Role of Protein-Protein Interactions in Metabolism: Genetics, Structure, Function

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The catalytic mechanism of steroidogenic cytochromes P450 from all-atom simulations: Entwinement with membrane environment, redox partners, and post-transcriptional regulation

Cytochromes P450 (CYP450s) promote the biosynthesis of steroid hormones with major impact on the onset of diseases such as breast and prostate cancers. By merging distinct functions into the same catalytic scaffold, steroidogenic CYP450s enhance complex chemical transformations with extreme efficiency and selectivity. Mammalian CYP450s and their redox partners are membrane-anchored proteins, dynamically associating to form functional machineries. Mounting evidence signifies that environmental factors are strictly intertwined with CYP450s catalysis. Atomic-level simulations have the potential to provide insights into the catalytic mechanism of steroidogenic CYP450s and on its regulation by environmental factors, furnishing information often inaccessible to experimental means. In this review, after an introduction of computational methods commonly employed to tackle these systems, we report the current knowledge on three steroidogenic CYP450s\u2014CYP11A1, CYP17A1, and CYP19A1\u2014endowed with multiple catalytic functions and critically involved in cancer onset. In particular, besides discussing their catalytic mechanisms, we highlight how the membrane environment contributes to (i) regulate ligand channeling through these enzymes, (ii) modulate their interactions with specific protein partners, (iii) mediate post-transcriptional regulation induced by phosphorylation. The results presented set the basis for developing novel therapeutic strategies aimed at fighting diseases originating from steroid metabolism dysfunction

Hepatic cytochromes P450: structural degrons and barcodes, posttranslational modifications and cellular adapters in the ERAD-endgame.

The endoplasmic reticulum (ER)-anchored hepatic cytochromes P450 (P450s) are enzymes that metabolize endo- and xenobiotics i.e. drugs, carcinogens, toxins, natural and chemical products. These agents modulate liver P450 content through increased synthesis or reduction via inactivation and/or proteolytic degradation, resulting in clinically significant drug-drug interactions. P450 proteolytic degradation occurs via ER-associated degradation (ERAD) involving either of two distinct routes: Ubiquitin (Ub)-dependent 26S proteasomal degradation (ERAD/UPD) or autophagic lysosomal degradation (ERAD/ALD). CYP3A4, the major human liver/intestinal P450, and the fast-turnover CYP2E1 species are degraded via ERAD/UPD entailing multisite protein phosphorylation and subsequent ubiquitination by gp78 and CHIP E3 Ub-ligases. We are gaining insight into the nature of the structural determinants involved in CYP3A4 and CYP2E1 molecular recognition in ERAD/UPD [i.e. K48-linked polyUb chains and linear and/or "conformational" phosphodegrons consisting either of consecutive sequences on surface loops and/or disordered regions, or structurally-assembled surface clusters of negatively charged acidic (Asp/Glu) and phosphorylated (Ser/Thr) residues, within or vicinal to which, Lys-residues are targeted for ubiquitination]. Structural inspection of select human liver P450s reveals that such linear or conformational phosphodegrons may indeed be a common P450-ERAD/UPD feature. By contrast, although many P450s such as the slow-turnover CYP2E1 species and rat liver CYP2B1 and CYP2C11 are degraded via ERAD/ALD, little is known about the mechanism of their ALD-targeting. On the basis of our current knowledge of ALD-substrate targeting, we propose a tripartite conjunction of K63-linked Ub-chains, P450 structural "LIR" motifs and selective cellular "cargo receptors" as plausible P450-ALD determinants

Dynamics and Interactions of Membrane Proteins

Membrane proteins are members of the class of proteins that perform their functions while being associated with a lipid bilayer. In the cell, they serve as transporters, receptors, anchors and enzymes. The domain organisation of these proteins suggests importance of lipid membrane and protein-lipid interactions for protein function. The requirement of a membrane mimic and the level of its resemblance to a native one for protein investigation makes the studies of membrane proteins a challenging project. My research work is focusing on the biophysical and biochemical studies of membrane proteins. This dissertation outlines two separate projects, each with their own challenges. Ras proteins are members of a superfamily of small GTPases that act as molecular switches that are involved in signal transduction pathways responsible for cell division and proliferation and, as one might guess, protein malfunction can lead to cancer. Recently, there have been a number of studies that suggest Ras protein dimerization on lipid membranes through protein-protein interactions between G- domains. On the basis of the results obtained from solution NMR and fluorescence polarization anisotropy studies, we concluded that the G-domain of the Ras protein by itself is not prone to dimerization. The result of this work was later confirmed by publications from other groups that performed studies in the presence of the lipid bilayer. NADPH-cytochrome P450 oxidoreductase (POR) is an integral membrane protein involved in an electron transport pathway transferring electrons from NADPH to cytochrome P450. The goal was achieved by application of lipid nanodisc technology, 13C-methyl extrinsic labeling coupled with Methyl-TROSY NMR technique that resulted in signals that showed differential sensitivity towards the redox state of the protein cofactors and conformational transitions of the protein. Moreover, results were obtained on a 600MHz instrument under protonated conditions. The goal of this project was the development of methodology to obtain structural data on a high-molecular weight protein associated with lipid nanodiscs in the presence of paramagnetic cofactors. Membrane proteins are challenging systems to research due to diverse interactions they experience on the membrane surface. In this dissertation I successfully utilized two approaches investigating this interactions: in my first project, I separately studied protein-protein interaction underlying the dimerization hypothesis, while in my second project I suggested the approach to explore conformational details and diverse interactions in a lipoprotein complex

