos
Blastocisto/citologia , Padronização Corporal/genética , Embrião de Mamíferos , Desenvolvimento Embrionário/genética , Linhagem da Célula/genética , HumanosRESUMO
Biological energy currency ATP is produced by F1Fo-ATP synthase. However, the molecular mechanism for human ATP synthase action remains unknown. Here, we present snapshot images for three main rotational states and one substate of human ATP synthase using cryoelectron microscopy. These structures reveal that the release of ADP occurs when the ß subunit of F1Fo-ATP synthase is in the open conformation, showing how ADP binding is coordinated during synthesis. The accommodation of the symmetry mismatch between F1 and Fo motors is resolved by the torsional flexing of the entire complex, especially the γ subunit, and the rotational substep of the c subunit. Water molecules are identified in the inlet and outlet half-channels, suggesting that the proton transfer in these two half-channels proceed via a Grotthus mechanism. Clinically relevant mutations are mapped to the structure, showing that they are mainly located at the subunit-subunit interfaces, thus causing instability of the complex.
Assuntos
Trifosfato de Adenosina , ATPases Translocadoras de Prótons , Humanos , Microscopia Crioeletrônica , Trifosfato de Adenosina/metabolismo , ATPases Translocadoras de Prótons/química , Conformação ProteicaRESUMO
The voltage-gated ion channel activity depends on both activation (transition from the resting state to the open state) and inactivation. Inactivation is a self-restraint mechanism to limit ion conduction and is as crucial to membrane excitability as activation. Inactivation can occur when the channel is open or closed. Although open-state inactivation is well understood, the molecular basis of closed-state inactivation has remained elusive. We report cryo-EM structures of human KV4.2 channel complexes in inactivated, open, and closed states. Closed-state inactivation of KV4 involves an unprecedented symmetry breakdown for pore closure by only two of the four S4-S5 linkers, distinct from known mechanisms of open-state inactivation. We further capture KV4 in a putative resting state, revealing how voltage sensor movements control the pore. Moreover, our structures provide insights regarding channel modulation by KChIP2 and DPP6 auxiliary subunits. Our findings elucidate mechanisms of closed-state inactivation and voltage-dependent activation of the KV4 channel.
Assuntos
Ativação do Canal Iônico , Canais de Potássio Shal , Humanos , Ativação do Canal Iônico/fisiologia , Cinética , Potenciais da Membrana/fisiologia , Canais de Potássio Shal/genética , Canais de Potássio Shal/metabolismoRESUMO
AMPA receptors (AMPARs) mediate the majority of excitatory neurotransmission. Their surface expression, trafficking, gating, and pharmacology are regulated by auxiliary subunits. Of the two types of TARP auxiliary subunits, type I TARPs assume activating roles, while type II TARPs serve suppressive functions. We present cryo-EM structures of GluA2 AMPAR in complex with type II TARP γ5, which reduces steady-state currents, increases single-channel conductance, and slows recovery from desensitization. Regulation of AMPAR function depends on its ligand-binding domain (LBD) interaction with the γ5 head domain. GluA2-γ5 complex shows maximum stoichiometry of two TARPs per AMPAR tetramer, being different from type I TARPs but reminiscent of the auxiliary subunit GSG1L. Desensitization of both GluA2-GSG1L and GluA2-γ5 complexes is accompanied by rupture of LBD dimer interface, while GluA2-γ5 but not GluA2-GSG1L LBD dimers remain two-fold symmetric. Different structural architectures and desensitization mechanisms of complexes with auxiliary subunits endow AMPARs with broad functional capabilities.
