Lipid-protein Complexes Research Articles

Insights into Medication-Induced Osteonecrosis of the Jaw Through the Application of Salivary Proteomics and Bioinformatics.

Long-term treatment with bisphosphonates is accompanied by an increased risk of medication-related osteonecrosis of the jaw (MRONJ). Currently, no clinically useful biomarkers for the predictive diagnosis of MRONJ are available. To investigate the potential key proteins involved in the pathogenesis of MRONJ, a proteomic LC-MS/MS analysis of saliva was performed. Differentially expressed proteins (DEPs) were analyzed using BiNGO, ClueGO, cytoHubba, MCODE, KEGG, and ReactomeFI software packages using Cytoscape platforms. In total, 1545 DEPs were identified, including 43 up- and 11 down-regulated with a 1.5-fold cut-off value and adj. p-value < 0.05. The analysis provided a panel of hub genes, including APOA2, APOB, APOC2, APOC3, APOE, APOM, C4B, C4BPA, C9, FGG, GC, HP, HRG, LPA, SAA2-SAA4, and SERPIND1. The most prevalent terms in GO of the biological process were macromolecular complex remodeling, protein-lipid complex remodeling, and plasma lipoprotein particle remodeling. DEPs were mainly involved in signaling pathways associated with lipoproteins, the innate immune system, complement, and coagulation cascades. The current investigation advanced our knowledge of the molecular mechanisms underlying MRONJ. In particular, the research identified the principal salivary proteins that are implicated in the onset and progression of this condition.

Nonfunctional coq10 mutants maintain the ERMES complex and reveal true phenotypes associated with the loss of the coenzyme Q chaperone protein Coq10

Coenzyme Q (CoQ) is a redox-active lipid molecule that acts as an electron carrier in the mitochondrial electron transport chain. In Saccharomyces cerevisiae, CoQ is synthesized in the mitochondrial matrix by a multisubunit protein-lipid complex termed the CoQ synthome, the spatial positioning of which is coordinated by the endoplasmic reticulum-mitochondria encounter structure (ERMES). The MDM12 gene encoding the cytosolic subunit of ERMES is coexpressed with COQ10, which encodes the putative CoQ chaperone Coq10, via a shared bidirectional promoter. Deletion of COQ10 results in respiratory deficiency, impaired CoQ biosynthesis, and reduced spatial coordination between ERMES and the CoQ synthome. While Coq10 protein content is maintained upon deletion of MDM12, we show that deletion of COQ10 by replacement with a HIS3 marker results in diminished Mdm12 protein content. Since deletion of individual ERMES subunits prevents ERMES formation, we asked whether some or all of the phenotypes associated with COQ10 deletion result from ERMES dysfunction. To identify the phenotypes resulting solely due to the loss of Coq10, we constructed strains expressing a functionally impaired (coq10-L96S) or truncated (coq10-R147∗) Coq10 isoform using CRISPR-Cas9. We show that both coq10 mutants preserve Mdm12 protein content and exhibit impaired respiratory capacity like the coq10Δ mutant, indicating that Coq10's function is vital for respiration regardless of ERMES integrity. Moreover, the maintenance of CoQ synthome stability and efficient CoQ biosynthesis observed for the coq10-R147∗ mutant suggests these deleterious phenotypes in the coq10Δ mutant result from ERMES disruption. Overall, this study clarifies the role of Coq10 in modulating CoQ biosynthesis.

A methodology for gene level omics-WAS integration identifies genes influencing traits associated with cardiovascular risks: the Long Life Family Study.

The Long Life Family Study (LLFS) enrolled 4953 participants in 539 pedigrees displaying exceptional longevity. To identify genetic mechanisms that affect cardiovascular risks in the LLFS population, we developed a multi-omics integration pipeline and applied it to 11 traits associated with cardiovascular risks. Using our pipeline, we aggregated gene-level statistics from rare-variant analysis, GWAS, and gene expression-trait association by Correlated Meta-Analysis (CMA). Across all traits, CMA identified 64 significant genes after Bonferroni correction (p ≤ 2.8 × 10-7), 29 of which replicated in the Framingham Heart Study (FHS) cohort. Notably, 20 of the 29 replicated genes do not have a previously known trait-associated variant in the GWAS Catalog within 50kb. Thirteen modules in Protein-Protein Interaction (PPI) networks are significantly enriched in genes with low meta-analysis p-values for at least one trait, three of which are replicated in the FHS cohort. The functional annotation of genes in these modules showed a significant over-representation of trait-related biological processes including sterol transport, protein-lipid complex remodeling, and immune response regulation. Among major findings, our results suggest a role of triglyceride-associated and mast-cell functional genes FCER1A, MS4A2, GATA2, HDC, and HRH4 in atherosclerosis risks. Our findings also suggest that lower expression of ATG2A, a gene we found to be associated with BMI, may be both a cause and consequence of obesity. Finally, our results suggest that ENPP3 may play an intermediary role in triglyceride-induced inflammation. Our pipeline is freely available and implemented in the Nextflow workflow language, making it easily runnable on any compute platform ( https://nf-co.re/omicsgenetraitassociation ).

