Function Of Specific Proteins Research Articles

An overview of S100 proteins and their functions in skin homeostasis, interface dermatitis conditions and other skin pathologies.

S100 proteins comprise a family of structurally related proteins that are calcium-sensitive. S100 proteins have been found to play various roles in regulation of cell apoptosis, cell proliferation and differentiation, cell migration and invasion, energy metabolism, calcium homeostasis, protein phosphorylation, anti-microbial activity and inflammation in a variety of cell types. While the specific function of many S100 proteins remains unknown, some of the S100 proteins serve as disease biomarkers as well as possible therapeutic targets in skin diseases. Interface dermatitis (ID) is a histopathological term that covers many different skin conditions including cutaneous lupus erythematosus, lichen planus, and dermatomyositis. These pathologies share similar histological features, which include basal cell vacuolization and lymphocytic infiltration at the dermal-epidermal junction. In this review, we summarize how the S100 protein family contributes to both homeostatic and inflammatory processes in the skin. We also highlight the role of S100 proteins in neuronal signalling, describing how this might contribute to neuroimmune interactions in ID and other skin pathologies. Last, we discuss what is known about the S100 family proteins as both biomarkers and potential treatment targets in specific pathologies.

The Non-Histone Protein FgNhp6 Is Involved in the Regulation of the Development, DON Biosynthesis, and Virulence of Fusarium graminearum.

Fusarium graminearum is the primary causative agent of Fusarium head blight (FHB), a devastating disease affecting cereals globally. The high-mobility group (HMG) of non-histone proteins constitutes vital architectural elements within chromatin, playing diverse roles in various biological processes in eukaryotic cells. Nonetheless, the specific functions of HMG proteins in F. graminearum have yet to be elucidated. Here, we identified 10 HMG proteins in F. graminearum and extensively characterized the biological roles of one HMGB protein, FgNhp6. We constructed the FgNhp6 deletion mutant and its complementary strains. With these strains, we confirmed the nuclear localization of FgNhp6 and discovered that the absence of FgNhp6 led to reduced radial growth accompanied by severe pigmentation defects, a significant reduction in conidial production, and a failure to produce perithecia. The ∆FgNhp6 mutant exhibited a markedly reduced pathogenicity on wheat coleoptiles and spikes, coupled with a significant increase in deoxynivalenol production. An RNA sequencing (RNA-seq) analysis indicated that FgNhp6 deletion influenced a wide array of metabolic pathways, particularly affecting several secondary metabolic pathways, such as sterol biosynthesis and aurofusarin biosynthesis. The findings of this study highlight the essential role of FgNhp6 in the regulation of the asexual and sexual reproduction, deoxynivalenol (DON) production, and pathogenicity of F. graminearum.

Unveiling the repressive mechanism of a PPS-like regulator (PspR) in polyhydroxyalkanoates biosynthesis network.

Poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) is a type of polyhydroxyalkanoates (PHA) that exhibits numerous outstanding properties and is naturally synthesized and elaborately regulated in various microorganisms. However, the regulatory mechanism involving the specific regulator PhaR in Haloferax mediterranei, a major PHBV production model among Haloarchaea, is not well understood. In our previous study, we showed that deletion of the phosphoenolpyruvate (PEP) synthetase-like (pps-like) gene activates the cryptic phaC genes in H. mediterranei, resulting in enhanced PHBV accumulation. In this study, we demonstrated the specific function of the PPS-like protein as a negative regulator of phaR gene expression and PHBV synthesis. Chromatin immunoprecipitation (ChIP), in situ fluorescence reporting system, and in vitro electrophoretic mobility shift assay (EMSA) showed that the PPS-like protein can bind to the promoter region of phaRP. Computational modeling revealed a high structural similarity between the rifampin phosphotransferase (RPH) protein and the PPS-like protein, which has a conserved ATP-binding domain, a His domain, and a predicted DNA-binding domain. Key residues within this unique DNA-binding domain were subsequently validated through point mutation and functional evaluations. Based on these findings, we concluded that PPS-like protein, which we now renamed as PspR, has evolved into a repressor capable of regulating the key regulator PhaR, and thereby modulating PHBV synthesis. This regulatory network (PspR-PhaR) for PHA biosynthesis is likely widespread among haloarchaea, providing a novel approach to manipulate haloarchaea as a production platform for high-yielding PHA. KEY POINTS: • The repressive mechanism of a novel inhibitor PspR in the PHBV biosynthesis was demonstrated • PspR is widespread among the PHA accumulating haloarchaea • It is the first report of functional conversion from an enzyme to a trans-acting regulator in haloarchaea.

