Anatomy & Physiology
Clustering-based Method for Constructing the Phase Diagram of the van der Waals Model Fluid
Membraneless organelles such as nucleoli stress granules and P-bodies are not enclosed by lipid membranes; rather they are formed through a process known as liquid-liquid phase separation. To fully understand the biophysics behind the formation and regulation of these organelles knowledge that has significant implications for cellular biology and disease research the creation of phase diagrams is essential. Phase diagrams help clarify the physical and chemical conditions under which these organelles form exist and function within cells. However methods for creating phase diagrams are often limited when the equation of state is unknown a challenge that becomes more pronounced with increasing system complexity. While several methods exist to address this issue their application is not universal.
We present a new method based on the SPACEBALL algorithm and cluster size monitoring which enables the determination of binodal and spinodal line positions by analyzing system clustering during molecular dynamics simulations of a well-studied van der Waals fluid under various conditions.
Based on an analysis of the system’s clustering behavior we constructed the phase diagram for the monoatomic van der Waals fluid simulated at various densities and temperatures observing that uniformly distributed van der Waals beads aggregate causing changes in the system’s density.
Using the generated data we discuss how a fitting function can be used to determine the binodal line location and how observations of the system’s density fluctuations can be used to determine the spinodal line location and assess the critical temperature.
We have presented alternative methods for locating phase boundaries in protein solutions where the absence of a validated equation of state necessitates innovative approaches and makes traditional methods challenging to apply. Our SPACEBALL-based approach enables the creation of phase diagrams using pure trajectories obtained from molecular dynamics simulations.
Coupling of SARS-CoV-2 to Amyloid Fibrils and Liquid-Liquid Phase Separation
COVID-19 is a respiratory disease caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) but because the receptor protein of this virus can appear not only in the lungs and throat but also in various parts of the host's body it causes different diseases. Recent observations have suggested that SARS-CoV-2 damages the central nervous system of patients in a manner similar to amyloid-associated neurodegenerative diseases such as Alzheimer's and Parkinson's. Neurodegenerative diseases are believed to be associated with the self-assembly of amyloid proteins and peptides. On the other hand whole proteins or parts of them encoded by SARS-CoV-2 can form amyloid fibrils which may play an important role in amyloid-related diseases. Motivated by this evidence this mini-review discusses experimental and computational studies of SARS-CoV-2 proteins that can form amyloid aggregates. Liquid-Liquid Phase Separation (LLPS) is a dynamic and reversible process leading to the creation of membrane-less organelles within the cytoplasm which is not bound by a membrane that concentrates specific types of biomolecules. These organelles play pivotal roles in cellular signaling stress response and the regulation of biomolecular condensates. Recently LLPS of the Nucleocapsid (N) protein and SARS-CoV-2 RNA has been disclosed but many questions about the phase separation mechanism and the formation of the virion core are still unclear. We summarize the results of this phenomenon and suggest potentially intriguing issues for future research.
Protein Misfolding and Aggregation of Pathological IgG Light Chains in Oncohematological Dyscrasias: From Molecular Pathways to Clinical Implications
Neoplastic transformation of B cells of the post-germinative center can lead to oncohematological dyscrasias which often results in an abnormal production of monoclonal immunoglobulin light chains. The non-physiological production of large amounts of IgG light chains leads to the formation of extracellular deposits called 'aggregomas' and rare conditions such as light chain crystal deposition disease. Kidney manifestations and heavy-chain deposition disease can also occur in plasma cell dyscrasias emphasizing the role of IgG misfolding and aggregation. This minireview describes molecular mechanisms of IgG light-chain aggregation as well as the consequences and therapeutic implications of IgG light chain misfolding in these disorders. By elucidating the mechanisms of IgG light chain misfolding and aggregation researchers can identify specific molecular and cellular pathways. This knowledge opens the door to novel therapeutic targets offering the potential for interventions that can either prevent the initial misfolding events promote the proper folding and processing of immunoglobulins or enhance the clearance of misfolded proteins and aggregates. These protein folding-related issues persist even after the successful elimination of the malignant B cells. Such targeted protein-folding therapies could significantly improve patients' quality of life and contribute to their recovery. Thus a deep understanding of IgG light chain misfolding and its consequences not only sheds light on the complex biology of oncohematological dyscrasias but also opens the way for innovative treatment strategies that could transform patient care in these conditions instilling hope and motivation in the healthcare professionals and researchers in this field.
Utilizing AfDesign for Developing a Small Molecule Inhibitor of PICK1-PDZ
The PICK1 PDZ domain has been identified as a potential drug target for neurological disorders. After many years of effort a few inhibitors such as TAT-C5 and mPD5 have been discovered experimentally to bind to the PDZ domain with a relatively high binding affinity. With the rapid growth of computational research there is an urgent need for more efficient computational methods to design viable ligands that target proteins.
