Correct Conformation Research Articles

Sanyensin with an Unprecedented Architecture: An Effective Strategy from Discovery to Stereochemical Identification of Flexible Natural Products.

Under the guidance of genome mining combined with bioassay-coupled metabolomic analyses, an unprecedented macrodiolide sanyensin (1), with two flexible macrolides fused by the rigid oxabicyclo[3.3.1]nonane core, was isolated from the deep-sea-derived Streptomyces sp. OUCT16-30. The stereochemistry of 1 was established by NOEs (nuclear Overhauser effects), J-based configuration analysis, Marfey's analysis, and together with a newly introduced stereochemical study workflow, which greatly shortens the time to obtain correct conformations of flexible structures based on the NMR constraints, thus leading to reliable quantum chemical calculations to establish the absolute configurations. This workflow is expected to have broad applicability for elucidating the stereochemistry of flexible natural products. The macrodiolide framework of 1 is proposed to be formed through a biocatalytic cyclodimerization, followed by a series of nonenzymatic reactions. This work leads to new insights into the unexplored biosynthetic potential of deep-sea microbes and also provides a practical streamline for efficient mining of novel natural products, from discovery to stereochemical finalization.

Adenoviral fiber-knob based vaccination elicits efficient neutralizing antibodies and T cell responses against adenovirus infection

BackgroundHuman adenoviruses (HAdVs) frequently cause common respiratory or gastrointestinal infections among children, adults, individuals with immune deficiencies, and other vulnerable populations with varying degree of symptoms, ranging from mild to server, and in some cases, even fatalities. Despite the significant clinical impact of HAdVs, there is currently no approved vaccine available.MethodsThis study explores the potential of the adenovirus type 5 fiber knob (Ad5-FK) to stimulate the production of Ad-specific neutralizing antibodies and T-cell responses in mice. Based on structure predictions, we first expressed Ad5-FK in E. coli and confirmed the assembly of FK into its trimeric form. After testing the binding capability of the trimeric FK to susceptible cells, the immunogenicity of the protein in combination with the c-di-AMP adjuvant was assessed in BALB/c mice.ResultsThe purified Ad5-FK exhibited self-trimerization and maintained correct conformation akin to the authentic FK structure. This facilitated effective binding to susceptible HEK293 cells. Notably, the protein demonstrated significant inhibition of HEK293 cells infection by rAd5-GFP. Immunization of BALB/c mice with Ad5-FK, or Ad5-FK mixed with c-di-AMP yielded FK-specific antibodies with potent neutralization capacity. Significantly, Ad5-FK was found to elicit a vigorous CD4+ T-cell response in the immunized mice.ConclusionOur findings underscore the efficacy of FK-based vaccine in eliciting anti-Ad humoral immune response and CD4 T-cell immune reactions essential for protection against viral infections.

A Method for Treating Significant Conformational Changes in Alchemical Free Energy Simulations of Protein-Ligand Binding.

Relative binding free energy (RBFE) simulation is a rigorous approach to the calculation of quantitatively accurate binding free energy values for protein-ligand binding in which a reference binder is gradually converted to a target binder through alchemical transformation during the simulation. The success of such simulations relies on being able to accurately sample the correct conformational phase space for each alchemical state; however, this becomes a challenge when a significant conformation change occurs between the reference and target binder-receptor complexes. Increasing the simulation time and using enhanced sampling methods can be helpful, but effects can be limited, especially when the free energy barrier between conformations is high or when the correct target complex conformation is difficult to find and maintain. Current RBFE protocols seed the reference complex structure into every alchemical window of the simulation. In our study, we describe an improved protocol in which the reference structure is seeded into the first half of the alchemical windows, and the target structure is seeded into the second half of the alchemical windows. By applying information about the relevant correct end point conformations to different simulation windows from the beginning, the need for large barrier crossings or simulation prediction of the correct structures during an alchemical simulation is in many cases obviated. In the diverse cases we examine below, the simulations yielded free energy predictions that are satisfactory as compared to experiment and superior to running the simulations utilizing the conventional protocol. The method is straightforward to implement for publicly available FEP workflows.

