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At least 1,189 records · Page 66

Accurate prediction of protein structures and interactions using a three-track neural network

DeepMind presented notably accurate predictions at the recent 14th Critical Assessment of Structure Prediction (CASP14) conference. We explored network architectures that incorporate related ideas and obtained the best performance with a three-track network in which information at the one-dimensional (1D) sequence level, the 2D distance map level, and the 3D coordinate level is successively transformed and integrated. The three-track network produces structure predictions with accuracies approaching those of DeepMind in CASP14, enables the rapid solution of challenging x-ray crystallography and cryo–electron microscopy structure modeling problems, and provides insights into the functions of proteins of currently unknown structure. The network also enables rapid generation of accurate protein-protein complex models from sequence information alone, short-circuiting traditional approaches that require modeling of individual subunits followed by docking. Here, we make the method available to the scientific community to speed biological research.

59 BASIC BIOLOGICAL SCIENCES↗

Structure of a ribonucleotide reductase R2 protein radical

Aerobic ribonucleotide reductases (RNRs) initiate synthesis of DNA building blocks by generating a free radical within the R2 subunit; the radical is subsequently shuttled to the catalytic R1 subunit through proton-coupled electron transfer (PCET). Here we present a high-resolution room temperature structure of the class Ie R2 protein radical captured by x-ray free electron laser serial femtosecond crystallography. The structure reveals conformational reorganization to shield the radical and connect it to the translocation path, with structural changes propagating to the surface where the protein interacts with the catalytic R1 subunit. Restructuring of the hydrogen bond network, including a notably short O–O interaction of 2.41 angstroms, likely tunes and gates the radical during PCET. These structural results help explain radical handling and mobilization in RNR and have general implications for radical transfer in proteins.

59 BASIC BIOLOGICAL SCIENCES↗

Structural analysis of extracellular ATP-independent chaperones of streptococcal species and protein substrate interactions

ABSTRACT During infection, bacterial pathogens rely on secreted virulence factors to manipulate the host cell. However, in gram-positive bacteria, the molecular mechanisms underlying the folding and activity of these virulence factors after membrane translocation are not clear. Here, we solved the protein structures of two secreted parvulin and two secreted cyclophilin-like peptidyl-prolyl isomerase (PPIase) ATP-independent chaperones found in gram-positive streptococcal species. The extracellular parvulin-type PPIase, PrsA inStreptococcus pneumoniaeandStreptococcus mutansmaintain dimeric crystal structures reminiscent of folding catalysts that consist of two domains, a PPIase and foldase domain. Structural comparison of the two cyclophilin-like extracellular chaperones fromS. pneumoniaeandStreptococcus pyogeneswith other cyclophilins demonstrates that this group of cyclophilin-like chaperones has novel structural appendages formed by 9- and 24-residue insertions. Furthermore, we demonstrate that deletion ofprsAandslrAgenes impairs the secretion of the cholesterol-dependent pore-forming toxin, pneumolysin inS. pneumoniae. Using protein pull-down and biophysical assays, we demonstrate a direct interaction between PrsA and SlrA with Ply. Then, we developed chaperone-assisted folding assays that show that theS. pneumoniaePrsA and SlrA extracellular chaperones accelerate pneumolysin folding. In addition, we demonstrate that SlrA and, for the first time,S. pyogenes PpiA exhibit PPIase activity and can bind the immunosuppressive drug, cyclosporine A. Altogether, these findings suggest a mechanistic role for streptococcal PPIase chaperones in the activity and folding of secreted virulence factors such as pneumolysin. IMPORTANCE Streptococcal species are a leading cause of lower respiratory infections that annually affect millions of people worldwide. During infection, streptococcal species secrete a medley of virulence factors that allow the bacteria to colonize and translocate to deeper tissues. In many gram-positive bacteria, virulence factors are secreted from the cytosol across the bacterial membrane in an unfolded state. The bacterial membrane-cell wall interface is exposed to the potentially harsh extracellular environment, making it difficult for native virulence factors to fold before being released into the host. ATP-independent PPIase-type chaperones, PrsA and SlrA, are thought to facilitate folding and stabilization of several unfolded proteins to promote the colonization and spread of streptococci. Here, we present crystal structures of the molecular chaperones of PrsA and SlrA homologs from streptococcal species. We provide evidence that theStreptococcus pyogenesSlrA homolog, PpiA, has PPIase activity and binds to cyclosporine A. In addition, we show thatStreptococcus pneumoniaePrsA and SlrA directly interact and fold the cholesterol-dependent pore-forming toxin and critical virulence determinant, pneumolysin.

