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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 -
Current Protein & Peptide Science 2016Earlier, we have collected an experimental evidence showing that low molecular weight chiral carboxylic acids (amino acids included) can spontaneously undergo an... (Review)
Review
Earlier, we have collected an experimental evidence showing that low molecular weight chiral carboxylic acids (amino acids included) can spontaneously undergo an oscillatory chiral conversion and an oscillatory condensation in abiotic aqueous and non-aqueous liquid systems, stored for certain amount of time under mild external conditions. These earlier findings are summarized in the introductory part of this study. In the second part, a preliminary report is given on spontaneous pulsation of peptide microfibers in the aged proline-phenylalanine (Pro-Phe) solution in 70% aqueous acetonitrile. The experimental evidence originates from a number of advanced analytical techniques. In view of our earlier and present findings, a presumption is made that the mechanism of spontaneous pulsation (formation and decay) of Pro-Phe microfibers is directly related to the oscillatory chiral conversion and oscillatory peptidization. The entity of the discussed results pointing out to spontaneous and uncontrolled instability of peptide structures might be a bad prognostic for employing such structures in nanobiotechnology.
Topics: Carboxylic Acids; Nanofibers; Peptides; Phenylalanine; Proline
PubMed: 26521956
DOI: 10.2174/138920371702160209121513 -
Amino Acids Nov 2023Vitamin C plays a very important role in the repair of connective tissue, especially for sports whose training causes the most damage to this tissue. Therefore, many...
Vitamin C plays a very important role in the repair of connective tissue, especially for sports whose training causes the most damage to this tissue. Therefore, many people believe that L-ascorbic acid (CHO: vitamin C) reduces the recovery time between sports exercises. The most abundant form of structural protein in the body is collagen. Collagen is characterized by a high concentration of the three amino acids glycine (Gly), proline (Pro), and hydroxyproline (Hyp), which creates its characteristic triple helix structure. Therefore, in this study, the effect of vitamin C presence on the sequence, interaction, and orientation of amino acids for collagen formation is investigated using computational simulation. This study aimed to investigate the mechanism of action of vitamin C in terms of thermodynamics and structure of the reaction. The calculations are performed using density function theory (DFT) by the base set of B3LYP/6-311++G (p,d). The results show that the presence of vitamin C is effective in the formation of collagen protein for this interaction and the mechanism of amino acid sequence (Gly-Hyp-Pro) is better in the formation of collagen protein in the presence of vitamin C. The presence of Vit-C in the formation and direction of hydroxyproline (Hyp) causes its separation from the prolyl 5-hydroxylase enzyme. In the absence of vitamin C, the reaction stops at this stage and proline cannot be converted into hydroxyproline. The computational data shows vitamin C prevents unwanted interactions and directs amino acid reactions to repair connective tissue (collagen). Therefore, vitamin C acts as a cofactor in the Prolyl 5-Hydroxylase enzyme and causes it to convert proline to hydroxyl.
Topics: Humans; Hydroxyproline; Amino Acids; Protein Structure, Secondary; Proline; Collagen; Glycine; Ascorbic Acid; Mixed Function Oxygenases
PubMed: 37782378
DOI: 10.1007/s00726-023-03339-5 -
Molecules (Basel, Switzerland) Oct 2022An efficient way to access highly functionalized proline derivatives was developed based on a Cu(I)-catalyzed reaction between CF-substituted allenynes and tosylazide,...
An efficient way to access highly functionalized proline derivatives was developed based on a Cu(I)-catalyzed reaction between CF-substituted allenynes and tosylazide, which involved a cascade of [3 + 2]-cycloaddition/ketenimine and a rearrangement/Alder-ene cyclization to afford the new proline framework with a high diastereoselectivity.
Topics: Proline; Stereoisomerism; Catalysis; Cyclization; Cycloaddition Reaction; Molecular Structure
PubMed: 36296490
DOI: 10.3390/molecules27206898 -
Protein Engineering, Design & Selection... Feb 2022Proline dehydrogenase (PRODH) catalyzes the FAD-dependent oxidation of l-proline to Δ1-pyrroline-5-carboxylate and is a target for inhibitor discovery because of its...
