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1.
Int J Mol Sci ; 25(8)2024 Apr 12.
Artigo em Inglês | MEDLINE | ID: mdl-38673873

RESUMO

The lipocalin proteins are a large family of small extracellular proteins that demonstrate significant heterogeneity in sequence similarity and have highly conserved crystal structures. They have a variety of functions, including acting as carrier proteins, transporting retinol, participating in olfaction, and synthesizing prostaglandins. Importantly, they also play a critical role in human diseases, including cancer. Additionally, they are involved in regulating cellular homeostasis and immune response and dispensing various compounds. This comprehensive review provides information on the lipocalin family, including their structure, functions, and implications in various diseases. It focuses on selective important human lipocalin proteins, such as lipocalin 2 (LCN2), retinol binding protein 4 (RBP4), prostaglandin D2 synthase (PTGDS), and α1-microglobulin (A1M).


Assuntos
Oxirredutases Intramoleculares , Lipocalinas , Humanos , Lipocalinas/metabolismo , Lipocalinas/química , Lipocalinas/genética , Neoplasias/metabolismo , Relação Estrutura-Atividade , Animais
2.
Biomol NMR Assign ; 18(1): 79-84, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38564159

RESUMO

The lipocalin protein family is a structurally conserved group of proteins with a variety of biological functions defined by their ability to bind small molecule ligands and interact with partner proteins. One member of this family is siderocalin, a protein found in mammals. Its role is discussed in inflammatory processes, iron trafficking, protection against bacterial infections and oxidative stress, cell migration, induction of apoptosis, and cancer. Though it seems to be involved in numerous essential pathways, the exact mechanisms are often not fully understood. The NMR backbone assignments for the human siderocalin and its rat ortholog have been published before. In this work we describe the backbone NMR assignments of siderocalin for another important model organism, the mouse - data that might become important for structure-based drug discovery. Secondary structure elements were predicted based on the assigned backbone chemical shifts using TALOS-N and CSI 3.0, revealing a high content of beta strands and one prominent alpha helical region. Our findings correlate well with the known crystal structure and the overall conserved fold of the lipocalin family.


Assuntos
Lipocalinas , Ressonância Magnética Nuclear Biomolecular , Estrutura Secundária de Proteína , Animais , Camundongos , Sequência de Aminoácidos , Lipocalina-2/química , Lipocalinas/química
3.
Glycobiology ; 34(2)2024 Mar 26.
Artigo em Inglês | MEDLINE | ID: mdl-38015986

RESUMO

The unique viviparous Pacific Beetle cockroaches provide nutrition to their embryo by secreting milk proteins Lili-Mip, a lipid-binding glycoprotein that crystallises in-vivo. The resolved in-vivo crystal structure of variably glycosylated Lili-Mip shows a classical Lipocalin fold with an eight-stranded antiparallel beta-barrel enclosing a fatty acid. The availability of physiologically unaltered glycoprotein structure makes Lili-Mip a very attractive model system to investigate the role of glycans on protein structure, dynamics, and function. Towards that end, we have employed all-atom molecular dynamics simulations on various glycosylated stages of a bound and free Lili-Mip protein and characterised the impact of glycans and the bound lipid on the dynamics of this glycoconjugate. Our work provides important molecular-level mechanistic insights into the role of glycans in the nutrient storage function of the Lili-Mip protein. Our analyses show that the glycans stabilise spatially proximal residues and regulate the low amplitude opening motions of the residues at the entrance of the binding pocket. Glycans also preserve the native orientation and conformational flexibility of the ligand. However, we find that either deglycosylation or glycosylation with high-mannose and paucimannose on the core glycans, which better mimic the natural insect glycosylation state, significantly affects the conformation and dynamics. A simple but effective distance- and correlation-based network analysis of the protein also reveals the key residues regulating the barrel's architecture and ligand binding characteristics in response to glycosylation.


