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The Journal of Physical Chemistry... Jul 2021The presence of metamorphism in the protein's native state is not yet fully understood. To shed light on this issue, we present an assessment, in terms of the amide...
The presence of metamorphism in the protein's native state is not yet fully understood. To shed light on this issue, we present an assessment, in terms of the amide hydrogen exchange protection factor, that aims to determine the possible existence of structural fluctuations in the native-state consistent with both the upper-bound marginal stability of proteins and the presence of metamorphism. The preliminary results enable us to conclude that the native-state metamorphism is, indeed, more probable than previously thought.
Topics: Amides; Protein Stability; Proteins
PubMed: 34192878
DOI: 10.1021/acs.jpclett.1c01831 -
Biochemical Pharmacology Mar 2022Phosphorylation of proteins is one of the most extensively investigated post-translational protein modifications. Threonine, serine and tyrosine in proteins are the most... (Review)
Review
Phosphorylation of proteins is one of the most extensively investigated post-translational protein modifications. Threonine, serine and tyrosine in proteins are the most commonly phosphorylated amino acids. Dysregulated cancer-related signaling pathways due to aberrant phosphorylation status of the key protein(s) in these pathways exist in most malignancies. Intensive studies in the recent decade have implicated long non-coding RNAs (lncRNAs) in the precise regulation of protein phosphorylation in cancers. In this review, we systematically delve into recent advance that underlines the multidimensional role of lncRNAs in modulating protein phosphorylation, regulating cancerous signaling and impacting prognosis of gastrointestinal (GI) cancers including hepatocellular carcinoma, colorectal cancer, gastric cancer, esophageal cancer, and pancreatic cancer. LncRNAs regulate protein phosphorylation via directly binding to the target protein(s), interacting with the partner protein(s) of the target protein(s) or lncRNAs-encoded small peptides. Although there are still extensive studies on disclosing the intricate interactions between lncRNAs and proteins and their impacts on protein phosphorylation, we believe that targeting lncRNAs controlling phosphorylation of key protein(s) in cancerous signaling pathways might provide novel paths for precision therapeutics of GI cancers in the future.
Topics: Animals; Antineoplastic Agents; Biomarkers, Tumor; Gastrointestinal Neoplasms; Humans; Phosphorylation; Protein Processing, Post-Translational; RNA, Long Noncoding
PubMed: 35007523
DOI: 10.1016/j.bcp.2022.114907 -
Disease Markers 2019Increasing evidence suggests that pathogenic mechanisms underlying neurodegeneration are strongly linked with neuroinflammatory responses. Tyro3, Axl, and Mertk (TAM... (Review)
Review
Increasing evidence suggests that pathogenic mechanisms underlying neurodegeneration are strongly linked with neuroinflammatory responses. Tyro3, Axl, and Mertk (TAM receptors) constitute a subgroup of the receptor tyrosine kinase family, cell surface receptors which transmit signals from the extracellular space to the cytoplasm and nucleus. TAM receptors and the corresponding ligands, Growth Arrest Specific 6 and Protein S, are expressed in different tissues, including the nervous system, playing complex roles in tissue repair, inflammation and cell survival, proliferation, and migration. In the nervous system, TAM receptor signalling modulates neurogenesis and neuronal migration, synaptic plasticity, microglial activation, phagocytosis, myelination, and peripheral nerve repair, resulting in potential interest in neuroinflammatory and neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, and Multiple Sclerosis. In Alzheimer and Parkinson diseases, a role of TAM receptors in neuronal survival and pathological protein aggregate clearance has been suggested, while in Multiple Sclerosis TAM receptors are involved in myelination and demyelination processes. To better clarify roles and pathways involving TAM receptors may have important therapeutic implications, given the fine modulation of multiple molecular processes which could be reached. In this review, we summarise the roles of TAM receptors in the central nervous system, focusing on the regulation of immune responses and microglial activities and analysing in vitro and in vivo studies regarding TAM signalling involvement in neurodegeneration.
Topics: Alzheimer Disease; Animals; Calcium-Binding Proteins; Cell Nucleus; Cell Proliferation; Cell Survival; Central Nervous System; Cytoplasm; Humans; Inflammation; Intercellular Signaling Peptides and Proteins; Ligands; Mice; Microglia; Multiple Sclerosis; Neurodegenerative Diseases; Neurogenesis; Parkinson Disease; Protein S; Proto-Oncogene Proteins; Receptor Protein-Tyrosine Kinases; Signal Transduction; c-Mer Tyrosine Kinase; Axl Receptor Tyrosine Kinase
PubMed: 31636733
DOI: 10.1155/2019/2387614 -
Nucleic Acids Research Sep 2023In meiosis, Dmc1 recombinase and the general recombinase Rad51 are responsible for pairing homologous chromosomes and exchanging strands. Fission yeast...