Transgenic Expression of Haemonchus contortus Cytochrome P450 Hco-cyp-13A11 Decreases Susceptibility to Particular but Not All Macrocyclic Lactones in the Model Organism Caenorhabditis elegans

The number of reported macrocyclic lactones (ML) resistance cases across all livestock hosts is steadily increasing. Different studies in the parasitic nematode Haemonchus contortus assume the participation of cytochrome P450s (Cyps) enzymes in ML resistance. Still, functional data about their individual contribution to resistance or substrate specificity is missing. Via microinjection, transgenic Caenorhabditis elegans expressing HCON_00141052 (transgene-Hco-cyp-13A11) from extrachromosomal arrays were generated. After 24 h of exposure to different concentrations of ivermectin (IVM), ivermectin aglycone (IVMa), selamectin (SEL), doramectin (DRM), eprinomectin (EPR), and moxidectin (MOX), motility assays were performed to determine the impact of the H. contortus Cyp to the susceptibility of the worms against each ML. While transgene-Hco-cyp-13A11 significantly decreased susceptibility to IVM (four-fold), IVMa (2-fold), and SEL (3-fold), a slight effect for DRM and no effect for MOX, and EPR was observed. This substrate specificity of Hco-cyp-13A11 could not be explained by molecular modeling and docking studies. Hco-Cyp-13A11 molecular models were obtained for alleles from isolates with different resistance statuses. Although 14 amino acid polymorphisms were detected, none was resistance specific. In conclusion, Hco-cyp-13A11 decreased IVM, IVMa, and SEL susceptibility to a different extent, but its potential impact on ML resistance is not driven by polymorphisms

Use of protein immobilization to measure cytochrome P450 conduction and metabolism kinetics

Cytochrome P450s (P450s) are a large family (\u3e11,000) of heme thiolated proteins that are responsible for ~ 75% of the metabolism of pharmaceuticals on the market. Understanding P450 mediated metabolism is crucial for accurate in vitro predictions of drug metabolism. P450 protein-protein interactions have been shown to alter enzyme catalytic activity. Furthermore, these interactions are isoform specific, and can elicit activation, inhibition, or no effect on enzymatic activity. Studies show these effects are also dependent on the protein binding partner cytochrome P450 reductase (CPR), and the order of protein addition to purified reconstituted enzyme systems. In the current work, we use controlled immobilization of P450s to a gold surface to gain a better understanding of P450-P450 interactions between three key drug-metabolizing isoforms (CYP2C9, CYP3A4, and CYP2D6). Molecular modeling was used to assess the favorability of homo/heteromeric P450 complex formation. P450 complex formation in vitro was analyzed in real-time utilizing surface plasmon resonance (SPR). Lastly, the effects of P450 complex formation were investigated utilizing our immobilized platform and reconstituted enzyme systems.;Molecular modeling shows favorable binding of CYP2C9-CPR, CYP2C9-CYP2D6, CYP2C9-CYP2C9, and CYP2C9-CYP3A4 in rank order. KD values obtained via SPR show strong binding, in the nanomolar range, of the above pairs, with CYP2D6 yielding the lowest KD, followed by CYP2C9, CPR, and CYP3A4. Metabolic incubations show immobilized CYP2C9 metabolism was activated by homomeric complex formation. CYP2C9 metabolism was not affected by the presence of CYP3A4 with saturating CPR concentrations. CYP2C9 metabolism was activated by CYP2D6 in solution, but inhibited when CYP2C9 was immobilized, both at saturating and sub-saturating CPR concentrations. Order of addition of proteins (CYP2C9, CYP2D6, CYP3A4, and CPR) influenced magnitude of inhibition for CYP3A4, but not CYP2D6. These results indicate isoform specific P450 interactions and effects on P450 mediated-metabolism. These findings are important in evaluating how in vitro results are obtained for measuring P450 kinetics, and provide a better mechanistic understanding of P450-P450 interactions to allow for better prediction of in vivo metabolism from in vitro data.;We also demonstrate that gold nanopillars, functionalized with an organic self-assembled monolayer, can be used to measure the electrical conductance properties of immobilized P450s without aggregation. Given that transfer of the 1st electron to the P450 heme group acts as the gating step for the catalytic cycle, understanding electron transfer in P450s could shed light on metabolism kinetics. Conductance measurements of nanopillars with immobilized CYP2C9 using conducting probe atomic force microscopy demonstrate that a correlation exists between the energy barrier height between hopping sites and CYP2C9 metabolic activity. Measurements performed as a function of tip force indicate that, when subjected to a large force, the protein is more stable in the presence of a substrate. This agrees with the hypothesis that substrate entry into the active site helps to stabilize the enzyme.;The relative distance between hopping sites also increases with increasing force, possibly because protein functional groups responsible for electron transport depend on the structure of the protein. The inhibitor sulfaphenazole, in addition to the previously studied aniline, increased the barrier height for electron transfer and thereby makes CYP2C9 reduction more difficult and inhibits metabolism. This suggests that P450 Type II ligands may decrease the ease of electron transport processes in the enzyme, in addition to occupying the active site. These findings further our understanding of how P450 metabolism is mediated through substrates, and provides an important technological advancement for studying P450s that avoids complications found in current methodologies. These two studies demonstrate the ability of an immobilized P450 platform to provide information on protein-protein interactions, substrate protein interactions, and atypical enzyme kinetics