Assuntos
Canais de Cálcio/química , Claudinas/química , Receptores de AMPA/química , Motivos de Aminoácidos , Animais , Microscopia Crioeletrônica , Dimerização , Células HEK293 , Humanos , Processamento de Imagem Assistida por Computador , Bicamadas Lipídicas/química , Proteínas de Membrana , Conformação Molecular , Técnicas de Patch-Clamp , Polímeros , Ligação Proteica , Conformação Proteica , Domínios Proteicos , Ratos , Transmissão SinápticaRESUMO
This Review elucidates the regulatory principles of random monoallelic expression by focusing on two well-studied examples: the X-chromosome inactivation regulator Xist and the olfactory receptor gene family. Although the choice of a single X chromosome or olfactory receptor occurs in different developmental contexts, common gene regulatory principles guide monoallelic expression in both systems. In both cases, an event breaks the symmetry between genetically and epigenetically identical copies of the gene, leading to the expression of one single random allele, stabilized through negative feedback control. Although many regulatory steps that govern the establishment and maintenance of monoallelic expression have been identified, key pieces of the puzzle are still missing. We provide an overview of the current knowledge and models for the monoallelic expression of Xist and olfactory receptors. We discuss their similarities and differences, and highlight open questions and approaches that could guide the study of other monoallelically expressed genes.
Assuntos
Alelos , RNA Longo não Codificante , Receptores Odorantes , Inativação do Cromossomo X , Animais , Humanos , Inativação do Cromossomo X/genética , RNA Longo não Codificante/genética , RNA Longo não Codificante/metabolismo , Receptores Odorantes/genética , Receptores Odorantes/metabolismo , Regulação da Expressão Gênica no DesenvolvimentoRESUMO
Degeneracy and symmetry have a profound relation in quantum systems. Here, we report gate-tunable subband degeneracy in PbTe nanowires with a nearly symmetric cross-sectional shape. The degeneracy is revealed in electron transport by the absence of a quantized plateau. Utilizing a dual gate design, we can apply an electric field to lift the degeneracy, reflected as emergence of the plateau. This degeneracy and its tunable lifting were challenging to observe in previous nanowire experiments, possibly due to disorder. Numerical simulations can qualitatively capture our observation, shedding light on device parameters for future applications.
RESUMO
The intricate interplay between biomechanical and biochemical pathways in modulating morphogenesis is an interesting research topic. How biomechanical force regulates epithelial cell tubulogenesis remains poorly understood. Here, we established a model of tubulogenesis by culturing renal proximal tubular epithelial cells on a collagen gel while manipulating contractile force. Epithelial cells were dynamically self-organized into tubule-like structures by augmentation of cell protrusions and cell-cell association. Reduction and asymmetric distribution of phosphorylated myosin light chain 2, the actomyosin contractility, in cells grown on soft matrix preceded tube connection. Notably, reducing matrix stiffness via sonication of collagen fibrils and inhibiting actomyosin contractility with blebbistatin promoted tubulogenesis, whereas inhibition of cytoskeleton polymerization suppressed it. CXC chemokine ligand 1 (CXCL1) expression was transcriptionally upregulated in cells undergoing tubulogenesis. Additionally, inhibiting actomyosin contractility facilitated CXCL1 polarization and cell protrusions preceding tube formation. Conversely, inhibiting the CXCL1-CXC receptor 1 pathway hindered cell protrusions and tubulogenesis. Mechanical property asymmetry with cell-collagen fibril interaction patterns at cell protrusions and along the tube structure supported the association of anisotropic contraction with tube formation. Furthermore, suppressing the mechanosensing machinery of integrin subunit beta 1 reduced CXCL1 expression, collagen remodeling, and impaired tubulogenesis. In summary, symmetry breaking of cell contractility on a soft collagen gel promotes CXCL1 polarization at cell protrusions which in turn facilitates cell-cell association and thus tubule connection.
Assuntos
Actomiosina , Colágeno , Actomiosina/metabolismo , Matriz Extracelular/metabolismo , Morfogênese , Células Epiteliais/metabolismoRESUMO
Covalent bonding interactions determine the energy-momentum (E-k) dispersion (band structure) of solid-state materials. Here, we show that noncovalent interactions can modulate the E-k dispersion near the Fermi level of a low-dimensional nanoscale conductor. We demonstrate that low energy band gaps may be opened in metallic carbon nanotubes through polymer wrapping of the nanotube surface at fixed helical periodicity. Electronic spectral, chiro-optic, potentiometric, electronic device, and work function data corroborate that the magnitude of band gap opening depends on the nature of the polymer electronic structure. Polymer dewrapping reverses the conducting-to-semiconducting phase transition, restoring the native metallic carbon nanotube electronic structure. These results address a long-standing challenge to develop carbon nanotube electronic structures that are not realized through disruption of π conjugation, and establish a roadmap for designing and tuning specialized semiconductors that feature band gaps on the order of a few hundred meV.