In meiosis, Dmc1 recombinase and the general recombinase Rad51 are responsible for pairing homologous chromosomes and exchanging strands. Fission yeast (Schizosaccharomyces pombe) Swi5-Sfr1 and Hop2-Mnd1 stimulate Dmc1-driven recombination, but the stimulation mechanism is unclear. Using single-molecule fluorescence resonance energy transfer (smFRET) and tethered particle motion (TPM) experiments, we showed that Hop2-Mnd1 and Swi5-Sfr1 individually enhance Dmc1 filament assembly on single-stranded DNA (ssDNA) and adding both proteins together allows further stimulation. FRET analysis showed that Hop2-Mnd1 enhances the binding rate of Dmc1 while Swi5-Sfr1 specifically reduces the dissociation rate during the nucleation, about 2-fold. In the presence of Hop2-Mnd1, the nucleation time of Dmc1 filaments shortens, and doubling the ss/double-stranded DNA (ss/dsDNA) junctions of DNA substrates reduces the nucleation times in half. Order of addition experiments confirmed that Hop2-Mnd1 binds on DNA to recruit and stimulate Dmc1 nucleation at the ss/dsDNA junction. Our studies directly support the molecular basis of how Hop2-Mnd1 and Swi5-Sfr1 act on different steps during the Dmc1 filament assembly. DNA binding of these accessory proteins and nucleation preferences of recombinases thus dictate how their regulation can take place.
Topics: Cell Cycle Proteins; DNA; DNA, Single-Stranded; Meiosis; Rad51 Recombinase; Recombinases; Schizosaccharomyces
PubMed: 37395447
DOI: 10.1093/nar/gkad561 -
Blood Advances Jan 2022Protein S is a cofactor in the tissue factor pathway inhibitor (TFPI) anticoagulant pathway. It enhances TFPIα-mediated inhibition of factor (F)Xa activity and...
Protein S is a cofactor in the tissue factor pathway inhibitor (TFPI) anticoagulant pathway. It enhances TFPIα-mediated inhibition of factor (F)Xa activity and generation. The enhancement is dependent on a TFPIα-protein S interaction involving TFPIα Kunitz 3 and protein S laminin G-type (LG)-1. C4b binding protein (C4BP), which binds to protein S LG1, almost completely abolishes its TFPI cofactor function. However, neither the amino acids involved in TFPIα enhancement nor the mechanisms underlying the reduced TFPI cofactor function of C4BP-bound protein S are known. To screen for functionally important regions within protein S LG1, we generated 7 variants with inserted N-linked glycosylation attachment sites. Protein S D253T and Q427N/K429T displayed severely reduced TFPI cofactor function while showing normal activated protein C (APC) cofactor function and C4BP binding. Based on these results, we designed 4 protein S variants in which 4 to 6 surface-exposed charged residues were substituted for alanine. One variant, protein S K255A/E257A/D287A/R410A/K423A/E424A, exhibited either abolished or severely reduced TFPI cofactor function in plasma and FXa inhibition assays, both in the presence or absence of FV-short, but retained normal APC cofactor function and high-affinity C4BP binding. The C4BP β-chain was expressed to determine the mechanisms behind the reduced TFPI cofactor function of C4BP-bound protein S. Like C4BP-bound protein S, C4BP β-chain-bound protein S had severely reduced TFPI cofactor function. These results show that protein S Lys255, Glu257, Asp287, Arg410, Lys423, and Glu424 are critical for protein S-mediated enhancement of TFPIα and that binding of the C4BP β-chain blocks this function.