An overview of the role of cytochrome P450 enzyme system in food-drug interactions and possible applications in veterinary medicine

Dissertação de Mestrado Integrado em Medicina VeterináriaCytochrome P450 enzymes (CYP) are hemoproteins belonging to the group of monooxygenases and one of the main enzymatic systems responsible for drug metabolism. In the present study, in vitro approach was applied to evaluate the relation of CYP-catalyzed activities between human, rabbit, minipig and mouse, using single substrate assays (MultiCYP 7-ethoxycoumarin 0-deethylase (ECOD), CYP1A1/2 7-ethoxyresorufin 0- deethylase (EROD), CYP2A6 coumarin 7-hydroxylase (COH), CYP3A4 midazolam 1- hydroxylase (OH-MDZ), and CYP2E1 chlorzoxazone 6-hydroxylase (OH-CLZ)). It was also studied plant extracts (Pinus sylvestris, Angelica archangelica, Mentha sp., Citrus grandis) and phytochemicals (8-Hydroxybergapten, 5,6-dihydroxyangelicin, α, β-Thujone, α-Thujone, angelicin, bergamottin, bergapten, bergaptol, cnidilin, imperatorin, isobergapten, isopimpinellin, lanatin, phellopterin, psoralen, sphondin, xanthotoxin) as potential inhibitors in CYP-related activities of hepatic human microsomes (CYP1A1/2 (EROD), CYP2A6 (COH), CYP3A4 (OH-MDZ)). This study showed that the lowest ECOD activity was detected in humans and there was no similarity between other species. CYP1A1/2 showed equivalent activities. The highest CYP activities in humans were found for CYP2A6 and CYP3A4. In CYP2E1 activity, two similar groups were recognized: human and mouse versus rabbit and minipig. EROD reaction was the most inhibited CYP-mediated reaction. COH reaction was inhibited by few compounds. The highest inhibition was detected among angular furocoumarins. Linear furocoumarins group had the lower inhibitory concentration of CYP3A4. Thujone showed weak inhibition of CYP activities.RESUMO - As enzimas do sistema citocromo P450 (CYP) são hemoproteinas pertencentes ao grupo das monoxigenases e um dos principais sistemas enzimáticos responsáveis pela metabolização de fármacos. Neste estudo foi avaliada a relação da actividade catalítica de diferentes CYPs entre humanos, coelhos, minipig e murganhos, recorrendo a substratos como sondas individuais in vitro para mensurar reacções especificas (MultiCYP 7-etoxicumarina 0-deetilase (ECOD), CYP1A1/2 7-etoxiresorufina 0-deetilase (EROD), CYP2A6 cumarina 7-hidroxilase (COH), CYP3A4 midazolam 1-hidroxilase (OH-MDZ), e CYP2E1 clorozoxazona 6-hidroxilase (OH-CLZ)). Também foram estudados extractos de plantas (Pinus sylvestris, Angelica archangelica, Mentha sp., Citrus grandis) e fitoquímicos (8-hidroxibergaptem, 5,6-dihidroxiangelicina, α, β-tujona, α-tujona, angelicina, bergamottin, bergapteno, bergaptol, cnidilina, imperatorina, isobergapteno, isopimpinelina, lanatin, felopterina, psoraleno, sphondin, xantotoxina) como potenciais inibidores da actividade catalítica dos CYPs microssomais hepáticos humanos (CYP1A1/2 (EROD), CYP2A6 (COH), CYP3A4 (OH-MDZ)). Neste estudo não foram detectadas actividades similires entre espécies na reacção ECOD e a actividade mais baixa foi detectada nos humanos. A reacção EROD dos CYP1A1/2 demonstrou actividades similares entre as diferentes espécies. As maiores actividades cataliticas verificadas nos humanos correspondem aos CYP2A6 e CYP3A4. No estudo da reacção do CYP2E1 foram determinados dois grupos distintos com actividades cataliticas similares: 1) humanos e murganhos, 2) coelhos e minipigs. No estudo de potenciais inibidores dos CYPs, a reacção EROD foi a mais inibida. Pelo contrário, a reacção COH foi inibida por poucos compostos. A maioria das inibições ocorreu por exposição a furocumarinas angulares. O grupo de furocumarinas lineares teve a menor concentração inibitória da reacção OH-MDZ do CYP3A4. Os fitoquímicos α, β-tujona e α- tujona demonstraram ter um fraco poder inibitório na actividade dos CYPs analisados

