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1.
Int J Mol Sci ; 25(11)2024 May 26.
Artigo em Inglês | MEDLINE | ID: mdl-38891976

RESUMO

In recent years, the awareness that pesticides can have other effects apart from generic toxicity is growing. In particular, several pieces of evidence highlight their influence on human fertility. In this study, we investigated, by a virtual screening approach, the binding between pesticides and proteins present in human gametes or associated with reproduction, in order to identify new interactions that could affect human fertility. To this aim, we prepared ligand (pesticides) and receptor (proteins) 3D structure datasets from online structural databases (such as PubChem and RCSB), and performed a virtual screening analysis using Autodock Vina. In the comparison of the predicted interactions, we found that famoxadone was predicted to bind Cellular Retinol Binding Protein-III in the retinol-binding site with a better minimum energy value of -10.4 Kcal/mol and an RMSD of 3.77 with respect to retinol (-7.1 Kcal/mol). In addition to a similar network of interactions, famoxadone binding is more stabilized by additional hydrophobic patches including L20, V29, A33, F57, L117, and L118 amino acid residues and hydrogen bonds with Y19 and K40. These results support a possible competitive effect of famoxadone on retinol binding with impacts on the ability of developing the cardiac tissue, in accordance with the literature data on zebrafish embryos. Moreover, famoxadone binds, with a minimum energy value between -8.3 and -8.0 Kcal/mol, to the IZUMO Sperm-Egg Fusion Protein, interacting with a network of polar and hydrophobic amino acid residues in the cavity between the 4HB and Ig-like domains. This binding is more stabilized by a predicted hydrogen bond with the N185 residue of the protein. A hindrance in this position can probably affect the conformational change for JUNO binding, avoiding the gamete membrane fusion to form the zygote. This work opens new interesting perspectives of study on the effects of pesticides on fertility, extending the knowledge to other typologies of interaction which can affect different steps of the reproductive process.


Assuntos
Simulação de Acoplamento Molecular , Praguicidas , Ligação Proteica , Humanos , Praguicidas/metabolismo , Praguicidas/química , Proteínas Celulares de Ligação ao Retinol/metabolismo , Proteínas Celulares de Ligação ao Retinol/química , Sítios de Ligação , Reprodução/efeitos dos fármacos , Animais , Ligação de Hidrogênio , Ligantes
2.
Artigo em Inglês | MEDLINE | ID: mdl-35533980

RESUMO

Retinol-binding protein 2 (RBP2, also known as cellular retinol-binding protein 2 (CRBP2)) is a member of the fatty acid-binding protein family and has been extensively studied for its role in facilitating dietary vitamin A (retinol) uptake and metabolism within enterocytes of the small intestine. RBP2 is present in highest concentrations in the proximal small intestine where it constitutes approximately 0.1-0.5% of soluble protein. Recent reports have established that RBP2 binds monoacylglycerols (MAGs) with high affinity, including the canonical endocannabinoid 2-arachidonoylglycerol (2-AG). Crystallographic studies reveal that retinol, 2-AG, or other long-chain MAGs alternatively can bind in the retinol-binding pocket of RBP2. It also has been demonstrated recently that Rbp2-deficient mice are more susceptible to developing obesity and associated metabolic phenotypes when exposed to a high fat diet, or as they age when fed a conventional chow diet. When subjected to an oral fat challenge, the Rbp2-deficient mice release into the circulation significantly more, compared to littermate controls, of the intestinal hormone glucose-dependent insulinotropic polypeptide (GIP). These new findings regarding RBP2 structure and actions within the intestine are the focus of this review.


Assuntos
Retinoides , Vitamina A , Animais , Transporte Biológico , Dieta Hiperlipídica , Camundongos , Monoglicerídeos/metabolismo , Retinoides/metabolismo , Proteínas Celulares de Ligação ao Retinol/química , Proteínas Celulares de Ligação ao Retinol/genética , Proteínas Celulares de Ligação ao Retinol/metabolismo , Vitamina A/metabolismo
3.
J Biol Chem ; 297(4): 101142, 2021 10.
Artigo em Inglês | MEDLINE | ID: mdl-34480899

