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The omnipresence and diversity of allosteric regulation in proteins and protein associations complemented by the potential for the design of allosterically acting biologics and drugs call for the development of a new generation of computational models for the analysis of allostery and rational engineering/design of desired signaling and effector molecules determining it. One of the most important challenges is the consideration of the role of amino acid sequence in forming the protein's allosteric communication, including the mode and strength of the allosteric signal that is communicated to the regulated functional site. Here, we present the network-based model with a sequence dependence added in consideration of allosteric communication by combining the structure-based statistical mechanical model of allostery with the Miyazawa-Jernigan residue–residue potential. Applying the model in the analysis of five classical allosteric proteins, we found that it is necessary to consider the following two major determinants: (i) the free energy exerted by the allosteric site on the regulated one and (ii) the background (average) change in dynamics of the overall structure. We show that working together these two components determine the allosteric modulation, calling one to study their dependence on structures, oligomerization states, and sequence divergence in different proteins. [ABSTRACT FROM AUTHOR]

SUMMARY: The sugarcane (Saccharum spp.) genome is one of the most complex of all. Modern varieties are highly polyploid and aneuploid as a result of hybridization between Saccharum officinarum and S. spontaneum. Little research has been done on meiotic control in polyploid species, with the exception of the wheat Ph1 locus harboring the ZIP4 gene (TaZIP4‐B2) which promotes pairing between homologous chromosomes while suppressing crossover between homeologs. In sugarcane, despite its interspecific origin, bivalent association is favored, and multivalents, if any, are resolved at the end of prophase I. Thus, our aim herein was to investigate the purported genetic control of meiosis in the parental species and in sugarcane itself. We investigated the ZIP4 gene and immunolocalized meiotic proteins, namely synaptonemal complex proteins Zyp1 and Asy1. The sugarcane ZIP4 gene is located on chromosome 2 and expressed more abundantly in flowers, a similar profile to that found for TaZIP4‐B2. ZIP4 expression is higher in S. spontaneum a neoautopolyploid, with lower expression in S. officinarum, a stable octoploid species. The sugarcane Zip4 protein contains a TPR domain, essential for scaffolding. Its 3D structure was also predicted, and it was found to be very similar to that of TaZIP4‐B2, reflecting their functional relatedness. Immunolocalization of the Asy1 and Zyp1 proteins revealed that S. officinarum completes synapsis. However, in S. spontaneum and SP80‐3280 (a modern variety), no nuclei with complete synapsis were observed. Importantly, our results have implications for sugarcane cytogenetics, genetic mapping, and genomics. Significance Statement: Our work provides insights into the genetic control of meiosis in sugarcane (Saccharum spp.), a man made polyploid and fertile plant of interspecific constitution. Inspired by the discoveries of the Ph1 locus, which harbors the ZIP4 gene in wheat, we identified this meiotic gene in both parental species and in two current sugarcane varieties. We analyzed both gene and protein sequence conservation, protein domains, and predicted the 3D‐protein structure. We also investigated the level of ZIP4 expression in different sugarcane tissues. Like its role in wheat, ZIP4 seems to promote pairing between homologous chromosomes while suppressing crossover between homeologs in Saccharum. Using immunocytology, we were able to determine synaptonemal complex polymerization during prophase I, using Asy1 and Zyp1 sugarcane specific antibodies, revealing synapsis defects in all genotypes except Saccharum officinarum, a parental species with regular meiotic behavior. [ABSTRACT FROM AUTHOR]

Insertion of electrophilic species on the structure of small molecule ligands or peptides is a well‐known strategy to increase their binding affinity for the target protein of interest. Among these reactive units, the salicylaldehyde (SA) tag can form remarkably stable imine bonds with the ϵ‐amino group of lysine, a highly frequent residue in proteins. In this work, we describe the optimized synthesis of two new noncoded α‐amino acids, starting from l‐homoserine and featuring the SA tag on the side chain. One of these final compounds was successfully inserted into a model tripeptide through in‐solution synthesis. These building blocks will allow the versatile insertion of the SA tag at suitable position of peptide sequences, opening to a tailored design of Lys‐engaging peptide ligands. [ABSTRACT FROM AUTHOR]

This review gathers all, to the best of our current knowledge, known lysins, mainly bacteriophage-derived, that have demonstrated activity against Bacillus anthracis strains. B. anthracis is a spore-forming, toxin-producing bacteria, naturally dwelling in soil. It is best known as a potential biowarfare threat, an etiological agent of anthrax, and a severe zoonotic disease. Anthrax can be treated with antibiotics (ciprofloxacin, penicillin, doxycycline); however, their administration may take up even to 60 days, and different factors can compromise their effectiveness. Bacterial viruses, bacteriophages (phages), are natural enemies of bacteria and use their lytic enzymes, endolysins (lysins), to specifically kill bacterial cells. Harnessing the potential of lysins to combat bacterial infections holds promise for diminishing antibiotic usage and, consequently, addressing the escalating antibiotic resistance in bacteria. In this context, we list the lysins with the activity against B. anthracis, providing a summary of their lytic properties in vitro and the outcomes observed in animal models. Bacillus cereus strain ATCC 4342/RSVF1, a surrogate for B. anthracis, was also included as a target bacteria. Key points: • More than a dozen different B. anthracis lysins have been identified and studied. • They fall into three blocks regarding their amino acid sequence similarity and most of them are amidases. • Lysins could be used in treating B. anthracis infections. [ABSTRACT FROM AUTHOR]

Background: Gene families are groups of homologous genes that often have similar biological functions. These families are formed by gene duplication events throughout evolution, resulting in multiple copies of an ancestral gene. Over time, these copies can acquire mutations and structural variations, resulting in members that may vary in size, motif ordering and sequence. Multigene families have been described in a broad range of organisms, from single-celled bacteria to complex multicellular organisms, and have been linked to an array of phenomena, such as host–pathogen interactions, immune evasion and embryonic development. Despite the importance of gene families, few approaches have been developed for estimating and graphically visualizing their diversity patterns and expression profiles in genome-wide studies. Results: Here, we introduce an R package named dgfr, which estimates and enables the visualization of sequence divergence within gene families, as well as the visualization of secondary data such as gene expression. The package takes as input a multi-fasta file containing the coding sequences (CDS) or amino acid sequences from a multigene family, performs a pairwise alignment among all sequences, and estimates their distance, which is subjected to dimension reduction, optimal cluster determination, and gene assignment to each cluster. The result is a dataset that allows for the visualization of sequence divergence and expression within the gene family, an approximation of the number of clusters present in the family. Conclusions: dgfr provides a way to estimate and study the diversity of gene families, as well as visualize the dispersion and secondary profile of the sequences. The dgfr package is available at https://github.com/lailaviana/dgfr under the GPL-3 license. [ABSTRACT FROM AUTHOR]

Short peptide sequences consisting of two cysteine residues separated by three other amino acids display complete change from random coil to α‐helical secondary structure in response to addition of Ag+ ions. The folded CXXXC/Ag+ complex involves formation of multinuclear Ag+ species and is stable in a wide pH range from below 3 to above 8. The complex is stable through reversed‐phase HPLC separation as well as towards a physiological level of chloride ions, based on far‐UV circular dichroism spectroscopy. In electrospray MS under acidic conditions a peptide dimer with four Ag+ ions bound was observed, and modelling based on potentiometric experiments supported this to be the dominating complex at neutral pH together with a peptide dimer with 3 Ag+ and one proton at lower pH. The complex was demonstrated to work as a N‐terminal nucleation site for inducing α‐helicity into longer peptides. This type of silver‐mediated peptide assembly and folding may be of more general use for stabilizing not only peptide folding but also for controlling oligomerization even under acidic conditions. [ABSTRACT FROM AUTHOR]