Microbiology↗

A microfluidic platform for the synthesis of polymer and polymer-protein-based protocells

In this study, we demonstrate the fabrication of polymersomes, protein-blended polymersomes, and polymeric microcapsules using droplet microfluidics. Polymersomes with uniform, single bilayers and controlled diameters are assembled from water-in-oil-in-water double-emulsion droplets. This technique relies on adjusting the interfacial energies of the droplet to completely separate the polymer-stabilized inner core from the oil shell. Protein-blended polymersomes are prepared by dissolving protein in the inner and outer phases of polymer-stabilized droplets. Cell-sized polymeric microcapsules are assembled by size reduction in the inner core through osmosis followed by evaporation of the middle phase. All methods are developed and validated using the same glass-capillary microfluidic apparatus. This integrative approach not only demonstrates the versatility of our setup, but also holds significant promise for standardizing and customizing the production of polymer-based artificial cells.

36 MATERIALS SCIENCE↗

Modeling protein structures from predicted contacts with modern molecular dynamics potentials: accuracy, sensitivity, and refinement

Protein structure prediction has become increasingly popular and successful in recent years. An essential step for fragment-free, template-free methods is the generation of a final three-dimensional protein model from a set of predicted amino acid contacts that are often described by interresidue pairwise atomic distances. Here we explore the use of modern, open-source molecular dynamics (MD) engines, which have been continually developed over the last three decades with all-atom Hamiltonians to model biomolecular structure and dynamics, to generate accurate protein structures starting from a set of inferred pairwise distances. Additionally, the ability of MD empirical physical potentials to correct inaccuracies in the predicted geometries is tested. We rigorously characterize the effect of modeling parameters on results, the effect of different amounts of error in the predicted distances on the final structures, and test the ability of post-processing analysis to sort the best models out of a set of statistical replicas. We find that with exact distances and with noisy distances, the method can produce excellent structural models, and that the molecular dynamics force field seems to help correct errors in distance predictions, resisting the effects of applied noise.

Davidson, Russ↗

EvoProtGrad (Directed Evolution for Proteins with Gradients) [SWR-23-48]

A Python package for directed evolution on a protein sequence with gradient-based discrete Markov chain monte carlo (MCMC). Users are able to compose custom models that map sequence to function with pretrained models, including protein language models (PLMs), to guide and constrain search. Our package natively integrates with the HuggingFace platform and supports PLMs from transformers. Our MCMC sampler identifies promising amino acids to mutate via model gradients taken with respect to the input (i.e., sensitivity analysis). We allow users to compose their own custom target function for MCMC by leveraging the Product of Experts MCMC paradigm. Each model is an "expert" that contributes its own knowledge about the protein's fitness landscape to the overall target function. The sampler is designed to be more efficient and effective than brute force and random search while maintaining most of the generality and flexibility. Additional information can be found in the related publication: https://iopscience.iop.org/article/10.1088/2632-2153/accacd

Emami, Patrick↗

PRIME: Protein Representation Inference for Mutation Evaluation

Protein language machine learning models built upon existing ESM-2 model developed by Evolutionary Scale (evolutionaryscale.ai) and an in-house protein language model based on the BERT model developed by Google. The code also includes model training scripts and saved checkpoints from our own training using publicly available SARS-CoV-2 protein sequences.

Gibson, Kaetlyn [Los Alamos National Lab]↗

TwoFold: Highly accurate structure and affinity prediction for protein-ligand complexes from sequences

We describe our development of ab initio protein-ligand binding pose prediction models based on transformers and binding affinity prediction models based on the neural tangent kernel (NTK). Folding both protein and ligand, the TwoFold models achieve efficient and quality predictions matching state-of-the-art implementations while additionally reconstructing protein structures. In conclusion, solving NTK models points to a new use case for highly optimized linear solver benchmarking codes on HPC.