Investigating Associations between Horse Hoof Conformation and Presence of Lameness.

Hoof trimming and shoeing determine the horse's hoof shape and balance. Hoof conformation plays a crucial role in limb biomechanics and can consequently prevent or predispose to injury. This study investigated the relationship between the morphometric characteristics of the horse's hoof, specifically, the dorsal hoof wall angle (DHWA), the coronet band circumference (CBC), and lameness in 73 horses categorised as undertaking either show jumping, dressage, or riding school activities. Results from logistic regression indicated that horses with either a combination of acute DHWA with large CBC, or more upright feet with larger DHWA and smaller CBC have higher probabilities of lameness. Show jumping and dressage horses showed a higher prevalence of lameness. Hoof morphometry should be monitored, and podiatric interventions should be regularly scheduled for the maintenance of correct hoof conformation to prevent injury. This study suggests that an aligned hoof-pastern axis managed by a DHWA of around 50 degrees may prevent lameness, with special emphasis on horses in dressage and show jumping activities. On the other hand, we can also speculate that the disturbed axis alignment of DHWA may be a cause of lameness.

Peroxiredoxin 4 deficiency induces accelerated ovarian aging through destroyed proteostasis in granulosa cells

Ovarian aging, a complex and challenging concern within the realm of reproductive medicine, is associated with reduced fertility, menopausal symptoms and long-term health risks. Our previous investigation revealed a correlation between Peroxiredoxin 4 (PRDX4) and human ovarian aging. The purpose of this research was to substantiate the protective role of PRDX4 against ovarian aging and elucidate the underlying molecular mechanism in mice. In this study, a Prdx4−/− mouse model was established and it was observed that the deficiency of PRDX4 led to only an accelerated decline of ovarian function in comparison to wild-type (WT) mice. The impaired ovarian function observed in this study can be attributed to an imbalance in protein homeostasis, an exacerbation of endoplasmic reticulum stress (ER stress), and ultimately an increase in apoptosis of granulosa cells. Furthermore, our research reveals a noteworthy decline in the expression of Follicle-stimulating hormone receptor (FSHR) in aging Prdx4−/− mice, especially the functional trimer, due to impaired disulfide bond formation. Contrarily, the overexpression of PRDX4 facilitated the maintenance of protein homeostasis, mitigated ER stress, and consequently elevated E2 levels in a simulated KGN cell aging model. Additionally, the overexpression of PRDX4 restored the expression of the correct spatial conformation of FSHR, the functional trimer. In summary, our research reveals the significant contribution of PRDX4 in delaying ovarian aging, presenting a novel and promising therapeutic target for ovarian aging from the perspective of endoplasmic reticulum protein homeostasis.

Catalytic Relaxation of Kinetically Trapped Intermediates by DNA Chaperones.

Common in biomacromolecules, kinetically trapped misfolded intermediates are often detrimental to the structures, properties, or functions of proteins or nucleic acids. Nature employs chaperone proteins but not nucleic acids to escort intermediates to correct conformations. Herein, we constructed a Jablonski-like diagram of a mechanochemical cycle in which individual DNA hairpins were mechanically unfolded to high-energy states, misfolded into kinetically trapped states, and catalytically relaxed back to ground-state hairpins by a DNA chaperone. The capacity of catalytic relaxation was demonstrated in a 1D DNA hairpin array mimicking nanoassembled materials. At ≥1 μM, the diffusive (or self-walking) DNA chaperone converted the entire array of misfolded intermediates to correct conformation in less than 15 s, which is essential to rapidly prepare homogeneous nanoassemblies. Such an efficient self-walking amplification increases the signal-to-noise ratio, facilitating catalytic relaxation to recognize a 1 fM DNA chaperone in 10 min, a detection limit comparable to the best biosensing strategies.