Proteins and nucleic-acids are essential components of living organisms that interact in critical cellular processes. Accurate prediction of nucleic acid-binding residues in proteins can contribute to a better understanding of protein function. However, the discrepancy between protein sequence information and obtained structural and functional data renders most current computational models ineffective. Therefore, it is vital to design computational models based on protein sequence information to identify nucleic acid binding sites in proteins. Here, we implement an ensemble deep learning model-based nucleic-acid-binding residues on proteins identification method, called SOFB, which characterizes protein sequences by learning the semantics of biological dynamics contexts, and then develop an ensemble deep learning-based sequence network to learn feature representation and classification by explicitly modeling dynamic semantic information. Among them, the language learning model, which is constructed from natural language to biological language, captures the underlying relationships of protein sequences, and the ensemble deep learning-based sequence network consisting of different convolutional layers together with Bi-LSTM refines various features for optimal performance. Meanwhile, to address the imbalanced issue, we adopt ensemble learning to train multiple models and then incorporate them. Our experimental results on several DNA/RNA nucleic-acid-binding residue datasets demonstrate that our proposed model outperforms other state-of-the-art methods. In addition, we conduct an interpretability analysis of the identified nucleic acid binding residue sequences based on the attention weights of the language learning model, revealing novel insights into the dynamic semantic information that supports the identified nucleic acid binding residues. SOFB is available at https://github.com/Encryptional/SOFB and https://figshare.com/articles/online_resource/SOFB_figshare_rar/25499452. We implement SOFB, an ensemble deep learning model-based nucleic-acid-binding residues on proteins identification method to characterize protein sequences by learning the semantics of biological dynamics contexts. [ABSTRACT FROM AUTHOR]

Background: Protein solubility is a critically important physicochemical property closely related to protein expression. For example, it is one of the main factors to be considered in the design and production of antibody drugs and a prerequisite for realizing various protein functions. Although several solubility prediction models have emerged in recent years, many of these models are limited to capturing information embedded in one-dimensional amino acid sequences, resulting in unsatisfactory predictive performance. Results: In this study, we introduce a novel Graph Attention network-based protein Solubility model, GATSol, which represents the 3D structure of proteins as a protein graph. In addition to the node features of amino acids extracted by the state-of-the-art protein large language model, GATSol utilizes amino acid distance maps generated using the latest AlphaFold technology. Rigorous testing on independent eSOL and the Saccharomyces cerevisiae test datasets has shown that GATSol outperforms most recently introduced models, especially with respect to the coefficient of determination R2, which reaches 0.517 and 0.424, respectively. It outperforms the current state-of-the-art GraphSol by 18.4% on the S. cerevisiae_test set. Conclusions: GATSol captures 3D dimensional features of proteins by building protein graphs, which significantly improves the accuracy of protein solubility prediction. Recent advances in protein structure modeling allow our method to incorporate spatial structure features extracted from predicted structures into the model by relying only on the input of protein sequences, which simplifies the entire graph neural network prediction process, making it more user-friendly and efficient. As a result, GATSol may help prioritize highly soluble proteins, ultimately reducing the cost and effort of experimental work. The source code and data of the GATSol model are freely available at https://github.com/binbinbinv/GATSol. [ABSTRACT FROM AUTHOR]

Diseases caused by Rickettsiales are often overlooked, although they pose important public health concerns. The Rickettsiales family comprises a broad range of intracellular bacteria with distinct evolutionary adaptations, making the development of treatment measures to combat infections, such as vaccines or antibiotics, a challenge. Interestingly, the outer membrane protein A (OmpA) was found to exist in the cell surface of most human pathogenic bacteria in the order Rickettsiales. However, knowledge about OmpA in each species and strain is scattered and ambiguous. In this study, we systematically compiled the existing information on OmpA and its relationship with human pathogenic rickettsiae to serve as a reference for future research. A comprehensive literature search was conducted using specific keywords across five databases. According to the literature, OmpA of spotted fever group rickettsia plays a crucial role as an adhesin and invasin that directly interacts with the surface of mammalian host cells to mediate bacterial localization in host cells. The presence of a premature stop codon in the amino acid sequence resulted in the secretion of non-functional OmpA, which is one of the main reasons for rickettsial strains or species to become avirulent. Similarly, OmpA also functions as an important adhesin in the Anaplasma family when it interacts with the sLex and sLex -like glycan of myeloid and endothelial cells, respectively. However, the OmpA of Anaplasma must be co-functional with the other two adhesins to promote bacterial internalization. Interestingly, certain sites in the amino acid residues of Ehrlichia and Orientia OmpA are predicted to be homologous to the binding domain region of Anaplasma OmpA. It is therefore suggested that OmpA is an important adhesin for bacteria to bind to their specific mammalian host cells. [ABSTRACT FROM AUTHOR]

Foot and mouth disease (FMD) is an infectious vesicular disease of cloven-hoofed animals caused by the FMD virus. It is acute, highly contagious, and has a lot of genetic diversity. The aim of this study was to confirm cases diagnosed in the field as FMD virus (FMDV) infection through identification and molecular characterization based on the amplification of the VP1 gene of FMDV to provide information about serotype, virus clustering, and additional molecular scientific data on FMDV circulating in Indonesia. The samples used in this study were Madura cattle and Ongole Grade cattle, which showed clinical signs of FMD. Twenty-six samples were collected from the vesicular fluid of blister epithelial cells (tongue, gum, and hard palate), oral, and nasal swabs. Those samples underwent a screening test using the real-time reverse transcription-polymerase chain reaction (RT-qPCR) method with a 3D gene target to detect FMDV infection. About 46.15% of samples (12/26) were detected as RT-qPCR positive for FMDV. Those positive results were then amplified by reverse transcription-polymerase chain reaction (RT-PCR) and sequenced using the Sanger sequencing technique targeting the VP1 gene fragment of the FMDV. The sequencing results were analyzed by the Molecular Evolutionary Genetics Analysis (MEGA) software X version, which includes assembly, alignment using ClustalW, amino acid prediction, genetic distance, and phylogenetic tree construction. The result showed that amino acid sequence variations were found in this gene, including at positions 96, 99, 129, 134, 138, 140, 156, 158, and 197, and no changes were found either at the critical amino acid sites at positions 144 (V), 148 (L), 154 (K), and 208 (P) or in the arginine-glycine-aspartic acid (RGD) motif at positions 145-147. Phylogenetic analysis indicated that FMD viruses detected in this study were identified as serotype "O", topotype "Middle East South Asia (ME-SA)", lineage "Ind-2001", and sub-lineage "e" (O/ME-SA/Ind-2001e), which have high homology to the VP1 gene (99-100%) between the viruses studied and the viruses found at the beginning of the FMD outbreak in Indonesia in 2022. [ABSTRACT FROM AUTHOR]

Objective: Although main components of the venoms from Viperidae snakes are hemotoxins, several studies indicate the presence of neurotoxins in these venoms. We previously found that the venom of pit viper Gloydius saxatilis inhibited the muscle-type nicotinic acetylcholine receptor (nAChR). The objective of present work is to isolate and characterize a neurotoxic protein from this venom. Methods: The protein was isolated by liquid chromatography and characterized using high resolution mass-spectrometry. Results and Discussion: The isolated protein called glosaxin inhibited the binding of the α-bungarotoxin to the nAChR of muscle type from Torpedo californica. Investigation of the amino acid sequence of the isolated protein by high resolution mass spectrometry and the subsequent bioinformatic analysis showed that it is homologous to the amino acid sequences of disintegrin-like proteins, consisting of non-catalytic domains of class PIII metalloproteinases from the venom of pit vipers of genus Gloydius. Glosaxin was shown to inhibit the binding of α-bungarotoxin to T. californica nAChR with IC50 = 51 μM. It also inhibited ACh-induced functional responses of the human neuronal nAChR of α3β2 subtype. Conclusions: This is the first evidence for the ability of proteins consisting of non-catalytic domains of snake venom class PIII metalloproteinase to inhibit the nAChR. [ABSTRACT FROM AUTHOR]