Proline dehydrogenase (PRODH) catalyzes the FAD-dependent oxidation of l-proline to Δ1-pyrroline-5-carboxylate and is a target for inhibitor discovery because of its importance in cancer cell metabolism. Because human PRODH is challenging to purify, the PRODH domains of the bacterial bifunctional enzyme proline utilization A (PutA) have been used for inhibitor development. These systems have limitations due to large polypeptide chain length, conformational flexibility and the presence of domains unrelated to PRODH activity. Herein, we report the engineering of minimal PRODH domains for inhibitor discovery. The best designs contain one-third of the 1233-residue PutA from Sinorhizobium meliloti and include a linker that replaces the PutA α-domain. The minimal PRODHs exhibit near wild-type enzymatic activity and are susceptible to known inhibitors and inactivators. Crystal structures of minimal PRODHs inhibited by S-(-)-tetrahydro-2-furoic acid and 2-(furan-2-yl)acetic acid were determined at 1.23 and 1.72 Å resolution. Minimal PRODHs should be useful in chemical probe discovery.
Topics: Humans; Proline Oxidase; Proline; Bacterial Proteins
PubMed: 36448708
DOI: 10.1093/protein/gzac016 -
Angewandte Chemie (International Ed. in... Jan 2022Protein stability and evolvability influence each other. Although protein dynamics play essential roles in various catalytically important properties, their high...
Protein stability and evolvability influence each other. Although protein dynamics play essential roles in various catalytically important properties, their high flexibility and diversity makes it difficult to incorporate such properties into rational engineering. Therefore, how to unlock the potential evolvability in a user-friendly rational design process remains a challenge. In this endeavor, we describe a method for engineering an enantioselective alcohol dehydrogenase. It enables synthetically important substrate acceptance for 4-chlorophenyl pyridine-2-yl ketone, and perfect stereocontrol of both (S)- and (R)-configured products. Thermodynamic analysis unveiled the subtle interaction between enzyme stability and evolvability, while computational studies provided insights into the origin of selectivity and substrate recognition. Preparative-scale synthesis of the (S)-product (73 % yield; >99 % ee) was performed on a gram-scale. This proof-of-principle study demonstrates that interfaced proline residues can be rationally engineered to unlock evolvability and thus provide access to new biocatalysts with highly improved catalytic performance.
Topics: Alcohol Dehydrogenase; Proline; Protein Conformation; Protein Engineering; Stereoisomerism; Substrate Specificity
PubMed: 34658118
DOI: 10.1002/anie.202110793 -
Journal of the American Chemical Society Jul 2014The synthetic modification of proteins plays an important role in chemical biology and biomaterials science. These fields provide a constant need for chemical tools that...
The synthetic modification of proteins plays an important role in chemical biology and biomaterials science. These fields provide a constant need for chemical tools that can introduce new functionality in specific locations on protein surfaces. In this work, an oxidative strategy is demonstrated for the efficient modification of N-terminal residues on peptides and N-terminal proline residues on proteins. The strategy uses o-aminophenols or o-catechols that are oxidized to active coupling species in situ using potassium ferricyanide. Peptide screening results have revealed that many N-terminal amino acids can participate in this reaction, and that proline residues are particularly reactive. When applied to protein substrates, the reaction shows a stronger requirement for the proline group. Key advantages of the reaction include its fast second-order kinetics and ability to achieve site-selective modification in a single step using low concentrations of reagent. Although free cysteines are also modified by the coupling reaction, they can be protected through disulfide formation and then liberated after N-terminal coupling is complete. This allows access to doubly functionalized bioconjugates that can be difficult to access using other methods.
Topics: Aminophenols; Models, Molecular; Molecular Structure; Oxidation-Reduction; Peptides; Proline; Proteins
PubMed: 24963951
DOI: 10.1021/ja500728c -
ACS Chemical Neuroscience Sep 2021There is a plethora of significant research that illustrates toxic self-assemblies formed by the aggregation of single amino acids, such as phenylalanine, tyrosine,...
There is a plethora of significant research that illustrates toxic self-assemblies formed by the aggregation of single amino acids, such as phenylalanine, tyrosine, tryptophan, cysteine, and methionine, and their implication on the etiology of inborn errors of metabolisms (IEMs), such as phenylketonuria, tyrosinemia, hypertryptophanemia, cystinuria, and hypermethioninemia, respectively. Hence, studying the aggregation behavior of single amino acids is very crucial from the chemical neuroscience perspective to understanding the common etiology between single amino acid metabolite disorders and amyloid diseases like Alzheimer's and Parkinson's. Herein we report the aggregation properties of nonaromatic single amino acids l-proline (Pro), l-hydroxyproline (Hyp), and l-lysine hydrochloride (Lys). The morphologies of the self-assembled structures formed by Pro, Hyp, and Lys were extensively studied by various microscopic techniques, and controlled morphological transitions were observed under varied concentrations and aging times. The mechanism of structure formation was deciphered by concentration-dependent H NMR analysis, which revealed the crucial role of hydrogen bonding and hydrophobic interactions in the structure formation of Pro, Hyp, and Lys. MTT assays on neural (SHSY5Y) cell lines revealed that aggregates formed by Pro, Hyp, and Lys reduced cell viability in a dose-dependent manner. These results may have important implications in the understanding of the patho-physiology of disorders such as hyperprolinemia, hyperhydroxyprolinemia, and hyperlysinemia since all these IEMs are associated with severe neurodegenerative symptoms, including intellectual disability, seizures, and psychiatric problems. Our future studies will endeavor to study these biomolecular assemblies in greater detail by immuno-histochemical analysis and advanced biophysical assays.