RESUMO

Cytochrome P450 27C1 (P450 27C1) is a retinoid desaturase expressed in the skin that catalyzes the formation of 3,4-dehydroretinoids from all-trans retinoids. Within the skin, retinoids are important regulators of proliferation and differentiation. In vivo, retinoids are bound to cellular retinol-binding proteins (CRBPs) and cellular retinoic acid-binding proteins (CRABPs). Interaction with these binding proteins is a defining characteristic of physiologically relevant enzymes in retinoid metabolism. Previous studies that characterized the catalytic activity of human P450 27C1 utilized a reconstituted in vitro system with free retinoids. However, it was unknown whether P450 27C1 could directly interact with holo-retinoid-binding proteins to receive all-trans retinoid substrates. To assess this, steady-state kinetic assays were conducted with free all-trans retinoids and holo-CRBP-1, holo-CRABP-1, and holo-CRABP-2. For holo-CRBP-1 and holo-CRABP-2, the kcat/Km values either decreased 5-fold or were equal to the respective free retinoid values. The kcat/Km value for holo-CRABP-1, however, decreased ∼65-fold in comparison with reactions with free all-trans retinoic acid. These results suggest that P450 27C1 directly accepts all-trans retinol and retinaldehyde from CRBP-1 and all-trans retinoic acid from CRABP-2, but not from CRABP-1. A difference in substrate channeling between CRABP-1 and CRABP-2 was also supported by isotope dilution experiments. Analysis of retinoid transfer from holo-CRABPs to P450 27C1 suggests that the decrease in kcat observed in steady-state kinetic assays is due to retinoid transfer becoming rate-limiting in the P450 27C1 catalytic cycle. Overall, these results illustrate that, like the CYP26 enzymes involved in retinoic acid metabolism, P450 27C1 interacts with cellular retinoid-binding proteins.


Assuntos
Família 27 do Citocromo P450/química , Receptores do Ácido Retinoico/química , Retinoides/química , Proteínas Celulares de Ligação ao Retinol/química , Família 27 do Citocromo P450/metabolismo , Humanos , Receptores do Ácido Retinoico/metabolismo , Retinoides/metabolismo , Proteínas Celulares de Ligação ao Retinol/metabolismo
4.
Anal Chem ; 92(17): 11553-11557, 2020 09 01.
Artigo em Inglês | MEDLINE | ID: mdl-32867496

RESUMO

Protein digestion is a key challenge in mass spectrometry (MS)-based structural proteomics. Although using hydrogen-deuterium exchange kinetics with MS (HDX-MS) to interrogate the high-order structure of proteins is now established, it can be challenging for ß-barrel proteins, which are important in cellular transport. These proteins contain a continuous chain of H-bonds that impart stability, causing difficulty in digestion for bottom-up measurements. To overcome this impediment, we tested organic solvents as denaturants during on-line pepsin digestion of soluble ß-barrel proteins. We selected green fluorescent protein (GFP), siderocalin (Scn), and retinol-binding protein 4 (RBP4) as model proteins and screened six different polar-aprotic and polar-protic solvent combinations to disrupt the H-bonds and hydrophobic interactions holding together the ß-sheets. The use of organic solvents improves digestion, generating more peptides from the rigid ß-barrel regions, without compromising the ability to predict the retinol binding site on RBP4 when adopting this proteolysis with HDX.


Assuntos
Espectrometria de Massa com Troca Hidrogênio-Deutério/métodos , Proteínas/química , Melhoramento Biomédico , Deutério/química , Proteínas de Fluorescência Verde/química , Hidrogênio/química , Ligação de Hidrogênio , Interações Hidrofóbicas e Hidrofílicas , Lipocalina-2/química , Pepsina A/metabolismo , Proteólise , Proteínas Celulares de Ligação ao Retinol/química , Solventes/química
5.
Chembiochem ; 21(22): 3192-3196, 2020 11 16.
Artigo em Inglês | MEDLINE | ID: mdl-32608180

RESUMO

Domain-swapping is a mechanism for evolving new protein structure from extant scaffolds, and has been an efficient protein-engineering strategy for tailoring functional diversity. However, domain swapping can only be exploited if it can be controlled, especially in cases where various folds can coexist. Herein, we describe the structure of a domain-swapped trimer of the iLBP family member hCRBPII, and suggest a mechanism for domain-swapped trimerization. It is further shown that domain-swapped trimerization can be favored by strategic installation of a disulfide bond, thus demonstrating a strategy for fold control. We further show the domain-swapped trimer to be a useful protein design template by installing a high-affinity metal binding site through the introduction of a single mutation, taking advantage of its threefold symmetry. Together, these studies show how nature can promote oligomerization, stabilize a specific oligomer, and generate new function with minimal changes to the protein sequence.