60 APPLIED LIFE SCIENCES↗

Identification and characterization of proteins of unknown function (PUFs) in Clostridium thermocellum DSM 1313 strains as potential genetic engineering targets

Abstract Background Mass spectrometry-based proteomics can identify and quantify thousands of proteins from individual microbial species, but a significant percentage of these proteins are unannotated and hence classified as proteins of unknown function (PUFs). Due to the difficulty in extracting meaningful metabolic information, PUFs are often overlooked or discarded during data analysis, even though they might be critically important in functional activities, in particular for metabolic engineering research. Results We optimized and employed a pipeline integrating various “guilt-by-association” (GBA) metrics, including differential expression and co-expression analyses of high-throughput mass spectrometry proteome data and phylogenetic coevolution analysis, and sequence homology-based approaches to determine putative functions for PUFs in Clostridium thermocellum . Our various analyses provided putative functional information for over 95% of the PUFs detected by mass spectrometry in a wild-type and/or an engineered strain of C. thermocellum . In particular, we validated a predicted acyltransferase PUF (WP_003519433.1) with functional activity towards 2-phenylethyl alcohol, consistent with our GBA and sequence homology-based predictions. Conclusions This work demonstrates the value of leveraging sequence homology-based annotations with empirical evidence based on the concept of GBA to broadly predict putative functions for PUFs, opening avenues to further interrogation via targeted experiments.

09 BIOMASS FUELS↗

Nitrogen limitation causes a seismic shift in redox state and phosphorylation of proteins implicated in carbon flux and lipidome remodeling in Rhodotorula toruloides

Background: Oleaginous yeast are prodigious producers of oleochemicals, offering alternative and secure sources for applications in foodstuff, skincare, biofuels, and bioplastics. Nitrogen starvation is the primary strategy used to induce oil accumulation in oleaginous yeast as part of a global stress response. While research has demonstrated that post-translational modifications (PTMs), including phosphorylation and protein cysteine thiol oxidation (redox PTMs), are involved in signaling pathways that regulate stress responses in metazoa and algae, their role in oleaginous yeast remain understudied and unexplored. Results: Towards linking the yeast oleaginous phenotype to protein function, we integrated lipidomics, redox proteomics, and phosphoproteomics to investigate Rhodotorula toruloides under nitrogen-rich and starved conditions over time. Our lipidomics results unearthed interactions involving sphingolipids and cardiolipins with ER stress and mitophagy. Our redox and phosphoproteomics data highlighted the roles of the AMPK, TOR, and calcium signaling pathways in regulation of lipogenesis, autophagy, and oxidative stress response. As a first, we also demonstrated that lipogenic enzymes including fatty acid synthase are modified as a consequence of shifts in cellular redox states due to nutrient availability. Conclusions: We conclude that lipid accumulation is largely a consequence of carbon rerouting and autophagy governed by changes to PTMs, and not increases in the abundance of enzymes involved in central carbon metabolism and fatty acid biosynthesis. Our systems-level approach sets the stage for acquiring multidimensional data sets for protein structural modeling and predicting the functional relevance of PTMs using Artificial Intelligence/Machine Learning (AI/ML). Coupled to those bioinformatics approaches, the putative PTM switches that we delineate will enable advanced metabolic engineering strategies to decouple lipid accumulation from nitrogen limitation.

Lipid Signalling↗

Cortical Proteins and Individual Differences in Cognitive Resilience in Older Adults