Recently a newly developed program called AfDesign (part of ColabDesign) at https://github.com/sokrypton/ColabDesign) an open-source software built on AlphaFold has been suggested to be capable of generating ligands that bind to targeted proteins thus potentially facilitating the ligand development process. To evaluate the performance of this program we explored its ability to target the PICK1 PDZ domain given our current understanding of it. We found that the designated length of the ligand and the number of recycles play vital roles in generating ligands with optimal properties.
Utilizing AfDesign with a sequence length of 5 for the ligand produced the highest comparable ligands to that of prior identified ligands. Moreover these designed ligands displayed significantly lower binding energy compared to manually created sequences.
This work demonstrated that AfDesign can potentially be a powerful tool to facilitate the exploration of the ligand space for the purpose of targeting PDZ domains.
Recent Advances in Co-Condensation and Co-Aggregation of Amyloid Proteins Linked to Neurodegenerative Diseases
The misfolding and aggregation of amyloid proteins are closely associated with a range of neurodegenerative diseases. Liquid-liquid phase separation (LLPS) can initiate the aggregation of proteins indicating that LLPS may serve as an alternative pathway for the pathological aggregation of amyloid proteins. The co-occurrence of two or more amyloid pathologies has been observed in extensive pathophysiological studies and is linked to faster disease progression. The co-LLPS (also known as co-condensation) and co-aggregation of different disease-related proteins have been proposed as a potential molecular mechanism for combined neuropathology. Here we reviewed the current state of knowledge regarding the co-aggregation and co-condensation of various amyloid proteins including Aβ tau α-synuclein TDP-43 FUS and hnRNPA/B protein family C9orf72 dipeptide repeats and prion protein. We briefly introduced the epidemiological correlation among different neurodegenerative diseases and specifically presented recent experimental findings about co-aggregation and co-condensation of two different amyloid proteins. Additionally we discussed computational studies focusing on the molecular interactions between amyloid proteins to offer mechanistic insights into the co-LLPS and co-aggregation processes. This review provides an overview of the synergistic interactions between different disease-related proteins which is helpful for understanding the mechanisms of combined neuropathology and developing targeted therapeutic strategies.
Liquid-Liquid Phase Separation Associated with Intrinsically Disordered Proteins: Experimental and Computational Tools
The phenomenon of Liquid-Liquid Phase Separation (LLPS) serves as a vital mechanism for the spatial organization of biomolecules significantly influencing the elementary processes within the cellular milieu. Intrinsically disordered proteins or proteins endowed with intrinsically disordered regions are pivotal in driving this biophysical process thereby dictating the formation of non-membranous cellular compartments. Compelling evidence has linked aberrations in LLPS to the pathogenesis of various neurodegenerative diseases underscored by the disordered proteins’ proclivity to form pathological aggregates. This study meticulously evaluates the arsenal of contemporary experimental and computational methodologies dedicated to the examination of intrinsically disordered proteins within the context of LLPS. Through a discerning discourse on the capabilities and constraints of these investigative techniques we unravel the intricate contributions of these ubiquitous proteins to LLPS and neurodegeneration. Moreover we project a future trajectory for the field contemplating on innovative research tools and their potential to elucidate the underlying mechanisms of LLPS with the ultimate goal of fostering new therapeutic avenues for combating neurodegenerative disorders.
Design and Characterization of Antibacterial Peptide Nanofibrils as Components of Composites for Biomaterial Applications
The objective of this study was to design and synthesize the ug46 peptide incorporate its fibrils into composite materials and evaluate its structural and antimicrobial properties. Another objective was to utilize spectroscopy and molecular simulation enhanced by Machine Vision methods to monitor the aggregation process of the ug46 peptide and assess its potential as a scaffold for an antimicrobial peptide.
The structural analysis of the ug46 peptide reveals its dynamic conformational changes. Initially the peptide exhibits a disordered structure with minimal α-helix content but as incubation progresses it aggregates into fibrils rich in β-sheets. This transformation was validated by CD and ThT assays which showed decreased molar ellipticity and an increase in ThT fluorescence.
Laser-induced fluorescence and molecular dynamics simulations further revealed the transition from a compact native state to extended “worm-like” filament structures influenced by peptide concentration and temperature. TEM and AFM confirmed these changes showing the evolution of protofibrils into mature fibrils with characteristic twists. When incorporated into chitosan-bioglass composites these fibrils significantly enhanced antimicrobial activity against pathogens such as Staphylococcus aureus and Pseudomonas aeruginosa.
Overall ug46 peptide fibrils show promise as a multifunctional scaffold with structural and antimicrobial benefits in composite biomaterials.