RESUMO
Proteomics has been revolutionized by large protein language models (PLMs), which learn unsupervised representations from large corpora of sequences. These models are typically fine-tuned in a supervised setting to adapt the model to specific downstream tasks. However, the computational and memory footprint of fine-tuning (FT) large PLMs presents a barrier for many research groups with limited computational resources. Natural language processing has seen a similar explosion in the size of models, where these challenges have been addressed by methods for parameter-efficient fine-tuning (PEFT). In this work, we introduce this paradigm to proteomics through leveraging the parameter-efficient method LoRA and training new models for two important tasks: predicting protein-protein interactions (PPIs) and predicting the symmetry of homooligomer quaternary structures. We show that these approaches are competitive with traditional FT while requiring reduced memory and substantially fewer parameters. We additionally show that for the PPI prediction task, training only the classification head also remains competitive with full FT, using five orders of magnitude fewer parameters, and that each of these methods outperform state-of-the-art PPI prediction methods with substantially reduced compute. We further perform a comprehensive evaluation of the hyperparameter space, demonstrate that PEFT of PLMs is robust to variations in these hyperparameters, and elucidate where best practices for PEFT in proteomics differ from those in natural language processing. All our model adaptation and evaluation code is available open-source at https://github.com/microsoft/peft_proteomics. Thus, we provide a blueprint to democratize the power of PLM adaptation to groups with limited computational resources.
Assuntos
Proteômica , Proteômica/métodos , Proteínas/química , Proteínas/metabolismo , Processamento de Linguagem Natural , Mapeamento de Interação de Proteínas/métodos , Biologia Computacional/métodos , Humanos , AlgoritmosRESUMO
Collective cell rotations are widely used during animal organogenesis. Theoretical and in vitro studies have conceptualized rotating cells as identical rigid-point objects that stochastically break symmetry to move monotonously and perpetually within an inert environment. However, it is unclear whether this notion can be extrapolated to a natural context, where rotations are ephemeral and heterogeneous cellular cohorts interact with an active epithelium. In zebrafish neuromasts, nascent sibling hair cells invert positions by rotating ≤180° around their geometric center after acquiring different identities via Notch1a-mediated asymmetric repression of Emx2. Here, we show that this multicellular rotation is a three-phasic movement that progresses via coherent homotypic coupling and heterotypic junction remodeling. We found no correlation between rotations and epithelium-wide cellular flow or anisotropic resistive forces. Moreover, the Notch/Emx2 status of the cell dyad does not determine asymmetric interactions with the surrounding epithelium. Aided by computer modeling, we suggest that initial stochastic inhomogeneities generate a metastable state that poises cells to move and spontaneous intercellular coordination of the resulting instabilities enables persistently directional rotations, whereas Notch1a-determined symmetry breaking buffers rotational noise.
Assuntos
Células Ciliadas Auditivas , Peixe-Zebra , Animais , Microscopia de Vídeo , Epitélio , MecanorreceptoresRESUMO
Vertebrate podocytes and Drosophila nephrocytes display slit diaphragms, specialised cell junctions that are essential for the execution of the basic excretory function of ultrafiltration. To elucidate the mechanisms of slit diaphragm assembly we have studied their formation in Drosophila embryonic garland nephrocytes. These cells of mesenchymal origin lack overt apical-basal polarity. We find that their initial membrane symmetry is broken by an acytokinetic cell division that generates PIP2-enriched domains at their equator. The PIP2-enriched equatorial cortex becomes a favourable domain for hosting slit diaphragm proteins and the assembly of the first slit diaphragms. Indeed, when this division is either prevented or forced to complete cytokinesis, the formation of diaphragms is delayed to larval stages. Furthermore, although apical polarity determinants also accumulate at the equatorial cortex, they do not appear to participate in the recruitment of slit diaphragm proteins. The mechanisms we describe allow the acquisition of functional nephrocytes in embryos, which may confer on them a biological advantage similar to the formation of the first vertebrate kidney, the pronephros.