Background and objectives: Cognitive resilience is a well-recognized concept, but knowledge gaps about its underlying mechanisms have made it difficult to develop instruments that identify older adults with high or low resilience. We tested whether aggregating cortical peptides associated with cognitive resilience into an index can identify adults with higher or lower cognitive resilience. Methods: We used data from 1,192 older decedents, including annual clinical testing, indices of 10 Alzheimer disease (AD) and related dementia (ADRD) pathologies, and 226 proteotypic peptides measured in the dorsal lateral prefrontal cortex. We used linear mixed-effects models to identify peptides that were related to cognitive resilience (i.e., cognitive decline not explained by ADRD pathologies [false discovery rate <0.05]). We aggregated the expression levels of these resilience peptides into a person-specific cognitive resilience index and examined its association with AD clinical and pathologic phenotypes. Results: We constructed a resilience index from 52 of 226 peptides related to cognitive resilience. A higher index was associated with slower cognitive decline (estimate 0.05, SE 0.003, p < 0.001) and slower motor decline (estimate 0.005, SE 0.001, p < 0.001). Most resilience peptides (70%) were specific to cognitive decline, but 30% also provided resilience for motor decline. A higher index was also related to a lower burden of AD pathologies (odds ratio [OR] 0.41, SE 0.01, p < 0.001) and modified the association of AD pathology with cognition in that a higher index modified the negative effects of AD pathology on AD dementia proximate to death (OR 0.70, SE 0.14, p = 0.010). Up to 90% of cognitive resilience peptides were related to AD pathologic phenotypes. Discussion: Cortical proteins may provide some degree of cognitive resilience. These multifunctional proteins also seem to provide resilience to other AD clinical phenotypes and have independent associations with ADRD pathologies. Resilience proteins may be high-value therapeutic targets for drug discovery of interventions that maintain brain health in aging adults via multiple pathways.

60 APPLIED LIFE SCIENCES↗

Cysteine Rich Intestinal Protein 2 is a copper-responsive regulator of skeletal muscle differentiation and metal homeostasis

Copper (Cu) is essential for respiration, neurotransmitter synthesis, oxidative stress response, and transcription regulation, with imbalances leading to neurological, cognitive, and muscular disorders. Here we show the role of a novel Cu-binding protein (Cu-BP) in mammalian transcriptional regulation, specifically on skeletal muscle differentiation using murine primary myoblasts. Utilizing synchrotron X-ray fluorescence-mass spectrometry, we identified murine cysteine-rich intestinal protein 2 (mCrip2) as a key Cu-BP abundant in both nuclear and cytosolic fractions. mCrip2 binds two to four Cu + ions with high affinity and presents limited redox potential. CRISPR/Cas9-mediated deletion of mCrip2 impaired myogenesis, likely due to Cu accumulation in cells. CUT&RUN and transcriptome analyses revealed its association with gene promoters, including MyoD1 and metallothioneins, suggesting a novel Cu-responsive regulatory role for mCrip2. Our work describes the significance of mCrip2 in skeletal muscle differentiation and metal homeostasis, expanding understanding of the Cu-network in myoblasts. Copper (Cu) is essential for various cellular processes, including respiration and stress response, but imbalances can cause serious health issues. This study reveals a new Cu-binding protein (Cu-BP) involved in muscle development in primary myoblasts. Using unbiased metalloproteomic techniques and high throughput sequencing, we identified mCrip2 as a key Cu-BP found in cell nuclei and cytoplasm. mCrip2 binds up to four Cu + ions and has a limited redox potential. Deleting mCrip2 using CRISPR/Cas9 disrupted muscle formation due to Cu accumulation. Further analyses showed that mCrip2 regulates the expression of genes like MyoD1, essential for muscle differentiation, and metallothioneins in response to copper supplementation. This research highlights the importance of mCrip2 in muscle development and metal homeostasis, providing new insights into the Cu-network in cells.

59 BASIC BIOLOGICAL SCIENCES↗

Exploiting bacterial effector proteins to uncover evolutionarily conserved antiviral host machinery

Arboviruses are a diverse group of insect-transmitted pathogens that pose global public health challenges. Identifying evolutionarily conserved host factors that combat arbovirus replication in disparate eukaryotic hosts is important as they may tip the balance between productive and abortive viral replication, and thus determine virus host range. Here, we exploit naturally abortive arbovirus infections that we identified in lepidopteran cells and use bacterial effector proteins to uncover host factors restricting arbovirus replication. Bacterial effectors are proteins secreted by pathogenic bacteria into eukaryotic hosts cells that can inhibit antimicrobial defenses. Since bacteria and viruses can encounter common host defenses, we hypothesized that some bacterial effectors may inhibit host factors that restrict arbovirus replication in lepidopteran cells. Thus, we used bacterial effectors as molecular tools to identify host factors that restrict four distinct arboviruses in lepidopteran cells. By screening 210 effectors encoded by seven different bacterial pathogens, we identify several effectors that individually rescue the replication of all four arboviruses. We show that these effectors encode diverse enzymatic activities that are required to break arbovirus restriction. We further characterize Shigella flexneri-encoded IpaH4 as an E3 ubiquitin ligase that directly ubiquitinates two evolutionarily conserved proteins, SHOC2 and PSMC1, promoting their degradation in insect and human cells. We show that depletion of either SHOC2 or PSMC1 in insect or human cells promotes arbovirus replication, indicating that these are ancient virus restriction factors conserved across invertebrate and vertebrate hosts. Collectively, our study reveals a novel pathogen-guided approach to identify conserved antimicrobial machinery, new effector functions, and conserved roles for SHOC2 and PSMC1 in virus restriction.