Topics: Complement C4b-Binding Protein; Factor V; Laminin; Lipoproteins; Protein S; Thrombin
PubMed: 34731882
DOI: 10.1182/bloodadvances.2021005382 -
Scientific Reports May 2021Protein S (PS) is a multifunctional glycoprotein that ameliorates the detrimental effects of diabetes mellitus (DM). The aim of this study was to evaluate the... (Observational Study)
Observational Study
Protein S (PS) is a multifunctional glycoprotein that ameliorates the detrimental effects of diabetes mellitus (DM). The aim of this study was to evaluate the distribution of PS in diabetic retinopathy (DR) and diabetic macular edema (DME). This was a study of 50 eyes with DM (37 with DME, 6 with proliferative DR, and 7 with no DR) and 19 eyes without DM. The level of PS was measured by enzyme immunoassay and was compared between eyes with or without DM, with or without DME, and with severe DME (≥ 350 μm) or mild DME (< 350 μm). We also performed immunohistopathologic evaluations of post-mortem eyes and the cystoid lesions excised during surgery. The aqueous free PS was significantly higher with DM (7.9 ± 1.2 ng/ml, P < 0.01) than without DM (6.1 ± 0.7). The aqueous free PS was significantly elevated with DME (8.2 ± 1.2, P < 0.05) compared to proliferative DR (7.0 ± 1.0) and no DR (7.0 ± 0.7). Eyes with severe DME had significantly higher aqueous free PS than mild DME (8.5 ± 1.3 vs. 7.7 ± 1.0, P < 0.05). Immunohistochemistry showed PS in the outer plexiform layer of the retina and cystoid lesion. The higher expression of PS with DR and DME suggests that PS is involved in their pathogenesis.
Topics: Aged; Aged, 80 and over; Aqueous Humor; Diabetes Mellitus, Type 2; Diabetic Retinopathy; Female; Humans; Macular Edema; Male; Middle Aged; Protein S; Retina; Severity of Illness Index; Tomography, Optical Coherence
PubMed: 34001977
DOI: 10.1038/s41598-021-89870-5 -
Frontiers in Cardiovascular Medicine 2021Binge drinking has become the most common and deadly pattern of excessive alcohol use in the United States, especially among younger adults. It is closely related to...
Binge drinking has become the most common and deadly pattern of excessive alcohol use in the United States, especially among younger adults. It is closely related to the increased risk of cardiovascular disease. Oxidative stress as a result of ethanol metabolism is the primary pathogenic factor for alcohol-induced end organ injury, but the role of protein S-glutathionylation-a reversible oxidative modification of protein cysteine thiol groups that mediates cellular actions by oxidants-in binge drinking-associated cardiovascular disease has not been explored. The present study defines the effect of alcohol binge drinking on the formation of protein S-glutathionylation in a mouse model of atherosclerosis. To mimic the weekend binge drinking pattern in humans, ApoE deficient ( ) mice on the Lieber-DeCarli liquid diet received ethanol or isocaloric maltose (as a control) gavages (5 g/kg/day, 2 consecutive days/week) for 6 weeks. The primary alcohol-targeted organs (liver, brain), and cardiovascular system (heart, aorta, lung) of these two groups of the mice were determined by measuring the protein S-glutathionylation levels and its regulatory enzymes including [Glutaredoxin1(Grx1), glutathione reductase (GR), glutathione-S-transferase Pi (GST-π)], as well as by assessing aortic endothelial function and liver lipid levels. Our results showed that binge drinking selectively stimulated protein S-glutathionylation in aorta, liver, and brain, which coincided with altered glutathionylation regulatory enzyme expression that is downregulated Grx1 and upregulated GST-π in aorta, massive upregulation of GST-π in liver, and no changes in Grx1 and GST-π in brain. Functionally, binge drinking induced aortic endothelial cell function, as reflected by increased aortic permeability and reduced flow-mediated vasodilation. This study is the first to provide evidence for differential effects of binge drinking on formation of protein S-glutathionylation and its enzymatic regulation system in major alcohol-target organs and cardiovascular system. The selective induction of protein S-glutathionylation in aorta and liver is associated with aortic endothelial dysfunction and fatty liver, which may be a potential redox mechanism for the increased risk of vascular disease in human binge-drinkers.
PubMed: 33796575
DOI: 10.3389/fcvm.2021.649813 -
Biomolecules Mar 2022Covalent binding between nitric oxide (NO) and a protein's free thiol group (SH) is termed protein S-nitrosylation. Protein S-nitrosylation is involved in cellular...