Probing solution conformations of l-DOPA: Integration of experiment and simulation via vibrational optical activity

l-DOPA plays a critical role as a precursor to dopamine and is a standard treatment for Parkinson's disease. Recent research has highlighted the potential therapeutic advantages of deuterated l-DOPA analogs having a longer biological half-life. For their spectroscopic characterization, the in-detail characterization of l-DOPA itself is necessary. This article presents a thorough examination of the vibrational spectra of l-DOPA, with a particular emphasis on chirally sensitive VOA techniques. We successfully obtained high-quality Raman and ROA spectra of l-DOPA in its cationic form, under low pH conditions, and at a high concentration of 100 mg/ml. These spectra cover a broad spectral range, allowing for precise comparisons with theoretical simulations. We also obtained IR and VCD spectra, but they faced limitations due to the narrow accessible spectral region. Exploration of l-DOPA's conformational landscape revealed its intrinsic flexibility, with multiple coexisting conformations. To characterize these conformations, we employed two methods: one involved potential energy surface scans with implicit solvation, and the other utilized molecular dynamics simulations with explicit solvation. Comparing ROA spectra from different conformer groups and applying spectral decomposition proved crucial in determining the correct conformer ratios. The use of explicit solvation significantly improved the quality of the final simulated spectral profiles. The accurate determination of conformer ratios, rather than solely relying on the number of averaged spectra, played a crucial role in simulation accuracy. In conclusion, our study offers valuable insights into the structure and conformational behavior of l-DOPA and represents a valuable resource for subsequent spectroscopic studies of its deuterated analogs.

Exploring the surface epitope and nuclear localization analysis of porcine circovirus type 3 capsid protein

Porcine circovirus 3 (PCV3) is a newly emerging virus associated with porcine dermatitis and nephropathy syndrome (PDNS) and reproductive disorders, impacting global pig populations. Porcine circoviruses contain two major open reading frames (ORFs), and the ORF2 encodes the viral capsid protein (Cap). Cap is the most antigenic structural protein and an ideal candidate for the development of vaccines and diagnostic reagents. This study generated a monoclonal antibody (MAb) specific to PCV3 Cap, MAb CCC160, for diagnosis and pathogenesis studies of this novel virus. The MAb specifically recognized PCV3-infected swine lymph node tissue in an immunohistochemical analysis confirming its clinical diagnostic potential. In addition, a novel linear B-cell epitope recognized by MAb CCC160 was identified at the amino acid region 120–134 of Cap. Nuclear localization analysis of PCV3 Cap revealed a potential nuclear localization signal (NLS) in the middle region (aa 131–143) in addition to the dominant N-terminal NLS that is already known. A cell viability assay further demonstrated that the cytotoxicity of PCV3 Cap is correlated with its nuclear localization, indicating a crucial role of Cap in the pathogenic mechanism of PCV3. A full-length construct of PCV3 Cap was successfully expressed using a baculovirus expression system and purified recombinant proteins self-assembled into virus-like particles (VLPs). The protein constitution of the VLPs was confirmed by MAb CCC160 recognition, indicating the correct conformation and specificity of VLP and exhibiting the linear epitope aa 120–134 on the VLP surface. These results provide insights for developing diagnostic tools and potential VLP vaccines for PCV3, revealing its pathogenesis and antigenic properties.

Strategies for the production of isotopically labelled Fab fragments of therapeutic antibodies in Komagataella phaffii (Pichia pastoris) and Escherichia coli for NMR studies.