Assuntos
Citocinese , Drosophila , Animais , Divisão Celular , Córtex Cerebral , DiafragmaRESUMO
Inspired by the superrotation of the Earth's solid core, we investigate the dynamics of a free-rotating body as it interacts with the large-scale circulation (LSC) of the Rayleigh-Bénard thermal convection in a cylindrical container. A surprising and persistent corotation of both the free body and the LSC emerges, breaking the axial symmetry of the system. The corotational speed increases monotonically with the intensity of thermal convection, measured by the Rayleigh number Ra, which is proportional to the temperature difference between the heated bottom and cooled top. The rotational direction occasionally and spontaneously reverses, occurring more frequently at higher Ra. The reversal events follow a Poisson process; it is feasible that flow fluctuations randomly interrupt and reestablish the rotation-sustaining mechanism. This corotation is powered by thermal convection alone and promoted by the addition of a free body, enriching the classical dynamical system.
RESUMO
Understanding how to utilize symmetry-breaking charge separation (SB-CS) offers a path toward increasingly efficient light-harvesting technologies. This process plays a central role in the first step of photosynthesis, in which the dimeric "special pair" of the photosynthetic reaction center enters a coherent SB-CS state after photoexcitation. Previous research on SB-CS in both biological and synthetic chromophore dimers has focused on increasing the efficiency of light-driven processes. In a chromophore dimer undergoing SB-CS, the energy of the radical ion pair product is nearly isoenergetic with that of the lowest excited singlet (S1) state of the dimer. This means that very little energy is lost from the absorbed photon. In principle, the relatively high energy electron and hole generated by SB-CS within the chromophore dimer can each be transferred to adjacent charge acceptors to extend the lifetime of the electron-hole pair, which can increase the efficiency of solar energy conversion. To investigate this possibility, we have designed a bis-perylenediimide cyclophane (mPDI2) covalently linked to a secondary electron donor, peri-xanthenoxanthene (PXX) and a secondary electron acceptor, partially fluorinated naphthalenediimide (FNDI). Upon selective photoexcitation of mPDI2, transient absorption spectroscopy shows that mPDI2 undergoes SB-CS, followed by two secondary charge transfer reactions to generate a PXXâ¢+-mPDI2-FNDIâ¢- radical ion pair having a nearly 3 µs lifetime. This strategy has the potential to increase the efficiency of molecular systems for artificial photosynthesis and photovoltaics.
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Protein nanoparticles play pivotal roles in many areas of bionanotechnology, including drug delivery, vaccination, and diagnostics. These technologies require control over the distinct particle morphologies that protein nanocontainers can adopt during self-assembly from their constituent protein components. The geometric construction principle of virus-derived protein cages is by now fairly well understood by analogy to viral protein shells in terms of Caspar and Klug's quasi-equivalence principle. However, many artificial, or genetically modified, protein containers exhibit varying degrees of quasi-equivalence in the interactions between identical protein subunits. They can also contain a subset of protein subunits that do not participate in interactions with other assembly units, called capsomers, leading to gaps in the particle surface. We introduce a method that exploits information on the local interactions between the capsomers to infer the geometric construction principle of these nanoparticle architectures. The predictive power of this approach is demonstrated here for a prominent system in nanotechnology, the AaLS pentamer. Our method not only rationalises hitherto discovered cage structures but also predicts geometrically viable options that have not yet been observed. The classification of nanoparticle architecture based on the geometric properties of the interaction network closes a gap in our current understanding of protein container structure and can be widely applied in protein nanotechnology, paving the way to programmable control over particle polymorphism.