Objective: Hair ageing is accompanied by hair fibres becoming irregularly shaped causing them to stick out in irregular directions or have more curliness and being spread out. This is believed to be due to changes within the hair fibre structure which occur with ageing, and one of the causes of these changes could be an increase in the number of protein carbonyl groups present in the hair. The aim of this study is to investigate the internal denaturation of hair related to protein carbonyls in attempt to gain new insight into age‐related changes that occur in hair. Methods: The degree of carbonylation of the hair structural protein as determined by fluorescent labelling and Western blotting analysis was used to investigate the primary structure of hair protein. The amount of helix, a common conformation in the secondary structure of proteins, in hair in groups of women with different ages was also analysed using infrared microscopy coupled with multivariate curve resolution (MCR). From the results of this, an image of the two‐dimensional distribution of the α‐helices was generated for the hair taken from each age group. Also, high‐pressure differential scanning calorimetry (HPDSC) of the hair in water was performed on the hair taken from each age group to determine the peak temperature of endothermic effect and the enthalpy of denaturation. Results: We found that the amino group content in hair proteins decreased and Type II keratin, one of the subunits of intermediate filament, was more carbonylated with age. The results of the MCR indicated eight separate components, including components of the secondary structure of proteins, such as α helices and β sheets. Two‐dimensional images of the hair cross‐sections revealed that the presence of α helices decreased with age. In addition, data from the HPDSC showed that the enthalpy associated with the denaturing temperature also significantly decreased with age. Conclusion: These results suggest that there is a negative correlation between age and structural integrity of the helix segment in intermediate filament. The results of this study also show that there is a positive correlation between age‐related hair denaturation and protein carbonyls. [ABSTRACT FROM AUTHOR]

Background: Tralokinumab is a monoclonal antibody that specifically neutralizes interleukin (IL)‐13, a key driver of skin inflammation and barrier abnormalities in atopic dermatitis (AD). This study evaluated early and 2‐year impacts of IL‐13 neutralization on skin and serum biomarkers following tralokinumab treatment in adults with moderate‐to‐severe AD. Methods: Skin biopsies and blood samples were evaluated from a subset of patients enrolled in the Phase 3 ECZTRA 1 (NCT03131648) and the long‐term extension ECZTEND (NCT03587805) trials. Gene expression was assessed by RNA sequencing; protein expression was assessed by immunohistochemistry and immunoassay. Results: Tralokinumab improved the transcriptomic profile of lesional skin by Week 4. Mean improvements in the expression of genes dysregulated in AD were 39% at Week 16 and 85% at 2 years with tralokinumab, with 15% worsening at Week 16 with placebo. At Week 16, tralokinumab significantly decreased type 2 serum biomarkers (CCL17/TARC, periostin, and IgE), reduced epidermal thickness versus placebo, and increased loricrin coverage versus baseline. Two years of tralokinumab treatment significantly reduced expression of genes in the Th2 (IL4R, IL31, CCL17, and CCL26), Th1 (IFNG), and Th17/Th22 (IL22, S100A7, S100A8, and S100A9) pathways as well as increased expression of epidermal differentiation and barrier genes (CLDN1 and LOR). Tralokinumab also shifted atherosclerosis signaling pathway genes (SELE, IL‐37, and S100A8) toward non‐lesional expression. Conclusion: Tralokinumab treatment improved epidermal pathology, reduced systemic markers of type 2 inflammation, and shifted expression of key AD biomarkers in skin towards non‐lesional levels, further highlighting the key role of IL‐13 in the pathogenesis of AD. Clinical Trial Registration: NCT03131648, NCT03587805. [ABSTRACT FROM AUTHOR]

In this study, we purified a lectin isolated from the seeds of Dioclea bicolor (DBL) via affinity purification. Electrophoresis analysis revealed that DBL had three bands, α, β, and γ chains, with molecular masses of approximately 29, 14, and 12 kDa, respectively. Gel filtration chromatography revealed that the native form of DBL had a molecular mass of approximately 100 kDa, indicating that it is a tetramer. Interestingly, DBL-induced hemagglutination was inhibited by several glucosides, mannosides, ampicillin, and tetracycline with minimum inhibitory concentration (MIC) values of 1.56–50 mM. Analysis of the complete amino acid sequence of DBL revealed the presence of 237 amino acids with high similarity to other Diocleinae lectins. Circular dichroism showed the prominent β-sheet secondary structure of DBL. Furthermore, DBL structure prediction revealed a Discrete Optimized Protein Energy (DOPE) score of –26,642.69141/Normalized DOPE score of –1.84041. The DBL monomer was found to consist a β-sandwich based on its 3D structure. Molecular docking showed the interactions between DBL and α-D-glucose, N-acetyl-D-glucosamine, α-D-mannose, α-methyl-D-mannoside, ampicillin, and tetracycline. In addition, DBL showed antimicrobial activity with an MIC of 125 μg/mL and exerted synergistic effects in combination with ampicillin and tetracycline (fractional inhibitory concentration index ≤ 0.5). Additionally, DBL significantly inhibited biofilm formation and showed no toxicity in murine fibroblasts (p < 0.05). These results suggest that DBL exhibits antimicrobial activity and works synergistically with antibiotics. [ABSTRACT FROM AUTHOR]

Biological macromolecules are found in different shapes and sizes. Among these, enzymes catalyze biochemical reactions and are essential in all organisms, but is there a limit size for them to function properly? Large enzymes such as catalases have hundreds of kDa and are formed by multiple subunits, whereas most enzymes are smaller, with molecular weights of 20–60 kDa. Enzymes smaller than 10 kDa could be called microenzymes and the present literature review brings together evidence of their occurrence in nature. Additionally, bioactive peptides could be a natural source for novel microenzymes hidden in larger peptides and molecular downsizing could be useful to engineer artificial enzymes with low molecular weight improving their stability and heterologous expression. An integrative approach is crucial to discover and determine the amino acid sequences of novel microenzymes, together with their genomic identification and their biochemical biological and evolutionary functions. [ABSTRACT FROM AUTHOR]

Heterologous production of proteins in Escherichia coli has raised several challenges including soluble production of target proteins, high levels of expression and purification. Fusion tags can serve as the important tools to overcome these challenges. SUMO (small ubiquitin-related modifier) is one of these tags whose fusion to native protein sequence can enhance its solubility and stability. In current research, a simple, efficient and cost-effective method is being discussed for the construction of pET28a-SUMO vector. In order to improve the stability and activity of lysophospholipase from Pyrococcus abyssi (Pa-LPL), a 6xHis-SUMO tag was fused to N-terminal of Pa-LPL by using pET28a-SUMO vector. Recombinant SUMO-fused enzyme (6 H-S-PaLPL) works optimally at 35 °C and pH 6.5 with remarkable thermostability at 35–95 °C. Thermo-inactivation kinetics of 6 H-S-PaLPL were also studied at 35–95 °C with first order rate constant (kIN) of 5.58 × 10− 2 h-1 and half-life of 12 ± 0 h at 95 °C. Km and Vmax for the hydrolysis of 4-nitrophenyl butyrate were calculated to be 2 ± 0.015 mM and 3882 ± 22.368 U/mg, respectively. 2.4-fold increase in Vmax of Pa-LPL was observed after fusion of 6xHis-SUMO tag to its N-terminal. It is the first report on the utilization of SUMO fusion tag to enhance the overall stability and activity of Pa-LPL. Fusion of 6xHis-SUMO tag not only aided in the purification process but also played a crucial role in increasing the thermostability and activity of the enzyme. SUMO-fused enzyme, thus generated, can serve as an important candidate for degumming of vegetable oils at industrial scale. [ABSTRACT FROM AUTHOR]

