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At least 595 records · Page 33

FLS2-BAK1 Extracellular Domain Interaction Sites Required for Defense Signaling Activation

Signaling initiation by receptor-like kinases (RLKs) at the plasma membrane of plant cells often requires regulatory leucine-rich repeat (LRR) RLK proteins such as SERK or BIR proteins. The present work examined how the microbe-associated molecular pattern (MAMP) receptor FLS2 builds signaling complexes with BAK1 (SERK3). We first, using in vivo methods that validate separate findings by others, demonstrated that flg22 (flagellin epitope) ligand-initiated FLS2-BAK1 extracellular domain interactions can proceed independent of intracellular domain interactions. We then explored a candidate SERK protein interaction site in the extracellular domains (ectodomains; ECDs) of the significantly different receptors FLS2, EFR (MAMP receptors), PEPR1 (damage-associated molecular pattern (DAMP) receptor), and BRI1 (hormone receptor). Repeat conservation mapping revealed a cluster of conserved solvent-exposed residues near the C-terminus of models of the folded LRR domains. However, site-directed mutagenesis of this conserved site in FLS2 did not impair FLS2-BAK1 ECD interactions, and mutations in the analogous site of EFR caused receptor maturation defects. Hence this conserved LRR C-terminal region apparently has functions other than mediating interactions with BAK1. In vivo tests of the subsequently published FLS2-flg22-BAK1 ECD co-crystal structure were then performed to functionally evaluate some of the unexpected configurations predicted by that crystal structure. In support of the crystal structure data, FLS2-BAK1 ECD interactions were no longer detected in in vivo co-immunoprecipitation experiments after site-directed mutagenesis of the FLS2 BAK1-interaction residues S554, Q530, Q627 or N674. In contrast, in vivo FLS2-mediated signaling persisted and was only minimally reduced, suggesting residual FLS2-BAK1 interaction and the limited sensitivity of co-immunoprecipitation data relative to in vivo assays for signaling outputs. However, Arabidopsis plants expressing FLS2 with the Q530A+Q627A double mutation were impaired both in detectable interaction with BAK1 and in FLS2-mediated responses, lending overall support to current models of FLS2 structure and function.

59 BASIC BIOLOGICAL SCIENCES↗

Utilizing genome-scale models to optimize nutrient supply for sustained algal growth and lipid productivity

Nutrient availability is critical for growth of algae and other microbes used for generating valuable biochemical products. Determining the optimal levels of nutrient supplies to cultures can eliminate feeding of excess nutrients, lowering production costs and reducing nutrient pollution into the environment. With the advent of omics and bioinformatics methods, it is now possible to construct genome-scale models that accurately describe the metabolism of microorganisms. In this study, a genome-scale model of the green alga Chlorella vulgaris (iCZ946) was applied to predict feeding of multiple nutrients, including nitrate and glucose, under both autotrophic and heterotrophic conditions. The objective function was changed from optimizing growth to instead minimizing nitrate and glucose uptake rates, enabling predictions of feed rates for these nutrients. The metabolic model control (MMC) algorithm was validated for autotrophic growth, saving 18% nitrate while sustaining algal growth. Additionally, we obtained similar growth profiles by simultaneously controlling glucose and nitrate supplies under heterotrophic conditions for both high and low levels of glucose and nitrate. Finally, the nitrate supply was controlled in order to retain protein and chlorophyll synthesis, albeit at a lower rate, under nitrogen-limiting conditions. This model-driven cultivation strategy doubled the total volumetric yield of biomass, increased fatty acid methyl ester (FAME) yield by 61%, and enhanced lutein yield nearly 3 fold compared to nitrogen starvation. This study introduces a control methodology that integrates omics data and genome-scale models in order to optimize nutrient supplies based on the metabolic state of algal cells in different nutrient environments. This approach could transform bioprocessing control into a systems biology-based paradigm suitable for a wide range of species in order to limit nutrient inputs, reduce processing costs, and optimize biomanufacturing for the next generation of desirable biotechnology products.