Klotho in pregnancy and intrauterine development - Potential clinical implications: a review from the European Renal Association CKD-MBD Working Group.

Intrauterine development is crucial for life-long health; therefore, elucidation of its key regulators is of interest for their potential prognostic and therapeutic implications. Originally described as a membrane-bound anti-aging protein, Klotho has evolved as a regulator of numerous functions in different organ systems. Circulating Klotho is generated by alternative splicing or active shedding from cell membranes. Recently, Klotho was identified as a regulator of placental function, and while Klotho does not cross the placental barrier, increased levels of circulating α-Klotho have been identified in umbilical cord blood compared to maternal blood, indicating that Klotho may also play a role in intrauterine development. In this narrative review, we discuss novel insights into the specific functions of the Klotho proteins in the placenta and in intrauterine development, while summarizing up-to-date knowledge about their structures and functions. Klotho plays a role in stem cell functioning, organogenesis, and haematopoiesis. Low circulating maternal and foetal levels of Klotho are associated with preeclampsia, intra-uterine growth restriction, and an increased perinatal risk for newborns, indicating a potential used of Klotho as biomarker and therapeutic target. Experimental administration of Klotho protein indicates a neuro- and nephroprotective potential, suggesting a possible future role of Klotho as a therapeutic agent. However, the use of Klotho as intervention during pregnancy is yet unproven. Here, we summarize novel evidence, suggesting Klotho as a key regulator for healthy pregnancies and intrauterine development with promising potential for clinical use.

Pronucleotide Probes Reveal a Diverging Specificity for AMPylation vs UMPylation of Human and Bacterial Nucleotide Transferases.

AMPylation is a post-translational modification utilized by human and bacterial cells to modulate the activity and function of specific proteins. Major AMPylators such as human FICD and bacterial VopS have been studied extensively for their substrate and target scope in vitro. Recently, an AMP pronucleotide probe also facilitated the in situ analysis of AMPylation in living cells. Based on this technology, we here introduce a novel UMP pronucleotide probe and utilize it to profile uninfected and Vibrio parahaemolyticus infected human cells. Mass spectrometric analysis of labeled protein targets reveals an unexpected promiscuity of human nucleotide transferases with an almost identical target set of AMP- and UMPylated proteins. Vice versa, studies in cells infected by V. parahaemolyticus and its effector VopS revealed solely AMPylation of host enzymes, highlighting a so far unknown specificity of this transferase for ATP. Taken together, pronucleotide probes provide an unprecedented insight into the in situ activity profile of crucial nucleotide transferases, which can largely differ from their in vitro activity.

Thiolation-Based Protein-Protein Hydrogels for Improved Wound Healing.

The limitations of protein-based hydrogels, including their insufficient mechanical properties and restricted biological functions, arise from the highly specific functions of proteins as natural building blocks. A potential solution to overcome these shortcomings is the development of protein-protein hydrogels, which integrate structural and functional proteins. In this study, a protein-protein hydrogel formed by crosslinking bovine serum albumin (BSA) and a genetically engineered intrinsically disordered collagen-like protein (CLP) through Ag─S bonding is introduced. The approach involves thiolating lysine residues of BSA and crosslinking CLP with Ag+ ions, utilizing thiolation of BSA and the free-cysteines of CLP. The resulting protein-protein hydrogels exhibit exceptional properties, including notable plasticity, inherent self-healing capabilities, and gel-sol transition in response to redox conditions. In comparison to standalone BSA hydrogels, these protein-protein hydrogels demonstrate enhanced cellular viability, and improved cellular migration. In vivo experiments provide conclusive evidence of accelerated wound healing, observed not only in murine models with streptozotocin (Step)-induced diabetes but also in zebrafish models subjected to UV-burn injuries. Detailed mechanistic insights, combined with assessments of proinflammatory cytokines and the expression of epidermal differentiation-related proteins, robustly validate the protein-protein hydrogel's effectiveness in promoting wound repair.