Assuntos
Engenharia de Proteínas , Proteínas Celulares de Ligação ao Retinol/química , Cristalografia por Raios X , Humanos , Modelos Moleculares , Conformação Proteica , Dobramento de Proteína
6.
Crit Rev Biochem Mol Biol ; 55(2): 197-218, 2020 04.
Artigo em Inglês | MEDLINE | ID: mdl-32466661

RESUMO

Retinol-binding protein 2 (RBP2; originally cellular retinol-binding protein, type II (CRBPII)) is a 16 kDa cytosolic protein that in the adult is localized predominantly to absorptive cells of the proximal small intestine. It is well established that RBP2 plays a central role in facilitating uptake of dietary retinoid, retinoid metabolism in enterocytes, and retinoid actions locally within the intestine. Studies of mice lacking Rbp2 establish that Rbp2 is not required in times of dietary retinoid-sufficiency. However, in times of dietary retinoid-insufficiency, the complete lack of Rbp2 gives rise to perinatal lethality owing to RBP2 absence in both placental (maternal) and neonatal tissues. Moreover, when maintained on a high-fat diet, Rbp2-knockout mice develop obesity, glucose intolerance and a fatty liver. Unexpectedly, recent investigations have demonstrated that RBP2 binds long-chain 2-monoacylglycerols (2-MAGs), including the canonical endocannabinoid 2-arachidonoylglycerol, with very high affinity, equivalent to that of retinol binding. Crystallographic studies establish that 2-MAGs bind to a site within RBP2 that fully overlaps with the retinol binding site. When challenged orally with fat, mucosal levels of 2-MAGs in Rbp2 null mice are significantly greater than those of matched controls establishing that RBP2 is a physiologically relevant MAG-binding protein. The rise in MAG levels is accompanied by elevations in circulating levels of the hormone glucose-dependent insulinotropic polypeptide (GIP). It is not understood how retinoid and/or MAG binding to RBP2 affects the functions of this protein, nor is it presently understood how these contribute to the metabolic and hormonal phenotypes observed for Rbp2-deficient mice.


Assuntos
Proteínas Celulares de Ligação ao Retinol/química , Proteínas Celulares de Ligação ao Retinol/metabolismo , Adulto , Animais , Desenvolvimento Embrionário/fisiologia , Feminino , Humanos , Imunidade Inata , Intestino Delgado/embriologia , Intestino Delgado/imunologia , Intestino Delgado/metabolismo , Fígado/embriologia , Fígado/metabolismo , Masculino , Monoglicerídeos/metabolismo , Obesidade/metabolismo , Gravidez , Retinoides/metabolismo , Proteínas Celulares de Ligação ao Retinol/genética , Vitamina A/metabolismo
7.
Fish Shellfish Immunol ; 100: 476-488, 2020 May.
Artigo em Inglês | MEDLINE | ID: mdl-32209398

RESUMO

Retinol-binding protein 4 (RBP4) is known as a highly conserved adipokine for immune activation. Aeromonas hydrophila (A. hydrophila) is the most common zoonotic pathogen in aquaculture, which causes serious economic losses to aquaculture, especially to bighead carp (Hypophthalmichthys nobilis, H. nobilis) and silver carp (Hypophthalmichthys molitrix, H. molitrix). Recent studies along with our previous findings have shown that synthetic oligodeoxynucleotides containing CpG motifs (CpG ODN) can play a good role in aquatic animals against infection. In order to clarify the relationship between CpG ODN and RBP4 under A. hydrophila infection, firstly, full-length RBP4 cDNAs from H. nobilis and H. molitrix were cloned. And characteristics of RBP4, including sequence and structure, tissue distribution and genetic evolution were analyzed. In addition, mRNA expression levels of RBP4, cytokine, toll-like receptors (TLRs), morbidity and survival rates of H. nobilis and H. molitrix were observed post CpG ODN immunization or following challenge. The results indicated that hn/hm_RBP4 (RBP4 genes obtained from H. nobilis and H. molitrix) had the highest homology with Megalobrama amblycephala. Distribution data showed that the expression level of hn_RBP4 mRNA was higher than that of hm_RBP4. After CpG ODN immunization followed by A.hydrophila challenge, significantly higher survival was observed in both carps, together with up-regulated RBP4 expression. Meanwhile, hn/hm_IL-1ß level was relatively flat (and decreased), hn/hm_IFN-γ, hn/hm_TLR4 and hn/hm_TLR9 levels increased significantly, but hn/hm_STRA6 showed no significant change, compared with control. Moreover, CpG ODN immunization could induce stronger immune protective responses (higher IFN-γ/gentle IL-1ß level and lower morbidity/higher survival rate) against A. hydrophila in H. nobilis, along with higher RBP4 level, when compared with that in H. molitrix. These results demonstrated that RBP4 was well involved in the immune protection of CpG ODN. Based on the results, we speculated that in the case of A. hydrophila infection, TLR9 signaling pathway was activated by CpG ODN. Subsequently, CpG ODN up-regulated RBP4, and RBP4 activated TLR4 signaling pathway. Then TLR4 and TLR9 synergistically improved the anti-infection responses. Our findings have good significance for improving resistance to pathogen infection in freshwater fish.


