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Protein Science : a Publication of the... Mar 2024Domains known as von Willebrand factor type D (VWD) are found in extracellular and cell-surface proteins including von Willebrand factor, mucins, and various signaling...
Domains known as von Willebrand factor type D (VWD) are found in extracellular and cell-surface proteins including von Willebrand factor, mucins, and various signaling molecules and receptors. Many VWD domains have a glycine-aspartate-proline-histidine (GDPH) amino-acid sequence motif, which is hydrolytically cleaved post-translationally between the aspartate (Asp) and proline (Pro). The Fc IgG binding protein (FCGBP), found in intestinal mucus secretions and other extracellular environments, contains 13 VWD domains, 11 of which have a GDPH cleavage site. In this study, we investigated the structural and biophysical consequences of Asp-Pro peptide cleavage in a representative FCGBP VWD domain. We found that endogenous Asp-Pro cleavage increases the resistance of the domain to exogenous proteolytic degradation. Tertiary structural interactions made by the newly generated chain termini, as revealed by a crystal structure of an FCGBP segment containing the VWD domain, may explain this observation. Notably, the Gly-Asp peptide bond, upstream of the cleavage site, assumed the cis configuration in the structure. In addition to these local features of the cleavage site, a global organizational difference was seen when comparing the FCGBP segment structure with the numerous other structures containing the same set of domains. Together, these data illuminate the outcome of GDPH cleavage and demonstrate the plasticity of proteins with VWD domains, which may contribute to their evolution for function in a dynamic extracellular environment.
Topics: von Willebrand Factor; Proline; Aspartic Acid; Peptides; Dipeptides
PubMed: 38380729
DOI: 10.1002/pro.4929 -
The Journal of Experimental Medicine Mar 2020Cancer cells often proliferate under hypoxia and reprogram their metabolism. However, how to find targets to effectively block the hypoxia-associated metabolic pathways...
Cancer cells often proliferate under hypoxia and reprogram their metabolism. However, how to find targets to effectively block the hypoxia-associated metabolic pathways remains unclear. Here, we developed a tool to conveniently calculate electrons dissipated in metabolic transformations. Based on the law of conservation of electrons in chemical reactions, we further built up an electron balance model for central carbon metabolism, and it can accurately outline metabolic plasticity under hypoxia. Our model specifies that glutamine metabolism reprogrammed for biosynthesis of lipid and/or proline actually acts as the alternative electron bin to enable electron transfer in proliferating cells under hypoxia. Inhibition of both proline biosynthesis and lipogenesis can synergistically suppress cancer cell growth under hypoxia and in vivo tumor onset. Therefore, our model helps to reveal combinations of potential targets to inhibit tumor growth by blocking hypoxia-rewired metabolism and provides a useful tool for future studies on cancer metabolism.
Topics: A549 Cells; Animals; Cell Hypoxia; Cell Line, Tumor; Cell Proliferation; Female; Glutamine; HeLa Cells; Hep G2 Cells; Humans; Lipogenesis; MCF-7 Cells; Metabolic Networks and Pathways; Mice; Mice, Nude; Neoplasms; Proline
PubMed: 31961917
DOI: 10.1084/jem.20191226 -
Marine Drugs Jul 2022Investigation of the cytotoxic fractions of the ethyl acetate extract of the fermentation broth of the tunicate-derived sp. DY001 afforded two new dipeptides,...
Investigation of the cytotoxic fractions of the ethyl acetate extract of the fermentation broth of the tunicate-derived sp. DY001 afforded two new dipeptides, asperopiperazines A and B ( and ), along with the previously reported compounds (+)-citreoisocoumarin () and (-)-6,8-di--methylcitreoisocoumarin (). Analyses of the 1D and 2D NMR spectroscopic data of the compounds supported their structural assignments. Asperopiperazine A () is a cyclic dipeptide of leucine and phenylalanine moieties, which are substituted with an -methyl and an -acetyl group, respectively. On the other hand, asperopiperazine B () is a cyclic dipeptide of proline and phenylalanine moieties with a hydroxyl group at C-2 of the proline part. The absolute configuration of the amino acid moieties in and were determined by Marfey's analyses and DFT NMR chemical shift calculations, leading to their assignment as cyclo(l-Me-Leu-l-Ac-Phe) and cyclo(d-6-OH-Pro-l-Phe), respectively. Asperopiperazines A and B displayed higher antimicrobial effects against and than Furthermore, compounds - displayed variable growth inhibitory effects towards HCT 116 and MDA-MB-231 cells, with asperopiperazine A as the most active one towards HCT 116.