59 BASIC BIOLOGICAL SCIENCES↗

Atypical Divergence of SARS-CoV-2 Orf8 from Orf7a within the Coronavirus Lineage Suggests Potential Stealthy Viral Strategies in Immune Evasion

Orf8, one of the most puzzling genes in the SARS lineage of coronaviruses, marks a unique and striking difference in genome organization between SARS-CoV-2 and SARS-CoV-1. Here, using sequence comparisons, we unequivocally reveal the distant sequence similarities between SARS-CoV-2 Orf8 with its SARS-CoV-1 counterparts and the X4-like genes of coronaviruses, including its highly divergent “paralog” gene Orf7a, whose product is a potential immune antagonist of known structure. Supervised sequence space walks unravel identity levels that drop below 10% and yet exhibit subtle conservation patterns in this novel superfamily, characterized by an immunoglobulin-like beta sandwich topology. We document the high accuracy of the sequence space walk process in detail and characterize the subgroups of the superfamily in sequence space by systematic annotation of gene and taxon groups. While SARS-CoV-1 Orf7a and Orf8 genes are most similar to bat virus sequences, their SARS-CoV-2 counterparts are closer to pangolin virus homologs, reflecting the fine structure of conservation patterns within the SARS-CoV-2 genomes. The divergence between Orf7a and Orf8 is exceptionally idiosyncratic, since Orf7a is more constrained, whereas Orf8 is subject to rampant change, a peculiar feature that may be related to hitherto-unknown viral infection strategies. Despite their common origin, the Orf7a and Orf8 protein families exhibit different modes of evolutionary trajectories within the coronavirus lineage, which might be partly attributable to their complex interactions with the mammalian host cell, reflected by a multitude of functional associations of Orf8 in SARS-CoV-2 compared to a very small number of interactions discovered for Orf7a.

60 APPLIED LIFE SCIENCES↗

Curated BLAST for Genomes

Given a microbe’s genome sequence, we often want to predict what capabilities the organism has, such as which nutrients it requires or which energy sources it can use. Or, we know the organism has a capability and we want to find the genes involved. Scientists often use automated gene annotations to find relevant genes, but automated annotations are often vague or incorrect. Curated BLAST finds candidate genes for a capability without relying on automated annotations. First, Curated BLAST finds proteins (usually from other organisms) whose functions have been studied experimentally and whose curated descriptions match a query. Then, it searches the genome of interest for similar proteins and returns a list of candidates. Curated BLAST is fast and often finds relevant genes that are missed by automated annotation.

59 BASIC BIOLOGICAL SCIENCES↗

Data for Characterization of the Ghd8 Flowering Time Gene in a Mini-Core Collection of Miscanthus sinensis

The optimal flowering time for bioenergy crop miscanthus is essential for environmental adaptability and biomass accumulation. However, little is known about how genes controlling flowering in other grasses contribute to flowering regulation in miscanthus. Here, we report on the sequence characterization and gene expression of Miscanthus sinensisGhd8 , a transcription factor encoding a HAP3/NF-YB DNA-binding domain, which has been identified as a major quantitative trait locus in rice, with pleiotropic effects on grain yield, heading date and plant height. In M. sinensis , we identified two homoeologous loci, MsiGhd8A located on chromosome 13 and MsiGhd8B on chromosome 7, with one on each of this paleo-allotetraploid species’ subgenomes. A total of 46 alleles and 28 predicted protein sequence types were identified in 12 wild-collected accessions. Several variants of MsiGhd8 showed a geographic and latitudinal distribution. Quantitative real-time PCR revealed that MsiGhd8 expressed under both long days and short days, and MsiGhd8B showed a significantly higher expression than MsiGhd8A . The comparison between flowering time and gene expression indicated that MsiGhd8B affected flowering time in response to day length for some accessions. This study provides insight into the conserved function of Ghd8 in the Poaceae, and is an important initial step in elucidating the flowering regulatory network of Miscanthus.

Feedstock Production↗

The genotype-phenotype landscape of an allosteric protein

Allostery is a fundamental biophysical mechanism that underlies cellular sensing, signaling, and metabolism. Yet a quantitative understanding of allosteric genotype-phenotype relationships remains elusive. Here, we report the large-scale measurement of the genotype-phenotype landscape for an allosteric protein: the lac repressor from Escherichia coli , LacI. Using a method that combines long-read and short-read DNA sequencing, we quantitatively measure the dose-response curves for nearly 10 5 variants of the LacI genetic sensor. The resulting data provide a quantitative map of the effect of amino acid substitutions on LacI allostery and reveal systematic sequence-structure-function relationships. We find that in many cases, allosteric phenotypes can be quantitatively predicted with additive or neural-network models, but unpredictable changes also occur. For example, we were surprised to discover a new band-stop phenotype that challenges conventional models of allostery and that emerges from combinations of nearly silent amino acid substitutions.