Topics: Amino Acids; Hydroxyproline; Lysine; Proline; Tyrosine
PubMed: 34406754
DOI: 10.1021/acschemneuro.1c00427 -
European Journal of Medicinal Chemistry Feb 2022High temperature requirement A (HtrA) serine proteases have emerged as a novel class of antibacterial target, which are crucial in protein quality control and are...
High temperature requirement A (HtrA) serine proteases have emerged as a novel class of antibacterial target, which are crucial in protein quality control and are involved in the pathogenesis of a wide array of bacterial infections. Previously, we demonstrated that HtrA in Chlamydia is essential for bacterial survival, replication and virulence. Here, we report a new series of proline (P2)-modified inhibitors of Chlamydia trachomatis HtrA (CtHtrA) developed by proline ring expansion and Cγ-substitutions. The structure-based drug optimization process was guided by molecular modelling and in vitro pharmacological evaluation of inhibitory potency, selectivity and cytotoxicity. Compound 25 from the first-generation 4-substituted proline analogues increased antiCtHtrA potency and selectivity over human neutrophil elastase (HNE) by approximately 6- and 12-fold, respectively, relative to the peptidic lead compound 1. Based on this compound, second-generation substituted proline residues containing 1,2,3-triazole moieties were synthesized by regioselective azide-alkyne click chemistry. Compound 49 demonstrated significantly improved antichlamydial activity in whole cell assays, diminishing the bacterial infectious progeny below the detection limit at the lowest dose tested. Compound 49 resulted in approximately 9- and 22-fold improvement in the inhibitory potency and selectivity relative to 1, respectively. To date, compound 49 is the most potent HtrA inhibitor developed against Chlamydia spp.
Topics: Anti-Bacterial Agents; Chlamydia trachomatis; Humans; Peptides; Proline; Serine Proteases
PubMed: 35007862
DOI: 10.1016/j.ejmech.2021.114064 -
Molecules (Basel, Switzerland) Jun 2023L-Azetidine-2-carboxylic acid (AZE) is a non-protein amino acid that shares structural similarities with its proteogenic L-proline amino acid counterpart. For this...
L-Azetidine-2-carboxylic acid (AZE) is a non-protein amino acid that shares structural similarities with its proteogenic L-proline amino acid counterpart. For this reason, AZE can be misincorporated in place of L-proline, contributing to AZE toxicity. In previous work, we have shown that AZE induces both polarization and apoptosis in BV2 microglial cells. However, it is still unknown if these detrimental effects involve endoplasmic reticulum (ER) stress and whether L-proline co-administration prevents AZE-induced damage to microglia. Here, we investigated the gene expression of ER stress markers in BV2 microglial cells treated with AZE alone (1000 µM), or co-treated with L-proline (50 µM), for 6 or 24 h. AZE reduced cell viability, nitric oxide (NO) secretion and caused a robust activation of the unfolded protein response (UPR) genes (ATF4, ATF6, ERN1, PERK, XBP1, DDIT3, GADD34). These results were confirmed by immunofluorescence in BV2 and primary microglial cultures. AZE also altered the expression of microglial M1 phenotypic markers (increased IL-6, decreased CD206 and TREM2 expression). These effects were almost completely prevented upon L-proline co-administration. Finally, triple/quadrupole mass spectrometry demonstrated a robust increase in AZE-bound proteins after AZE treatment, which was reduced by 84% upon L-proline co-supplementation. This study identified ER stress as a pathogenic mechanism for AZE-induced microglial activation and death, which is reversed by co-administration of L-proline.
Topics: Proline; Microglia; Azetidinecarboxylic Acid; Amino Acids; Endoplasmic Reticulum Stress
PubMed: 37375363
DOI: 10.3390/molecules28124808