Herbs and their Active Constituents for Gastric Cancer and Related Problems - Preclinical and Clinical Studies
Gastric cancer remains one of the leading cancer-related deaths worldwide. Despite the research advances many challenges persist because the diseases are usually diagnosed at an advanced stage and have a complex treatment protocol. Conventional treatments such as chemotherapy radiation and surgery pose several side effects and low efficiency. The growing worldwide interest in herbal products particularly their bioactive ingredients presents a promising prospect for auxiliary or alternative therapies for gastric cancer. In vivo experiments show that the given compounds increase the effectiveness and decrease the cumulative harmful impact of conventional anticancer treatments which may have additive effects. Furthermore clinical trials have revealed that phytoconstituents have possible anti-gastric cancer properties in humans. Nonetheless these encouraging preclinical observations have not progressed into clinical practice all that much due to the absence of adequately powered Phase III trials for GC. Therefore this review stresses the need for well-controlled human interventions to confirm the effectiveness and safety of herb-based therapies. In the long run the incorporation of these herbal products could present a new approach to constructing the gastric cancer prevention and treatment outlook while minimizing the side effects of conventional treatments and opening up arenas of functional foods and pharmaceuticals.
From Bugs to Benefits: Edible Insects as Exceptional Protein Sources
Eating insects may be healthier and more sustainable than eating animals. Various insect protein hydrolysates are assessed for therapeutic potential in this review.
A wide range of literature pertaining to nutrition compositions and the biological activity of edible insects has been compiled and meticulously examined through the utilization of various scholarly databases including PubMed and ScienceDirect.
Different insect protein hydrolysates had anti-inflammatory anti-cancer and antioxidant characteristics in addition to controlling blood sugar and cholesterol. These findings suggest that insect-derived bioactive peptides have health benefits and therapeutic uses.
Edible insects may replace traditional foods due to their nutritional and environmental benefits. The biological activity of their protein hydrolysates suggests they could be beneficial food additives or medicines.
What Can Proteomics Tell us About COVID-19 Infections? Mass Spectrometry as a Tool to Find New Proteins as Biomarkers
The COVID-19 outbreak caused by the SARS-CoV-2 coronavirus has threatened and taken many lives since the end of 2019. Given the importance of COVID-19 worldwide since its spread many research groups have been seeking blood markers that could help to understand the disease establishment and prognosis. Usually those markers are proteins with a differential accumulation only during infection. Based on that proteomic studies have played a crucial role in elucidating diseases. Mass spectrometry (MS) is a promising technique in COVID-19 studies allowing the identification and quantification of proteins present in the plasma or serum of affected patients. It helps us to understand pathological mechanisms predict clinical outcomes and develop specific therapies. MS proteomics revealed biomarkers associated with infection disease severity and immune response. Plasma or blood serum is easy to collect and store; however its composition and the higher concentration of proteins (e.g. albumins) shadow the identification of less abundant proteins which usually are essential markers. So clean-up approaches such as depletion strategies and fractionating are often required to analyze blood samples allowing the identification of low-abundant proteins. This review will discuss many proteomic approaches to discovering new plasma biomarkers of COVID-19 employed in recently published studies. The challenges inherent to blood samples will also be discussed such as sample preparation data processing and identifying reliable biomarkers.
A2 Milk: The Impact of Genetic Variation in Milk Protein on Human Health
Recently a new type of cow’s milk has been commercialized in the markets called A2 milk. It is derived from a specific allelic composition on chromosome 6. The only difference between A1 and A2 milk results from the polymorphism at the 67 amino acid chain. In this position A2 milk has a proline amino acid while A1 milk has a histidine amino acid. Proteins are one of the most important components of milk especially casein and have received significant attention as they are the source of bioactive opioid peptides called beta-casomorphin-7. Peptides are released through enzymatic digestion of casein and whey proteins. More precisely this bioactive peptide is produced by sequential gastrointestinal digestion of bovine A1 variants proteins while this phenomenon is not present in variant A2. Studies have reported that A1 milk can be harmful to health not only for adults but also for infants and that β-casein A2 becomes a safer choice following the relationship between disease risk and consumption of the beta-casomorphin-7 peptide. Indeed epidemiological studies suggest that the released beta-casomorphin-7 peptide is a risk factor for the development of diseases in humans but this has not yet been validated by other studies. In contrast A2 milk has been suggested as an appropriate substitute for A1 milk since populations consuming milk containing high levels of the A2 beta-casein variant have lower rates of diseases such as diabetes coronary heart disease autism and schizophrenia.