Dynamic formation of the protein-lipid prefusion complex

Synaptic vesicles (SVs) fuse with the presynaptic membrane (PM) to release neuronal transmitters. The SV protein synaptotagmin 1 (Syt1) serves as a Ca2+ sensor for evoked fusion. Syt1 is thought to trigger fusion by penetrating the PM upon Ca2+ binding; however, the mechanistic detail of this process is still debated. Syt1 interacts with the SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptors) complex, a coiled-coil four-helical bundle that enables the SV-PM attachment. The SNARE-associated protein complexin (Cpx) promotes Ca2+-dependent fusion, possibly interacting with Syt1. We employed all-atom molecular dynamics to investigate the formation of the Syt1-SNARE-Cpx complex interacting with the lipid bilayers of the PM and SVs. Our simulations demonstrated that the PM-Syt1-SNARE-Cpx complex can transition to a “dead-end” state, wherein Syt1 attaches tightly to the PM but does not immerse into it, as opposed to a prefusion state, which has the tips of the Ca2+-bound C2 domains of Syt1 inserted into the PM. Our simulations unraveled the sequence of Syt1 conformational transitions, including the simultaneous docking of Syt1 to the SNARE-Cpx bundle and the PM, followed by Ca2+ chelation and the penetration of the tips of Syt1 domains into the PM, leading to the prefusion state of the protein-lipid complex. Importantly, we found that direct Syt1-Cpx interactions are required to promote these transitions. Thus, we developed the all-atom dynamic model of the conformational transitions that lead to the formation of the prefusion PM-Syt1-SNARE-Cpx complex. Our simulations also revealed an alternative dead-end state of the protein-lipid complex that can be formed if this pathway is disrupted.

Catalase: A Potential Pharmacologic Target for Hydrogen Peroxide in the Treatment of COVID-19.

Acute respiratory distress syndrome in the elderly with COVID-19 complicated by airway obstruction with sputum and mucus, and cases of asphyxia with blood, serous fluid, pus, or meconium in newborns and people of different ages can sometimes cause hypoxemia and death from hypoxic damage to brain cells, because the medical standard does not include intrapulmonary injections of oxygen-producing solutions. The physical-chemical repurposing of hydrogen peroxide from an antiseptic to an oxygen-producing antihypoxant offers hope for the development of new drugs. This manuscript is a meta-analysis performed according to PRISMA guidelines. It is shown that replacement of the traditional acidic activity of hydrogen peroxide solutions by alkaline activity with pH 8.4 and heating the solutions to the temperature of +37 - +42 °C allows to repurpose hydrogen peroxide from antiseptics into inhalation and intrapulmonary mucolytics, pyolytics and antihypoxants releasing oxygen. The fact is that warm alkaline hydrogen peroxide solution (WAHPS) in local interaction with sputum, mucus, pus, blood and meconium provides optimal conditions for the metabolism of hydrogen peroxide to oxygen gas under the action of the enzyme catalase, always present in these tissues. It was established that WAHPS liquefies these biological masses due to alkaline saponification of lipid and protein-lipid complexes and simultaneously transforms dense masses into soft oxygen foam due to active enzymatic metabolism of hydrogen peroxide to oxygen gas, the rapidly appearing bubbles of which are formed by the type of "cold boiling" and literally explode these masses. The results of the first experiments showed that inhalation and intrapulmonary injections of WAHPS can significantly optimize the treatment of suffocation and hypoxemia. The results showed that catalase, which is found in sputum, mucus, pus, and blood, may be a target for localized WAHPS because this enzyme provides an intensive metabolism of hydrogen peroxide to oxygen gas up to the formation of the cold boiling process. These data provide a new perspective way for intrapulmonary drugs and new technologies for the emergency increase of blood oxygenation through the lungs in asphyxia with thick sputum, mucus, pus, meconium and blood.