Assuntos
Glicoproteínas , Lipocalinas , Lipocalinas/química , Lipocalinas/metabolismo , Ligantes , Glicoproteínas/metabolismo , Polissacarídeos/química , Lipídeos , Ligação Proteica
4.
Biochemistry (Mosc) ; 88(9): 1232-1247, 2023 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-37770391

RESUMO

Extensive application of technologies like phage display in screening peptide and protein combinatorial libraries has not only facilitated creation of new recombinant antibodies but has also significantly enriched repertoire of the protein binders that have polypeptide scaffolds without homology to immunoglobulins. These innovative synthetic binding protein (SBP) platforms have grown in number and now encompass monobodies/adnectins, DARPins, lipocalins/anticalins, and a variety of miniproteins such as affibodies and knottins, among others. They serve as versatile modules for developing complex affinity tools that hold promise in both diagnostic and therapeutic settings. An optimal scaffold typically has low molecular weight, minimal immunogenicity, and demonstrates resistance against various challenging conditions, including proteolysis - making it potentially suitable for peroral administration. Retaining functionality under reducing intracellular milieu is also advantageous. However, paramount to its functionality is the scaffold's ability to tolerate mutations across numerous positions, allowing for the formation of a sufficiently large target binding region. This is achieved through the library construction, screening, and subsequent expression in an appropriate system. Scaffolds that exhibit high thermodynamic stability are especially coveted by the developers of new SBPs. These are steadily making their way into clinical settings, notably as antagonists of oncoproteins in signaling pathways. This review surveys the diverse landscape of SBPs, placing particular emphasis on the inhibitors targeting the oncoprotein KRAS, and highlights groundbreaking opportunities for SBPs in oncology.


Assuntos
Lipocalinas , Peptídeos , Peptídeos/química , Proteínas Recombinantes/química , Lipocalinas/química , Lipocalinas/uso terapêutico , Clonagem Molecular , Biblioteca de Peptídeos , Ligação Proteica
5.
Acta Crystallogr F Struct Biol Commun ; 79(Pt 9): 231-239, 2023 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-37584182

RESUMO

Using Anticalin technology, a lipocalin protein dubbed Colchicalin, with the ability to bind the toxic plant alkaloid colchicine with picomolar affinity, has previously been engineered, thus offering a potential antidote in vivo and also allowing its sensitive detection in biological samples. To further analyze the mode of ligand recognition, the crystal structure of Colchicalin is now reported in its unliganded form and is compared with the colchicine complex. A superposition of the protein structures revealed major rearrangements in the four structurally variable loops of the engineered lipocalin. Notably, the binding pocket in the unbound protein is largely occupied by the inward-bent loop #3, in particular Ile97, as well as by the phenylalanine side chain at position 71 in loop #2. Upon binding of colchicine, a dramatic shift of loop #3 by up to 11.1 Šoccurs, in combination with a side-chain flip of Phe71, thus liberating the necessary space within the ligand pocket. Interestingly, the proline residue at the neighboring position 72, which arose during the combinatorial engineering of Colchicalin, remained in a cis configuration in both structures. These findings provide a striking example of a conformational adaptation mechanism, which is a long-known phenomenon for antibodies in immunochemistry, during the recognition of a small ligand by an engineered lipocalin, thus illustrating the general similarity between the mode of antigen/ligand binding by immunoglobulins and lipocalins.


Assuntos
Colchicina , Lipocalinas , Lipocalinas/genética , Lipocalinas/química , Lipocalinas/metabolismo , Engenharia de Proteínas , Ligantes , Cristalografia por Raios X
6.
Artigo em Inglês | MEDLINE | ID: mdl-37207740

RESUMO

Tributyltin (TBT)-binding protein type 1 in Japanese medaka (Oryzias latipes) (O.latTBT-bp1) is a fish lipocalin implicated in TBT binding and detoxification. We purified recombinant O.latTBT-bp1 (rO.latTBT-bp1; ca. 30 kDa) by using a baculovirus expression system and His- and Strep-tag chromatography process. Then, we examined O.latTBT-bp1 binding to several endo/exogenous steroid hormones by means of competitive binding assay. The dissociation constants for the binding of rO.latTBT-bp1 to DAUDA and ANS, two fluorescent ligands of lipocalin, were 7.06 and 13.6 µM, respectively. Multiple model validations indicated that a single-binding-site model was the most appropriate for evaluating rO.latTBT-bp1 binding. In the competitive binding assay, testosterone, 11-ketotestosterone, and 17ß-estradiol were each bound by rO.latTBT-bp1; rO.latTBT-bp1 showed the strongest affinity for testosterone (inhibition constant, Ki = 3.47 µM). Endocrine-disrupting chemical (synthetic steroid) also bound to rO.latTBT-bp1; the affinity for ethinylestradiol (Ki = 9.29 µM) was stronger than that for 17ß-estradiol (Ki = 30.0 µM). To determine the function of O.latTBT-bp1, we produced TBT-bp1 knockout medaka (TBT-bp1 KO), which we exposed to ethinylestradiol for 28 days. After exposure, the number of papillary processes in TBT-bp1 KO genotypic male medaka was significantly fewer (3.5), compared to that in wild-type male medaka (22). Thus, TBT-bp1 KO medaka were more sensitive to the anti-androgenic effects of ethinylestradiol than wild-type medaka. These results indicate that O.latTBT-bp1 may bind to steroids and act as a gatekeeper of ethinylestradiol action by regulating the androgen-estrogen balance.