Decoding the secrets: how conformational and structural regulators inhibit the human 20S proteasome.

Acquired resistance to drugs that modulate specific protein functions, such as the human proteasome, presents a significant challenge in targeted therapies. This underscores the importance of devising new methodologies to predict drug binding and potential resistance due to specific protein mutations. In this work, we conducted an extensive computational analysis to ascertain the effects of selected mutations (Ala49Thr, Ala50Val, and Cys52Phe) within the active site of the human proteasome. Specifically, we sought to understand how these mutations might disrupt protein function either by altering protein stability or by impeding interactions with a clinical administered drug. Leveraging molecular dynamics simulations and molecular docking calculations, we assessed the effect of these mutations on protein stability and ligand affinity. Notably, our results indicate that the Cys52Phe mutation critically impacts protein-ligand binding, providing valuable insights into potential proteasome inhibitor resistance.

Examining Protein Translocation by β-Barrel Membrane Proteins Using Reconstituted Proteoliposomes.

β-barrel membrane proteins populate the outer membrane of Gram-negative bacteria, mitochondria, and chloroplasts, playing significant roles in multiple key cellular pathways. Characterizing the functions of these membrane proteins in vivo is often challenging due to the complex protein network in the periplasm of Gram-negative bacteria (or intermembrane space in mitochondria and chloroplasts) and the presence of other outer membrane proteins. In vitro reconstitution into lipid-bilayer-like environments such as nanodiscs or proteoliposomes provides an excellent method for examining the specific function and mechanism of these membrane proteins in an isolated system. Here, we describe the methodologies employed to investigate Slam, a 14-stranded β-barrel membrane protein also known as the type XI secretion system that is responsible for translocating proteins across the outer membrane of many bacterial species.

Protein Sequence Classification Through Deep Learning and Encoding Strategies

Protein sequence classification is vital for understanding protein functionalities, aiding in the inference of novel protein functions. Machine learning and deep learning algorithms have revolutionized this field, offering insights into specific protein classes and functions. This study employs Natural Language Processing (NLP) techniques, including Integer and Blosum encoding, for efficient classification. SVM with count vectorizer achieves the highest accuracy of 92%, while Integer encoding with CNN surpasses NLP embedding techniques by 4%. The goal is to develop an automated system for predicting protein functionality based on sequence classification, contributing to advancements in proteomics and computational biology.

Crosstalk of ubiquitin system and non-coding RNA in fibrosis.

Chronic tissue injury triggers changes in the cell type and microenvironment at the site of injury and eventually fibrosis develops. Current research suggests that fibrosis is a highly dynamic and reversible process, which means that human intervention after fibrosis has occurred has the potential to slow down or cure fibrosis. The ubiquitin system regulates the biological functions of specific proteins involved in the development of fibrosis, and researchers have designed small molecule drugs to treat fibrotic diseases on this basis, but their therapeutic effects are still limited. With the development of molecular biology technology, researchers have found that non-coding RNA (ncRNA) can interact with the ubiquitin system to jointly regulate the development of fibrosis. More in-depth explorations of the interaction between ncRNA and ubiquitin system will provide new ideas for the clinical treatment of fibrotic diseases.