HAMLET, a human milk protein-lipid complex, modulates amoxicillin induced changes in an ex vivo biofilm model of the oral microbiome.

Challenges from infections caused by biofilms and antimicrobial resistance highlight the need for novel antimicrobials that work in conjunction with antibiotics and minimize resistance risk. In this study we investigated the composite effect of HAMLET (human alpha-lactalbumin made lethal to tumor cells), a human milk protein-lipid complex and amoxicillin on microbial ecology using an ex vivo oral biofilm model with pooled saliva samples. HAMLET was chosen due to its multi-targeted antimicrobial mechanism, together with its synergistic effect with antibiotics on single species pathogens, and low risk of resistance development. The combination of HAMLET and low concentrations of amoxicillin significantly reduced biofilm viability, while each of them alone had little or no impact. Using a whole metagenomics approach, we found that the combination promoted a remarkable shift in overall microbial composition compared to the untreated samples. A large proportion of the bacterial species in the combined treatment were Lactobacillus crispatus, a species with probiotic effects, whereas it was only detected in a minor fraction in untreated samples. Although resistome analysis indicated no major shifts in alpha-diversity, the results showed the presence of TEM beta-lactamase genes in low proportions in all treated samples but absence in untreated samples. Our study illustrates HAMLET's capability to alter the effects of amoxicillin on the oral microbiome and potentially favor the growth of selected probiotic bacteria when in combination. The findings extend previous knowledge on the combined effects of HAMLET and antibiotics against target pathogens to include potential modulatory effects on polymicrobial biofilms of human origin.

Identification of biomarkers and molecular mechanisms implicated in genetic variations underlying Alzheimer's disease pathogenesis

We analyzed data from human genome-wide association studies (GWASs) to identify genetic variants and biological pathways linked to Alzheimer's disease (AD). Ten AD biomarkers (APOE, NECTIN2, APOC1, APOC1P1, TOMM40, RNU4-67P, KRAS, Y_RNA, THORLNC, LINC01956) were found across studies, including six central genetic variants (MAPT (rs242557-A), GRIN2B (rs74442473-G), APOE (rs438811-T), ANK3 (rs438811-T), BIN1 (rs744373-G), and BDNF (rs7481773-A)). ANK3 (rs438811-T) and GRIN2B (rs74442473-G) were essential hub biomarkers for amyloid plaques, while MAPT (rs242557-A) and BIN1 (rs744373-G) were crucial for neurofibrillary tangles (NFTs). Higher-risk AD biomarkers were associated with increased protein-lipid complex formation, while lower-risk AD biomarkers were correlated with improved synaptic function. Six essential miRNAs (hsa-miR-124–3p, 15a-5p, 16–5p, 204–5p, 520g-3p, 520h) and three transcription factors (ZMAT4, ZBED6, FOXG1) emerged as possible candidates to reveal the genetic differences that lead to amyloid plaques, NFTs, and ultimately AD. These findings serve as a basis for potential AD treatments and offer new avenues for therapeutic approaches to directly target the genetic variations and processes associated with the disease.

The joint action of yeast eisosomes and membraneless organelles in response to ethanol stress

Elevated ethanol concentrations in yeast affect the plasma membrane. The plasma membrane in yeast has many lipid-protein complexes, such as Pma1 (MCP), Can1 (MCC), and the eisosome complex. We investigated the response of eisosomes, MCPs, and membraneless structures to ethanol stress. We found a correlation between ethanol stress and proton flux with quick acidification of the medium. Moreover, ethanol stress influences the symporter expression in stressed cells. We also suggest that acute stress from ethanol leads to increases in eisosome size and SG number: we hypothesized that eisosomes may protect APC symporters and accumulate an mRNA decay protein in ethanol-stressed cells. Our findings suggest that the joint action of these factors may provide a protective effect on cells under ethanol stress.