The importance and fast growth of therapeutic monoclonal antibodies, both innovator and biosimilar products, have triggered the need for the development of characterization methods at high resolution such as nuclear magnetic resonance (NMR) spectroscopy. However, the full power of NMR spectroscopy cannot be unleashed without labelling the mAb of interest with NMR-active isotopes. Here, we present strategies using either Komagataella phaffii (Pichia pastoris) or Escherichia coli that can be widely applied for the production of the antigen-binding fragment (Fab) of therapeutic antibodies of immunoglobulin G1 kappa isotype. The E. coli approach consists of expressing Fab fragments as a single polypeptide chain with a cleavable linker between the heavy and light chain in inclusion bodies, while K. phaffii secretes a properly folded fragment in the culture media. After optimization, the protocol yielded 10-45 mg of single chain adalimumab-Fab, trastuzumab-Fab, rituximab-Fab, and NISTmAb-Fab per liter of culture. Comparison of the 2D-1H-15N-HSQC spectra of each Fab fragment, without their polyhistidine tag and linker, with the corresponding Fab from the innovator product showed that all four fragments have folded into the correct conformation. Production of 2H-13C-15N-adalimumab-scFab and 2H-13C-15N-trastuzumab-scFab (>98% enrichment for all three isotopes) yielded NMR samples where all amide deuterons have completely exchanged back to proton during the refolding procedure.

Genetically Encoded RNA Sensors for Ratiometric and Multiplexed Imaging of Small Molecules in Living Cells.

Genetically encoded sensors afford powerful tools for studying small molecules and metabolites in live cells. However, genetically encoded sensors with a general design remain to be developed. Here we develop genetically encoded RNA sensors with a modular design for ratiometric and multiplexed imaging of small molecules in live cells. The sensor utilizes aptazyme as a recognition module and the light-up RNA aptamer as a signal reporter. The conformation of light-up aptamers is abrogated by a blocking sequence, and aptazyme-mediated cleavage restores the correct conformation, delivering activated fluorescence for small molecule imaging. We first developed a genetically encoded ratiometric sensor using Mango aptamer as a reference and SRB2 as a reporter. It is shown that the sensor allows quantitative imaging and detection of theophylline in live cells. The generality of the design is further demonstrated for imaging other small molecules by replacing the aptazymes. Its ability for multiplexed imaging of small molecules is further explored via the integration of different small-molecule responsive aptazymes and light-up RNA aptamers. This modular design could offer a versatile platform for imaging diverse molecules in living cells.

Molecular Dynamics as a Tool for Virtual Ligand Screening.

Rational drug design is essential for new drugs to emerge, especially when the structure of a target protein or nucleic acid is known. To that purpose, high-throughput virtual ligand screening campaigns aim at discovering computationally new binding molecules or fragments to modulate particular biomolecular interactions or biological activities, related to a disease process. The structure-based virtual ligand screening process primarily relies on docking methods which allow predicting the binding of a molecule to a biological target structure with a correct conformation and the best possible affinity. The docking method itself is not sufficient as it suffers from several and crucial limitations (lack of full protein flexibility information, no solvation and ion effects, poor scoring functions, and unreliable molecular affinity estimation).At the interface of computer techniques and drug discovery, molecular dynamics (MD) allows introducing protein flexibility before or after a docking protocol, refining the structure of protein-drug complexes in the presence of water, ions, and even in membrane-like environments, describing more precisely the temporal evolution of the biological complex and ranking these complexes with more accurate binding energy calculations. In this chapter, we describe the up-to-date MD, which plays the role of supporting tools in the virtual ligand screening (VS) process.Without a doubt, using docking in combination with MD is an attractive approach in structure-based drug discovery protocols nowadays. It has proved its efficiency through many examples in the literature and is a powerful method to significantly reduce the amount of required wet experimentations (Tarcsay et al, J Chem Inf Model 53:2990-2999, 2013; Barakat et al, PLoS One 7:e51329, 2012; De Vivo et al, J Med Chem 59:4035-4061, 2016; Durrant, McCammon, BMC Biol 9:71-79, 2011; Galeazzi, Curr Comput Aided Drug Des 5:225-240, 2009; Hospital et al, Adv Appl Bioinforma Chem 8:37-47, 2015; Jiang et al, Molecules 20:12769-12786, 2015; Kundu et al, J Mol Graph Model 61:160-174, 2015; Mirza et al, J Mol Graph Model 66:99-107, 2016; Moroy et al, Future Med Chem 7:2317-2331, 2015; Naresh et al, J Mol Graph Model 61:272-280, 2015; Nichols et al, J Chem Inf Model 51:1439-1446, 2011; Nichols et al, Methods Mol Biol 819:93-103, 2012; Okimoto et al, PLoS Comput Biol 5:e1000528, 2009; Rodriguez-Bussey et al, Biopolymers 105:35-42, 2016; Sliwoski et al, Pharmacol Rev 66:334-395, 2014).