Assuntos
Carpas/genética , Carpas/microbiologia , Infecções por Bactérias Gram-Negativas/veterinária , Imunização/veterinária , Oligodesoxirribonucleotídeos/administração & dosagem , Proteínas Celulares de Ligação ao Retinol/genética , Aeromonas hydrophila/patogenicidade , Animais , Carpas/imunologia , DNA Complementar , Infecções por Bactérias Gram-Negativas/imunologia , Infecções por Bactérias Gram-Negativas/prevenção & controle , Oligodesoxirribonucleotídeos/imunologia , Proteínas Celulares de Ligação ao Retinol/química , Proteínas Celulares de Ligação ao Retinol/imunologia , Regulação para Cima
8.
Chembiochem ; 21(5): 723-729, 2020 03 02.
Artigo em Inglês | MEDLINE | ID: mdl-31482666

RESUMO

A reengineered human cellular retinol binding protein II (hCRBPII), a 15-kDa protein belonging to the intracellular lipid binding protein (iLBP) family, generates a highly fluorescent red pigment through the covalent linkage of a merocyanine aldehyde to an active site lysine residue. The complex exhibits "turn-on" fluorescence, due to a weakly fluorescent aldehyde that "lights up" with subsequent formation of a strongly fluorescent merocyanine dye within the binding pocket of the protein. Cellular penetration of merocyanine is rapid, and fluorophore maturation is nearly instantaneous. The hCRBPII/merocyanine complex displays high quantum yield, low cytotoxicity, specificity in labeling organelles, and compatibility in both cancer cell lines and yeast cells. The hCRBPII/merocyanine tag is brighter than most common red fluorescent proteins.


Assuntos
Benzopiranos/química , Corantes Fluorescentes/química , Indóis/química , Proteínas Celulares de Ligação ao Retinol/química , Animais , Células COS , Chlorocebus aethiops , Células HeLa , Humanos , Saccharomyces cerevisiae
9.
J Phys Chem Lett ; 10(23): 7333-7339, 2019 Dec 05.
Artigo em Inglês | MEDLINE | ID: mdl-31714784

RESUMO

Due to the poor aqueous solubility of retinoids, evolution has tuned their binding to cellular proteins to address specialized physiological roles by modulating uptake, storage, and delivery to specific targets. With the aim to disentangle the structure-function relationships in these proteins and disclose clues for engineering selective carriers, the binding mechanism of the two most abundant retinol-binding isoforms was explored by using enhanced sampling molecular dynamics simulations and surface plasmon resonance. The distinctive dynamics of the entry portal site in the holo species was crucial to modulate retinol dissociation. Remarkably, this process is controlled to a large extent by the replacement of Ile by Leu in the two isoforms, thus suggesting that fine control of ligand release can be achieved through a rigorous selection of conservative mutations in accessory sites.


Assuntos
Proteínas Celulares de Ligação ao Retinol/metabolismo , Vitamina A/metabolismo , Sítios de Ligação , Humanos , Isomerismo , Cinética , Ligantes , Simulação de Dinâmica Molecular , Ligação Proteica , Isoformas de Proteínas/química , Isoformas de Proteínas/metabolismo , Proteínas Celulares de Ligação ao Retinol/química , Termodinâmica , Vitamina A/química
10.
J Am Chem Soc ; 141(43): 17125-17132, 2019 10 30.
Artigo em Inglês | MEDLINE | ID: mdl-31557439

RESUMO

Protein conformational switches or allosteric proteins play a key role in the regulation of many essential biological pathways. Nonetheless, the implementation of protein conformational switches in protein design applications has proven challenging, with only a few known examples that are not derivatives of naturally occurring allosteric systems. We have discovered that the domain-swapped (DS) dimer of hCRBPII undergoes a large and robust conformational change upon retinal binding, making it a potentially powerful template for the design of protein conformational switches. Atomic resolution structures of the apo- and holo-forms illuminate a simple, mechanical movement involving sterically driven torsion angle flipping of two residues that drive the motion. We further demonstrate that the conformational "readout" can be altered by addition of cross-domain disulfide bonds, also visualized at atomic resolution. Finally, as a proof of principle, we have created an allosteric metal binding site in the DS dimer, where ligand binding results in a reversible 5-fold loss of metal binding affinity. The high resolution structure of the metal-bound variant illustrates a well-formed metal binding site at the interface of the two domains of the DS dimer and confirms the design strategy for allosteric regulation.