Clinical case of pulmonary alveolar proteinosis in a newborn

Pulmonary alveolar proteinosis (PAP) is a rare disease characterized by the accumulation of protein-lipid complexes in the alveoli due to impaired utilization of surfactant by alveolar macrophages; it is most often idiopathic and occurs in healthy men and women aged 30–50 years. The congenital form of PAP is extremely rare, its diagnosis is complicated by the fact that it is impossible to conduct functional lung tests in newborns, and lung biopsy is used extremely rarely. Against this background, data obtained by computed tomography (CT) of the lungs of newborns are of particular importance. The article presents a clinical case of treatment of a newborn with respiratory failure (RF) and signs of pulmonary hypertension, who was admitted to the neonatal intensive care unit of the Children’s City Multidisciplinary Clinical Specialized Center for High Medical Technologies at the age of the first day of life. The article reflects the role of computed tomography in diagnosing the causes of respiratory failure in newborns, as well as the importance of anamnesis and a thorough clinical examination of patients. The presented clinical case demonstrates the need for a multidisciplinary approach to the diagnosis of newborns with pulmonary alveolar proteinosis.

Lipoprotein Particles in Cerebrospinal Fluid.

The brain is the most lipid-rich organ in the body, and the intricate interplay between lipid metabolism and pathologies associated with neurodegenerative disorders is being increasingly recognized. The brain is bathed in cerebrospinal fluid (CSF), which, like plasma, contains lipid-protein complexes called lipoproteins that are responsible for extracellular lipid transport. Multiple CSF lipoprotein populations exist, some of which are produced de novo in the central nervous system and others that appear to be generated from protein constituents that are produced in the periphery. These CSF lipoproteins are thought to play key roles in maintaining lipid homeostasis in the central nervous system, while little else is known due to their limited accessibility and their low abundance in CSF. Recent work has provided new insights into the compositional complexity of CSF lipoprotein families and their metabolism in cerebral circulation. The purpose of this review is to summarize our current state of knowledge on the composition, origin, and metabolism of CSF lipoproteins.

Evaluation of Plasma Biomarkers for Causal Association With Peripheral Artery Disease.

Hundreds of biomarkers for peripheral artery disease (PAD) have been reported in the literature; however, the observational nature of these studies limits causal inference due to the potential of reverse causality and residual confounding. We sought to evaluate the potential causal impact of putative PAD biomarkers identified in human observational studies through genetic causal inference methods. Putative circulating PAD biomarkers were identified from human observational studies through a comprehensive literature search based on terms related to PAD using PubMed, Cochrane, and Embase. Genetic instruments were generated from publicly available genome-wide association studies of circulating biomarkers. Two-sample Mendelian randomization was used to test the association of genetically determined biomarker levels with PAD using summary statistics from a genome-wide association study of 31 307 individuals with and 211 753 individuals without PAD in the Veterans Affairs Million Veteran Program and replicated in data from FinnGen comprised of 11 924 individuals with and 288 638 individuals without PAD. We identified 204 unique circulating biomarkers for PAD from the observational literature, of which 173 were genetically instrumented using genome-wide association study results. After accounting for multiple testing (false discovery rate, <0.05), 10 of 173 (5.8%) biomarkers had significant associations with PAD. These 10 biomarkers represented categories including plasma lipoprotein regulation, lipid homeostasis, and protein-lipid complex remodeling. Observational literature highlighted different pathways including inflammatory response, negative regulation of multicellular organismal processes, and regulation of response to external stimuli. Integrating human observational studies and genetic causal inference highlights several key pathways in PAD pathophysiology. This work demonstrates that a substantial portion of biomarkers identified in observational studies are not well supported by human genetic evidence and emphasizes the importance of triangulating evidence to understand PAD pathophysiology. Although the identified biomarkers offer insights into atherosclerotic development in the lower limb, their specificity to PAD compared with more widespread atherosclerosis requires further study.

Direct determination of membrane protein lipid complexes from cellular membranes through native top-down MS

Direct determination of membrane protein lipid complexes from cellular membranes through native top-down MS

Evidence for alterations in lipid profiles and biophysical properties of lipid rafts from spinal cord in sporadic amyotrophic lateral sclerosis