Comprehensive analysis of Pigeon egg proteins: Composition, function, and health significance

Pigeon eggs have been used as a valuable source of high-quality proteins, which play a crucial role to regulate metabolism, immunity, and other physiological functions in humans. However, the specific composition and function of pigeon egg proteins remain underexplored. In this study, a comprehensive into the common proteome and modified proteins (phosphorylated proteins and N-glycosylated proteins) of whole pigeon eggs was carried out using proteomics. The results showed that a total of 189 proteins were identified, including 27 phosphorylated proteins (containing 90 phosphorylation modification sites) and 73 N-glycosylated proteins (containing 203 N-glycosylation modification sites). Motif analysis indicated that serine (Ser) accounted for 72.6% of the phosphorylation events, while the sequence "N-X-T" emerged as the predominant motif for N-glycosylation, representing 58.7% of such modifications. Functional enrichment analysis further demonstrated that the majority of pigeon egg proteins, modified proteins were involved in binding and catalytic activities and contributed to enzyme activity regulation and inhibition. Pigeon egg proteins were predominantly associated with the lysosomal pathway, as outlined in the KEGG database. This study could pave the way for the development of innovative food products and nutritional interventions based on pigeon egg proteins.

Effects of Mirror Therapy Combined With Task-Oriented Training on Limb Function Recovery in Stroke Patients With Hemiplegia

To explore the effects of mirror therapy combined with task-oriented training on limb function recovery in stroke patients with hemiplegia. A total of 304 older patients with post-stroke hemiplegia who received treatment in Nanyang Third People's Hospital between March 2020 and March 2022 were enrolled as the subjects. They were assigned to the intervention group and the control group through a systematic randomization method, with 152 patients in each group. The control group was treated with conventional medication and task-oriented training, while the intervention group received a combined mirror therapy in addition to the treatment given to the control group. Both groups received continuous treatment for 3 months. The pre-treatment findings and those obtained after 3 month of treatment were compared between the two groups in the following areas, the neurological functions, including the levels of neuron-specific enolase (NSE) and S100β, a central nervous system specific protein, upper and lower limb motor function as reflected by Fugl-Meyer Assessment (FMA) score, balance ability as measured by Berg Balance Scale (BBS), and the integrated electromyography (iEMG) values of quadriceps femoris, gastrocnemius, and tibialis anterior muscles, three-dimensional gait spatiotemporal parameters, and quality of life as reflected by the assessment results for the National Institute of Stroke Scale (NIHSS) and Stroke-Specific Quality of Life Scale (SS-QOL). The findings were compared to identify changes. After 3 months of treatment, the FMA and BBS scores and three-dimensional gait spatio-temporal parameters in the intervention group were significantly better than those in the control group (all P<0.05). Mirror therapy combined with task-oriented training promotes the function recovery of the affected limbs in older patients with post-stroke hemiplegia, effectively improves their motor function and quality of life, and helps improve patient prognosis.

MAPK11 (p38β) is a major determinant of cellular radiosensitivity by controlling ionizing radiation-associated senescence: An in vitro study

MAPKs are among the most relevant signalling pathways involved in coordinating cell responses to different stimuli. This group includes p38MAPKs, constituted by 4 different proteins with a high sequence homology: MAPK14 (p38α), MAPK11 (p38β), MAPK12 (p38γ) and MAPK13 (p38δ). Despite their high similarity, each member shows unique expression patterns and even exclusive functions. Thus, analysing protein-specific functions of MAPK members is necessary to unequivocally uncover the roles of this signalling pathway. Here, we investigate the possible role of MAPK11 in the cell response to ionizing radiation (IR).We developed MAPK11/14 knockdown through shRNA and CRISPR interference gene perturbation approaches and analysed the downstream effects on cell responses to ionizing radiation in A549, HCT-116 and MCF-7 cancer cell lines. Specifically, we assessed IR toxicity by clonogenic assays; DNA damage response activity by immunocytochemistry; apoptosis and cell cycle by flow cytometry (Annexin V and propidium iodide, respectively); DNA repair by comet assay; and senescence induction by both X-Gal staining and gene expression of senescence-associated genes by RT-qPCR.Our findings demonstrate a critical role of MAPK11 in the cellular response to IR by controlling the associated senescent phenotype, and without observable effects on DNA damage response, apoptosis, cell cycle or DNA damage repair.Our results highlight MAPK11 as a novel mediator of the cellular response to ionizing radiation through the control exerted onto IR-associated senescence.

Construction of Five Tryptophan Isomers and Application of the Isomers to Solid-Phase Total Syntheses of Lysocin E Derivatives.