59 BASIC BIOLOGICAL SCIENCES↗

Characterization of the Ghd8 Flowering Time Gene in a Mini-Core Collection of Miscanthus sinensis

The optimal flowering time for bioenergy crop Miscanthus is essential for environmental adaptability and biomass accumulation. However, little is known about how genes controlling flowering in other grasses contribute to flowering regulation in Miscanthus. Here, we report on the sequence characterization and gene expression of Miscanthus sinensisGhd8, a transcription factor encoding a HAP3/NF-YB DNA-binding domain, which has been identified as a major quantitative trait locus in rice, with pleiotropic effects on grain yield, heading date and plant height. In M. sinensis, we identified two homoeologous loci, MsiGhd8A located on chromosome 13 and MsiGhd8B on chromosome 7, with one on each of this paleo-allotetraploid species’ subgenomes. A total of 46 alleles and 28 predicted protein sequence types were identified in 12 wild-collected accessions. Several variants of MsiGhd8 showed a geographic and latitudinal distribution. Quantitative real-time PCR revealed that MsiGhd8 expressed under both long days and short days, and MsiGhd8B showed a significantly higher expression than MsiGhd8A. The comparison between flowering time and gene expression indicated that MsiGhd8B affected flowering time in response to day length for some accessions. This study provides insight into the conserved function of Ghd8 in the Poaceae, and is an important initial step in elucidating the flowering regulatory network of Miscanthus.

geographic distribution↗

Codominant grasses differ in gene expression under experimental climate extremes in native tallgrass prairie

Extremes in climate, such as heat waves and drought, are expected to become more frequent and intense with forecasted climate change. Plant species will almost certainly differ in their responses to these stressors. We experimentally imposed a heat wave and drought in the tallgrass prairie ecosystem near Manhattan, Kansas, USA to assess transcriptional responses of two ecologically important C 4 grass species, Andropogon gerardii and Sorghastrum nutans . Based on previous research, we expected that S. nutans would regulate more genes, particularly those related to stress response, under high heat and drought. Across all treatments, S. nutans showed greater expression of negative regulatory and catabolism genes while A. gerardii upregulated cellular and protein metabolism. As predicted, S. nutans showed greater sensitivity to water stress, particularly with downregulation of non-coding RNAs and upregulation of water stress and catabolism genes. A. gerardii was less sensitive to drought , although A. gerardii tended to respond with upregulation in response to drought versus S. nutans which downregulated more genes under drier conditions. Surprisingly, A. gerardii only showed minimal gene expression response to increased temperature, while S. nutans showed no response. Gene functional annotation suggested that these two species may respond to stress via different mechanisms. Specifically, A. gerardii tends to maintain molecular function while S. nutans prioritizes avoidance. Sorghastrum nutans may strategize abscisic acid response and catabolism to respond rapidly to stress. These results have important implications for success of these two important grass species under a more variable and extreme climate forecast for the future.

59 BASIC BIOLOGICAL SCIENCES↗

Ceruloplasmin and cardiovascular disease

Transition metal ion-mediated oxidation is a commonly used model system for studies of the chemical, structural, and functional modifications of low-density lipoprotein (LDL). The physiological relevance of studies using free metal ions is unclear and has led to an exploration of free metal ion-independent mechanisms of oxidation. We and others have investigated the role of human ceruloplasmin (Cp) in oxidative processes because it the principal copper-containing protein in serum. There is an abundance of epidemiological data that suggests that serum Cp may be an important risk factor predicting myocardial infarction and cardiovascular disease. Biochemical studies have shown that Cp is a potent catalyst of LDL oxidation in vitro. The pro-oxidant activity of Cp requires an intact structure, and a single copper atom at the surface of the protein, near His(426), is required for LDL oxidation. Under conditions where inhibitory protein (such as albumin) is present, LDL oxidation by Cp is optimal in the presence of superoxide, which reduces the surface copper atom of Cp. Cultured vascular endothelial and smooth muscle cells also oxidize LDL in the presence of Cp. Superoxide release by these cells is a critical factor regulating the rate of oxidation. Cultured monocytic cells, when activated by zymosan, can oxidize LDL, but these cells are unique in their secretion of Cp. Inhibitor studies using Cp-specific antibodies and antisense oligonucleotides show that Cp is a major contributor to LDL oxidation by these cells. The role of Cp in lipoprotein oxidation and atherosclerotic lesion progression in vivo has not been directly assessed and is an important area for future studies.