Modeling Side Chains in the Three-Dimensional Structure of Proteins for Post-Translational Modifications.

Amino acid substitutions and post-translational modifications (PTMs) play a crucial role in many cellular processes by directly affecting the structural and dynamic features of protein interaction. Despite their importance, the understanding of protein PTMs at the structural level is still largely incomplete. The Protein Data Bank contains a relatively small number of 3D structures having post-translational modifications. Although recent years have witnessed significant progress in three-dimensional modeling (3D) of proteins using neural networks, the problem related to predicting accurate PTMs in proteins has been largely ignored. Predicting accurate 3D PTM models in proteins is closely related to another fundamental problem: predicting the correct side-chain conformations of amino acid residues in proteins. An analysis of publications as well as the paid and free software packages for modeling three-dimensional structures showed that most of them focus on working with unmodified proteins and canonical amino acid residues; the number of articles and software packages placing emphasis on modeling three-dimensional PTM structures is an order of magnitude smaller. This paper focuses on modeling the side-chain conformations of proteins containing PTMs (nonstandard amino acid residues). We collected our own libraries comprising the most frequently observed PTMs from the PDB and implemented a number of algorithms for predicting the side-chain conformation at modification points and in the immediate environment of the protein. A comprehensive analysis of both the algorithms per se and compared to the common Rosetta and FoldX structure modeling packages was also carried out. The proposed algorithmic solutions are comparable in their characteristics to the well-known Rosetta and FoldX packages for the modeling of three-dimensional structures and have great potential for further development and optimization. The source code of algorithmic solutions has been deposited to and is available at the GitHub source.

Expression and purification of Drosophila OBP44a with the aids of LC-MS and NMR

The production of highly purified native soluble proteins in large quantities is crucial for studying protein structure and function. Odorant binding proteins (OBPs) are small, soluble, extracellular proteins with multiple disulfide bonds, whose functions include, but are not limited to, binding hydrophobic molecules and delivering them to their corresponding receptors expressed on insect olfactory receptor neurons. Expression of proteins with multiple disulfide bonds like OBPs usually results in insolubility and low yield, which has been a significant barrier to understanding their biological roles and physiological functions. In the E. coli system, expression of OBPs often results in insoluble inclusion bodies or a limited amount of periplasmic soluble proteins. Although expression of OBPs in eukaryotic systems such as Sf9 insect cells or yeast Pichia pastoris can increase the solubility of the protein, the process remains insufficient. Additionally, monitoring the purity and native apo state of the protein is critical for establishing the correct conformation of the protein. In this study, we employed an E. coli host with an altered intracellular environment to produce cytosolic soluble OBP44a protein, which yielded over 100 mg/L. We monitored the integrity of disulfide bonds throughout the purification process using LC-MS and used NMR to ensure the final product adopted a single conformation. Our study presents an efficient method for obtaining large quantities of soluble proteins in a single conformation, which enables extensive in vitro studies of secreted proteins like OBPs.