Topics: Animals; Anti-Bacterial Agents; Anti-Infective Agents; Antineoplastic Agents; Aspergillus; Dipeptides; Fungi; Microbial Sensitivity Tests; Peptides, Cyclic; Phenylalanine; Proline; Urochordata
PubMed: 35877744
DOI: 10.3390/md20070451 -
Scientific Reports Oct 2023Silicon (Si) and/or proline (Pro) are natural supplements that are considered to induce plants' stress tolerance against various abiotic stresses. Sweet corn (Zea mays...
Silicon (Si) and/or proline (Pro) are natural supplements that are considered to induce plants' stress tolerance against various abiotic stresses. Sweet corn (Zea mays L. saccharata) production is severely afflicted by salinity stress. Therefore, two field tests were conducted to evaluate the potential effects of Si and/or Pro (6mM) used as seed soaking (SS) and/or foliar spray (FS) on Sweet corn plant growth and yield, physio-biochemical attributes, and antioxidant defense systems grown in a saline (EC = 7.14dS m) soil. The Si and/or Pro significantly increased growth and yield, photosynthetic pigments, free proline, total soluble sugars (TSS), K/Naratios, relative water content (RWC), membrane stability index (MSI), α-Tocopherol (α-TOC), Ascorbate (AsA), glutathione (GSH), enzymatic antioxidants activities and other anatomical features as compared to controls. In contrast, electrolytes, such as SS and/or FS under salt stress compared to controls (SS and FS using tap water) were significantly decreased. The best results were obtained when SS was combined with FS via Si or Pro. These alterations are brought about by the exogenous application of Si and/or Pro rendering these elements potentially useful in aiding sweet corn plants to acclimate successfully to saline soil.
Topics: Antioxidants; Zea mays; Silicon; Proline; Salt Stress; Glutathione; Water; Soil
PubMed: 37880216
DOI: 10.1038/s41598-023-45003-8 -
Folia Histochemica Et Cytobiologica 2021Extracellular matrix (ECM) proteins have been associated with atherosclerotic complications, such as plaque rupture, calcification and aneurysm. It is not clear what...
INTRODUCTION
Extracellular matrix (ECM) proteins have been associated with atherosclerotic complications, such as plaque rupture, calcification and aneurysm. It is not clear what role different types of collagen play in the pathomechanism of atherosclerosis. The aim of the study was to analyze the content of elastin and major types of collagen in the aortic wall and how they associated are with course of atherosclerosis.
MATERIAL AND METHODS
In this work we present six biochemical parameters related to ECM proteins and collagen-specific amino acids (collagen type I, III, and IV, elastin, proline and hydroxyproline) analyzed in 106 patients' aortic wall specimens characterized by different degree of atherosclerosis. Liquid Chromatography Electrospray Ionization Tandem Mass Spectrometry (LC/ESI-MS/MS), ELISA and immunohistochemical methods were used. The severity of atherosclerosis was assessed on the six-point scale of the American Heart Association, taking into account the number and location of foam cells, the presence of a fatty core, calcium deposits and other characteristic atherosclerotic features.
RESULTS
The results show that there is a relationship between the content of collagen-specific amino acids and development of atherosclerosis. The degree of atherosclerotic lesions was negatively correlated with the content of proline, hydroxyproline and the ratio of these two amino acids. Calcium deposits and surrounding tissue were compared and it was demonstrated that the ratio of type I collagen to type III collagen was higher in the aortic tissue than in aortic calcification areas, while the ratio of collagen type III to elastin was smaller in the artery than in the calcium deposits.
CONCLUSIONS
We suggest that increase in collagen type III presence in the calcification matrix may stem from disorders in the structure of the type I and III collagen fibers. These anomalous fibers are likely to favor accumulation of the calcium salts, an important feature of the process of atheromatosis.
