Beyond the MUN domain, Munc13 controls priming and depriming of synaptic vesicles.

Synaptic vesicle docking and priming are dynamic processes. At the molecular level, SNAREs (soluble NSF attachment protein receptors), synaptotagmins, and other factors are critical for Ca2+-triggered vesicle exocytosis, while disassembly factors, including NSF (N-ethylmaleimide-sensitive factor) and α-SNAP (soluble NSF attachment protein), disassemble and recycle SNAREs and antagonize fusion under some conditions. Here, we introduce a hybrid fusion assay that uses synaptic vesicles isolated from mouse brains and synthetic plasma membrane mimics. We included Munc18, Munc13, complexin, NSF, α-SNAP, and an ATP-regeneration system and maintained them continuously-as in the neuron-to investigate how these opposing processes yield fusogenic synaptic vesicles. In this setting, synaptic vesicle association is reversible, and the ATP-regeneration system produces the most synchronous Ca2+-triggered fusion, suggesting that disassembly factors perform quality control at the early stages of synaptic vesicle association to establish a highly fusogenic state. We uncovered a functional role for Munc13 ancillary to the MUN domain that alleviates an α-SNAP-dependent inhibition of Ca2+-triggered fusion.

Machine learning-based prediction of proteins' architecture using sequences of amino acids and structural alphabets.

In addition to the growth of protein structures generated through wet laboratory experiments and deposited in the PDB repository, AlphaFold predictions have significantly contributed to the creation of a much larger database of protein structures. Annotating such a vast number of structures has become an increasingly challenging task. CATH is widely recognized as one the most common platforms for addressing this challenge, as it classifies proteins based on their structural and evolutionary relationships, offering the scientific community an invaluable resource for uncovering various properties, including functional annotations. While CATH annotation involves - to some extent - human intervention, keeping up with the classification of the rapidly expanding repositories of protein structures has become exceedingly difficult. Therefore, there is a pressing need for a fully automated approach. On the other hand, the abundance of protein sequences stemming from next generation sequencing technologies, lacking structural annotations, presents an additional challenge to the scientific community. Consequently, 'pre-annotating' protein sequences with structural features, ensuring a high level of precision, could prove highly advantageous. In this paper, after a thorough investigation, we introduce a novel machine-learning model capable of classifying any protein domain, whether it has a known structure or not, into one of the 40 main CATH Architectures. We achieve an F1 Score of 0.92 using only the amino acid sequence and a score of 0.94 using both the sequence of amino acids and the sequence of structural alphabets.Communicated by Ramaswamy H. Sarma.

Varying protein architectures in 3-dimensions for scaffolding and modulating properties of catalytic gold nanoparticles.

Fabrication and development of nanoscale materials with tunable structural and functional properties require a dynamic arrangement of nanoparticles on architectural templates. The function of nanoparticles not only depends on the property of the nanoparticles but also on their spatial orientations. Proteins with self-assembling properties which can be genetically engineered to varying architectural designs for scaffolds can be used to develop different orientations of nanoparticles in three dimensions. Here, we report the use of naturally self-assembling bacterial micro-compartment shell protein (PduA) assemblies in 2D and its single-point mutant variant (PduA[K26A]) in 3D architectures for the reduction and fabrication of gold nanoparticles. Interestingly, the different spatial organization of gold nanoparticles resulted in a smaller size in the 3D architect scaffold. Here, we observed a two-fold increase in catalytic activity and six-fold higher affinity toward TMB (3,3',5,5'-tetramethylbenzidine) substrate as a measure of higher peroxidase activity (nanozymatic) in the case of PduA[K26A] 3D scaffold. This approach demonstrates that the hierarchical organization of scaffold enables the fine-tuning of nanoparticle properties, thus paving the way toward the design of new nanoscale materials.

Promiscuous Domains in Eukaryotes and HAT Proteins in FUNGI Have Followed Different Evolutionary Paths.