NASA Discipline Cell Biology↗

Biogenesis of non-structural protein 1 (nsp1) and nsp1-mediated type I interferon modulation in arteriviruses

Type I interferons (IFNs-α/β) play a key role for the antiviral state of host, and the porcine arterivirus; porcine reproductive and respiratory syndrome virus (PRRSV), has been shown to down-regulate the production of IFNs during infection. Non-structural protein (nsp) 1 of PRRSV has been identified as a viral IFN antagonist, and the nsp1α subunit of nsp1 has been shown to degrade the CREB-binding protein (CBP) and to inhibit the formation of enhanceosome thus resulting in the suppression of IFN production. The study was expanded to other member viruses in the family Arteriviridae: equine arteritis virus (EAV), murine lactate dehydrogenase-elevating virus (LDV), and simian hemorrhagic fever virus (SHFV). While PRRSV–nsp1 and LDV–nsp1 were auto-cleaved to produce the nsp1α and nsp1β subunits, EAV–nsp1 remained uncleaved. SHFV–nsp1 was initially predicted to be cleaved to generate three subunits (nsp1α, nsp1β, and nsp1γ), but only two subunits were generated as SHFV–nsp1αβ and SHFV–nsp1γ. The papain-like cysteine protease (PLP) 1α motif in nsp1α remained inactive for SHFV, and only the PLP1β motif of nsp1β was functional to generate SHFV–nsp1γ subunit. All subunits of arterivirus nsp1 were localized in the both nucleus and cytoplasm, but PRRSV–nsp1β, LDV–nsp1β, EAV–nsp1, and SHFV–nsp1γ were predominantly found in the nucleus. All subunits of arterivirus nsp1 contained the IFN suppressive activity and inhibited both interferon regulatory factor 3 (IRF3) and NF-κB mediated IFN promoter activities. Similar to PRRSV–nsp1α, CBP degradation was evident in cells expressing LDV–nsp1α and SHFV–nsp1γ, but no such degradation was observed for EAV–nsp1. Regardless of CBP degradation, all subunits of arterivirus nsp1 suppressed the IFN-sensitive response element (ISRE)-promoter activities. Our data show that the nsp1-mediated IFN modulation is a common strategy for all arteriviruses but their mechanism of action may differ from each other. - Highlights: • LDV–nsp1 was cleaved to nsp1α and nsp1β whereas EAV–nsp1 was uncleaved. • SHFV–nsp1 was cleaved to nsp1αβ and nsp1γ. • PRRSV–nsp1β, LDV–nsp1β, EAV–nsp1, and SHFV–nsp1γ were nuclear proteins. • PRRSV–nsp1α, LDV–nsp1α, and SHFV–nsp1γ caused CBP degradation. • All nsp1 subunits contained interferon and ISRE suppressive activities.

60 APPLIED LIFE SCIENCES↗

ppdx : Automated modeling of protein–protein interaction descriptors for use with machine learning

This paper describes ppdx, a python workflow tool that combines protein sequence alignment, homology modeling, and structural refinement, to compute a broad array of descriptors for characterizing protein–protein interactions. The descriptors can be used to predict various properties of interest, such as protein–protein binding affinities, or inhibitory concentrations (IC 50 ), using approaches that range from simple regression to more complex machine learning models. The software is highly modular. It supports different protocols for generating structures, and 95 descriptors can be currently computed. More protocols and descriptors can be easily added. The implementation is highly parallel and can fully exploit the available cores in a single workstation, or multiple nodes on a supercomputer, allowing many systems to be analyzed simultaneously. As an illustrative application, ppdx is used to parametrize a model that predicts the IC 50 of a set of antigens and a class of antibodies directed to the influenza hemagglutinin stalk.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

SPOP promotes FADD degradation and inhibits NF-κB activity in non-small cell lung cancer

Highlights: • FADD protein level predicts poor prognosis of NSCLC patients. • SPOP binds to FADD and mediates its degradation. • SPOP inhibits NF-κB activity and its target genes expression. FAS-associated protein with death domain (FADD) is the pivotal adaptor protein, which transmits apoptotic signals mediated by the death receptors. Here we report that high FADD protein level predicts poor prognosis of non-small cell lung cancer (NSCLC) patients and its protein level is mainly regulated by the 26S proteasome. We also found that ubiquitin ligase SPOP (speckle-type POZ protein) binds to FADD and mediates its degradation, which can be blocked by MG132 treatment. Notably, SPOP inhibits NF-κB (nuclear factor kappa-light-chain-enhancer of activated B cells) activity and its target genes expression via FADD. These results reveal the function of SPOP-FADDNFκB axis in NSCLC cells, which is associated with prognosis of NSCLC patients.

