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Abstract
Fatty acid-binding proteins (FABPs) are small lipid-binding proteins abundantly expressed in tissues that are highly active in fatty acid (FA) metabolism. Ten mammalian FABPs have been identified, with tissue-specific expression patterns and highly conserved tertiary structures. FABPs were initially studied as intracellular FA transport proteins. Further investigation has demonstrated their participation in lipid metabolism, both directly and via regulation of gene expression, and in signaling within their cells of expression. There is also evidence that they may be secreted and have functional impact via the circulation. It has also been shown that the FABP ligand binding repertoire extends beyond long-chain FAs and that their functional properties also involve participation in systemic metabolism. This article reviews the present understanding of FABP functions and their apparent roles in disease, particularly metabolic and inflammation-related disorders and cancers.
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Affiliation(s)
- Judith Storch
- Department of Nutritional Sciences and Rutgers Center for Lipid Research, Rutgers University, New Brunswick, New Jersey, United States;
| | - Betina Corsico
- Instituto de Investigaciones Bioquímicas de La Plata, CONICET-UNLP, Facultad de Ciencias Médicas, La Plata, Argentina;
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2
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Horváth G, Balterer B, Micsonai A, Kardos J, Toke O. Multiple Timescale Dynamic Analysis of Functionally-Impairing Mutations in Human Ileal Bile Acid-Binding Protein. Int J Mol Sci 2022; 23:ijms231911346. [PMID: 36232642 PMCID: PMC9569817 DOI: 10.3390/ijms231911346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/16/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022] Open
Abstract
Human ileal bile acid-binding protein (hI-BABP) has a key role in the enterohepatic circulation of bile salts. Its two internal binding sites exhibit positive cooperativity accompanied by a site-selectivity of glycocholate (GCA) and glycochenodeoxycholate (GCDA), the two most abundant bile salts in humans. To improve our understanding of the role of dynamics in ligand binding, we introduced functionally impairing single-residue mutations at two key regions of the protein and subjected the mutants to NMR relaxation analysis and MD simulations. According to our results, mutation in both the vicinity of the C/D (Q51A) and the G/H (Q99A) turns results in a redistribution of motional freedom in apo hI-BABP. Mutation Q51A, deteriorating the site-selectivity of GCA and GCDA, results in the channeling of ms fluctuations into faster motions in the binding pocket hampering the realization of key side chain interactions. Mutation Q99A, abolishing positive binding cooperativity for GCDA, leaves ms motions in the C-terminal half unchanged but by decoupling βD from a dynamic cluster of the N-terminal half displays an increased flexibility in the vicinity of site 1. MD simulations of the variants indicate structural differences in the portal region and mutation-induced changes in dynamics, which depend on the protonation state of histidines. A dynamic coupling between the EFGH portal, the C/D-region, and the helical cap is evidenced highlighting the interplay of structural and dynamic effects in bile salt recognition in hI-BABP.
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Affiliation(s)
- Gergő Horváth
- NMR Research Laboratory, Centre for Structural Science, Research Centre for Natural Sciences, 2 Magyar Tudósok Körútja, H-1117 Budapest, Hungary
| | - Bence Balterer
- NMR Research Laboratory, Centre for Structural Science, Research Centre for Natural Sciences, 2 Magyar Tudósok Körútja, H-1117 Budapest, Hungary
| | - András Micsonai
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, H-1117 Budapest, Hungary
| | - József Kardos
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, H-1117 Budapest, Hungary
| | - Orsolya Toke
- NMR Research Laboratory, Centre for Structural Science, Research Centre for Natural Sciences, 2 Magyar Tudósok Körútja, H-1117 Budapest, Hungary
- Correspondence: ; Tel.: +36-1-382-6575
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Mei L, Fu Q, Guo T, Ji Q, Zhou Y. Structural changes and cholesterol-lowering in denatured whey protein isolate: Malic acid combined enzymolysis. Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2022.107502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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4
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Toke O. Structural and Dynamic Determinants of Molecular Recognition in Bile Acid-Binding Proteins. Int J Mol Sci 2022; 23:ijms23010505. [PMID: 35008930 PMCID: PMC8745080 DOI: 10.3390/ijms23010505] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/30/2021] [Accepted: 12/31/2021] [Indexed: 12/12/2022] Open
Abstract
Disorders in bile acid transport and metabolism have been related to a number of metabolic disease states, atherosclerosis, type-II diabetes, and cancer. Bile acid-binding proteins (BABPs), a subfamily of intracellular lipid-binding proteins (iLBPs), have a key role in the cellular trafficking and metabolic targeting of bile salts. Within the family of iLBPs, BABPs exhibit unique binding properties including positive binding cooperativity and site-selectivity, which in different tissues and organisms appears to be tailored to the local bile salt pool. Structural and biophysical studies of the past two decades have shed light on the mechanism of bile salt binding at the atomic level, providing us with a mechanistic picture of ligand entry and release, and the communication between the binding sites. In this review, we discuss the emerging view of bile salt recognition in intestinal- and liver-BABPs, with examples from both mammalian and non-mammalian species. The structural and dynamic determinants of the BABP-bile–salt interaction reviewed herein set the basis for the design and development of drug candidates targeting the transcellular traffic of bile salts in enterocytes and hepatocytes.