Unveiling the Role of DPYS: A New Prognostic Biomarker in Sarcoma
Dihydropyrimidinase (DPYS) a pivotal enzyme in the pyrimidine synthesis pathway has been increasingly studied for its potential role in cancer therapy. While its presence has been noted in various cancers its specific impact on sarcoma (SARC) still needs to be fully understood.
This study sought to explore the correlation between DPYS expression and SARC utilizing data from The Cancer Genome Atlas (TCGA) bioinformatics tools and experimental validation.
The study employed statistical analysis and logistic regression to assess the link between DPYS expression levels and clinical features in SARC patients. Survival analysis was conducted using the Kaplan-Meier method and Cox regression evaluating the prognostic significance of DPYS expression. Gene set enrichment analysis and immuno-infiltration analysis were conducted to uncover the potential regulatory mechanisms of the DPYS gene. We validated the expression of DPYS using GSE17674. Quantitative reverse transcription PCR was utilized to measure DPYS expression levels in SARC cell lines.
The study found that reduced DPYS expression in SARC correlated with therapeutic response (P = 0.011) histological subtype (P = 0.003) and the presence of residual tumor (P = 0.043). Reduced DPYS expression was a predictor of inferior Overall Survival (OS) with a Hazard Ratio (HR) of 0.56 and a 95% Confidence Interval (CI) of 0.37-0.84 (P = 0.005) as well as Disease-Specific Survival (DSS) with an HR of 0.64 and a 95% CI of 0.41-1.00 (P = 0.048). DPYS expression was also identified as an independent factor for OS in SARC (HR: 0.335; 95% CI: 0.169-0.664; P = 0.002). The gene was associated with various pathways including GPCR ligand binding signaling by interleukins G alpha (i) signaling events Class A/1 Rhodopsin-like receptors cytokine-cytokine receptor interaction and platelet activation. DPYS expression also showed a correlation with certain immune cell infiltrates and was found to be significantly downregulated in SARC cell lines.
DPYS may serve as a potential prognostic biomarker and therapeutic target for SARC.
Potential of Circular RNAs (circRNAs) Neoantigen Vaccines in Tumor Immunotherapy
Circular RNAs (circRNAs) have emerged as promising candidates for neoantigen vaccine development due to their unique structural stability enhanced translational efficiency and immunostimulatory properties. Unlike linear RNAs circRNAs exhibit exonuclease resistance prolonged antigen expression and increased activation of innate immune receptors such as RIG-I and MDA5 thereby enhancing anti-tumor immune responses. Preclinical studies have demonstrated that circRNA-based vaccines encoding tumor-specific neoantigens effectively stimulate Antigen-Presenting Cells (APCs) particularly Dendritic Cells (DCs) leading to robust CD8+ Cytotoxic T Lymphocyte (CTL) activation. This results in increased cytokine production T-cell proliferation and durable anti-tumor immunity. Compared to conventional neoantigen vaccine platforms circRNA vaccines offer distinct advantages including higher immunogenicity improved cytosolic delivery and minimal risk of genomic integration. CircRNA vaccines have demonstrated efficacy in preclinical tumor models with studies highlighting their ability to induce long-term memory T-cell responses and enhance the efficacy of immune checkpoint blockade therapies. However challenges remain in optimizing circRNA delivery mitigating unintended immune activation and scaling up manufacturing processes. The translational potential of circRNA vaccines in tumor immunotherapy is significant offering a novel and scalable approach to personalized cancer treatment. Further research and clinical validation are needed to optimize their design improve manufacturing efficiency and assess their efficacy in human trials. CircRNA vaccines represent a next-generation platform with the potential to revolutionize cancer immunotherapy by harnessing durable and targeted anti-tumor immune responses.
Phylogenetic Analysis of SOD Gene Isolated from Indian Variety of Mud Crabs: Scylla serrata and Scylla olivacea
Our research aimed to isolate and sequence the SOD gene from the genomic DNA of Scylla serrata and Scylla olivacea and to study its phylogeny.
In crustaceans superoxide dismutase (SOD) serves as the first line of defense against stress. Extracellular Cu/Zn-SOD has been demonstrated in several investigations involving crustaceans. Crustaceans do not have a distinct immune system. They entirely depend on the innate immune system triggered when they come in contact with any pathogen.
Partial SOD gene was isolated from the genomic DNA of S. serrata and S. olivacea through polymerase chain reaction.
We successfully isolated partial SOD genes of 942bp and 957bp from S. serrata and S. olivacea respectively. The sequences were submitted to the NCBI GenBank database.
The phylogenetic study suggests their clustering with the genus Scylla species. Investigating the SOD gene sequences across diverse crustacean lineages can reveal profound insights into their evolutionary history and the intricate relationships among species concerning their SOD development.
This research holds the potential to enhance our understanding of the evolutionary adaptations that have shaped these organisms.