Amyotrophic lateral sclerosis (ALS) is an age-dependent neurodegenerative disease affecting motor neurons in the spinal cord and brainstem whose etiopathogenesis remains unclear. Recent studies have linked major neurodegenerative diseases with altered function of multimolecular lipid-protein complexes named lipid rafts. In the present study, we have isolated lipid rafts from the anterior horn of the spinal cords of controls and ALS individuals and analysed their lipid composition. We found that ALS affects levels of different fatty acids, lipid classes and related ratios and indexes. The most significant changes affected the contents of n-9/n-7 monounsaturated fatty acids and arachidonic acid, the main n-6 long-chain polyunsaturated fatty acid (LCPUFA), which were higher in ALS lipid rafts. Paralleling these findings, ALS lipid rafts lower saturates-to-unsaturates ratio compared to controls. Further, levels of cholesteryl ester (SE) and anionic-to-zwitterionic phospholipids ratio were augmented in ALS lipid rafts, while sulfatide contents were reduced. Further, regression analyses revealed augmented SE esterification to (mono)unsaturated fatty acids in ALS, but to saturates in controls. Overall, these changes indicate that lipid rafts from ALS spinal cord undergo destabilization of the lipid structure, which might impact their biophysical properties, likely leading to more fluid membranes. Indeed, estimations of membrane microviscosity confirmed less viscous membranes in ALS, as well as more mobile yet smaller lipid rafts compared to surrounding membranes. Overall, these results demonstrate that the changes in ALS lipid rafts are unrelated to oxidative stress, but to anomalies in lipid metabolism and/or lipid raft membrane biogenesis in motor neurons.Key messagesThe lipid matrix of multimolecular membrane complexes named lipid rafts are altered in human spinal cord in sporadic amyotrophic lateral sclerosis (ALS).Lipid rafts from ALS spinal cord contain higher levels of n-6 LCPUFA (but not n-3 LCPUFA), n-7/n-9 monounsaturates and lower saturates-to-unsaturates ratio.ALS lipid rafts display increased contents of cholesteryl esters, anomalous anionic-to-zwitterionic phospholipids and phospholipid remodelling and reduced sulphated and total sphingolipid levels, compared to control lipid rafts.Destabilization of the lipid structure of lipid raft affects their biophysical properties and leads to more fluid, less viscous membrane microdomains.The changes in ALS lipid rafts are unlikely related to increased oxidative stress, but to anomalies in lipid metabolism and/or raft membrane biogenesis in motor neurons.

Liprotide-encapsulated vitamin D3 modulates circulated PTH levels and improved bone microstructure

Background: vitamin D (25(OH)D) is a fat-soluble vitamin that is unstable in the gastrointestinal environment and has low bioavailability. A protein-lipid complex (liprotide) can be used as a shell to increase vitamin D stability and bioavailability. Liprotide can also serve as a delivery system for transporting vitamin D to its intended site. Little attention has been paid to utilizing liprotide as a delivery system for vitamin D and evaluating its functional activity.Objective: to investigate the effect of liprotide-encapsulated vitamin D3 on PTH levels and bone microstructure in vitamin D and calcium (VD-Ca) deficient rats.Materials and Methods: an overall of 24 Wistar rats had been divided into four groups, a normal control group (K), a VD-Ca group without treatment (K-), a VD-Ca group with 180 IU/200 gBW/day free vitamin D3 (FVD3), and a VD-Ca group with 180 IU/200 gBW/day liprotide-encapsulated vitamin D3 (LVD3). Before and after 28 days of vitamin D intervention, blood samples were taken and analysed for serum PTH levels. The microstructure of the bone was analyzed using the Scanning Electron Microscope (SEM).Results: the VD-Ca rats supplemented with vitamin D3 (FVD3 and LVD3) had a significant decrease in serum PTH levels (p&lt;0.001) and improved bone microstructure (p&lt;0.05) compared to the (K-) group. The reduction of PTH in the LVD3 group was higher compared to the FVD3 group. The bone microstructure between the FVD3 and LVD3 groups is significantly different, as seen in the Ct.Wi parameter, with the LVD3 group having a higher Ct.Wi than the FVD3 group.Conclusion: liprotide-encapsulated vitamin D3 improves the serum PTH level and bone microstructure in a rat model of vitamin D and calcium deficiency.

Exploring protein-protein interactions and oligomerization state of pulmonary surfactant protein C (SP-C) through FRET and fluorescence self-quenching.