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Affiliation(s)
- Orsolya Toke
- Laboratory for NMR Spectroscopy, Structural Research Centre, Research Centre for Natural Sciences, 2 Magyar Tudósok Körútja, H-1117 Budapest, Hungary
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Validation of Recombinant Chicken Liver Bile Acid Binding Protein as a Tool for Cholic Acid Hosting. Biomolecules 2021; 11:biom11050645. [PMID: 33925706 PMCID: PMC8146743 DOI: 10.3390/biom11050645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/24/2021] [Accepted: 04/26/2021] [Indexed: 02/02/2023] Open
Abstract
Bile acids (BAs) are hydroxylated steroids derived from cholesterol that act at the intestinal level to facilitate the absorption of several nutrients and also play a role as signaling molecules. In the liver of various vertebrates, the trafficking of BAs is mediated by bile acid-binding proteins (L-BABPs). The ability to host hydrophobic or amphipathic molecules makes BABPs suitable for the distribution of a variety of physiological and exogenous substances. Thus, BABPs have been proposed as drug carriers, and more recently, they have also been employed to develop innovative nanotechnology and biotechnology systems. Here, we report an efficient protocol for the production, purification, and crystallization of chicken liver BABP (cL-BABP). By means of target expression as His6-tag cL-BABP, we obtained a large amount of pure and homogeneous proteins through a simple purification procedure relying on affinity chromatography. The recombinant cL-BABP showed a raised propensity to crystallize, allowing us to obtain its structure at high resolution and, in turn, assess the structural conservation of the recombinant cL-BABP with respect to the liver-extracted protein. The results support the use of recombinant cL-BABP for the development of drug carriers, nanotechnologies, and innovative synthetic photoswitch systems.
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Harjula SKE, Saralahti AK, Ojanen MJT, Rantapero T, Uusi-Mäkelä MIE, Nykter M, Lohi O, Parikka M, Rämet M. Characterization of immune response against Mycobacterium marinum infection in the main hematopoietic organ of adult zebrafish (Danio rerio). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2020; 103:103523. [PMID: 31626817 DOI: 10.1016/j.dci.2019.103523] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/09/2019] [Accepted: 10/14/2019] [Indexed: 06/10/2023]
Abstract
Tuberculosis remains a major global health challenge. To gain information about genes important for defense against tuberculosis, we used a well-established tuberculosis model; Mycobacterium marinum infection in adult zebrafish. To characterize the immunological response to mycobacterial infection at 14 days post infection, we performed a whole-genome level transcriptome analysis using cells from kidney, the main hematopoietic organ of adult zebrafish. Among the upregulated genes, those associated with immune signaling and regulation formed the largest category, whereas the largest group of downregulated genes had a metabolic role. We also performed a forward genetic screen in adult zebrafish and identified a fish line with severely impaired survival during chronic mycobacterial infection. Based on transcriptome analysis, these fish have decreased expression of several immunological genes. Taken together, these results give new information about the genes involved in the defense against mycobacterial infection in zebrafish.
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Affiliation(s)
- Sanna-Kaisa E Harjula
- Laboratory of Experimental Immunology, BioMediTech, Faculty of Medicine and Health Technology, FI-33014, Tampere University, Finland.
| | - Anni K Saralahti
- Laboratory of Experimental Immunology, BioMediTech, Faculty of Medicine and Health Technology, FI-33014, Tampere University, Finland.
| | - Markus J T Ojanen
- Laboratory of Experimental Immunology, BioMediTech, Faculty of Medicine and Health Technology, FI-33014, Tampere University, Finland; Laboratory of Immunoregulation, BioMediTech, Faculty of Medicine and Health Technology, FI-33014, Tampere University, Finland.
| | - Tommi Rantapero
- Laboratory of Computational Biology, BioMediTech, Faculty of Medicine and Health Technology, FI-33014, Tampere University, Finland.
| | - Meri I E Uusi-Mäkelä
- Laboratory of Experimental Immunology, BioMediTech, Faculty of Medicine and Health Technology, FI-33014, Tampere University, Finland.
| | - Matti Nykter
- Laboratory of Computational Biology, BioMediTech, Faculty of Medicine and Health Technology, FI-33014, Tampere University, Finland.
| | - Olli Lohi
- Tampere Center for Child Health Research, Tampere University and Tays Cancer Center, Tampere University Hospital, FI-33014, Tampere University, Finland.
| | - Mataleena Parikka
- Laboratory of Infection Biology, BioMediTech, Faculty of Medicine and Health Technology, FI-33014, Tampere University, Finland; Oral and Maxillofacial Unit, Tampere University Hospital, P.O. Box 2000, FI-33521, Tampere, Finland.
| | - Mika Rämet
- Laboratory of Experimental Immunology, BioMediTech, Faculty of Medicine and Health Technology, FI-33014, Tampere University, Finland; Department of Pediatrics, Tampere University Hospital, P.O. Box 2000, FI-33521, Tampere, Finland; PEDEGO Research Unit, Medical Research Center Oulu, P.O. Box 8000, FI-90014, University of Oulu, Finland; Department of Children and Adolescents, Oulu University Hospital, P.O. Box 10, FI-90029, OYS, Finland.