Preliminary biometric characteristics of Huacaya alpacas

The purpose of this study was to analyze and measure the biometrics of huacaya alpacas. The results were compared with various animal species in which biometrics is much better studied, including horses, dogs and camels. Index calculations used in other works on biometrics were performed. Animals were divided into males and females, and a group of young animals under 24 months old and older was distinguished. The results in this paper provide preliminary information for further research on the biometrics of this species. Chest circumference is greater than height at the withers, and their ratio, expressed by the massiveness index, is similar to that of the Felinsky pony, a horse designed for riding. According to the company's research, the eurystomy index in alpacas is high, far exceeding that of the one-humped camel. The greater limb length of males than females in both age groups is also an interesting parameter. Further studies are needed to obtain a complete set of biometric traits of alpacas. The results, at this stage, may be useful for determining the correct conformation of the animal and for breeding selection purposes.

Structural insights into the substrate specificity and activity of a novel mannose 2-epimerase from Runella slithyformis.

Mannose 2-epimerase (ME), a member of the acylglucosamine 2-epimerase (AGE) superfamily that catalyzes epimerization of D-mannose and D-glucose, has recently been characterized to have potential for D-mannose production. However, the substrate-recognition and catalytic mechanism of ME remains unknown. In this study, structures of Runella slithyformis ME (RsME) and its D254A mutant [RsME(D254A)] were determined in their apo forms and asintermediate-analog complexes [RsME-D-glucitol and RsME(D254A)-D-glucitol]. RsME possesses the (α/α)6-barrel of the AGE superfamily members but has a unique pocket-covering long loop (loopα7-α8). The RsME-D-glucitol structure showed that loopα7-α8 moves towards D-glucitol and closes the active pocket. Trp251 and Asp254 in loopα7-α8 are only conserved in MEs and interact with D-glucitol. Kinetic analyses of the mutants confirmed the importance of these residues for RsME activity. Moreover, the structures of RsME(D254A) and RsME(D254A)-D-glucitol revealed that Asp254 is vital for binding the ligand in a correct conformation and for active-pocket closure. Docking calculations and structural comparison with other 2-epimerases show that the longer loopα7-α8 in RsME causes steric hindrance upon binding to disaccharides. A detailed substrate-recognition and catalytic mechanism for monosaccharide-specific epimerization in RsME has been proposed.

ENHANCER RNAS (ERNAS) PLAY A ROLE IN THE RESPONSE TO SMALL MOLECULES AND IN THE DEVELOPMENT OF ACQUIRED RESISTANCE IN MARGINAL ZONE LYMPHOMA (MZL)

Introduction: The therapeutic options for MZL patients with disseminated disease include chemotherapy, rituximab alone or rituximab with chemotherapy but several small molecules are also available. Resistance development is always an issue. Stable non-genetic resistance can be acquired by transcriptional adaptation through alternative pattern of enhancers sustaining the expression of survival genes. Most active enhancers are also transcribed in long noncoding RNAs (lncRNAs) called eRNAs. They play a regulatory role helping the correct chromatin conformation required to transactivate promoters. eRNAs can occasionally be stabilized and regulate distal loci in trans. We studied the contribution of eRNAs, but also other lincRNAs, expressed in MZL in the response to agents as inhibitors of PI3K (copanlisib, umbralisib), BTK (ibrutinib), BCL2 (venetoclax) or anti CD20 (rituximab). In particular, for ibrutinib we took advantage of a resistant cell line in vitro stabilized by prolonged exposure to the drug. Methods: To identify eRNAs expressed in MZL, we applied de novo reconstruction to total RNA-Seq profiling of VL51 parental, ibrutinib-Res and idelalisib-Res derivatives (Arribas et al., Haematologica 2022). We looked for novel and known reconstructed transcripts associated to the superenhancers (SEs), identified by ROSE algorithm. We associated to these eRNAs a TSS derived from publicly available CAGE data sets. We designed 5825 paired gRNAs against 659 targets (312 eRNAs, 255 lincRNAs) and, as controls, 90 essential and 30 not expressed genes. The pgRNAs were included in a custom lentiviral library to infect VL51 expressing dCas9KRAB-ZIM3 mCherry. Cells were kept for 14 days under DMSO, ibrutinib, rituximab, copanlisib, umbralisib or copanlisib/venetoclax and gRNAs dropout was measured. Results: Unsupervised clustering of eRNAs differentially enriched at day 14 ver sus day0 discriminated parental and ibrutinib-Res cells, indicating the dependency of the cells on different transcriptome program. A series of eRNAs and lincRNA were significantly enriched after DMSO (12 and 19, respectively) ibrutinib (27 and 28), rituximab (12 and 18), copanlisib (8 and 17), umbralisib (12 and 13) or copanlisib/venetoclax (14 and 15). The inhibition of transcription of those molecules in some cases represented a proliferative advantage under exposure to the drug, in other cases a disadvantage. For further investigation, we considered eRNAs essential under treatment since they may regulate pathways involved in therapeutic escape, as the calcium-calcineurin pathway, or G-protein coupled receptors or molecules already known to interact with epigenetic regulators as EZH2. Conclusions: Individual eRNAs revealed to be essential in drug response, in a treatment specific manner and to play a role in resistance development, as regulator of relevant pathways. Encore Abstract—previously submitted to regional or national meetings (up to <1000 attendees) The research was funded by: Work supported from the Swiss National Science Foundation (SNSF Sparks CRSK-3_190808 and SNSF 310030_197466). Keywords: genomics, epigenomics, and other-omics, molecular targeted therapies, tumor biology and heterogeneity No conflicts of interests pertinent to the abstract.