Diverse studies have shown that the content of genes present in sequenced genomes does not seem to correlate with the complexity of the organisms. However, various studies have shown that organism complexity and the size of the proteome has, indeed, a significant correlation. This characteristic allows us to postulate that some molecular mechanisms have permitted a greater functional diversity to some proteins to increase their participation in developing organisms with higher complexity. Among those mechanisms, the domain promiscuity, defined as the ability of the domains to organize in combination with other distinct domains, is of great importance for the evolution of organisms. Previous works have analyzed the degree of domain promiscuity of the proteomes showing how it seems to have paralleled the evolution of eukaryotic organisms. The latter has motivated the present study, where we analyzed the domain promiscuity in a collection of 84 eukaryotic proteomes representative of all the taxonomy groups of the tree of life. Using a grammar definition approach, we determined the architecture of 1,223,227 proteins, conformed by 2,296,371 domains, which established 839,184 bigram types. The phylogenetic reconstructions based on differences in the content of information from measures of proteome promiscuity confirm that the evolution of the promiscuity of domains in eukaryotic organisms resembles the evolutionary history of the species. However, a close analysis of the PHD and RING domains, the most promiscuous domains found in fungi and functional components of chromatin remodeling enzymes and important expression regulators, suggests an evolution according to their function.

An Interfacial Sodium Ion is an Essential Structural Feature of Fluc Family Fluoride Channels.

Fluc family fluoride channels are assembled as primitive antiparallel homodimers. Crystallographic studies revealed a cation bound at the center of the protein, where it is coordinated at the dimer interface by main chain carbonyl oxygen atoms from the midmembrane breaks in two corresponding transmembrane helices. Here, we show that this cation is a stably bound sodium ion, and although it is not a transported substrate, its presence is required for the channel to adopt an open, fluoride-conducting conformation. The interfacial site is selective for sodium over other cations, except for Li+, which competes with Na+ for binding, but does not support channel activity. The strictly structural role fulfilled by this sodium provides new context to understand the structures, mechanisms, and evolutionary origins of widespread Na+-coupled transporters.

Prediction of protein architectures involved in the signaling-pathway initiating sporulation in Firmicutes.

OBJECTIVES: Like many other proteins, those belonging to the signal transduction cascade initiating sporulation (Spo0 pathway) have conserved protein domains (Capra and Laub in Annu Rev Microbiol 66:325-47, 2012). Improvements in bioinformatics applications to discover proteins involved in the initiation of the sporulating cascade in newly sequenced genomes is an important task that requires rigorous comparative genomic methods and manual curation to identify endospore-forming bacteria. This note aims to present a collection of predicted proteins involved in the Spo0 pathway found in the proteomes of fully sequenced and manually curated endospore-forming Firmicutes species. This collection may serve as a guide to conduct future experiments in endospore formers in genomic and metagenomic projects. DATA DESCRIPTION: Similar to the report of Davidson et al. (PLoS Genet 14:1-33, 2018), we used Pfam profiles (El-Gebali et al. in Nucleic Acids Res 47:D427-32, 2019) defining each protein and the genomic context surrounding the query gene to predict probable orthologs of the Spo0 pathway in Firmicutes. We present in this note a collection of 325 Firmicutes species organized by phylogenetic class and classified as spore formers, non-spore formers or unknown spore phenotype based on published literature, for which we predicted probable orthologs defining the signal transduction pathway initiating sporulation.

Structural Analysis of Protein Complexes by Cross-Linking and Mass Spectrometry.

Cross-linking and mass spectrometry is used more and more for the structural analysis of large proteins and protein complexes. Although essentially a low-resolution method, it avoids the main drawbacks of established structural techniques. Particularly, it is largely insensitive to the inherent flexibility of the studied complexes and is applied under native conditions. It is also applicable to nearly every structural system. Therefore, cross-linking and mass spectrometry is the method of choice for elucidating the general architecture of protein complexes. Advances in instrumentation, techniques, and software now allow every lab that is working with proteins to apply the approach without much difficulty. The most specialized step in the workflow, the mass spectrometry measurement, can be done in most facilities that are performing standard proteomics. We detail here a step-by-step protocol of how to successfully apply the approach in collaboration with the mass spectrometry facility in your institution.