Covalent binding between nitric oxide (NO) and a protein's free thiol group (SH) is termed protein S-nitrosylation. Protein S-nitrosylation is involved in cellular regulation mechanisms that underlie a wide range of critical functions, such as apoptosis, alteration of enzyme activities, and transcription-factor stability. Impaired protein S-nitrosylation is associated with a growing list of pathophysiological conditions, such as cardiovascular disease, multiple sclerosis, pulmonary hypertension, and sickle cell disease. The enzyme paraoxonase 1 (PON1) binds to high-density lipoprotein to provide many of its antiatherogenic properties. The enzyme has a strong antioxidant capacity, which protects fats, lipids, and lipoproteins from oxidation, in addition to breaking down oxidized fats. We investigated the effect of S-S transnitrosylation on PON1 activities. Incubation of recombinant PON1 (rePON1) with nitrosylated human serum albumin (HSA-NO) resulted in S-nitrosylation of about 70% of the rePON1, as measured by Q-TOF LC/MS. S-nitrosylation significantly increased rePON1 hydrolytic activities. It also increased rePON1's ability to inhibit low-density lipoprotein oxidation induced by Cu. Finally, it increased the enzyme's penetration into macrophage cells by 31%. Our findings suggest that S-nitrosylation of rePON1 improves its biological functions which may positively affect atherosclerosis disease progression.
Topics: Antioxidants; Aryldialkylphosphatase; Humans; Lipoproteins, HDL; Lipoproteins, LDL; Protein S
PubMed: 35327606
DOI: 10.3390/biom12030414 -
Blood Coagulation & Fibrinolysis : An... Dec 2019: Protein S Tokushima (p.Lys196Glu) and two protein C gene variants (p.Arg189Trp, p.Lys193del) are hereditary thrombophilia in Japanese and Chinese populations,...
: Protein S Tokushima (p.Lys196Glu) and two protein C gene variants (p.Arg189Trp, p.Lys193del) are hereditary thrombophilia in Japanese and Chinese populations, respectively; however, their diagnosis by plasma analyses is difficult because of the type II deficiency phenotype. Three gene variant genotypes were examined in young Japanese women (n = 231). Plasma total protein S activity and total protein S antigen levels were measured using a total protein S assay system, protein C and protein S activities by clot-based methods, and protein C and free protein S antigen levels by latex agglutination methods. protein S Tokushima (p.Lys196Glu) and protein C p.Lys193del variants were prevalent among participants with allele frequencies of 1.08 and 0.86%, respectively, whereas any carrier of protein C p.Arg189Trp variant was not identified. The plasma phenotype of the type II deficiency of protein S Tokushima heterozygotes was demonstrated by decreased total protein S activity with a normal total protein S antigen level; however, the protein C activities of protein C p.Lys193del heterozygotes were within reference intervals, whereas their protein C antigen levels were elevated. We compared the diagnostic accuracy of the total protein S activity/total protein S antigen ratio for identifying protein S Tokushima heterozygotes with that of the clot-based protein S activity/free protein S antigen ratio and found that sensitivity and specificity of 100% each was only achieved by the former. Protein S Tokushima and protein C p.Lys193del are prevalent among young Japanese women, and a plasma analysis using the total protein S assay system is more accurate than the clot-based protein S activity/free protein S antigen ratio for diagnosing protein S Tokushima carriers.
Topics: Adult; Antigens; Asian People; Female; Gene Frequency; Heterozygote; Humans; Japan; Mutation; Phenotype; Plasma; Protein C; Protein S; Thrombophilia; Young Adult
PubMed: 31490209
DOI: 10.1097/MBC.0000000000000854 -
Open Biology Apr 2022Protein S-acylation, more commonly known as protein palmitoylation, is a biological process defined by the covalent attachment of long chain fatty acids onto cysteine... (Review)
Review
Protein S-acylation, more commonly known as protein palmitoylation, is a biological process defined by the covalent attachment of long chain fatty acids onto cysteine residues of a protein, effectively altering the local hydrophobicity and influencing its stability, localization and overall function. Observed ubiquitously in all eukaryotes, this post translational modification is mediated by the 23-member family of zDHHC protein acyltransferases in mammals. There are thousands of proteins that are S-acylated and multiple zDHHC enzymes can potentially act on a single substrate. Since its discovery, numerous methods have been developed for the identification of zDHHC substrates and the individual members of the family that catalyse their acylation. Despite these recent advances in assay development, there is a persistent gap in knowledge relating to zDHHC substrate specificity and recognition, that can only be thoroughly addressed through reconstitution. Herein, we will review the various methods currently available for reconstitution of protein S-acylation for the purposes of identifying enzyme-substrate pairs with a particular emphasis on the advantages and disadvantages of each approach.
Topics: Acetyltransferases; Acylation; Animals; Mammals; Protein Processing, Post-Translational; Protein S; Substrate Specificity
PubMed: 35414257
DOI: 10.1098/rsob.210390