Assuntos
Etinilestradiol , Oryzias , Animais , Masculino , Etinilestradiol/toxicidade , Etinilestradiol/metabolismo , Peixes/metabolismo , Lipocalinas/química , Lipocalinas/metabolismo , Estradiol/metabolismo , Testosterona/metabolismo , Oryzias/metabolismo
7.
FEBS J ; 290(16): 3983-3996, 2023 08.
Artigo em Inglês | MEDLINE | ID: mdl-37021622

RESUMO

Lipocalin-type prostaglandin D synthase (L-PGDS) is a secretory lipid-transporter protein that was shown to bind a wide variety of hydrophobic ligands in vitro. Exploiting this function, we previously examined the feasibility of using L-PGDS as a novel delivery vehicle for poorly water-soluble drugs. However, the mechanism by which human L-PGDS binds to poorly water-soluble drugs is unclear. In this study, we determined the solution structure of human L-PGDS and investigated the mechanism of L-PGDS binding to 6-nitro-7-sulfamoyl-benzo[f]quinoxalin-2,3-dione (NBQX), an α-amino-3-hydroxy-5-methyl-4-isoxazole-propionic acid receptor antagonist. NMR experiments showed that human L-PGDS has an eight-stranded antiparallel ß-barrel structure that forms a central cavity, a short 310 -helix and two α-helices. Titration with NBQX was monitored using 1 H-15 N HSQC spectroscopy. At higher NBQX concentrations, some cross-peaks of the protein exhibited fast-exchanging shifts with a curvature, indicating at least two binding sites. These residues were located in the upper portion of the cavity. Singular value decomposition analysis revealed that human L-PGDS has two NBQX binding sites. Large chemical shift changes were observed in the H2-helix and A-, B-, C-, D-, H- and I-strands and H2-helix upon NBQX binding. Calorimetric experiments revealed that human L-PGDS binds two NBQX molecules with dissociation constants of 46.7 µm for primary binding and 185.0 µm for secondary binding. Molecular docking simulations indicated that these NBQX binding sites are located within the ß-barrel. These results provide new insights into the interaction between poorly water-soluble drugs and human L-PGDS as a drug carrier.


Assuntos
Lipocalinas , Água , Humanos , Preparações Farmacêuticas , Simulação de Acoplamento Molecular , Ligação Proteica , Água/química , Lipocalinas/química , Prostaglandina D2/metabolismo
8.
Pharmacol Ther ; 244: 108385, 2023 04.
Artigo em Inglês | MEDLINE | ID: mdl-36966973

RESUMO

The lipocalin (LCN) family members, a group of small extracellular proteins with 160-180 amino acids in length, can be detected in all kingdoms of life from bacteria to human beings. They are characterized by low similarity of amino acid sequence but highly conserved tertiary structures with an eight-stranded antiparallel ß-barrel which forms a cup-shaped ligand binding pocket. In addition to bind small hydrophobic ligands (i.e., fatty acids, odorants, retinoids, and steroids) and transport them to specific cells, lipocalins (LCNs) can interact with specific cell membrane receptors to activate their downstream signaling pathways, and with soluble macromolecules to form the complex. Consequently, LCNs exhibit great functional diversity. Accumulating evidence has demonstrated that LCN family proteins exert multiple layers of function in the regulation of many physiological processes and human diseases (i.e., cancers, immune disorders, metabolic disease, neurological/psychiatric disorders, and cardiovascular disease). In this review, we firstly introduce the structural and sequence properties of LCNs. Next, six LCNs including apolipoprotein D (ApoD), ApoM, lipocalin 2 (LCN2), LCN10, retinol-binding protein 4 (RBP4), and Lipocalin-type prostaglandin D synthase (L-PGDS) which have been characterized so far are highlighted for their diagnostic/prognostic values and their potential effects on coronary artery disease and myocardial infarction injury. The roles of these 6 LCNs in cardiac hypertrophy, heart failure, diabetes-induced cardiac disorder, and septic cardiomyopathy are also summarized. Finally, their therapeutic potential for cardiovascular disease is discussed in each section.