Symposium Report The Role of Protein-Protein and Protein-Membrane Interactions on P450 Function

ABSTRACT This symposium summary, sponsored by the ASPET, was held at Experimental Biology 2015 on March 29, 2015, in Boston, Massachusetts. The symposium focused on: 1) the interactions of cytochrome P450s (P450s) with their redox partners; and 2) the role of the lipid membrane in their orientation and stabilization. Two presentations discussed the interactions of P450s with NADPH-P450 reductase (CPR) and cytochrome b 5 . First, solution nuclear magnetic resonance was used to compare the protein interactions that facilitated either the hydroxylase or lyase activities of CYP17A1. The lyase interaction was stimulated by the presence of b 5 and 17a-hydroxypregnenolone, whereas the hydroxylase reaction was predominant in the absence of b 5 . The role of b 5 was also shown in vivo by selective hepatic knockout of b 5 from mice expressing CYP3A4 and CYP2D6; the lack of b 5 caused a decrease in the clearance of several substrates. The role of the membrane on P450 orientation was examined using computational methods, showing that the proximal region of the P450 molecule faced the aqueous phase. The distal region, containing the substrate-access channel, was associated with the membrane. The interaction of NADPH-P450 reductase (CPR) with the membrane was also described, showing the ability of CPR to "helicopter" above the membrane. Finally, the endoplasmic reticulum (ER) was shown to be heterogeneous, having ordered membrane regions containing cholesterol and more disordered regions. Interestingly, two closely related P450s, CYP1A1 and CYP1A2, resided in different regions of the ER. The structural characteristics of their localization were examined. These studies emphasize the importance of P450 protein organization to their function

Cytochromes P450: Drug Metabolism, Bioactivation and Biodiversity 2.0

This book, "Cytochromes P450: Drug Metabolism, Bioactivation and Biodiversity", presents five papers on human cytochrome P450 (CYP) and P450 reductase, three reviews on the role of CYPs in humans and their use as biomarkers, six papers on CYPs in microorganisms, and one study on CYP in insects. The first paper reports the in silico modeling of human CYP3A4 access channels. The second uses structural methods to explain the mechanism-based inactivation of CYP3A4 by mibefradil, 6,7-dihydroxy-bergamottin, and azamulin. The third article compares electron transfer in CYP2C9 and CYP2C19 using structural and biochemical methods, and the fourth uses kinetic methods to study electron transfer to CYP2C8 allelic mutants. The fifth article characterizes electron transfer between the reductase and CYP using in silico and in vitro methods, focusing on the conformations of the reductase. Then, two reviews describe clinical implications in cardiology and oncology and the role of fatty acid metabolism in cardiology and skin diseases. The second review is on the potential use of circulating extracellular vesicles as biomarkers. Five papers analyze the CYPomes of diverse microorganisms: the Bacillus genus, Mycobacteria, the fungi Tremellomycetes, Cyanobacteria, and Streptomyces. The sixth focuses on a specific Mycobacterium CYP, CYP128, and its importance in M. tuberculosis. The subject of the last paper is CYP in Sogatella furcifera, a plant pest, and its resistance to the insecticide sulfoxaflor