Assuntos
Engenharia de Proteínas/métodos , Proteínas Celulares de Ligação ao Retinol/química , Proteínas Celulares de Ligação ao Retinol/metabolismo , Regulação Alostérica , Sítios de Ligação , Dicroísmo Circular , Cristalografia por Raios X , Dissulfetos/química , Ligantes , Metais/metabolismo , Modelos Moleculares , Mutação , Domínios Proteicos , Multimerização Proteica , Proteínas Celulares de Ligação ao Retinol/genética , Treonina/genética , Tirosina/genética , Zinco/metabolismo
11.
Adv Exp Med Biol ; 1162: 39-50, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31332733

RESUMO

Cannabinoids have been widely used for recreational and medicinal purposes. The increasing legalization of cannabinoid use and the growing success in Medicinal Chemistry of cannabinoids have fueled recent interest in cannabinoid-sensing sites in receptor proteins. Here, we review structural data from high-resolution cryo-EM and crystallography studies that depict phytocannabinoid, endocannabinoid, and synthetic cannabinoid molecules bound to various proteins. The latter include antigen-binding fragment (Fab), cellular retinol binding protein 2 (CRBP2), fatty acid-binding protein 5 (FABP5), peroxisome proliferator-activated receptor γ (PPAR γ), and cannabinoid receptor types 1 and 2 (CB1 and CB2). Cannabinoid-protein complexes reveal the complex design of cannabinoid binding sites that are usually presented by conventional ligand-binding pockets on respective proteins. However, subtle differences in cannabinoid interaction with amino acids within the binding pocket often result in diverse consequences for protein function. The rapid increase in available structural data on cannabinoid-protein interactions will ultimately direct drug design efforts toward rendering highly potent cannabinoid-related pharmacotherapies that are devoid of side effects.


Assuntos
Canabinoides/química , Endocanabinoides/química , Sítios de Ligação , Proteínas de Ligação a Ácido Graxo/química , Humanos , Fragmentos Fab das Imunoglobulinas/química , PPAR gama/química , Mapeamento de Interação de Proteínas , Receptores de Canabinoides/química , Proteínas Celulares de Ligação ao Retinol/química
12.
Chembiochem ; 19(12): 1288-1295, 2018 06 18.
Artigo em Inglês | MEDLINE | ID: mdl-29645331

RESUMO

Mutants of human cellular retinol-binding protein II (hCRBPII) were engineered to bind a julolidine retinal analogue for the purpose of developing a ratiometric pH sensor. The design relied on the electrostatic influence of a titratable amino acid side chain, which affects the absorption and, thus, the emission of the protein/fluorophore complex. The ratio of emissions obtained at two excitation wavelengths that correspond to the absorption of the two forms of the protein/fluorophore complex, leads to a concentration-independent measure of pH.


Assuntos
Técnicas Biossensoriais/métodos , Corantes Fluorescentes/metabolismo , Retinaldeído/metabolismo , Proteínas Celulares de Ligação ao Retinol/metabolismo , Fluorescência , Corantes Fluorescentes/química , Humanos , Concentração de Íons de Hidrogênio , Modelos Moleculares , Mutagênese Sítio-Dirigida/métodos , Conformação Proteica , Retinaldeído/análogos & derivados , Proteínas Celulares de Ligação ao Retinol/química , Proteínas Celulares de Ligação ao Retinol/genética , Espectrometria de Fluorescência/métodos
13.
Arch Biochem Biophys ; 645: 107-116, 2018 05 01.
Artigo em Inglês | MEDLINE | ID: mdl-29567208

RESUMO

Four Cellular Retinol-binding Proteins (CRBP 1, 2, 3, 4) are encoded in the human genome. CRBP 1 and 2, sharing a 56% amino acid sequence identity, exhibit the highest binding affinities for retinol. Previous NMR studies provided some insights into the mechanism of retinol uptake, but details of such mechanism remain to be elucidated. Herein, the results of molecular dynamics simulations for the uptake of retinol by CRBP 1 and 2 are consistent with the presence of two different retinol entry points, both involving the 'cap region' (α-helices I and II and neighboring loops). We observed that a hydrophobic patch at the surface of the 'portal region' (α-helix II, CD and EF loops) of CRBP 1 attracts retinol, which accesses the binding cavity through an opening generated by the concerted movements of Arg58 and Phe57, present in the CD loop. In CRBP 2 a different distribution of the surface residues of the 'cap region' allows retinol to access the binding cavity by sinking in a hydrophobic matrix between the two α-helices. Polar interactions mainly affect retinol movements inside the ß-barrel cavities of both CRBPs. The interaction energy profiles are in agreement with the different behavior of the two protein systems.