Assuntos
Doenças Cardiovasculares , Humanos , Lipocalinas/química , Lipocalinas/metabolismo , Sequência de Aminoácidos , Receptores de Superfície Celular/metabolismo , Ligantes , Proteínas Plasmáticas de Ligação ao Retinol/metabolismo
9.
J Biochem ; 174(1): 21-31, 2023 Jun 30.
Artigo em Inglês | MEDLINE | ID: mdl-36762787

RESUMO

Lipocalin-type prostaglandin D synthase (L-PGDS) binds various hydrophobic small molecules. Since we aim to use human L-PGDS as a carrier in a drug delivery system (DDS) for poorly water-soluble drugs, quality control of the protein is indispensable. In this study, we investigated the thermodynamic stability of human L-PGDS under various pH conditions. Differential scanning calorimetry revealed that the thermal unfolding of L-PGDS was an almost-reversible two-state transition between the native and unfolded states over the pH range from 2.5 to 7.4. The linear relationship of ΔH(Tm) to Tm in this pH range gave a heat capacity change (ΔCp) of 4.76 kJ/(K·mol), which was small compared to those commonly found in globular proteins. The temperature-dependent free energy of unfolding, ΔG(T), specified by Tm, ΔH(Tm) and ΔCp, showed a pH dependence with the highest value at pH 7.4 closest to the isoelectric point of 8.3. The small value of Cp resulted in a large value of ΔG(T), which contributed to the stability of the protein. Taken together, these results demonstrated that human L-PGDS is sufficiently thermostable for storage and practical use and can be useful as a delivery vehicle of protein-based DDS.


Assuntos
Oxirredutases Intramoleculares , Lipocalinas , Humanos , Termodinâmica , Oxirredutases Intramoleculares/química , Oxirredutases Intramoleculares/metabolismo , Lipocalinas/química , Lipocalinas/metabolismo , Concentração de Íons de Hidrogênio
10.
Pharm Res ; 39(11): 2951-2963, 2022 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-35799081

RESUMO

Lipocalin-type prostaglandin D synthase was previously known as ß-trace protein (BTP), a low-molecular-weight glycoprotein that is heavily expressed in human cerebrospinal fluid. Nevertheless, it is also seen to be expressed in numerous other tissues including the kidney, liver, lung, heart, adipose, muscle, and pancreas. Functionally, L-PGDS behaves like a lipocalin type protein where it helps in binding and transportation of small lipophilic substances, such as steroids, retinoids, and other lipophilic ligands. Enzymatically, L-PGDS functions as a prostaglandin synthase where it helps in the production of PGD2 by catalyzing the isomerization of PGH2, a common precursor of the two series of prostaglandins. PGD2 regulates its physiological function through two individual receptors named DP1 and DP2. L-PGDS has been a central player in many diseases, its role in metabolism including diabetes, fatty liver disease, and obesity has gathered a large attention. In this review, we summarize the current state of knowledge about L-PGDS and it's signaling in adipose, hepatic, skeletal muscle, and pancreas tissues, which are core targets for metabolic studies. Modulation of L-PGDS signaling can be considered as a potential future therapeutic target for the treatment of insulin resistance as well as fatty liver disease.


Assuntos
Hepatopatias , Prostaglandina D2 , Humanos , Prostaglandina D2/metabolismo , Oxirredutases Intramoleculares/química , Oxirredutases Intramoleculares/metabolismo , Lipocalinas/química , Lipocalinas/metabolismo
11.
Biomol NMR Assign ; 16(2): 225-229, 2022 10.
Artigo em Inglês | MEDLINE | ID: mdl-35445291

RESUMO

Lipocalin-type prostaglandin (PG) D synthase (L-PGDS) catalyzes the isomerization of PGH2 to produce PGD2, an endogenous somenogen, in the brains of various mammalians. We recently reported that various other PGs also bind to L-PGDS, suggesting that it could serve as an extracellular carrier for PGs. Although the solution and crystal structure of L-PGDS has been determined, as has the structure of L-PGDS complexed PGH2 analog, a structural analysis of L-PGDS complexed with other PGs is needed in order to understand the mechanism responsible for the PG trapping. Here, we report the nearly complete 1H, 13C, and 15N backbone and side chain resonance assignments of the L-PGDS/PGJ2 complex and the binding site for PGJ2 on L-PGDS.