State of Vyatka horse population in regions of Russia

The current state of Vyatka horse breed gene pool was studied in the research. It was revealed that the main array of the breeding stock is concentrated in three populations of three regions - the Udmurt Republic, the Kirov region, the Central Federal District. The purpose of the research was to assess the state of gene pool of Vyatka breed in modern conditions. Population of breeding stock horses both in agricultural enterprises and on private farms was analyzed in the territory of three regions of the Russian Federation: the Udmurt Republic, the Kirov Region, the Central Federal District. According to the genetic characteristics, horses in each population were divided into groups based on the relation degree: group 1 - outbred, group 2 - with distant Fx inbreeding (0.21.55 %), group 3 - with moderate Fx inbreeding (1.5612.5 %), group 4 - with close Fx inbreeding (12.625 %). The coefficient of inbreeding was estimated according to the Wright-Kislovsky formula. The most typical horses with an inherent conformation were outbred horses from the population of the Central Federal District. Monitoring the quantitative composition of the breed showed that the number of mares increased from 73 to 287 heads over the period from 1995 to 2021. However, a sharp decrease in the number of mares (222 heads) was recorded at the beginning of 2022. This tendency creates certain difficulties in the selection process. The largest number of mares is concentrated in the Central Federal District - 83 heads nowadays. At the present stage of work with Vyatka breed the analysis of genetic diversity showed that 43.3 % of the representatives were outbred, it was based on the study of the increase in homozygosity of individuals in a limited gene pool. Representatives of the Vyatka breed were obtained in equal proportions by remote and moderate inbreeding - 28.1 and 27 %, respectively. The most typical with the correct conformation were outbred horses from the population of the Central Federal District.

DAQ-score database: Deep-learning based quality estimation of cryo-EM derived protein models

An increasing number of protein structures are determined by cryo-electron microscopy (cryo-EM) as cryo-EM has become one of the most important methods to determine structures. On the other hand, it has been noticed that errors occur in the model building process from cryo-EM maps, probably more frequently than one might think, particularly when the map resolution is not very high. Thus, establishing quality assessment methods has become a crucial and urgent task for biomolecular structure determination with cryo-EM. We have recently developed a quality assessment method to detect protein structural model outliers using machine learning techniques. Our method, called DAQ (Deep-learning-based Amino acid-wise model Quality) score, uses deep neural network to capture local density features of amino acids and atoms in proteins and assesses the likelihood that modeled residues in a structural model is correct (Terashi et al., Nature Methods, 2022). DAQ is also able to detect not only errors in conformations but also shifts in sequence assignment to otherwise correct main-chain conformations, which is often not easy to detect by checking density fitting. Here, we performed a PDB-scale model analysis by DAQ. We applied DAQ to around 10,000 protein structure models in PDB that were derived from cryo-EM maps deposited in Electron Microscopy Data Bank (EMDB). We report the tendency of common errors made in the models through the large-scale analysis. When authors deposited updated structure models to PDB over an initial model, we see clear improvement of DAQ score in the updated version of the model. A common type of errors observed include sequence shifts along alpha helices. Model assessment results with DAQ are made available in a database (https://daqdb.bio.purdue.edu/), where models can be searched by PDB IDs, EMDB IDs and keywords.