Assuntos
Proteínas Celulares de Ligação ao Retinol/química , Proteínas Celulares de Ligação ao Retinol/metabolismo , Vitamina A/metabolismo , Apoproteínas/química , Apoproteínas/metabolismo , Humanos , Simulação de Dinâmica Molecular , Ligação Proteica , Conformação Proteica em alfa-Hélice
14.
J Chem Theory Comput ; 13(12): 6391-6404, 2017 Dec 12.
Artigo em Inglês | MEDLINE | ID: mdl-29112449

RESUMO

A novel atomistic methodology to perform free energy geometry optimization of a retinal chromophore covalently bound to any rhodopsin-like protein cavity is presented and benchmarked by computing the absorption maxima wavelengths (λmax) of distant rhodopsin systems. The optimization is achieved by computing the Nagaoka's Free Energy Gradient (FEG) within an Average Solvent Electrostatic Configuration (ASEC) atomistic representation of the thermodynamic equilibrium and minimizing such quantity via an iterative procedure based on sequential classical MD and constrained QM/MM geometry optimization steps. The performance of such an ASEC-FEG protocol is assessed at the CASPT2//CASSCF/Amber level by reproducing the λmax values observed for 12 mutants of redesigned human cellular retinol binding protein II (hCRBPII) systems; a set of 10 distant wild-type rhodopsins from vertebrates, invertebrates, eubacteria, and archaea organisms; and finally a set of 10 rhodopsin mutants from an eubacterial rhodopsin. The results clearly show that the proposed protocol, which can be easily extended to any protein incorporating a covalently bound ligand, yields correct λmax trends with limited absolute errors.


Assuntos
Modelos Moleculares , Teoria Quântica , Rodopsina/química , Animais , Humanos , Ligação de Hidrogênio , Lignanas , Mutagênese , Proteínas Celulares de Ligação ao Retinol/química , Proteínas Celulares de Ligação ao Retinol/genética , Proteínas Celulares de Ligação ao Retinol/metabolismo , Rodopsina/genética , Rodopsina/metabolismo , Eletricidade Estática , Termodinâmica
15.
Biochem Biophys Res Commun ; 483(1): 203-208, 2017 01 29.
Artigo em Inglês | MEDLINE | ID: mdl-28034750

RESUMO

Computing the ligand-protein binding affinity (or the Gibbs free energy) with chemical accuracy has long been a challenge for which many methods/approaches have been developed and refined with various successful applications. False positives and, even more harmful, false negatives have been and still are a common occurrence in practical applications. Inevitable in all approaches are the errors in the force field parameters we obtain from quantum mechanical computation and/or empirical fittings for the intra- and inter-molecular interactions. These errors propagate to the final results of the computed binding affinities even if we were able to perfectly implement the statistical mechanics of all the processes relevant to a given problem. And they are actually amplified to various degrees even in the mature, sophisticated computational approaches. In particular, the free energy perturbation (alchemical) approaches amplify the errors in the force field parameters because they rely on extracting the small differences between similarly large numbers. In this paper, we develop a hybrid steered molecular dynamics (hSMD) approach to the difficult binding problems of a ligand buried deep inside a protein. Sampling the transition along a physical (not alchemical) dissociation path of opening up the binding cavity---pulling out the ligand---closing back the cavity, we can avoid the problem of error amplifications by not relying on small differences between similar numbers. We tested this new form of hSMD on retinol inside cellular retinol-binding protein 1 and three cases of a ligand (a benzylacetate, a 2-nitrothiophene, and a benzene) inside a T4 lysozyme L99A/M102Q(H) double mutant. In all cases, we obtained binding free energies in close agreement with the experimentally measured values. This indicates that the force field parameters we employed are accurate and that hSMD (a brute force, unsophisticated approach) is free from the problem of error amplification suffered by many sophisticated approaches in the literature.