Assuntos
Oxirredutases Intramoleculares , Lipocalinas , Animais , Oxirredutases Intramoleculares/química , Oxirredutases Intramoleculares/metabolismo , Lipocalinas/química , Lipocalinas/metabolismo , Mamíferos/metabolismo , Camundongos , Ressonância Magnética Nuclear Biomolecular , Prostaglandina H2/metabolismo
12.
Biol Chem ; 403(5-6): 557-571, 2022 04 26.
Artigo em Inglês | MEDLINE | ID: mdl-35355502

RESUMO

We describe the structural analysis of two Anticalin® proteins that tightly bind Aß40, a peptide involved in the pathophysiology of Alzheimer's disease. These anticalins, US7 and H1GA, were engineered on the basis of the human lipocalin 2, thus yielding compact single-domain binding proteins as an alternative to antibodies. Albeit selected under different conditions and mutually deviating in 13 amino acid positions within the binding pocket (of 17 mutated residues in total), both crystallised anticalins recognize the same epitope in the middle of the ß-amyloid peptide. In the two complexes with the Aß40 peptide, its central part comprising residues LysP16 to LysP28 shows well defined electron density whereas the flanking regions appear structurally disordered. The compact zigzag-bend conformation which is seen in both structures may indicate a role during conversion of the soluble monomeric form into pathogenic Aß state(s) and, thus, explain the aggregation-inhibiting effect of the anticalins. In contrast to solanezumab, which targets the same Aß region in a different conformation, the anticalin H1GA does not show cross-reactivity with sequence-related human plasma proteins. Consequently, anticalins offer promising reagents to prevent oligomerization of Aß peptides to neurotoxic species in vivo and their small size may enable new routes for brain delivery.


Assuntos
Doença de Alzheimer , Peptídeos beta-Amiloides , Doença de Alzheimer/metabolismo , Peptídeos beta-Amiloides/metabolismo , Epitopos , Humanos , Lipocalinas/química , Conformação Molecular , Fragmentos de Peptídeos/metabolismo
13.
Front Biosci (Landmark Ed) ; 27(3): 84, 2022 03 05.
Artigo em Inglês | MEDLINE | ID: mdl-35345316

RESUMO

BACKGROUND: Lipocalin belongs to the calcyin family, and its sequence length is generally between 165 and 200 residues. They are mainly stable and multifunctional extracellular proteins. Lipocalin plays an important role in several stress responses and allergic inflammations. Because the accurate identification of lipocalins could provide significant evidences for the study of their function, it is necessary to develop a machine learning-based model to recognize lipocalin. METHODS: In this study, we constructed a prediction model to identify lipocalin. Their sequences were encoded by six types of features, namely amino acid composition (AAC), composition of k-spaced amino acid pairs (CKSAAP), pseudo amino acid composition (PseAAC), Geary correlation (GD), normalized Moreau-Broto autocorrelation (NMBroto) and composition/transition/distribution (CTD). Subsequently, these features were optimized by using feature selection techniques. A classifier based on random forest was trained according to the optimal features. RESULTS: The results of 10-fold cross-validation showed that our computational model would classify lipocalins with accuracy of 95.03% and area under the curve of 0.987. On the independent dataset, our computational model could produce the accuracy of 89.90% which was 4.17% higher than the existing model. CONCLUSIONS: In this work, we developed an advanced computational model to discriminate lipocalin proteins from non-lipocalin proteins. In the proposed model, protein sequences were encoded by six descriptors. Then, feature selection was performed to pick out the best features which could produce the maximum accuracy. On the basis of the best feature subset, the RF-based classifier can obtained the best prediction results.