A histidine acid phosphatase (HAP) (PhySc) with 99.50% protein sequence similarity with PHO5 from Saccharomyces cerevisiae was expressed functionally with the molecular mass of ∼110 kDa through co-expression along with the set of molecular chaperones dnaK, dnaJ, GroESL. The purified HAP illustrated the optimum activity of 28.75 ± 0.39 U/mg at pH 5.5 and 40 ˚C. The Km and Kcat values towards calcium phytate were 0.608 ± 0.09 mM and 650.89 ± 3.6 s− 1. The half-lives (T1/2) at 55 and 60 ˚C were 2.75 min and 55 s, respectively. The circular dichroism (CD) demonstrated that PhySc includes 30.5, 28.1, 21.3, and 20.1% of random coils, α-Helix, β-Turns, and β-Sheet, respectively. The Tm recorded by CD for PhySc was 56.5 ± 0.34˚C. The molecular docking illustrated that His59 and Asp322 act as catalytic residues in the PhySc. MD simulation showed that PhySc at 40 ˚C has higher structural stability over those of the temperatures 60 and 80 ˚C that support the thermodynamic in vitro investigations. Secondary structure content results obtained from MD simulation indicated that PhySc consists of 34.03, 33.09, 17.5, 12.31, and 3.05% of coil, helix, turn, sheet, and helix310, respectively, which is almost consistent with the experimental results. [ABSTRACT FROM AUTHOR]

In bacteria, F-type ATPase (F-ATPase) plays a key role in bioenergetics and couples ATP synthesis/hydrolysis with the transport of ions (H+ or Na+) across the membrane. The ion specificity of the enzyme is determined by the amino acid sequence of subunits c and a. Here, we introduced several mutations (7 in subunit c and 6 in subunit a) into F-ATPase of thermophilic bacterium Bacillus sp. PS3 in order to change the ion specificity of the enzyme from proton to sodium. The mutations did not affect the ATPase activity of the enzyme, but led to loss of proton conductivity and impaired the binding of subunit a to the c-subunit oligomer, rather than changed the ion specificity. [ABSTRACT FROM AUTHOR]

The increasing prevalence of pathogenic and antimicrobial-resistant isolates of Salmonella Heidelberg (SH) represents a global concern. Consequently, novel strategies for preventing and controlling infections caused by this bacterium are needed. This study aimed to investigate the protective effects of in ovo injection with a formulation based on bacterial peptides, either alone or in combination with oligodeoxynucleotides containing cytosine-phosphodiester-guanine (CpG-ODN), against SH infection in chicks. Genomic data of SH available in public databases were analyzed to select amino acid sequences of structural proteins or those with greater relevance for intestinal colonization. These sequences were subjected to linear epitope prediction tools to identify highly immunogenic peptides. SPF eggs (n = 180) were incubated and injected via the allantoic cavity at day 18 of incubation. Results showed that in ovo injection of peptides + CpG-ODN reduced SH colonization in the caecal content during the first week post-infection, although it did not reduce overall faecal excretion throughout the study. Furthermore, CpG-ODN injection may positively affect intestinal health, as evidenced by reduced crypt depth at 21 dpi and increased villus height at 28 dpi. Levels of secretory IgA did not differ between chicks in any groups, and no detectable SH counts were found in the livers of chicks in any of the infected groups throughout the study. In conclusion, in ovo injection with peptides + CpG-ODN may help reduce caecal colonization by SH in the early stages of infection, but it does not impact total faecal excretion. Additionally, CpG-ODN injection may improve intestinal health parameters in chicks. Peptides + CpG-ODN reduced SH in caeca at the first week post-infection. Administered formulations did not reduce SH-faecal excretion. Levels of intestinal IgA were similar between all groups. CpG-ODN improved some parameters associated with chick intestinal health. [ABSTRACT FROM AUTHOR]

Summary: In the present study, rice bran protein (RBP) from the PB1121 variety was hydrolysed using trypsin and subjected to non‐targeted IMS profiling to identify antioxidant and antihypertensive amino acids in the resulting RBP hydrolysates. The hydrolysate was then separated into three fractions using ultrafiltration, and each fraction was tested for antioxidant and ACE inhibitory activities. The ACE activity was assessed using the tripeptide hippuryl‐histidyl‐leucine (HHL) as a model peptide via HPLC‐DAD. The fraction with the molecular weight (>3000 Da) displayed the strongest antioxidant and ACE inhibitory activity. This fraction was further divided into five fractions using gel Sephadex G‐25, and the greatest levels of antioxidant and ACE inhibitory activity were found in fraction F3B. Fraction F3B was then fractionated using HPLC, and the fraction with ACE inhibitory activity (IC50 of 43 mg mL−1) was analysed using MALDI‐TOF‐TOF mass spectrometry to determine its exact molecular mass and amino acid sequence. The amino acid sequence FMKSK (phe‐met‐lys‐ser‐lys) with a Mw of 655.376 Da was detected, and the molecular docking investigation revealed that FMKSK suppresses ACE by forming strong hydrogen bonds with the active pockets of human ACE. These findings suggest that rice bran contains bioactive peptides with antioxidant and ACE inhibitory effects, making it a promising raw material for the production of beneficial products. [ABSTRACT FROM AUTHOR]

Nucleotide-binding oligomerization domain containing 2 (NOD2), located in the cell cytoplasm, is a pattern recognition receptor belonging to the innate immune receptor family. It mediates the innate immune response by identifying conserved sequences in bacterial peptide glycans and plays an essential role in maintaining immune system homeostasis. Gene mutations of NOD2 lead to the development of autoimmune diseases such as Crohn's disease and Blau syndrome. Recently, NOD2 has been shown to be associated with the pathogenesis of diabetes, cardiac-cerebral diseases, and cancers. However, the function of NOD2 in these non-communicable diseases (CNCDs) is not well summarized in reviews. Our report mainly discusses the primary function and molecular mechanism of NOD2 as well as its potential clinical significance in CNCDs. [ABSTRACT FROM AUTHOR]

Human transglutaminase 1 (TG1) modulates skin development, while its involvement in diseases remains poorly understood, necessitating comprehensive exploration of its substrate interactions. To study the substrate profile of TG1, an in vitro selection system based on cDNA display technology was used to screen two peptide libraries with mutations at varying distance from the reactive glutamine. Next-generation sequencing and bioinformatics analysis of the selected DNA pools revealed a detailed TG1 substrate profile, indicating preferred and non-preferred amino acid sequences. The peptide sequence, AEQHKLPSKWPF, was identified showing high reactivity and specificity to TG1. The position weight matrix calculated from the per amino acid enrichment factors was employed to search human proteins using an in-house algorithm, revealing six known TG1 substrate proteins with high scores, alongside a list of candidate substrates currently under investigation. Our findings are expected to assist in future medical diagnoses and development of treatments for skin disorders. [ABSTRACT FROM AUTHOR]

ω-Transaminases (ω-TAs) are significant candidate enzymes in the biosynthesis of chiral amines for the pharmaceutical and chemical industries. Novel thermostable ω-TAs for potential use in these industries can be discovered using homologous sequence alignment. In this study, we used well-studied B3-TA from hot spring metagenomes, the Sbv333-TA from Streptomyces sp., and TATR from Thermomicrobium roseum as starting templates to BLAST search, and found a yet unidentified thermostable ω-TA (TATP) from Thermorudis peleae. We cloned TATP into vector pET28a, leading to pET28a-TATP, and overexpressed it in Escherichia coli. The enzyme showed the highest activity at pH 8.8 and 73.6 °C, with remarkable thermostability and tolerance toward organic solvents methanol and ethanol. Substrate specificity analysis showed that TATP enzyme is active toward a broad range of substrates including glyoxylate, pyruvate, 2-phenylpropionaldehyde, 2-oxobutyrate, propionaldehyde, acetaldehyde, ethyl acetoacetate, etc. Especially, TATP enzyme presented relatively good activity toward pyruvate and glyoxylate. In addition, the active sites of TATP were analyzed via the approaches of protein sequence alignment, three-dimensional structure simulation, and coenzyme pyridoxamine phosphate docking, which provided a guideline for further enzyme engineering and suggested a potential industrial thermostable ω-TA for chiral amines synthesis. [ABSTRACT FROM AUTHOR]