Topics: Adult; Aged; Aorta; Atherosclerosis; Collagen; Elastin; Female; Humans; Hydroxyproline; Male; Middle Aged; Proline; Vascular Calcification
PubMed: 33560515
DOI: 10.5603/FHC.a2021.0002 -
Journal of Experimental Botany Mar 2020Proline metabolism is an essential component of plant adaptation to multiple environmental stress conditions that is also known to participate in specific developmental...
Proline metabolism is an essential component of plant adaptation to multiple environmental stress conditions that is also known to participate in specific developmental phases, particularly in reproductive organs. Recent evidence suggested a possible role for proline catabolism in Brassica napus for nitrogen remobilization processes from source leaves at the vegetative stage. Here, we investigate transcript levels of Δ1-PYRROLINE-5-CARBOXYLATE SYNTHASE (P5CS) and PROLINE DEHYDROGENASE (ProDH) genes at the vegetative stage with respect to net proline biosynthesis and degradation fluxes in leaves having a different sink/source balance. We showed that the underexpression of three P5CS1 genes in source leaves was accompanied by a reduced commitment of de novo assimilated 15N towards proline biosynthesis and an overall depletion of free proline content. We found that the expression of ProDH genes was strongly induced by carbon starvation conditions (dark-induced senescence) compared with early senescing leaves. Our results suggested a role for proline catabolism in B. napus, but acting only at a late stage of senescence. In addition, we also identified some P5CS and ProDH genes that were differentially expressed during multiple processes (leaf status, dark to light transition, and stress response).
Topics: Brassica napus; Gene Expression Regulation, Plant; Nitrogen; Plant Leaves; Proline
PubMed: 31807778
DOI: 10.1093/jxb/erz538 -
Frontiers in Bioscience (Landmark... Jun 2023Intrinsically disordered proteins and protein regions (IDPs/IDRs) are important in diverse biological processes. Lacking a stable secondary structure, they display an...
BACKGROUND
Intrinsically disordered proteins and protein regions (IDPs/IDRs) are important in diverse biological processes. Lacking a stable secondary structure, they display an ensemble of conformations. One factor contributing to this conformational heterogeneity is the proline isomerization. The knowledge and value of a given proline ratio are paramount, as the different conformational states can be responsible for different biological functions. Nuclear Magnetic Resonance (NMR) spectroscopy is the only method to characterize the two co-existing isomers on an atomic level, and only a few works report on these data.
METHODS
After collecting the available experimental literature findings, we conducted a statistical analysis regarding the influence of the neighboring amino acid types ( ± 4 regions) on forming a -Pro isomer. Based on this, several regularities were formulated. NMR spectroscopy was then used to define the Pro content on model peptides and desired point mutations.
RESULTS
Analysis of NMR spectra prove the dependence of the Pro content on the type of the neighboring amino acid-with special attention on aromatic and positively charged sidechains.
CONCLUSIONS
Our results may benefit the design of protein regions with a given -Pro content, and contribute to a better understanding of the roles and functions of IDPs.
Topics: Isomerism; Intrinsically Disordered Proteins; Proline; Peptides; Magnetic Resonance Spectroscopy; Protein Conformation
PubMed: 37395034
DOI: 10.31083/j.fbl2806127 -
Cells Mar 2021The study examines the effect of acclimation on the antioxidant system and proline metabolism in cucumber leaves subjected to 100 and 150 NaCl stress. The levels of...
The study examines the effect of acclimation on the antioxidant system and proline metabolism in cucumber leaves subjected to 100 and 150 NaCl stress. The levels of protein carbonyl group, thiobarbituric acid reactive substances, α-tocopherol, and activity of ascorbate and glutathione peroxidases, catalase, glutathione -transferase, pyrroline-5-carboxylate: synthetase and reductase as well as proline dehydrogenase were determined after 24 and 72 h periods of salt stress in the acclimated and non-acclimated plants. Although both groups of plants showed high α-tocopherol levels, in acclimated plants was observed higher constitutive concentration of these compounds as well as after salt treatment. Furthermore, the activity of enzymatic antioxidants grew in response to salt stress, mainly in the acclimated plants. In the acclimated plants, protein carbonyl group levels collapsed on a constitutive level and in response to salt stress. Although both groups of plants showed a decrease in proline dehydrogenase activity, they differed with regard to the range and time. Differences in response to salt stress between the acclimated and non-acclimated plants may suggest a relationship between increased tolerance in acclimated plants and raised activity of antioxidant enzymes, high-level of α-tocopherol as well, as decrease enzyme activity incorporates in proline catabolism.