Assuntos
Inteligência Artificial , Lipocalinas , Aminoácidos , Biologia Computacional , Lipocalinas/química , Aprendizado de Máquina , Proteínas/química
14.
Int Arch Allergy Immunol ; 183(1): 93-104, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-34515139

RESUMO

BACKGROUND: Cow's milk allergy (CMA) is the most common IgE-mediated food allergy and Bos d 5 is the major allergen in cow's milk proteins. More than 60% of the patients with CMA are sensitized to this protein. METHODS AND RESULTS: A recombinant protein, encoded by a synthetic gene and consisting of reassembled Bos d 5 fragments, was expressed in E. coli strain BL21 (DE3) cells and purified to homogeneity. The B5M lacked relevant IgE-reactivity and allergenic activity compared with Bos d 5 in dot-blot and basophil activation assays. T-cell proliferation experiments demonstrated that B5M preserved the main T cell epitopes of Bos d 5. Immunization of rabbits with B5M induced protective IgG antibodies that blocked the binding of patients' IgE antibodies to the wild-type allergen and inhibited the degranulation of basophils induced by Bos d 5. CONCLUSION: Thus, we developed a new strategy, which was based on rational molecular reassembly for allergen-specific immunotherapy (AIT) of CMA and food allergy.


Assuntos
Alérgenos/imunologia , Lipocalinas/imunologia , Hipersensibilidade a Leite/imunologia , Leite/efeitos adversos , Vacinas/imunologia , Alérgenos/química , Alérgenos/genética , Animais , Especificidade de Anticorpos/imunologia , Basófilos/imunologia , Basófilos/metabolismo , Bovinos , Epitopos de Linfócito T/imunologia , Humanos , Imunoglobulina E/imunologia , Imunoglobulina G/imunologia , Imunoterapia , Lipocalinas/química , Lipocalinas/genética , Hipersensibilidade a Leite/prevenção & controle , Ligação Proteica/imunologia , Proteínas Recombinantes/química , Proteínas Recombinantes/imunologia , Subpopulações de Linfócitos T/imunologia , Subpopulações de Linfócitos T/metabolismo , Vacinas/administração & dosagem
15.
Science ; 373(6562): 1532-1536, 2021 Sep 24.
Artigo em Inglês | MEDLINE | ID: mdl-34446443

RESUMO

In Arabidopsis, de novo organogenesis of lateral roots is patterned by an oscillatory mechanism called the root clock, which is dependent on unidentified metabolites. To determine whether retinoids regulate the root clock, we used a chemical reporter for retinaldehyde (retinal)­binding proteins. We found that retinal binding precedes the root clock and predicts sites of lateral root organogenesis. Application of retinal increased root clock oscillations and promoted lateral root formation. Expression of an Arabidopsis protein with homology to vertebrate retinoid-binding proteins, TEMPERATURE INDUCED LIPOCALIN (TIL), oscillates in the region of retinal binding to the reporter, confers retinal-binding activity in a heterologous system, and, when mutated, decreases retinal sensitivity. These results demonstrate a role for retinal and its binding partner in lateral root organogenesis.


Assuntos
Proteínas de Arabidopsis/metabolismo , Arabidopsis/crescimento & desenvolvimento , Arabidopsis/metabolismo , Lipocalinas/metabolismo , Raízes de Plantas/crescimento & desenvolvimento , Retinaldeído/metabolismo , Arabidopsis/genética , Proteínas de Arabidopsis/química , Proteínas de Arabidopsis/genética , Fluorescência , Lipocalinas/química , Lipocalinas/genética , Meristema/metabolismo , Mutação , Organogênese Vegetal , Raízes de Plantas/metabolismo , Ligação Proteica , Pirimidinonas/metabolismo , Retinaldeído/farmacologia , Transdução de Sinais
16.
Biochem Biophys Res Commun ; 569: 66-71, 2021 09 10.
Artigo em Inglês | MEDLINE | ID: mdl-34237429

RESUMO

Prostaglandin D2 (PGD2), an endogenous somnogen, is a unique PG that is secreted into the cerebrospinal fluid. PGD2 is a relatively fragile molecule and should be transported to receptors localized in the basal forebrain without degradation. However, it remains unclear how PGD2 is stably carried to such remote receptors. Here, we demonstrate that the PGD2-synthesizing enzyme, Lipocalin-type prostaglandin D synthase (L-PGDS), binds not only its substrate PGH2 but also its product PGD2 at two distinct binding sites for both ligands. This behaviour implys its PGD2 carrier function. Nevertheless, since the high affinity (Kd = âˆ¼0.6 µM) of PGD2 in the catalytic binding site is comparable to that of PGH2, it may act as a competitive inhibitor, while our binding assay exhibits only weak inhibition (Ki = 189 µM) of the catalytic reaction. To clarify this enigmatic behavior, we determined the solution structure of L-PGDS bound to one substrate analog by NMR and compared it with the two structures: one in the apo form and the other in substrate analogue complex with 1:2 stoichiometry. The structural comparisons showed clearly that open or closed forms of loops at the entrance of ligand binding cavity are regulated by substrate binding to two sites, and that the binding to a second non-catalytic binding site, which apparently substrate concentration dependent, induces opening of the cavity that releases the product. From these results, we propose that L-PGDS is a unique enzyme having a carrier function and a substrate-induced product-release mechanism.