Tryptophan (Trp) plays a unique role in peptides and proteins as its indole ring possesses an electron-rich character and an N1-H hydrogen-bond donor. Because of its non-rotationally symmetric structure, synthetic alterations of the orientation of the indole ring would modulate the intrinsic structures and functions of peptides and proteins. Here we developed synthetic routes to the five Trp isomers in which the C3-substitution of the indole ring was changed to the C2/4/5/6/7-substitutions, and applied the five monomers to Fmoc-based solid-phase peptide synthesis. Specifically, the five monomers were prepared via Negishi cross-coupling reactions of C2/4/5/6/7-iodoindoles. To demonstrate the applicability of the monomers to the solid-phase synthesis, the five Trp isomers of macrocyclic antibiotic lysocin E were selected as target molecules and synthesized through peptide elongation, on-resin macrocyclization, and global deprotection. The Trp isomers displayed markedly weaker antibacterial activity than the parent natural product, revealing the biological importance of the precise three-dimensional shape of the original Trp residue of lysocin E. The present methods for the preparation and application of these five Trp isomers provide a new strategy for analyzing and modifying the specific functions of numerous Trp-containing peptides and proteins beyond this study.

Advances in machine learning for predicting protein functions

Proteins play a variety of functional roles in cellular activities and are indispensable for life. Understanding the functions of proteins is crucial in many fields such as medicine and drug development. In addition, the application of enzymes in green synthesis has been of great interest, but the high cost of obtaining specific functional enzymes as well as the variety of enzyme types and functions hamper their application. At present, the specific functions of proteins are mainly determined through tedious and time-consuming experimental characterization. With the rapid development of bioinformatics and sequencing technologies, the number of protein sequences that have been sequenced is much larger than those can be annotated, thus developing efficient methods for predicting protein functions becomes crucial. With the rapid development of computer technology, data-driven machine learning methods have become a promising solution to these challenges. This review provides an overview of protein function and its annotation methods as well as the development history and operation process of machine learning. In combination with the application of machine learning in the field of enzyme function prediction, we present an outlook on the future direction of efficient artificial intelligence-assisted protein function research.

Molecular insights on PS-PLA1 lipase activity of human ABHD16B

The human alpha beta hydrolase domain (ABHD) proteins are ubiquitous and regulate the cellular lipids' anabolic and catabolic processes. The structural aspects for specific biochemical function of many ABHD proteins related to physiological disorders and its link to pathological conditions remain unknown. Here putative human ABHD16B protein was overexpressed in Saccharomyces cerevisiae for its biological activity. In-vitro enzymatic assay of the recombinant ABHD16B protein with fluorescently tagged glycerophospholipids revealed that the PLA1 activity is observed with phosphatidylserine (PS). In addition, it efficiently hydrolyzed monoacylglycerol over triacylglycerols. Further, molecular dynamic simulations and per residue binding free energy decomposition analysis revealed that the origin of PS-specific PLA1 activity of ABHD16B is due to the electrostatic interaction of the PS head group with K8, R319, and E178, which led to having the hydrogen bond interaction of sn-1 acyl chain ester to the catalytic site residues. Site-directed mutagenesis of the 245GXSXG249 motif of ABHD16B reduced the maximal lipase activity of PS and MAG. In summary, these results revealed that ABHD16B plays a vital role in PS selectivity that in turn, controls the specific subcellular pools of 2-LPS metabolism in the tissues at low pH.

Investigating the role of computer simulations in modeling complex biological systems

The use of computer simulations in modeling complex biological systems has become an important tool for biotechnology research. This study investigates the role of computer simulations in modeling complex biological systems and their potential applications in biotechnology. The focus of the study was on protein folding, a complex biological process that plays a critical role in the structure and function of proteins. The simulation was carried out using molecular dynamics techniques that allowed the simulation of the movement of the protein molecules over time. The simulation results were compared to experimental data and showed a good agreement with the actual protein structure. Furthermore, the simulation provided insights into the dynamics of the protein folding process, such as the folding pathway and the stability of the intermediate states. These insights can be used to design new drugs and therapies that target specific protein structures and functions. The study concludes that computer simulations are a valuable tool in biotechnology research and have the potential to revolutionize the field by providing accurate and detailed information about complex biological systems. Future research could investigate the use of advanced computer simulations and machine learning algorithms in biotechnology applications to improve their accuracy and efficiency.