Bovine rhinitis B virus (BRBV) (genus Aphthovirus, family Picornaviridae) is a significant etiological agent of the bovine respiratory disease complex. Despite global reports on BRBV, genomic data for Japanese strains are not available. In this study, we aimed to obtain genomic information on BRBV in Japan and analyze its genetic characteristics. In nasal swabs from 66 cattle, BRBV was detected in 6 out of 10 symptomatic and 4 out of 56 asymptomatic cattle. Using metagenomic sequencing and Sanger sequencing, the nearly complete genome sequences of two Japanese BRBV strains, IBA/2211/2 and LAV/238002, from symptomatic and asymptomatic cattle, respectively, were determined. These viruses shared significant genetic similarity with known BRBV strains and exhibited unique mutations and recombination events, indicating dynamic evolution, influenced by regional environmental and biological factors. Notably, the leader gene was only approximately 80% and 90% identical in its nucleotide and amino acid sequence, respectively, to all of the BRBV strains with sequences in the GenBank database, indicating significant genetic divergence in the Japanese BRBV leader gene. These findings provide insights into the genetic makeup of Japanese BRBV strains, enriching our understanding of their genetic diversity and evolutionary mechanisms. [ABSTRACT FROM AUTHOR]

Chinese bayberry is a fruit that is appreciated for its taste. A novel totivirus associated with rolling, disfiguring, chlorotic and vein-clearing symptoms on the leaf apices of Chinese bayberry was identified by transcriptome sequencing and reverse transcription PCR (RT-PCR). The complete genome of the virus was determined to be 4959 nucleotides long, and it contains two open reading frames (ORFs). Its genomic organization is similar to that of previously reported totiviruses. ORF1 encodes a putative coat protein (CP) of 765 aa, and ORF2 encodes an RNA-dependent RNA polymerase (RdRp) of 815 aa. These two putative proteins share 55.1% and 62.6%, amino acid sequence identity, respectively, with the corresponding proteins of Panax notoginseng virus A, respectively. According to the demarcation criteria for totivirus species established by the International Committee on Taxonomy of Viruses (ICTV), the new virus should be considered a member of a new species in the genus totivirus, family Orthototiviridae, which we have tentatively named "Myrica rubra-associated totivirus" (MRaTV). [ABSTRACT FROM AUTHOR]

Channel catfish (Ictalurus punctatus) are a food fish extensively reared in aquaculture facilities throughout the world and are also among the most abundant wild catfish species in North America, making them a popular target of anglers. Furthermore, channel catfish are important members of aquatic ecosystems; for example, they serve as a glochidial host for the endangered winged mapleleaf mussel (Quadrula fragosa), making them critical for conserving this species through hatchery‐based restoration efforts. During a routine health inspection, a novel aquareovirus was isolated from channel catfish used in mussel propagation efforts at a fish hatchery in Wisconsin. This virus was isolated on brown bullhead cells (ATCC CCL‐59) and identified through metagenomic sequencing as a novel member of the family Spinareoviridae, genus Aquareovirus. The virus genome consists of 11 segments, as is typical of the aquareoviruses, with phylogenetic relationships based on RNA‐dependent RNA polymerase and major outer capsid protein amino acid sequences showing it to be most closely related to golden shiner virus (aquareovirus C) and aquareovirus C/American grass carp reovirus (aquareovirus G) respectively. The potential of the new virus, which we name genictpun virus 1 (GNIPV‐1), to cause disease in channel catfish or other species remains unknown. [ABSTRACT FROM AUTHOR]

Acetaminophen (APAP)-induced hepatotoxicity is comprised of an injury and recovery phase. While pharmacological interventions, such as N-acetylcysteine (NAC) and 4-methylpyrazole (4-MP), prevent injury there are no therapeutics that promote recovery. JNJ-26366821 (TPOm) is a novel thrombopoietin mimetic peptide with no sequence homology to endogenous thrombopoietin (TPO). Endogenous thrombopoietin is produced by hepatocytes and the TPO receptor is present on liver sinusoidal endothelial cells in addition to megakaryocytes and platelets, and we hypothesize that TPOm activity at the TPO receptor in the liver provides a beneficial effect following liver injury. Therefore, we evaluated the extent to which TPOm, NAC or 4-MP can provide a protective and regenerative effect in the liver when administered 2 h after an APAP overdose of 300 mg/kg in fasted male C57BL/6J mice. TPOm did not affect protein adducts, oxidant stress, DNA fragmentation and hepatic necrosis up to 12 h after APAP. In contrast, TPOm treatment was beneficial at 24 h, i.e., all injury parameters were reduced by 42–48%. Importantly, TPOm enhanced proliferation by 100% as indicated by PCNA-positive hepatocytes around the area of necrosis. When TPOm treatment was delayed by 6 h, there was no effect on the injury, but a proliferative effect was still evident. In contrast, 4MP and NAC treated at 2 h after APAP significantly attenuated all injury parameters at 24 h but failed to enhance hepatocyte proliferation. Thus, TPOm arrests the progression of liver injury by 24 h after APAP and accelerates the onset of the proliferative response which is essential for liver recovery. [ABSTRACT FROM AUTHOR]

A recessive haplotype resulting in elevated calf mortality but with apparent incomplete penetrance was previously linked to the end of chromosome 16 (78.7–80.7 Mbp). Genotype analysis of 5.6 million Holsteins indicated that the haplotype was common and traced back to 1952, with a key ancestor born in 1984 (HOUSA1964484, Southwind) identified from chip genotypes as homozygous for the suspect haplotype. Sequence data from Southwind (an affected calf) and the sire of the affected calf were scanned for candidate mutations. A missense mutation with a deleterious projected impact at 79,613,592 bp was homozygous in the affected calf and heterozygous in the calf's sire and Southwind. Sequence data available from the Cooperative Dairy DNA Repository for 299 other Holsteins indicated a 97% concordance with the haplotype and an 89% call rate. The exon amino acid sequence appears to be broadly conserved in the CACNA1S gene, and mutations in humans and mice can cause phenotypes of temporary or permanent paralysis analogous to those in calves with the haplotype causing muscle weakness (HMW). Improved methods for using pedigree to track new mutations within existing haplotypes were developed and applied to the haplotypes for both muscle weakness and Holstein cholesterol deficiency (HCD). For HCD, concordance of the gene test with its haplotype status was greatly improved. For both defects, haplotype status was matched to heifer livability records for 558,000 calves. For HMW, only 46 heifers with livability records were homozygous and traced only to Southwind on both sides. Of those, 52% died before 18 mo at an average age of 1.7 ± 1.6 mo, but that death rate may be underestimated if only healthier calves were genotyped. The death rate was 2.4% for noncarriers. Different reporting methods or dominance effects may be needed to include HMW and other partially lethal effects in selection and mating. Direct tests are needed for new mutations within existing common haplotypes because tracking can be difficult even with accurate pedigrees when the original haplotype has a high frequency. [ABSTRACT FROM AUTHOR]

Porcine reproductive and respiratory syndrome virus (PRRSV) critically threatens the pig industry in China. Lineage 1 PRRSV, which is divided into L1A–L1F and L1H–L1J, is widely recognized as the most extensively genetically diverse lineage globally. L1A (NADC34-like) and L1C (NADC30-like) PRRSVs have become the current major circulating strains in China. Notably, strains from other branches of L1 have not been reported in China. During our epidemiological investigation of PRRSV, we identified a new strain named HLJDZD55. Phylogenetic analysis of the ORF5 gene revealed that HLJDZD55 belongs to the L1B branch. Alignment of deduced amino acid sequences based on the Nsp2 gene indicated that HLJDZD55 has a discontinuous deletion of 131 amino acids (111 + 1 + 19). We further sequenced the whole genome of HLJDZD55, and phylogenetic analysis based on the whole-genome sequence revealed that HLJDZD55 belongs to the L1C branch. Recombination analysis of the whole genome demonstrated that HLJDZD55 is a recombinant strain of TJZH-1607 (L1C, identified in China) and Minnesota 14 (L1B, identified in the USA). These findings suggested that HLJDZD55 is a newly emerged lineage 1 PRRSV in China and is closely related to L1B PRRSV in the US, which may have been introduced from the U.S. strain and subsequently recombined with the local Chinese strain and underwent evolution. Taken together, these results demonstrated the emergence of L1B PRRSV in China for the first time. [ABSTRACT FROM AUTHOR]