An optimized method for 3D fluorescence co-localization applied to human kinetochore protein architecture.

Two-color fluorescence co-localization in 3D (three-dimension) has the potential to achieve accurate measurements at the nanometer length scale. Here, we optimized a 3D fluorescence co-localization method that uses mean values for chromatic aberration correction to yield the mean separation with ~10 nm accuracy between green and red fluorescently labeled protein epitopes within single human kinetochores. Accuracy depended critically on achieving small standard deviations in fluorescence centroid determination, chromatic aberration across the measurement field, and coverslip thickness. Computer simulations showed that large standard deviations in these parameters significantly increase 3D measurements from their true values. Our 3D results show that at metaphase, the protein linkage between CENP-A within the inner kinetochore and the microtubule-binding domain of the Ndc80 complex within the outer kinetochore is on average ~90 nm. The Ndc80 complex appears fully extended at metaphase and exhibits the same subunit structure in vivo as found in vitro by crystallography.

Rules for connectivity of secondary structure elements in protein: Two-layer αß sandwiches.

In protein structures, the fold is described according to the spatial arrangement of secondary structure elements (SSEs: α-helices and ß-strands) and their connectivity. The connectivity or the pattern of links among SSEs is one of the most important factors for understanding the variety of protein folds. In this study, we introduced the connectivity strings that encode the connectivities by using the types, positions, and connections of SSEs, and computationally enumerated all the connectivities of two-layer αß sandwiches. The calculated connectivities were compared with those in natural proteins determined using MICAN, a nonsequential structure comparison method. For 2α-4ß, among 23,000 of all connectivities, only 48 were free from irregular connectivities such as loop crossing. Of these, only 20 were found in natural proteins and the superfamilies were biased toward certain types of connectivities. A similar disproportional distribution was confirmed for most of other spatial arrangements of SSEs in the two-layer αß sandwiches. We found two connectivity rules that explain the bias well: the abundances of interlayer connecting loops that bridge SSEs in the distinct layers; and nonlocal ß-strand pairs, two spatially adjacent ß-strands located at discontinuous positions in the amino acid sequence. A two-dimensional plot of these two properties indicated that the two connectivity rules are not independent, which may be interpreted as a rule for the cooperativity of proteins.

Plasmobase: a comparative database of predicted domain architectures for Plasmodium genomes.

BACKGROUND: With the availability of complete genome sequences of both human and non-human Plasmodium parasites, it is now possible to use comparative genomics to look for orthology across Plasmodium species and for species specific genes. This comparative analyses could provide important clues for the development of new strategies to prevent and treat malaria in humans, however, the number of functionally annotated proteins is still low for all Plasmodium species. In the context of genomes that are hard to annotate because of sequence divergence, such as Plasmodium, domain co-occurrence becomes particularly important to trust predictions. In particular, domain architecture prediction can be used to improve the performance of existing annotation methods since homologous proteins might share their architectural context. RESULTS: Plasmobase is a unique database designed for the comparative study of Plasmodium genomes. Domain architecture reconstruction in Plasmobase relies on DAMA, the state-of-the-art method in architecture prediction, while domain annotation is realised with CLADE, a novel annotation tool based on a multi-source strategy. Plasmobase significantly increases the Pfam domain coverage of all Plasmodium genomes, it proposes new domain architectures as well as new domain families that have never been reported before for these genomes. It proposes a visualization of domain architectures and allows for an easy comparison among architectures within Plasmodium species and with other species, described in UniProt. CONCLUSIONS: Plasmobase is a valuable new resource for domain annotation in Plasmodium genomes. Its graphical presentation of protein sequences, based on domain architectures, will hopefully be of interest for comparative genomic studies. It should help to discover species-specific genes, possibly underlying important phenotypic differences between parasites, and orthologous gene families for deciphering the biology of these complex and important Apicomplexan organisms. In conclusion, Plasmobase is a flexible and rich site where any biologist can find something of his/her own interest. AVAILABILITY: Plasmobase is accessible at http://genome.lcqb.upmc.fr/plasmobase/ .