Assuntos
Domínio Catalítico , Oxirredutases Intramoleculares/metabolismo , Lipocalinas/metabolismo , Prostaglandina D2/metabolismo , Prostaglandina H2/metabolismo , Animais , Sítios de Ligação , Biocatálise , Oxirredutases Intramoleculares/química , Oxirredutases Intramoleculares/genética , Cinética , Lipocalinas/química , Lipocalinas/genética , Espectroscopia de Ressonância Magnética , Camundongos , Estrutura Molecular , Mutação , Prostaglandina D2/química , Prostaglandina H2/química , Ligação Proteica , Conformação Proteica , Especificidade por Substrato
17.
Biol Chem ; 402(4): 433-437, 2021 03 26.
Artigo em Inglês | MEDLINE | ID: mdl-33938175

RESUMO

Although some progress has been achieved in understanding certain aspects of the allergenic mechanism of animal lipocalins, they still remain largely enigmatic. One possibility to unravel this property is to investigate their interaction with components of the immune system. Since these components are highly complex we intended to use a high-throughput technology for this purpose. Therefore, we used phage-display of a random peptide library for panning against the dog allergen Can f 1. By this method we identified a Can f 1 binding peptide corresponding to the antigen-binding site of a putative γδT-cell receptor. Additional biochemical investigations confirmed this interaction.


Assuntos
Alérgenos/imunologia , Lipocalinas/imunologia , Peptídeos/imunologia , Receptores de Antígenos de Linfócitos T gama-delta/imunologia , Alérgenos/química , Sítios de Ligação/imunologia , Humanos , Lipocalinas/química , Modelos Moleculares , Peptídeos/química , Receptores de Antígenos de Linfócitos T gama-delta/química
18.
FEBS J ; 288(5): 1679-1695, 2021 03.
Artigo em Inglês | MEDLINE | ID: mdl-32679618

RESUMO

Hydroxynitrile lyases (HNLs) catalyze the cleavage of cyanohydrin into cyanide and the corresponding aldehyde or ketone. Moreover, they catalyze the synthesis of cyanohydrin in the reverse reaction, utilized in industry for preparation of enantiomeric pure pharmaceutical ingredients and fine chemicals. We discovered a new HNL from the cyanogenic millipede, Chamberlinius hualienensis. The enzyme displays several features including a new primary structure, high stability, and the highest specific activity in (R)-mandelonitrile ((R)-MAN) synthesis (7420 U·mg-1 ) among the reported HNLs. In this study, we elucidated the crystal structure and reaction mechanism of natural ChuaHNL in ligand-free form and its complexes with acetate, cyanide ion, and inhibitors (thiocyanate or iodoacetate) at 1.6, 1.5, 2.1, 1.55, and 1.55 Å resolutions, respectively. The structure of ChuaHNL revealed that it belongs to the lipocalin superfamily, despite low amino acid sequence identity. The docking model of (R)-MAN with ChuaHNL suggested that the hydroxyl group forms hydrogen bonds with R38 and K117, and the nitrile group forms hydrogen bonds with R38 and Y103. The mutational analysis showed the importance of these residues in the enzymatic reaction. From these results, we propose that K117 acts as a base to abstract a proton from the hydroxyl group of cyanohydrins and R38 acts as an acid to donate a proton to the cyanide ion during the cleavage reaction of cyanohydrins. The reverse mechanism would occur during the cyanohydrin synthesis. (Photo: Dr. Yuko Ishida) DATABASES: Structural data are available in PDB database under the accession numbers 6JHC, 6KFA, 6KFB, 6KFC, and 6KFD.