Histone variants are paralogs that replace canonical histones in nucleosomes, often imparting novel functions. However, how histone variants arise and evolve is poorly understood. Reconstruction of histone protein evolution is challenging due to large differences in evolutionary rates across gene lineages and sites. Here we used intron position data from 108 nematode genomes in combination with amino acid sequence data to find disparate evolutionary histories of the three H2A variants found in Caenorhabditis elegans: the ancient H2A.ZHTZ-1, the sperm-specific HTAS-1, and HIS-35, which differs from the canonical S-phase H2A by a single glycine-to-alanine C-terminal change. Although the H2A.ZHTZ-1 protein sequence is highly conserved, its gene exhibits recurrent intron gain and loss. This pattern suggests that specific intron sequences or positions may not be important to H2A.Z functionality. For HTAS-1 and HIS-35, we find variant-specific intron positions that are conserved across species. Patterns of intron position conservation indicate that the sperm-specific variant HTAS-1 arose more recently in the ancestor of a subset of Caenorhabditis species, while HIS-35 arose in the ancestor of Caenorhabditis and its sister group, including the genus Diploscapter. HIS-35 exhibits gene retention in some descendent lineages but gene loss in others, suggesting that histone variant use or functionality can be highly flexible. Surprisingly, we find the single amino acid differentiating HIS-35 from core H2A is ancestral and common across canonical Caenorhabditis H2A sequences. Thus, we speculate that the role of HIS-35 lies not in encoding a functionally distinct protein, but instead in enabling H2A expression across the cell cycle or in distinct tissues. This work illustrates how genes encoding such partially-redundant functions may be advantageous yet relatively replaceable over evolutionary timescales, consistent with the patchwork pattern of retention and loss of both genes. Our study shows the utility of intron positions for reconstructing evolutionary histories of gene families, particularly those undergoing idiosyncratic sequence evolution. [ABSTRACT FROM AUTHOR]

Background: The initial version of SEDA assists life science researchers without programming skills with the preparation of DNA and protein sequence FASTA files for multiple bioinformatics applications. However, the initial version of SEDA lacks a command-line interface for more advanced users and does not allow the creation of automated analysis pipelines. Results: The present paper discusses the updates of the new SEDA release, including the addition of a complete command-line interface, new functionalities like gene annotation, a framework for automated pipelines, and improved integration in Linux environments. Conclusion: SEDA is an open-source Java application and can be installed using the different distributions available (https://www.sing-group.org/seda/download.html) as well as through a Docker image (https://hub.docker.com/r/pegi3s/seda). It is released under a GPL-3.0 license, and its source code is publicly accessible on GitHub (https://github.com/sing-group/seda). The software version at the time of submission is archived at Zenodo (version v1.6.0, http://doi.org/10.5281/zenodo.10201605). [ABSTRACT FROM AUTHOR]

Blood–brain barrier (BBB) peptide-shuttles (BBBpS) are able to translocate the BBB and reach the brain. Despite the importance of brain targeting in pharmacology, BBBpS are poorly characterized. Currently, their development relies on the empiric assumption that cell-penetrating peptides (CPPs), with proven ability to traverse lipid membranes, will likewise behave as a BBBpS. The relationship between CPPs/BBBpS remains elusive and, to the best of our knowledge, has not hitherto been subject to thorough experimental scrutiny. In this work, we have identified/quantified the main physicochemical properties of BBBpS and then searched for CPPs with these properties, hence potential BBBpS. The specific features found for BBBpS are: (i) small size, (ii) none or few aromatic residues, (iii) hydrophobic, and (iv) slight cationic nature. Then, we selected the 10 scoring best in an ordinary least squares analysis, and tested them in vitro and in vivo. Overall, we identified the molecular determinants for brain targeting by peptides, devised a methodology that can be used to assist in the design of peptides with potential brain penetration from amino acid residue sequences, and found four new BBBpS within the CPP library. [ABSTRACT FROM AUTHOR]

Deep learning models adapted from natural language processing offer new opportunities for the prediction of active compounds via machine translation of sequential molecular data representations. For example, chemical language models are often derived for compound string transformation. Moreover, given the principal versatility of language models for translating different types of textual representations, off-the-beaten-path design tasks might be explored. In this work, we have investigated generative design of active compounds with desired potency from target sequence embeddings, representing a rather provoking prediction task. Therefore, a dual-component conditional language model was designed for learning from multimodal data. It comprised a protein language model component for generating target sequence embeddings and a conditional transformer for predicting new active compounds with desired potency. To this end, the designated "biochemical" language model was trained to learn mappings of combined protein sequence and compound potency value embeddings to corresponding compounds, fine-tuned on individual activity classes not encountered during model derivation, and evaluated on compound test sets that were structurally distinct from training sets. The biochemical language model correctly reproduced known compounds with different potency for all activity classes, providing proof-of-concept for the approach. Furthermore, the conditional model consistently reproduced larger numbers of known compounds as well as more potent compounds than an unconditional model, revealing a substantial effect of potency conditioning. The biochemical language model also generated structurally diverse candidate compounds departing from both fine-tuning and test compounds. Overall, generative compound design based on potency value-conditioned target sequence embeddings yielded promising results, rendering the approach attractive for further exploration and practical applications. Scientific contribution: The approach introduced herein combines protein language model and chemical language model components, representing an advanced architecture, and is the first methodology for predicting compounds with desired potency from conditioned protein sequence data. [ABSTRACT FROM AUTHOR]

Background: Cellobiose dehydrogenase (CDH) is an extracellular fungal oxidoreductase with multiple functions in plant biomass degradation. Its primary function as an auxiliary enzyme of lytic polysaccharide monooxygenase (LPMO) facilitates the efficient depolymerization of cellulose, hemicelluloses and other carbohydrate-based polymers. The synergistic action of CDH and LPMO that supports biomass-degrading hydrolases holds significant promise to harness renewable resources for the production of biofuels, chemicals, and modified materials in an environmentally sustainable manner. While previous phylogenetic analyses have identified four distinct classes of CDHs, only class I and II have been biochemically characterized so far. Results: Following a comprehensive database search aimed at identifying CDH sequences belonging to the so far uncharacterized class III for subsequent expression and biochemical characterization, we have curated an extensive compilation of putative CDH amino acid sequences. A sequence similarity network analysis was used to cluster them into the four distinct CDH classes. A total of 1237 sequences encoding putative class III CDHs were extracted from the network and used for phylogenetic analyses. The obtained phylogenetic tree was used to guide the selection of 11 cdhIII genes for recombinant expression in Komagataella phaffii. A small-scale expression screening procedure identified a promising cdhIII gene originating from the plant pathogen Fusarium solani (FsCDH), which was selected for expression optimization by signal peptide shuffling and subsequent production in a 5-L bioreactor. The purified FsCDH exhibits a UV-Vis spectrum and enzymatic activity similar to other characterized CDH classes. Conclusion: The successful production and functional characterization of FsCDH proved that class III CDHs are catalytical active enzymes resembling the key properties of class I and class II CDHs. A detailed biochemical characterization based on the established expression and purification strategy can provide new insights into the evolutionary process shaping CDHs and leading to their differentiation into the four distinct classes. The findings have the potential to broaden our understanding of the biocatalytic application of CDH and LPMO for the oxidative depolymerization of polysaccharides. [ABSTRACT FROM AUTHOR]