Structure, Substrate Specificity and Role of Lon Protease in Bacterial Pathogenesis and Survival

Proteases are the group of enzymes that carry out proteolysis in all forms of life and play an essential role in cell survival. By acting on specific functional proteins, proteases affect the transcriptional and post-translational pathways in a cell. Lon, FtsH, HslVU and the Clp family are among the ATP-dependent proteases responsible for intracellular proteolysis in bacteria. In bacteria, Lon protease acts as a global regulator, governs an array of important functions such as DNA replication and repair, virulence factors, stress response and biofilm formation, among others. Moreover, Lon is involved in the regulation of bacterial metabolism and toxin-antitoxin systems. Hence, understanding the contribution and mechanisms of Lon as a global regulator in bacterial pathogenesis is crucial. In this review, we discuss the structure and substrate specificity of the bacterial Lon protease, as well as its ability to regulate bacterial pathogenesis.

De novo design of β-barrel nanopore with Gly-kink towards single-molecule detection.

Nanopore sensing is a rapid and label-free method for single-molecule detection of DNA, peptides, and protein. However, it remains challenging to adjust the size and geometry of nanopores for each target molecule using biological nanopores. Therefore, constructing size and geometry controllable nanopore is highly demanded. Recently, de novo design has enabled the creation of specific structures and functions of proteins. We have previously designed a de novo β-hairpin peptide named SV28, which is assembled to form a multidisperse-sized β-barrel nanopore in a bilayer lipid membrane (BLM). A monodisperse-size nanopore is required for the highly sensitive detection of a specific target. Toward constructing a monodisperse-sized nanopore, we focused on Gly-kink. In the computational protein design, introducing the Gly-kink in a β-barrel structure makes the packing of the β-strands relaxed and the β-barrel structure to be more rigid. Then, we redesigned SVG28 with the introduction of Gly-kink into SV28. To evaluate the pore-forming ability of SVG28, we conducted channel current measurement with BLM in microdevices and signal classification analysis. As result, the SVG28 nanopore converged relatively monodisperse size (SVG28: φ = 1.7 nm, SV28: φ = 1.7-6.3 nm). Moreover, we carried out molecular dynamics simulations of peptide nanopores, indicating the stabilization of the β-barrel structure by introducing the Gly-kink. For future nanopore amino acid sequencing, we applied SVG28 nanopore to polypeptide detection. The SVG28 nanopore could detect and discriminate molecular weight difference of poly-l-lysine (PLL: φ = 1.1-1.4 nm). Furthermore, the SVG28 nanopore could identify the single amino acid in the oligo-arginine with several different types of single amino acids (R7X: φ = 1.0-1.5 nm). The above achievements are due to size and geometry matching between the SVG28 nanopore and the targets. Now, we are redesigning SVG28 to construct nanopores that have specific large pore sizes for protein detection.

Current Trends and Changes in Use of Membrane Molecular Dynamics Simulations within Academia and the Pharmaceutical Industry

There has been an almost exponential increase in the use of molecular dynamics simulations in basic research and industry over the last 5 years, with almost a doubling in the number of publications each year. Many of these are focused on neurological membranes, and biological membranes in general, applied to the medical industry. A smaller portion have utilized membrane simulations to answer more basic questions related to the function of specific proteins, chemicals or biological processes. This review covers some newer studies, alongside studies from the last two decades, to determine changes in the field. Some of these are basic, while others are more profound, such as multi-component embedded membrane machinery. It is clear that many facets of the discipline remain the same, while the focus on and uses of the technology are broadening in scope and utilization as a general research tool. Analysis of recent literature provides an overview of the current methodologies, covers some of the recent trends or advances and tries to make predictions of the overall path membrane molecular dynamics will follow in the coming years. In general, the overview presented is geared towards the general scientific community, who may wish to introduce the use of these methodologies in light of these changes, making molecular dynamic simulations more feasible for general scientific or medical research.