59 BASIC BIOLOGICAL SCIENCES↗

High-throughput screening of Protein-DNA interactions in Sorghum

Drought is the primary abiotic factors negatively affecting agriculture, causing tremendous reductions in yield world-wide. Drought responsive adaptation strategies require complex molecular responses to including hormone signaling and production of osmo-protectants, as well as developmental responses including stomatal closure, changes to leaf morphology, and altered root system architecture. A common strategy to better understand these adaptation mechanisms is to compare plants with differing drought tolerances and has been successful in multiple crop plants including wheat, rice, and maize. To better understand drought adaptation strategies, we compared the cytosolic- and organelle-enriched protein profiles of leaves from two Sorghum bicolor genotypes with differing pre-flowering drought tolerances after 8-weeks of growth under water limitation. In agreement with previous literature findings, we observed significant drought-induced changes in the abundance of multiple heat shock proteins and dehydrins in both genotypes. We also identified unique proteins that might play a role in genotype dependent drought adaptation.

60 APPLIED LIFE SCIENCES↗

Proteomics Analysis of Human Contaminant Proteins

Complete characterization of unknowns via proteomics remains challenging. There exist regions of mass spectrometry-based proteomics data where empirical measurements are not attributed to peptides, and/or sequenced peptides from mass spectra are not attributed to any source. These uncharacterized regions are known as the “dark” proteome. Many proteomics tools rely on some a priori knowledge of sample composition; few tools allow for investigation of unknowns without relying on composition assumptions. Further, the potential low abundance of minor traces in these uncharacterized regions can make elucidation of the “dark” proteome challenging. Herein, we describe the development and evaluation of approaches to study the “dark” proteome and move towards an untargeted approach for more complete characterization, namely by studying minor human protein traces in non-human samples and combining that approach with non-human source organism identification without relying on assumptions. Human protein markers, in the form of genetically variant peptides, have been extensively examined in a variety of human matrices, including blood, plasma, and hair, but have yet to be investigated in non-human samples, such as cell cultures, as human contaminant traces. Genetically variant peptides are those that are found in proteins carrying single nucleotide polymorphisms. In this work, we aimed to (1) investigate the feasibility of detecting human contaminant genetically variant peptides (GVPs) in a diverse set of non-human organisms using public proteomics data and a computational pipeline, as well as to (2) develop a combined capability for untargeted source organism characterization and GVP detection. To our knowledge, this is the first report of applying these approaches towards a more complete proteomic characterization of unknowns. We successfully demonstrate the feasibility of broad human contaminant GVP detection in proteomics data, develop a better understanding of GVP detectability, characterize the sample-to-sample variability in GVP detection, and identify a core set of GVPs that can potentially be used as markers indicative of the human contaminant traces portion of the “dark” proteome. Further, we developed and evaluated a combined pipeline, MARLOWE-GVP, that enables both untargeted source organism characterization and GVP detection. We show high accuracy of correct source organism characterization and high degree of similarity of human contaminant GVP detection compared to the conventional approach. Success on both these efforts have allowed us to advance our understanding and characterization of the “dark” proteome.