Pulmonary surfactant (PS) is a lipid-protein complex that forms films reducing surface tension at the alveolar air-liquid interface. Surfactant protein C (SP-C) plays a key role in rearranging the lipids at the PS surface layers during breathing. The N-terminal segment of SP-C, a lipopeptide of 35 amino acids, contains two palmitoylated cysteines, which affect the stability and structure of the molecule. The C-terminal region comprises a transmembrane α-helix that contains a ALLMG motif, supposedly analogous to a well-studied dimerization motif in glycophorin A. Previous studies have demonstrated the potential interaction between SP-C molecules using approaches such as Bimolecular Complementation assays or computational simulations. In this work, the oligomerization state of SP-C in membrane systems has been studied using fluorescence spectroscopy techniques. We have performed self-quenching and FRET assays to analyze dimerization of native palmitoylated SP-C and a non-palmitoylated recombinant version of SP-C (rSP-C) using fluorescently labeled versions of either protein reconstituted in different lipid systems mimicking pulmonary surfactant environments. Our results reveal that doubly palmitoylated native SP-C remains primarily monomeric. In contrast, non-palmitoylated recombinant SP-C exhibits dimerization, potentiated at high concentrations, especially in membranes with lipid phase separation. Therefore, palmitoylation could play a crucial role in stabilizing the monomeric α-helical conformation of SP-C. Depalmitoylation, high protein densities as a consequence of membrane compartmentalization, and other factors may all lead to the formation of protein dimers and higher-order oligomers, which could have functional implications under certain pathological conditions and contribute to membrane transformations associated with surfactant metabolism and alveolar homeostasis.

In vivo characterization of a podocyte-expressed short podocin isoform

The most common genetic causes of steroid-resistant nephrotic syndrome (SRNS) are mutations in the NPHS2 gene, which encodes the cholesterol-binding, lipid-raft associated protein podocin. Mass spectrometry and cDNA sequencing revealed the existence of a second shorter isoform in the human kidney in addition to the well-studied canonical full-length protein. Distinct subcellular localization of the shorter isoform that lacks part of the conserved PHB domain suggested a physiological role. Here, we analyzed whether this protein can substitute for the canonical full-length protein. The short isoform of podocin is not found in other organisms except humans. We therefore analysed a mouse line expressing the equivalent podocin isoform (podocinΔexon5) by CRISPR/Cas-mediated genome editing. We characterized the phenotype of these mice expressing podocinΔexon5 and used targeted mass spectrometry and qPCR to compare protein and mRNA levels of podocinwildtype and podocinΔexon5. After immunolabeling slit diaphragm components, STED microscopy was applied to visualize alterations of the podocytes’ foot process morphology.Mice homozygous for podocinΔexon5 were born heavily albuminuric and did not survive past the first 24 h after birth. Targeted mass spectrometry revealed massively decreased protein levels of podocinΔexon5, whereas mRNA abundance was not different from the canonical form of podocin. STED microscopy revealed the complete absence of podocin at the podocytes’ slit diaphragm and severe morphological alterations of podocyte foot processes. Mice heterozygous for podocinΔexon5 were phenotypically and morphologically unaffected despite decreased podocin and nephrin protein levels.The murine equivalent to the human short isoform of podocin cannot stabilize the lipid-protein complex at the podocyte slit diaphragm. Reduction of podocin levels at the site of the slit diaphragm complex has a detrimental effect on podocyte function and morphology. It is associated with decreased protein abundance of nephrin, the central component of the filtration-slit forming slit diaphragm protein complex.

Impact of lipid matrix composition on the activity of membranotropic enzymes galactonolactone oxidase from Trypanosoma cruzi and L-galactono-1,4-lactone dehydrogenase from &lt;i&gt;Arabidopsis thaliana&lt;/i&gt; in the system of reverse micelles

The study of many membrane enzymes in an aqueous medium is difficult due to the loss of their catalytic activity, which makes it necessary to use membrane-like systems, such as reverse micelles of surfactants in nonpolar organic solvents. However, it should be taken into account that micelles are a simplified model of natural membranes, since membranes contain many different components, a significant part of which are phospholipids. In this work, we studied the impact of the main phospholipids, phosphatidylcholine (PC) and phosphatidylethanolamine (PE), on the activity of membrane enzymes using galactonolactone oxidase from Trypanosoma cruzi (TcGAL) and L-galactono-1,4-lactone dehydrogenase from Arabidopsis thaliana (AtGALDH) as an examples. Effect of the structure (and charge) of the micelle-forming surfactant itself on the activity of both enzymes has been studied using an anionic surfactant (AOT), a neutral surfactant (Bridge-96), and a mixture of cationic and anionic surfactants (CTAB and AOT) as an examples. The pronounced effect of addition of PC and PE lipids on the activity of AtGALDH and TcGAL has been detected, which manifests as increase in catalytic activity and significant change in the activity profile. This can be explained by formation of the tetrameric form of enzymes and/or protein-lipid complexes. By varying composition and structure of the micelle-forming surfactants (AOT, CTAB, and Brijdge-96 and their combinations) it has been possible to change catalytic properties of the enzyme due to effect of the surfactant on the micelle size, lipid mobility, charge, and rigidity of the matrix itself.