Background: Signal peptide (SP) engineering has proven able to improve production of many proteins yet is a laborious process that still relies on trial and error. mRNA structure around the translational start site is important in translation initiation and has rarely been considered in this context, with recent improvements in in silico mRNA structure potentially rendering it a useful predictive tool for SP selection. Here we attempt to create a method to systematically screen candidate signal peptide sequences in silico based on both their nucleotide and amino acid sequences. Several recently released computational tools were used to predict signal peptide activity (SignalP), localization target (DeepLoc) and predicted mRNA structure (MXFold2). The method was tested with Bone Morphogenetic Protein 2 (BMP2), an osteogenic growth factor used clinically for bone regeneration. It was hoped more effective BMP2 SPs could improve BMP2-based gene therapies and reduce the cost of recombinant BMP2 production. Results: Amino acid sequence analysis indicated 2,611 SPs from the TGF-β superfamily were predicted to function when attached to BMP2. mRNA structure prediction indicated structures at the translational start site were likely highly variable. The five sequences with the most accessible translational start sites, a codon optimized BMP2 SP variant and the well-established hIL2 SP sequence were taken forward to in vitro testing. The top five candidates showed non-significant improvements in BMP2 secretion in HEK293T cells. All showed reductions in secretion versus the native sequence in C2C12 cells, with several showing large and significant decreases. None of the tested sequences were able to increase alkaline phosphatase activity above background in C2C12s. The codon optimized control sequence and hIL2 SP showed reasonable activity in HEK293T but very poor activity in C2C12. Conclusions: These results support the use of peptide sequence based in silico tools for basic predictions around signal peptide activity in a synthetic biology context. However, mRNA structure prediction requires improvement before it can produce reliable predictions for this application. The poor activity of the codon optimized BMP2 SP variant in C2C12 emphasizes the importance of codon choice, mRNA structure, and cellular context for SP activity. [ABSTRACT FROM AUTHOR]

Short amphipathic peptides are capable of binding to transcriptional coactivators, often targeting the same binding surfaces as native transcriptional activation domains. However, they do so with modest affinity and generally poor selectivity, limiting their utility as synthetic modulators. Here we show that incorporation of a medium‐chain, branched fatty acid to the N‐terminus of one such heptameric lipopeptidomimetic (LPPM‐8) increases the affinity for the coactivator Med25 >20‐fold (Ki >100 μM to 4 μM), rendering it an effective inhibitor of Med25 protein–protein interactions (PPIs). The lipid structure, the peptide sequence, and the C‐terminal functionalization of the lipopeptidomimetic each influence the structural propensity of LPPM‐8 and its effectiveness as an inhibitor. LPPM‐8 engages Med25 through interaction with the H2 face of its activator interaction domain and in doing so stabilizes full‐length protein in the cellular proteome. Further, genes regulated by Med25‐activator PPIs are inhibited in a cell model of triple‐negative breast cancer. Thus, LPPM‐8 is a useful tool for studying Med25 and mediator complex biology and the results indicate that lipopeptidomimetics may be a robust source of inhibitors for activator‐coactivator complexes. [ABSTRACT FROM AUTHOR]

In the realm of high‐throughput screening (HTS), macrocyclic peptide libraries traditionally necessitate decoding tags, essential for both library synthesis and identifying hit peptide sequences post‐screening. Our innovation introduces a tag‐free technology platform for synthesizing cyclic peptide libraries in solution and facilitates screening against biological targets to identify peptide binders through unconventional intramolecular CyClick and DeClick chemistries (CCDC) discovered through our research. This combination allows for the synthesis of diverse cyclic peptide libraries, the incorporation of various amino acids, and facile linearization and decoding of cyclic peptide binder sequences. Our sensitivity‐enhancing derivatization method, utilized in tandem with nano LC‐MS/MS, enables the sequencing of peptides even at exceedingly low picomolar concentrations. Employing our technology platform, we have successfully unearthed novel cyclic peptide binders against a monoclonal antibody and the first cyclic peptide binder of HIV capsid protein responsible for viral infections as validated by microscale thermal shift assays (TSA), biolayer interferometry (BLI) and functional assays. [ABSTRACT FROM AUTHOR]

Protein evolution is guided by structural, functional, and dynamical constraints ensuring organismal viability. Pseudogenes are genomic sequences identified in many eukaryotes that lack translational activity due to sequence degradation and thus over time have undergone "devolution." Previously pseudogenized genes sometimes regain their protein-coding function, suggesting they may still encode robust folding energy landscapes despite multiple mutations. We study both the physical folding landscapes of protein sequences corresponding to human pseudogenes using the Associative Memory, Water Mediated, Structure and Energy Model, and the evolutionary energy landscapes obtained using direct coupling analysis (DCA) on their parent protein families. We found that generally mutations that have occurred in pseudogene sequences have disrupted their native global network of stabilizing residue interactions, making it harder for them to fold if they were translated. In some cases, however, energetic frustration has apparently decreased when the functional constraints were removed. We analyzed this unexpected situation for Cyclophilin A, Profilin-1, and Small Ubiquitin-like Modifier 2 Protein. Our analysis reveals that when such mutations in the pseudogene ultimately stabilize folding, at the same time, they likely alter the pseudogenes' former biological activity, as estimated by DCA. We localize most of these stabilizing mutations generally to normally frustrated regions required for binding to other partners. [ABSTRACT FROM AUTHOR]

The activities of most enzymes and drugs depend on interactions between proteins and small molecules. Accurate prediction of these interactions could greatly accelerate pharmaceutical and biotechnological research. Current machine learning models designed for this task have a limited ability to generalize beyond the proteins used for training. This limitation is likely due to a lack of information exchange between the protein and the small molecule during the generation of the required numerical representations. Here, we introduce ProSmith, a machine learning framework that employs a multimodal Transformer Network to simultaneously process protein amino acid sequences and small molecule strings in the same input. This approach facilitates the exchange of all relevant information between the two molecule types during the computation of their numerical representations, allowing the model to account for their structural and functional interactions. Our final model combines gradient boosting predictions based on the resulting multimodal Transformer Network with independent predictions based on separate deep learning representations of the proteins and small molecules. The resulting predictions outperform recently published state-of-the-art models for predicting protein-small molecule interactions across three diverse tasks: predicting kinase inhibitions; inferring potential substrates for enzymes; and predicting Michaelis constants KM. The Python code provided can be used to easily implement and improve machine learning predictions involving arbitrary protein-small molecule interactions. Author summary: Understanding how proteins interact with small molecules, such as drugs, is critical to advancing medical, biological, and biotechnological research. Our work introduces ProSmith, a machine learning framework that improves the prediction of protein-small molecule interactions. Protein-small molecule interactions can be predicted by using numerical representations of proteins and small molecules as input to machine learning prediction models. Previous methods typically generated separate numerical representations for the proteins and small molecules without considering their interactions. ProSmith, however, combines both protein sequence and small molecule structural information in the input of a single multimodal Transformer Network to generate a joint numerical representation. Unlike previous methods, this allows for a comprehensive exchange of information between protein and small molecule, capturing the complex relationships and interactions between these two types of molecules. ProSmith successfully predicts several biological interactions, including kinase inhibitions, potential enzyme-substrate pairs, and enzyme kinetic parameters KM. We provide Python code that can be easily adapted to improve predictions for any protein-small molecule interaction. [ABSTRACT FROM AUTHOR]

Short amphipathic peptides are capable of binding to transcriptional coactivators, often targeting the same binding surfaces as native transcriptional activation domains. However, they do so with modest affinity and generally poor selectivity, limiting their utility as synthetic modulators. Here we show that incorporation of a medium‐chain, branched fatty acid to the N‐terminus of one such heptameric lipopeptidomimetic (LPPM‐8) increases the affinity for the coactivator Med25 >20‐fold (Ki >100 μM to 4 μM), rendering it an effective inhibitor of Med25 protein–protein interactions (PPIs). The lipid structure, the peptide sequence, and the C‐terminal functionalization of the lipopeptidomimetic each influence the structural propensity of LPPM‐8 and its effectiveness as an inhibitor. LPPM‐8 engages Med25 through interaction with the H2 face of its activator interaction domain and in doing so stabilizes full‐length protein in the cellular proteome. Further, genes regulated by Med25‐activator PPIs are inhibited in a cell model of triple‐negative breast cancer. Thus, LPPM‐8 is a useful tool for studying Med25 and mediator complex biology and the results indicate that lipopeptidomimetics may be a robust source of inhibitors for activator‐coactivator complexes. [ABSTRACT FROM AUTHOR]