Evolution of the Calcium-Based Intracellular Signaling System.

To progress our understanding of molecular evolution from a collection of well-studied genes toward the level of the cell, we must consider whole systems. Here, we reveal the evolution of an important intracellular signaling system. The calcium-signaling toolkit is made up of different multidomain proteins that have undergone duplication, recombination, sequence divergence, and selection. The picture of evolution, considering the repertoire of proteins in the toolkit of both extant organisms and ancestors, is radically different from that of other systems. In eukaryotes, the repertoire increased in both abundance and diversity at a far greater rate than general genomic expansion. We describe how calcium-based intracellular signaling evolution differs not only in rate but in nature, and how this correlates with the disparity of plants and animals.

Mechanistic signs of double-barreled structure in a fluoride ion channel.

The Fluc family of F(-) ion channels protects prokaryotes and lower eukaryotes from the toxicity of environmental F(-). In bacteria, these channels are built as dual-topology dimers whereby the two subunits assemble in antiparallel transmembrane orientation. Recent crystal structures suggested that Fluc channels contain two separate ion-conduction pathways, each with two F(-) binding sites, but no functional correlates of this unusual architecture have been reported. Experiments here fill this gap by examining the consequences of mutating two conserved F(-)-coordinating phenylalanine residues. Substitution of each phenylalanine specifically extinguishes its associated F(-) binding site in crystal structures and concomitantly inhibits F(-) permeation. Functional analysis of concatemeric channels, which permit mutagenic manipulation of individual pores, show that each pore can be separately inactivated without blocking F(-) conduction through its symmetry-related twin. The results strongly support dual-pathway architecture of Fluc channels.

Creating functional sophistication from simple protein building blocks, exemplified by factor H and the regulators of complement activation.

Complement control protein modules (CCPs) occur in numerous functionally diverse extracellular proteins. Also known as short consensus repeats (SCRs) or sushi domains each CCP contains approximately 60 amino acid residues, including four consensus cysteines participating in two disulfide bonds. Varying in length and sequence, CCPs adopt a ß-sandwich type fold and have an overall prolate spheroidal shape with N- and C-termini lying close to opposite poles of the long axis. CCP-containing proteins are important as cytokine receptors and in neurotransmission, cell adhesion, blood clotting, extracellular matrix formation, haemoglobin metabolism and development, but CCPs are particularly well represented in the vertebrate complement system. For example, factor H (FH), a key soluble regulator of the alternative pathway of complement activation, is made up entirely from a chain of 20 CCPs joined by short linkers. Collectively, therefore, the 20 CCPs of FH must mediate all its functional capabilities. This is achieved via collaboration and division of labour among these modules. Structural studies have illuminated the dynamic architectures that allow FH and other CCP-rich proteins to perform their biological functions. These are largely the products of a highly varied set of intramolecular interactions between CCPs. The CCP can act as building block, spacer, highly versatile recognition site or dimerization mediator. Tandem CCPs may form composite binding sites or contribute to flexible, rigid or conformationally 'switchable' segments of the parent proteins.

Identification of AHK2- and AHK3-like cytokinin receptors in Brassica napus reveals two subfamilies of AHK2 orthologues.