Assuntos
Acetonitrilas/química , Aldeído Liases/química , Proteínas de Artrópodes/química , Artrópodes/química , Lipocalinas/química , Acetonitrilas/metabolismo , Aldeído Liases/genética , Aldeído Liases/metabolismo , Sequência de Aminoácidos , Animais , Proteínas de Artrópodes/genética , Proteínas de Artrópodes/metabolismo , Artrópodes/enzimologia , Sítios de Ligação , Biocatálise , Clonagem Molecular , Cristalografia por Raios X , Inibidores Enzimáticos/química , Inibidores Enzimáticos/metabolismo , Escherichia coli/genética , Escherichia coli/metabolismo , Expressão Gênica , Vetores Genéticos/química , Vetores Genéticos/metabolismo , Ácido Iodoacético/química , Ácido Iodoacético/metabolismo , Cinética , Lipocalinas/genética , Lipocalinas/metabolismo , Simulação de Acoplamento Molecular , Ligação Proteica , Conformação Proteica em alfa-Hélice , Conformação Proteica em Folha beta , Domínios e Motivos de Interação entre Proteínas , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Alinhamento de Sequência , Homologia de Sequência de Aminoácidos , Especificidade por Substrato , Tiocianatos/química , Tiocianatos/metabolismo
19.
Plant Physiol Biochem ; 158: 265-274, 2021 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-33262014

RESUMO

The chloroplastic lipocalin (LCNP) is induced in response to various abiotic stresses including high light, dehydration and low temperature. It contributes to protection against oxidative damage promoted by adverse conditions by preventing accumulation of fatty acid hydroperoxides and lipid peroxidation. In contrast to animal lipocalins, LCNP is poorly characterized and the molecular mechanism by which it exerts protective effects during oxidative stress is largely unknown. LCNP is considered the ortholog of human apolipoprotein D (APOD), a protein whose lipid antioxidant function has been characterized. Here, we investigated whether APOD could functionally replace LCNP in Arabidopsis thaliana. We introduced APOD cDNA fused to a chloroplast transit peptide encoding sequence in an Arabidopsis LCNP KO mutant line and challenged the transgenic plants with different abiotic stresses. We demonstrated that expression of human APOD in Arabidopsis can partially compensate for the lack of the plastid lipocalin. The results are consistent with a conserved function of APOD and LCNP under stressful conditions. However, if the results obtained with the drought and oxidative stresses point to the protective effect of constitutive expression of APOD in plants lacking LCNP, this effect is not as effective as that conferred by LCNP overexpression. Moreover, when investigating APOD function in thylakoids after high light stress at low temperature, it appeared that APOD could not contribute to qH, a slowly reversible form of non-photochemical chlorophyll fluorescence quenching, as described for LCNP. This work provides a base of understanding the molecular mechanism underlying LCNP protective function.


Assuntos
Apolipoproteínas D/biossíntese , Arabidopsis/metabolismo , Desidratação , Lipocalinas/química , Estresse Oxidativo , Arabidopsis/genética , Cloroplastos/química , Secas , Expressão Ectópica do Gene , Humanos , Plantas Geneticamente Modificadas
20.
FEBS Lett ; 595(2): 206-219, 2021 01.
Artigo em Inglês | MEDLINE | ID: mdl-33210733

RESUMO

Lipocalins are a superfamily of functionally diverse proteins defined by a well-conserved tertiary structure despite variation in sequence. Lipocalins bind and transport small hydrophobic molecules in organisms of all kingdoms. However, there is still uncertainty regarding the function of some members of the family, including bacterial lipocalin Blc from Escherichia coli. Here, we present evidence that lipocalin Blc may be involved in heme binding, trans-periplasmic transport, or heme storage. This conclusion is supported by a cocrystal structure, mass-spectrometric data, absorption titration, and in silico analysis. Binding of heme is observed at low micromolar range with one-to-one ligand-to-protein stoichiometry. However, the absence of classical coordination to the iron atom leaves the possibility that the primary ligand of Blc is another tetrapyrrole.


Assuntos
Proteínas da Membrana Bacteriana Externa/química , Proteínas da Membrana Bacteriana Externa/metabolismo , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/metabolismo , Escherichia coli/metabolismo , Heme/metabolismo , Lipocalinas/química , Lipocalinas/metabolismo , Cromatografia Líquida , Simulação por Computador , Cristalografia por Raios X , Heme/química , Ligantes , Espectrometria de Massas , Modelos Moleculares , Simulação de Dinâmica Molecular , Ligação Proteica , Transporte Proteico
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