Assuntos
Simulação de Dinâmica Molecular , Proteínas/química , Proteínas/metabolismo , Benzeno/química , Benzeno/metabolismo , Compostos de Benzil/química , Compostos de Benzil/metabolismo , Sítios de Ligação , Ligantes , Muramidase/química , Muramidase/genética , Muramidase/metabolismo , Mutação , Conformação Proteica , Proteínas Celulares de Ligação ao Retinol/química , Proteínas Celulares de Ligação ao Retinol/metabolismo , Tiofenos/química , Tiofenos/metabolismo , Vitamina A/química , Vitamina A/metabolismo
16.
Subcell Biochem ; 81: 21-76, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27830500

RESUMO

Multiple binding and transport proteins facilitate many aspects of retinoid biology through effects on retinoid transport, cellular uptake, metabolism, and nuclear delivery. These include the serum retinol binding protein sRBP (aka Rbp4), the plasma membrane sRBP receptor Stra6, and the intracellular retinoid binding-proteins such as cellular retinol-binding proteins (CRBP) and cellular retinoic acid binding-proteins (CRABP). sRBP transports the highly lipophilic retinol through an aqueous medium. The major intracellular retinol-binding protein, CRBP1, likely enhances efficient retinoid use by providing a sink to facilitate retinol uptake from sRBP through the plasma membrane or via Stra6, delivering retinol or retinal to select enzymes that generate retinyl esters or retinoic acid, and protecting retinol/retinal from excess catabolism or opportunistic metabolism. Intracellular retinoic acid binding-proteins (CRABP1 and 2, and FABP5) seem to have more diverse functions distinctive to each, such as directing retinoic acid to catabolism, delivering retinoic acid to specific nuclear receptors, and generating non-canonical actions. Gene ablation of intracellular retinoid binding-proteins does not cause embryonic lethality or gross morphological defects. Metabolic and functional defects manifested in knockouts of CRBP1, CRBP2 and CRBP3, however, illustrate their essentiality to health, and in the case of CRBP2, to survival during limited dietary vitamin A. Future studies should continue to address the specific molecular interactions that occur between retinoid binding-proteins and their targets and their precise physiologic contributions to retinoid homeostasis and function.


Assuntos
Retinoides/fisiologia , Proteínas Celulares de Ligação ao Retinol/fisiologia , Oxirredutases do Álcool/metabolismo , Aldeído Desidrogenase/metabolismo , Animais , Transporte Biológico , Núcleo Celular/metabolismo , Olho/metabolismo , Técnicas de Inativação de Genes , Homeostase , Humanos , Mucosa Intestinal/metabolismo , Camundongos , Camundongos Knockout , Modelos Moleculares , Proteínas de Neoplasias/metabolismo , Conformação Proteica , Receptores Citoplasmáticos e Nucleares/metabolismo , Retinaldeído/metabolismo , Proteínas Celulares de Ligação ao Retinol/química , Proteínas Celulares de Ligação ao Retinol/deficiência , Proteínas Celulares de Ligação ao Retinol/genética , Transdução de Sinais/fisiologia , Tretinoína/metabolismo , Vitamina A/metabolismo , Vitamina A/toxicidade
17.
Structure ; 24(9): 1590-8, 2016 09 06.
Artigo em Inglês | MEDLINE | ID: mdl-27524203

RESUMO

Human Cellular Retinol Binding Protein II (hCRBPII), a member of the intracellular lipid-binding protein family, is a monomeric protein responsible for the intracellular transport of retinol and retinal. Herein we report that hCRBPII forms an extensive domain-swapped dimer during bacterial expression. The domain-swapped region encompasses almost half of the protein. The dimer represents a novel structural architecture with the mouths of the two binding cavities facing each other, producing a new binding cavity that spans the length of the protein complex. Although wild-type hCRBPII forms the dimer, the propensity for dimerization can be substantially increased via mutation at Tyr60. The monomeric form of the wild-type protein represents the thermodynamically more stable species, making the domain-swapped dimer a kinetically trapped entity. Hypothetically, the wild-type protein has evolved to minimize dimerization of the folding intermediate through a critical hydrogen bond (Tyr60-Glu72) that disfavors the dimeric form.


Assuntos
Substituição de Aminoácidos , Ácido Glutâmico/química , Proteínas Celulares de Ligação ao Retinol/química , Tirosina/química , Motivos de Aminoácidos , Sítios de Ligação , Cristalografia por Raios X , Expressão Gênica , Ácido Glutâmico/metabolismo , Humanos , Ligação de Hidrogênio , Cinética , Modelos Moleculares , Mutação , Ligação Proteica , Conformação Proteica em alfa-Hélice , Conformação Proteica em Folha beta , Domínios Proteicos , Dobramento de Proteína , Multimerização Proteica , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Proteínas Celulares de Ligação ao Retinol/genética , Proteínas Celulares de Ligação ao Retinol/metabolismo , Termodinâmica , Tirosina/metabolismo
18.
Chemistry ; 22(24): 8254-61, 2016 06 06.
Artigo em Inglês | MEDLINE | ID: mdl-27120137