Cytokinin (CK) signalling is known to play key roles in the regulation of plant growth and development, crop yields, and tolerance to both abiotic stress and pathogen defences, but the mechanisms involved are poorly characterized in dicotyledonous crops. Here the identification and functional characterization of sensor histidine kinases homologous to Arabidopsis CK receptors AHK2 and AHK3 in winter oilseed rape are presented. Five CHASE-containing His kinases were identified in Brassica napus var. Tapidor (BnCHK1-BnCHK5) by heterologous hybridization of its genomic library with gene-specific probes from Arabidopsis. The identified bacterial artificial chromosome (BAC) clones were fingerprinted and representative clones in five distinct groups were sequenced. Using a bioinformatic approach and cDNA cloning, the precise gene and putative protein domain structures were determined. Based on phylogenetic analysis, four AHK2 (BnCHK1-BnCHK4) homologues and one AHK3 (BnCHK5) homologue were defined. It is further suggested that BnCHK1 and BnCHK3, and BnCHK5 are orthologues of AHK2 and AHK3, originally from the B. rapa A genome, respectively. BnCHK1, BnCHK3, and BnCHK5 displayed high affinity for trans-zeatin (1-3nM) in a live-cell competitive receptor assay, but not with other plant hormones (indole acetic acid, GA3, and abscisic acid), confirming the prediction that they are genuine CK receptors. It is shown that BnCHK1 and BnCHK3, and BnCHK5 display distinct preferences for various CK bases and metabolites, characteristic of their AHK counterparts, AHK2 and AHK3, respectively. Interestingly, the AHK2 homologues could be divided into two subfamilies (BnCHK1/BnCK2 and BnCHK3/BnCHK4) that differ in putative transmembrane domain topology and CK binding specificity, thus implying potential functional divergence.

The chordate proteome history database.

The chordate proteome history database (http://ioda.univ-provence.fr) comprises some 20,000 evolutionary analyses of proteins from chordate species. Our main objective was to characterize and study the evolutionary histories of the chordate proteome, and in particular to detect genomic events and automatic functional searches. Firstly, phylogenetic analyses based on high quality multiple sequence alignments and a robust phylogenetic pipeline were performed for the whole protein and for each individual domain. Novel approaches were developed to identify orthologs/paralogs, and predict gene duplication/gain/loss events and the occurrence of new protein architectures (domain gains, losses and shuffling). These important genetic events were localized on the phylogenetic trees and on the genomic sequence. Secondly, the phylogenetic trees were enhanced by the creation of phylogroups, whereby groups of orthologous sequences created using OrthoMCL were corrected based on the phylogenetic trees; gene family size and gene gain/loss in a given lineage could be deduced from the phylogroups. For each ortholog group obtained from the phylogenetic or the phylogroup analysis, functional information and expression data can be retrieved. Database searches can be performed easily using biological objects: protein identifier, keyword or domain, but can also be based on events, eg, domain exchange events can be retrieved. To our knowledge, this is the first database that links group clustering, phylogeny and automatic functional searches along with the detection of important events occurring during genome evolution, such as the appearance of a new domain architecture.

Systematic alanine insertion reveals the essential regions that encode structure formation and activity of dihydrofolate reductase.

Decoding sequence information is equivalent to elucidating the design principles of proteins. For this purpose, we conducted systematic alanine insertion analysis to reveal the regions in the primary structure where the sequence continuity cannot be disrupted. We applied this method to dihydrofolate reductase (DHFR), and examined the effects of alanine insertion on structure and the enzymatic activity by solubility assay and trimethoprim resistance, respectively. We revealed that DHFR is composed of "Structure Elements", "Function Elements" and linkers connecting these elements. The "Elements" are defined as regions where the alanine insertion caused DHFR to become unstructured or inactive. Some "Structure Elements" overlap with "Function Elements", indicating that loss of structure leads to loss of function. However, other "Structure Elements" are not "Function Elements", in that alanine insertion mutants of these regions exhibit substrate- or inhibitor-induced folding. There are also some "Function Elements" which are not "Structure Elements"; alanine insertion into these elements deforms the catalytic site topology without the loss of tertiary structure. We hypothesize that these elements are involved essential interactions for structure formation and functional expression. The "Elements" are closely related to the module structure of DHFR. An "Element" belongs to a single module, and a single module is composed of some number of "Elements." We propose that properties of a module are determined by the "Elements" it contains. Systematic alanine insertion analysis is an effective and unique method for deriving the regions of a sequence that are essential for structure formation and functional expression.