Mitochondrial ferredoxin-like is essential for forming complex I-containing supercomplexes in Arabidopsis.

In eukaryotes, mitochondrial ATP is mainly produced by the oxidative phosphorylation (OXPHOS) system, which is composed of 5 multiprotein complexes (complexes I-V). Analyses of the OXPHOS system by native gel electrophoresis have revealed an organization of OXPHOS complexes into supercomplexes, but their roles and assembly pathways remain unclear. In this study, we characterized an atypical mitochondrial ferredoxin (mitochondrial ferredoxin-like, mFDX-like). This protein was previously found to be part of the bridge domain linking the matrix and membrane arms of the complex I. Phylogenetic analysis suggested that the Arabidopsis (Arabidopsis thaliana) mFDX-like evolved from classical mitochondrial ferredoxins (mFDXs) but lost one of the cysteines required for the coordination of the iron-sulfur (Fe-S) cluster, supposedly essential for the electron transfer function of FDXs. Accordingly, our biochemical study showed that AtmFDX-like does not bind an Fe-S cluster and is therefore unlikely to be involved in electron transfer reactions. To study the function of mFDX-like, we created deletion lines in Arabidopsis using a CRISPR/Cas9-based strategy. These lines did not show any abnormal phenotype under standard growth conditions. However, the characterization of the OXPHOS system demonstrated that mFDX-like is important for the assembly of complex I and essential for the formation of complex I-containing supercomplexes. We propose that mFDX-like and the bridge domain are required for the correct conformation of the membrane arm of complex I that is essential for the association of complex I with complex III2 to form supercomplexes.

The Molecular Basis of Heat-Stable Enterotoxin for Vaccine Development and Cancer Cell Detection.

Heat-stable enterotoxin (STa) produced by Enterotoxigenic E. coli is responsible for causing acute diarrhea in infants in developing countries. However, the chemical synthesis of STa peptides with the native conformation and the correct intra-molecular disulfide bonds is a major hurdle for vaccine development. To address this issue, we herein report on the design and preparation of STa analogs and a convenient chemical method for obtaining STa molecules with the correct conformation. To develop an STa vaccine, we focused on a structure in a type II β-turn in the STa molecule and introduced a D-Lys residue as a conjugation site for carrier proteins. In addition, the -Glu-Leu- sequence in the STa molecule was replaced with a -Asp-Val- sequence to decrease the toxic activity of the peptide to make it more amenable for use in vaccinations. To solve several issues associated with the synthesis of STa, such as the formation of non-native disulfide isomers, the native disulfide pairings were regioselectively formed in a stepwise manner. A native form or topological isomer of the designed STa peptide, which possesses a right-handed or a left-handed spiral structure, respectively, were synthesized in high synthetic yields. The conformation of the synthetic STa peptide was also confirmed by CD and NMR spectroscopy. To further utilize the designed STa peptide, it was labeled with fluorescein for fluorescent detection, since recent studies have also focused on the use of STa for detecting cancer cells, such as Caco-2 and T84. The labeled STa peptide was able to specifically and efficiently detect 293T cells expressing the recombinant STa receptor (GC-C) protein and Caco-2 cells. The findings reported here provide an outline of the molecular basis for using STa for vaccine development and in the detection of cancer cells.