Topics: Antioxidants; Cucumis sativus; Humans; Plant Leaves; Proline; Salt Stress
PubMed: 33801884
DOI: 10.3390/cells10030609 -
Biochemistry Feb 2020Pancreatic amyloid formation by the polypeptide IAPP contributes to β-cell dysfunction in type 2 diabetes. There is a 1:1 correspondence between the ability of IAPP...
Pancreatic amyloid formation by the polypeptide IAPP contributes to β-cell dysfunction in type 2 diabetes. There is a 1:1 correspondence between the ability of IAPP from different species to form amyloid and the susceptibility of the organism to develop diabetes. Rat IAPP is non-amyloidogenic and differs from human IAPP at six positions, including three proline replacements: A25P, S28P, and S29P. Incorporation of these proline residues into human IAPP leads to a non-amyloidogenic analogue that is used clinically. The role of the individual proline residues is not understood. We examine the three single and three double proline substitutions in the context of human IAPP. An S28P substitution significantly decreases amyloidogenicity and toxicity, while an S29P substitution has very modest effects despite being an identical replacement just one residue away. The consequences of the A25P substitution are between those of the two Ser to Pro substitutions. Double analogues containing an S28P replacement are less amyloidogenic and less toxic than the IAPP double analogue. Ion mobility mass spectrometry reveals that there is no correlation between the monomer or dimer conformation as reported by collision cross section measurements and the time to form amyloid. The work reveals both the plasticity of IAPP amyloid formation and the exquisite sequence sensitivity of IAPP amyloidogenicity and toxicity. The study highlights the key role of the S28P substitution and provides information that will aid in the rational design of soluble variants of IAPP. The variants studied here offer a system for further exploring features that control IAPP toxicity.
Topics: Algorithms; Amino Acid Sequence; Amino Acid Substitution; Amyloid; Genetic Variation; Humans; Islet Amyloid Polypeptide; Proline
PubMed: 31922743
DOI: 10.1021/acs.biochem.9b01109 -
Molecular and Cellular Biochemistry Mar 2020In stress conditions, as neoplastic transformation, amino acids serve not only as nutrients to maintain the cell survival but also as mediators of several regulatory... (Review)
Review
Understanding the role of key amino acids in regulation of proline dehydrogenase/proline oxidase (prodh/pox)-dependent apoptosis/autophagy as an approach to targeted cancer therapy.
In stress conditions, as neoplastic transformation, amino acids serve not only as nutrients to maintain the cell survival but also as mediators of several regulatory pathways which are involved in apoptosis and autophagy. Especially, under glucose deprivation, in order to maintain the cell survival, proline and glutamine together with other glutamine-derived products such as glutamate, alpha-ketoglutarate, and ornithine serve as alternative sources of energy. They are substrates for production of pyrroline-5-carboxylate which is the product of conversion of proline by proline dehydrogenase/ proline oxidase (PRODH/POX) to produce ATP for protective autophagy or reactive oxygen species for apoptosis. Interconversion of proline, ornithine, and glutamate may therefore regulate PRODH/POX-dependent apoptosis/autophagy. The key amino acid is proline, circulating between mitochondria and cytoplasm in the proline cycle. This shuttle is known as proline cycle. It is coupled to pentose phosphate pathway producing nucleotides for DNA biosynthesis. PRODH/POX is also linked to p53 and AMP-activated protein kinase (AMPK)-dependent pathways. Proline availability for PRODH/POX-dependent apoptosis/autophagy is regulated at the level of collagen biosynthesis (proline utilizing process) and prolidase activity (proline supporting process). In this review, we suggest that amino acid metabolism linking TCA and Urea cycles affect PRODH/POX-dependent apoptosis/autophagy and the knowledge might be useful to targeted cancer therapy.
Topics: Apoptosis; Autophagy; Humans; Neoplasm Proteins; Neoplasms; Proline; Proline Oxidase; Signal Transduction
PubMed: 31933109
DOI: 10.1007/s11010-020-03685-y