60 APPLIED LIFE SCIENCES↗

Transferable Dynamic Molecular Charge Assignment Using Deep Neural Networks

We report that the ability to accurately and efficiently compute quantum-mechanical partial atomistic charges has many practical applications, such as calculations of IR spectra, analysis of chemical bonding, and classical force field parametrization. Machine learning (ML) techniques provide a possible avenue for the efficient prediction of atomic partial charges. Modern ML advances in the prediction of molecular energies [i.e., the hierarchical interacting particle neural network (HIP-NN)] has provided the necessary model framework and architecture to predict transferable, extensible, and conformationally dynamic atomic partial charges based on reference density functional theory (DFT) simulations. Utilizing HIP-NN, we show that ML charge prediction can be highly accurate over a wide range of molecules (both small and large) across a variety of charge partitioning schemes such as the Hirshfeld, CM5, MSK, and NBO methods. To demonstrate transferability and size extensibility, we compare ML results with reference DFT calculations on the COMP6 benchmark, achieving errors of 0.004e – (elementary charge). This is remarkable since this benchmark contains two proteins that are multiple times larger than the largest molecules in the training set. An application of our atomic charge predictions on nonequilibrium geometries is the generation of IR spectra for organic molecules from dynamical trajectories on a variety of organic molecules, which show good agreement with calculated IR spectra with reference method. Critically, HIP-NN charge predictions are many orders of magnitude faster than direct DFT calculations. Lastly, these combined results provide further evidence that ML (specifically HIP-NN) provides a pathway to greatly increase the range of feasible simulations while retaining quantum-level accuracy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structure-Function and Nearest Neighbor Interactions of the Cytochrome b 6 f Complex

Test prediction from our (i) high resolution (2.5 Å) structure of cyanobacterial cytochrome b 6 f complex (Structure, 22, 1008-1015, 2014), and (ii) analysis of quinone/quinol traffic within the b 6 f complex (Biophys. J., 107, 1620-1628, 2014) concerning the rate-limiting step in the linear (non-cyclic) electron transport chain. It was concluded that it arises from access of plastoquinol, the electron/proton donor, to the high potential electron carriers, i. e., the Fe 2 S 2 and cytochrome f proteins. The directed motion of the quinol proceeds via a narrow channel on the lumen or electrochemically positive, p- (lumen) side of the b 6 f complex which was defined by crystal structures of the b 6 f complex with quinol analogue inhibitors (J. Mol. Biol., 370, 39-52, 2007).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Investigating Electron Conductivity Regimes in the Bacterial Cytochrome Wire OmcS

The anaerobic bacterium Geobacter sulfurreducens produces extracellular, electronically conductive cytochrome polymer wires that are conductive over micron length scales. Structure models from cryo-electron microscopy data show OmcS wires form a linear chain of hemes along the protein wire axis, which is proposed as the structural basis supporting their electronic properties. However, the mechanism by which this heme arrangement supports long-range electronic conduction remains unknown. Structure models from cryo-electron microscopy data show these wires form a linear chain of hemes along the protein wire axis, which is proposed as the structural basis supporting their electronic properties. Existing computational models using static heme redox potentials and coupling energies fail to explain experimental observations, predicting conductances 10,000 to 100,000 times lower than measured values. Here, we investigate how dynamic disorder affects site energies, interheme coupling, and long-range electronic conductivity within these cytochrome wires. We introduce an approach to extract charge carrier site information directly from Kohn–Sham density functional theory, without employing projector schemes, and show that site and coupling energies are highly sensitive to changes in interheme geometry and the surrounding electrostatic environment. Unlike models that incorporate dynamic disorder as a thermally averaged quantity, our quantum charge carrier model incorporates proxies for dynamic disorder through decoherence corrections, yielding predicted diffusion coefficient closer to what is expected from experiment and comparable with other organic-based electronic materials. Based on these simulations, we propose that the instantaneous fluctuations of the local electrostatic environment can transiently lift energy degeneracies and delocalize charge carriers. Furthermore, these studies reveal how incorporating dynamic fluctuations associated with the environment resolves the discrepancy between theory and experiment in microbial cytochrome wires and highlight design principles for bioinspired, heme-based conductive materials.