AQP1 as a novel biomarker to predict prognosis and tumor immunity in glioma patients

Abstract Background Glioma is a kind of nervous system cancer with a low overall survival rate. Aquaporin 1 (AQP1) is linked to a number of cancers. Its prognostic relevance and immunological consequences in gliomas, however, are unclear. Objectives Our objective was to thoroughly examine the modified expression of AQP1, its prognostic significance, and its correlation with immune cells and markers to discover innovative molecular immunotherapy strategies for glioma patients. Methods RNA sequencing data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases were used. In addition, we used real-time reverse transcription polymerase chain reaction (RT-PCR) and Western Blot methods to monitor AQP1 expression in glioma tissues. Results AQP1 expression was greater in gliomas than in traumatized brain tissues. The increased AQP1 expression in gliomas was additionally confirmed through immunohistochemical analysis in the Human Protein Atlas (HPA) repository. An elevated level of AQP1 expression was identified as a separate determinant of the overall survival (OS) and prognosis of individuals with glioma. AQP1 expression was shown to be tightly linked to the tumor immune milieu, immune checkpoint blockade (ICB) and temozolomide drug reaction. In conclusion, the 50 genes that show coexpression with AQP1 indicate that the predominant functions and pathways are related to anterior pattern specification, pattern specification, regionalization, high-density lipoprotein particles, protein–lipid complexes, glycosaminoglycan binding, DNA-binding transcription repressor specific activation to RNA polymerase II, DNA-binding transcription repressor activity, nitrogen metabolism, alpha-linolenic acid metabolism, and fat digestion and absorption. Conclusions The results indicate that AQP1 could serve as both a predictive marker and a potential treatment target in glioma.

Impact of Lipid Matrix Composition on Activity of Membranotropic Enzymes Galactonolactone Oxidase from Trypanosoma cruzi and L-Galactono-1,4-Lactone Dehydrogenase from Arabidopsis thaliana in the System of Reverse Micelles.

The study of many membrane enzymes in an aqueous medium is difficult due to the loss of their catalytic activity, which makes it necessary to use membrane-like systems, such as reverse micelles of surfactants in nonpolar organic solvents. However, it should be taken into account that the micelles are a simplified model of natural membranes, since membranes contain many different components, a significant part of which are phospholipids. In this work, we studied impact of the main phospholipids, phosphatidylcholine (PC) and phosphatidylethanolamine (PE), on activity of the membrane enzymes using galactonolactone oxidase from Trypanosoma cruzi (TcGAL) and L-galactono-1,4-lactone dehydrogenase from Arabidopsis thaliana (AtGALDH) as examples. Effect of the structure (and charge) of the micelle-forming surfactant itself on the activity of both enzymes has been studied using an anionic surfactant (AOT), a neutral surfactant (Brij-96), and a mixture of cationic and anionic surfactants (CTAB and AOT) as examples. The pronounced effect of addition of PC and PE lipids on the activity of AtGALDH and TcGAL has been detected, which manifests as increase in catalytic activity and significant change in the activity profile. This can be explained by formation of the tetrameric form of enzymes and/or protein-lipid complexes. By varying composition and structure of the micelle-forming surfactants (AOT, CTAB, and Brij-96) it has been possible to change catalytic properties of the enzyme due to effect of the surfactant on the micelle size, lipid mobility, charge, and rigidity of the matrix itself.

Alchemical Free Energy Calculations on Membrane-Associated Proteins.

Membrane proteins have diverse functions within cells and are well-established drug targets. The advances in membrane protein structural biology have revealed drug and lipid binding sites on membrane proteins, while computational methods such as molecular simulations can resolve the thermodynamic basis of these interactions. Particularly, alchemical free energy calculations have shown promise in the calculation of reliable and reproducible binding free energies of protein-ligand and protein-lipid complexes in membrane-associated systems. In this review, we present an overview of representative alchemical free energy studies on G-protein-coupled receptors, ion channels, transporters as well as protein-lipid interactions, with emphasis on best practices and critical aspects of running these simulations. Additionally, we analyze challenges and successes when running alchemical free energy calculations on membrane-associated proteins. Finally, we highlight the value of alchemical free energy calculations calculations in drug discovery and their applicability in the pharmaceutical industry.