In the realm of high‐throughput screening (HTS), macrocyclic peptide libraries traditionally necessitate decoding tags, essential for both library synthesis and identifying hit peptide sequences post‐screening. Our innovation introduces a tag‐free technology platform for synthesizing cyclic peptide libraries in solution and facilitates screening against biological targets to identify peptide binders through unconventional intramolecular CyClick and DeClick chemistries (CCDC) discovered through our research. This combination allows for the synthesis of diverse cyclic peptide libraries, the incorporation of various amino acids, and facile linearization and decoding of cyclic peptide binder sequences. Our sensitivity‐enhancing derivatization method, utilized in tandem with nano LC‐MS/MS, enables the sequencing of peptides even at exceedingly low picomolar concentrations. Employing our technology platform, we have successfully unearthed novel cyclic peptide binders against a monoclonal antibody and the first cyclic peptide binder of HIV capsid protein responsible for viral infections as validated by microscale thermal shift assays (TSA), biolayer interferometry (BLI) and functional assays. [ABSTRACT FROM AUTHOR]

This study presents the complete genome sequence of a novel nege-like virus identified in whiteflies (Bemisia tabaci MEAM1), provisionally designated as whitefly negevirus 1 (WfNgV1). The virus possesses a single-stranded RNA genome comprising 11,848 nucleotides, organized into four open reading frames (ORFs). These ORFs encode the putative RNA-dependent-RNA-polymerase (RdRp, ORF 1), a glycoprotein (ORF 2), a structural protein with homology to those in the SP24 family, (ORF 3), and a protein of unknown function (ORF 4). Phylogenetic analysis focusing on RdRp and SP24 amino acid sequences revealed a close relationship between WfNgV1 and Bemisia tabaci negevirus 1, a negevirus sequence recently discovered in whiteflies from Israel. Both viruses form a clade sharing a most recent common ancestor with the proposed nelorpivirus and centivirus taxa. The putative glycoprotein from ORF 2 and SP24 (ORF 3) of WfNgV1 exhibit the characteristic topologies previously reported for negevirus counterparts. This marks the first reported negevirus-like sequence from whiteflies in the Americas. [ABSTRACT FROM AUTHOR]

The standard genetic code defines the rules of translation for nearly every life form on Earth. It also determines the amino acid changes accessible via single-nucleotide mutations, thus influencing protein evolvability—the ability of mutation to bring forth adaptive variation in protein function. One of the most striking features of the standard genetic code is its robustness to mutation, yet it remains an open question whether such robustness facilitates or frustrates protein evolvability. To answer this question, we use data from massively parallel sequence-to-function assays to construct and analyze 6 empirical adaptive landscapes under hundreds of thousands of rewired genetic codes, including those of codon compression schemes relevant to protein engineering and synthetic biology. We find that robust genetic codes tend to enhance protein evolvability by rendering smooth adaptive landscapes with few peaks, which are readily accessible from throughout sequence space. However, the standard genetic code is rarely exceptional in this regard, because many alternative codes render smoother landscapes than the standard code. By constructing low-dimensional visualizations of these landscapes, which each comprise more than 16 million mRNA sequences, we show that such alternative codes radically alter the topological features of the network of high-fitness genotypes. Whereas the genetic codes that optimize evolvability depend to some extent on the detailed relationship between amino acid sequence and protein function, we also uncover general design principles for engineering nonstandard genetic codes for enhanced and diminished evolvability, which may facilitate directed protein evolution experiments and the bio-containment of synthetic organisms, respectively. Only "one in a million" possible genetic codes are as robust as the standard genetic code, but does this robustness accelerate or impede adaptive evolution? This study uses experimental data from six massively parallel sequence-to-function assays for four proteins to show that robust genetic codes enhance protein evolvability by producing smooth adaptive landscapes with few peaks. [ABSTRACT FROM AUTHOR]

[Display omitted] Tissue-specific homing peptides have been shown to improve chemotherapeutic efficacy due to their trophism for tumor cells. Other sequences that selectively home to the placenta are providing new and safer therapeutics to treat complications in pregnancy. Our hypothesis is that the placental homing peptide RSGVAKS (RSG) may have binding affinity to cancer cells, and that insight can be gained into the binding mechanisms of RSG and the tumor homing peptide CGKRK to model membranes that mimic the primary lipid compositions of the respective cells. Following cell culture studies on the binding efficacy of the peptides on a breast cancer cell line, a systematic translational characterization is delivered using ellipsometry, Brewster angle microscopy and neutron reflectometry of the extents, structures, and dynamics of the interactions of the peptides with the model membranes on a Langmuir trough. We start by revealing that RSG does indeed have binding affinity to breast cancer cells. The peptide is then shown to exhibit stronger interactions and greater penetration than CGKRK into both model membranes, combined with greater disruption to the lipid component. RSG also forms aggregates bound to the model membranes, yet both peptides bind to a greater extent to the placental than cancer model membranes. The results demonstrate the potential for varying local reservoirs of peptide within cell membranes that may influence receptor binding. The innovative nature of our findings motivates the urgent need for more studies involving multifaceted experimental platforms to explore the use of specific peptide sequences to home to different cellular targets. [ABSTRACT FROM AUTHOR]

Protein capsids are a widespread form of compartmentalization in nature. Icosahedral symmetry is ubiquitous in capsids derived from spherical viruses, as this geometry maximizes the internal volume that can be enclosed within. Despite the strong preference for icosahedral symmetry, we show that simple point mutations in a virus-like capsid can drive the assembly of unique symmetry-reduced structures. Starting with the encapsulin from Myxococcusxanthus, a 180-mer bacterial capsid that adopts the well-studied viral HK97 fold, we use mass photometry and native charge detection mass spectrometry to identify a triple histidine point mutant that forms smaller dimorphic assemblies. Using cryoelectron microscopy, we determine the structures of a precedented 60-mer icosahedral assembly and an unexpected 36-mer tetrahedron that features significant geometric rearrangements around a new interaction surface between capsid protomers. We subsequently find that the tetrahedral assembly can be generated by triple-point mutation to various amino acids and that even a single histidine point mutation is sufficient to form tetrahedra. These findings represent a unique example of tetrahedral geometry when surveying all characterized encapsulins, HK97-like capsids, or indeed any virus-derived capsids reported in the Protein Data Bank, revealing the surprising plasticity of capsid self-assembly that can be accessed through minimal changes in the protein sequence. [ABSTRACT FROM AUTHOR]

Synthetic polymers, commonly known as plastics, are currently present in all aspects of our lives. Although they are useful, they present the problem of what to do with them after their lifespan. There are currently mechanical and chemical methods to treat plastics, but these are methods that, among other disadvantages, can be expensive in terms of energy or produce polluting gases. A more environmentally friendly alternative is recycling, although this practice is not widespread. Based on the practice of the so-called circular economy, many studies are focused on the biodegradation of these polymers by enzymes. Using enzymes is a harmless method that can also generate substances with high added value. Novel and enhanced plastic-degrading enzymes have been obtained by modifying the amino acid sequence of existing ones, especially on their active site, using a wide variety of genetic approaches. Currently, many studies focus on the common aim of achieving strains with greater hydrolytic activity toward a different range of plastic polymers. Although in most cases the depolymerization rate is improved, more research is required to develop effective biodegradation strategies for plastic recycling or upcycling. This review focuses on a compilation and discussion of the most important research outcomes carried out on microbial biotechnology to degrade and recycle plastics. [ABSTRACT FROM AUTHOR]

The subcellular location of a protein provides valuable insights to bioinformaticians in terms of drug designs and discovery, genomics, and various other aspects of medical research. Experimental methods for protein subcellular localization determination are time-consuming and expensive, whereas computational methods, if accurate, would represent a much more efficient alternative. This article introduces an ab initio protein subcellular localization predictor based on an ensemble of Deep N-to-1 Convolutional Neural Networks. Our predictor is trained and tested on strict redundancy-reduced datasets and achieves 63% accuracy for the diverse number of classes. This predictor is a step towards bridging the gap between a protein sequence and the protein's function. It can potentially provide information about protein–protein interaction to facilitate drug design and processes like vaccine production that are essential to disease prevention. [ABSTRACT FROM AUTHOR]