Bioinorganic chemistry↗

The Exoproteome and Surfaceome of Toxigenic Corynebacterium diphtheriae 1737 and Its Response to Iron Restriction and Growth on Human Hemoglobin

Toxin-producing Corynebacterium diphtheriae strains are the etiological agents of the severe upper respiratory disease, diphtheria. A global phylogenetic analysis revealed that biotype gravis is particularly lethal as it produces diphtheria toxin and a range of other virulence factors, particularly when it encounters low levels of iron at sites of infection. Here, to gain insight into how it colonizes its host, we have identified iron-dependent changes in the exoproteome and surfaceome of C. diphtheriae strain 1737 using a combination of whole-cell fractionation, intact cell surface proteolysis, and quantitative proteomics. In total, we identified 1414 of the predicted 2265 proteins (62%) encoded by its reference genome. For each protein, we quantified its degree of secretion and surface exposure, revealing that exoproteases and hydrolases predominate in the exoproteome, while the surfaceome is enriched with adhesins, particularly DIP2093. Our analysis provides insight into how components in the heme-acquisition system are positioned, showing pronounced surface exposure of the strain-specific ChtA/ChtC paralogues and high secretion of the species-conserved heme-binding HtaA protein, suggesting it functions as a hemophore. Profiling the response of the exoproteome and surfaceome after microbial exposure to human hemoglobin and iron limitation reveals potential virulence factors that may be expressed at sites of infection. Data are available via ProteomeXchange with identifier PXD051674.

cell envelope↗

Diploid genomic architecture of Nitzschia inconspicua, an elite biomass production diatom

Abstract A near-complete diploid nuclear genome and accompanying circular mitochondrial and chloroplast genomes have been assembled from the elite commercial diatom species Nitzschia inconspicua . The 50 Mbp haploid size of the nuclear genome is nearly double that of model diatom Phaeodactylum tricornutum , but 30% smaller than closer relative Fragilariopsis cylindrus . Diploid assembly, which was facilitated by low levels of allelic heterozygosity (2.7%), included 14 candidate chromosome pairs composed of long, syntenic contigs, covering 93% of the total assembly. Telomeric ends were capped with an unusual 12-mer, G-rich, degenerate repeat sequence. Predicted proteins were highly enriched in strain-specific marker domains associated with cell-surface adhesion, biofilm formation, and raphe system gliding motility. Expanded species-specific families of carbonic anhydrases suggest potential enhancement of carbon concentration efficiency, and duplicated glycolysis and fatty acid synthesis pathways across cytosolic and organellar compartments may enhance peak metabolic output, contributing to competitive success over other organisms in mixed cultures. The N. inconspicua genome delivers a robust new reference for future functional and transcriptomic studies to illuminate the physiology of benthic pennate diatoms and harness their unique adaptations to support commercial algae biomass and bioproduct production.

09 BIOMASS FUELS↗

Functional Relevance of CASP16 Nucleic Acid Predictions as Evaluated by Structure Providers

ABSTRACT Accurate biomolecular structure prediction enables the prediction of mutational effects, the speculation of function based on predicted structural homology, the analysis of ligand binding modes, experimental model building, and many other applications. Such algorithms to predict essential functional and structural features remain out of reach for biomolecular complexes containing nucleic acids. Here, we report a quantitative and qualitative evaluation of nucleic acid structures for the CASP16 blind prediction challenge by 12 of the experimental groups who provided nucleic acid targets. Blind predictions accurately model secondary structure and some aspects of tertiary structure, including reasonable global folds for some complex RNAs; however, predictions often lack accuracy in the regions of highest functional importance. All models have inaccuracies in non‐canonical regions where, for example, the nucleic‐acid backbone bends, deviating from an A‐form helix geometry, or a base forms a non‐standard hydrogen bond (not a Watson‐Crick base pair). These bends and non‐canonical interactions are integral to forming functionally important regions such as RNA enzymatic active sites. Additionally, the modeling of conserved and functional interfaces between nucleic acids and ligands, proteins, or other nucleic acids remains poor. For some targets, the experimental structures may not represent the only structure the biomolecular complex occupies in solution or in its functional life cycle, posing a future challenge for the community.

Biochemistry & Molecular Biology↗