59 BASIC BIOLOGICAL SCIENCES↗

Plant sulfate transporter protein sequences for phylogenetic analysis

Sulfur is an essential macronutrient that supports plant growth, development, and responses to environmental stress. Sulfate is the predominant inorganic form of sulfur in soils, and its uptake by roots and translocation to shoots are facilitated by the sulfate transporter (SULTR) family of proteins. Although the first plant SULTR gene was identified nearly three decades ago, several subfamily members, particularly those in the expansive and angiosperm-specific SULTR3 group, remain poorly characterized. To support comprehensive phylogenetic and sequence-based analyses, we compiled a curated dataset of 262 SULTR protein sequences from 22 plant species spanning the evolutionary breadth of land plants. This collection includes representatives from two basal lineages, two early-divergent angiosperms, six monocots, and ten dicots. All sequences were extracted from genome assemblies available in Phytozome v13 (Joint Genome Institute) and manually curated, with cross-referencing to additional databases such as NCBI when needed. This dataset provides a valuable resource for reconstructing the evolutionary history of the SULTR family, with particular emphasis on the diversification of SULTR3 transporters in flowering plants. This resource may also support functional annotation, comparative genomics, and structural modeling of sulfate transport proteins.

CBI↗

Factor VIII moiety of recombinant Factor VIII Fc fusion protein impacts Fc effector function and CD16 + NK cell activation

Recombinant Factor VIII-Fc fusion protein (rFVIIIFc) is an enhanced half-life therapeutic protein product used for the management of hemophilia A. Recent studies have demonstrated that rFVIIIFc interacts with Fc gamma receptors (FcγR) resulting in the activation or inhibition of various FcγR-expressing immune cells. We previously demonstrated that rFVIIIFc, unlike recombinant Factor IX-Fc (rFIXFc), activates natural killer (NK) cells via Fc-mediated interactions with FcγRIIIA (CD16). Additionally, we showed that rFVIIIFc activated CD16 + NK cells to lyse a FVIII-specific B cell clone. Here, we used human NK cell lines and primary NK cells enriched from peripheral blood leukocytes to study the role of the FVIII moiety in rFVIIIFc-mediated NK cell activation. Following overnight incubation of NK cells with rFVIIIFc, cellular activation was assessed by measuring secretion of the inflammatory cytokine IFNγ by ELISA or by cellular degranulation. We show that anti-FVIII, anti-Fc, and anti-CD16 all inhibited indicating that these molecules were involved in rFVIIIFc-mediated NK cell activation. To define which domains of FVIII were involved, we used antibodies that are FVIII domain-specific and demonstrated that blocking FVIII C1 or C2 domain-mediated membrane binding potently inhibited rFVIIIFc-mediated CD16 + NK cell activation, while targeting the FVIII heavy chain domains did not. We also show that rFVIIIFc binds CD16 with about five-fold higher affinity than rFIXFc. Based on our results we propose that FVIII light chain-mediated membrane binding results in tethering of the fusion protein to the cell surface, and this, together with increased binding affinity for CD16, allows for Fc-CD16 interactions to proceed, resulting in NK cellular activation. Our working model may explain our previous results where we observed that rFVIIIFc activated NK cells via CD16, whereas rFIXFc did not despite having identical IgG1 Fc domains.

59 BASIC BIOLOGICAL SCIENCES↗

Identification, Expression, and Interaction Analysis of Ovate Family Proteins in Populus trichocarpa Reveals a Role of PtOFP1 Regulating Drought Stress Response

Ovate family proteins (OFPs) are a family of plant growth regulators that play diverse roles in many aspects of physiological processes. OFPs have been characterized in various plant species including tomato, Arabidopsis , and rice. However, little is known about OFPs in woody species. Here, a total of 30 PtOFP genes were identified from the genome of Populus trichocarpa and were further grouped into four subfamilies based on their sequence similarities. Gene expression analysis indicated that some members of the PtOFP gene family displayed tissue/organ-specific patterns. Analysis of cis -acting elements in the promoter as well as gene expression by hormone treatment revealed putative involvement of PtOFPs in hormonal response. Furthermore, PtOFP1 (Potri.006G107700) was further experimentally demonstrated to act as a transcriptional repressor. Yeast two-hybrid assay showed physical interactions of PtOFP1 with other proteins, which suggests that they might function in various cellular processes by forming protein complexes. In addition, overexpression of PtOFP1 in Arabidopsis conferred enhanced tolerance to PEG-induced drought stress at seedling stage, as well as a higher survival rate than the wild type at mature stage. These results provide a systematic analysis of the Populus OFP gene family and lay a foundation for functional characterization of this gene family.

59 BASIC BIOLOGICAL SCIENCES↗