RESUMO

Rational design of light-capturing properties requires understanding the molecular and electronic structure of chromophores in their native chemical or biological environment. We employ here large-scale quantum chemical calculations to study the light-capturing properties of retinal in recently designed human cellular retinol binding protein II (hCRBPII) variants (Wang et al. Science, 2012, 338, 1340-1343). Our calculations show that these proteins absorb across a large part of the visible spectrum by combined polarization and electrostatic effects. These effects stabilize the ground or excited state energy levels of the retinal by perturbing the Schiff-base or ß-ionone moieties of the chromophore, which in turn modulates the amount of charge transfer within the molecule. Based on the predicted tuning principles, we design putative in silico mutations that further shift the absorption properties of retinal in hCRBPII towards the ultraviolet and infrared regions of the spectrum.


Assuntos
Retinaldeído/química , Proteínas Celulares de Ligação ao Retinol/química , Humanos , Modelos Moleculares , Norisoprenoides/química , Teoria Quântica , Retinaldeído/metabolismo , Proteínas Celulares de Ligação ao Retinol/genética , Proteínas Celulares de Ligação ao Retinol/metabolismo , Bases de Schiff/química , Espectrofotometria Infravermelho , Espectrofotometria Ultravioleta , Eletricidade Estática , Termodinâmica
19.
J Biol Chem ; 291(16): 8528-40, 2016 Apr 15.
Artigo em Inglês | MEDLINE | ID: mdl-26900151

RESUMO

Important in regulating the uptake, storage, and metabolism of retinoids, cellular retinol-binding protein 1 (CRBP1) is essential for trafficking vitamin A through the cytoplasm. However, the molecular details of ligand uptake and targeted release by CRBP1 remain unclear. Here we report the first structure of CRBP1 in a ligand-free form as well as ultra-high resolution structures of this protein bound to either all-trans-retinol or retinylamine, the latter a therapeutic retinoid that prevents light-induced retinal degeneration. Superpositioning of human apo- and holo-CRBP1 revealed major differences within segments surrounding the entrance to the retinoid-binding site. These included α-helix II and hairpin turns between ß-strands ßC-ßD and ßE-ßF as well as several side chains, such as Phe-57, Tyr-60, and Ile-77, that change their orientations to accommodate the ligand. Additionally, we mapped hydrogen bond networks inside the retinoid-binding cavity and demonstrated their significance for the ligand affinity. Analyses of the crystallographic B-factors indicated several regions with higher backbone mobility in the apoprotein that became more rigid upon retinoid binding. This conformational flexibility of human apo-CRBP1 facilitates interaction with the ligands, whereas the more rigid holoprotein structure protects the labile retinoid moiety during vitamin A transport. These findings suggest a mechanism of induced fit upon ligand binding by mammalian cellular retinol-binding proteins.


Assuntos
Proteínas Celulares de Ligação ao Retinol/química , Vitamina A/química , Cristalografia por Raios X , Humanos , Ligação de Hidrogênio , Ligantes , Estrutura Secundária de Proteína
20.
Med Hypotheses ; 88: 60-2, 2016 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-26880640

RESUMO

Vitamin A is a fat-soluble vitamin required for many physiological functions. The intracellular transport of vitamin A is assisted by proteins called cellular retinol-binding proteins (CRBP I/II). The absorption, storage and usage of vitamin A are regulated by a protein called lecithin:retinol acyltransferase (LRAT), a retinol-related enzyme that transfers an acyl group derived from an sn-1 position of phosphatidylcholine to retinol. LRAT is a member of the protein family which includes HRAS-like tumor suppressors (HRASLS). However, the HRASLS proteins never use retinol as an acyl acceptor. The mechanisms underlying the different substrate specificities between LRAT and HRASLS proteins are unknown. We propose in this report that LRAT physically interacts with CRBP and the LRAT-CRBP complex represents the binding pockets for both an acyl group and retinol, thus assuring the substrate specificity of LRAT.


Assuntos
Aciltransferases/fisiologia , Proteínas Celulares de Ligação ao Retinol/fisiologia , Vitamina A/química , Aciltransferases/química , Esterificação , Ésteres/química , Humanos , Lecitinas/química , Fígado/metabolismo , Espectroscopia de Ressonância Magnética , Modelos Teóricos , Proteínas Celulares de Ligação ao Retinol/química , Especificidade por Substrato , Deficiência de Vitamina A/imunologia
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