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7
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Badiee M, Tochtrop GP. Bile Acid Recognition by Mouse Ileal Bile Acid Binding Protein. ACS Chem Biol 2017; 12:3049-3056. [PMID: 29058872 DOI: 10.1021/acschembio.7b00865] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Ileal bile acid binding protein (I-BABP, gene name FABP6) is a component of the bile acid recycling system, expressed in the ileal enterocyte. The physiological role of I-BABP has been hypothesized to be either an intracellular buffering agent to protect against excess intracellular bile acids or separately as a modulator of bile acid controlled transcription. We investigated mouse I-BABP (mI-BABP) to understand the function of this protein family. Here, we studied energetics and site selectivity of binding with physiological bile acids using a combination of isothermal calorimetric analysis and NMR spectroscopy. We found that the most abundant bile acid in the mouse (β-muricholic acid) binds with weak affinity individually and in combination with other bile acids. Further analysis showed that mI-BABP like human I-BABP (hI-BABP) specifically recognizes the conjugated form of cholic acid:chenodeoxycholic acid (CA:CDCA) in a site-selective manner, displaying the highest affinity of any bile acid combination tested. These results indicate that I-BABP specifically recognizes the ligand combination of CDCA and CA, even in a species such as the mouse where CDCA only represents a trace component of the physiological pool. Specific and conserved recognition of the CDCA and CA ligand combination suggests that I-BABP may play a critical role in the regulation of bile acid signaling in addition to its proposed role as a buffering agent.
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Affiliation(s)
- Mohsen Badiee
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Gregory P. Tochtrop
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
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D'Onofrio M, Zanzoni S, Munari F, Monaco HL, Assfalg M, Capaldi S. The long variant of human ileal bile acid-binding protein associated with colorectal cancer exhibits sub-cellular localization and lipid binding behaviour distinct from those of the common isoform. Biochim Biophys Acta Gen Subj 2017; 1861:2315-2324. [PMID: 28689989 DOI: 10.1016/j.bbagen.2017.07.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 06/09/2017] [Accepted: 07/05/2017] [Indexed: 12/29/2022]
Abstract
BACKGROUND Ileal bile acid-binding protein, IBABP, participates in the intracellular trafficking of bile salts and influences their signaling activities. The recently discovered variant, IBABP-L, bearing an N-terminal 49-amino acid extension, was found to be associated with colorectal cancer and to protect cancer cells from the cytotoxic effects of deoxycholate. However, the precise function and the molecular properties of this variant are currently unknown. METHODS Bioinformatics tools and confocal microscopy were used to investigate the sub-cellular localization of IBABP-L; protein dynamics, ligand binding and interaction with membrane models were studied by 2D NMR and fluorescence spectroscopy. RESULTS Based on sub-cellular localization experiments we conclude that IBABP-L is targeted to the secretory pathway by a 24-residue signal peptide and, upon its cleavage, the mature protein is constitutively released into the extracellular space. Site-resolved NMR experiments indicated the distinct preference of primary and secondary bile salts to form either heterotypic or homotypic complexes with IBABP-L. The presence of the relatively dynamic N-terminal extension, originating only subtle conformational perturbations in the globular domain, was found to influence binding site occupation in IBABP-L as compared to IBABP. Even more pronounced differences were found in the tendency of the two variants to associate with phospholipid bilayers. CONCLUSIONS IBABP-L exhibits different sub-cellular localization, ligand-binding properties and membrane interaction propensity compared to the canonical short isoform. GENERAL SIGNIFICANCE Our results constitute an essential first step towards an understanding of the role of IBABP-L in bile salt trafficking and signaling under healthy and pathological conditions.
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Affiliation(s)
- Mariapina D'Onofrio
- Biomolecular NMR Laboratory, Department of Biotechnology, University of Verona, Ca' Vignal 1, Strada Le Grazie 15, 37134 Verona, Italy
| | - Serena Zanzoni
- Biomolecular NMR Laboratory, Department of Biotechnology, University of Verona, Ca' Vignal 1, Strada Le Grazie 15, 37134 Verona, Italy
| | - Francesca Munari
- Biomolecular NMR Laboratory, Department of Biotechnology, University of Verona, Ca' Vignal 1, Strada Le Grazie 15, 37134 Verona, Italy
| | - Hugo L Monaco
- Biocrystallography Laboratory, Department of Biotechnology, University of Verona, Ca' Vignal 1, Strada Le Grazie 15, 37134 Verona, Italy
| | - Michael Assfalg
- Biomolecular NMR Laboratory, Department of Biotechnology, University of Verona, Ca' Vignal 1, Strada Le Grazie 15, 37134 Verona, Italy.
| | - Stefano Capaldi
- Biocrystallography Laboratory, Department of Biotechnology, University of Verona, Ca' Vignal 1, Strada Le Grazie 15, 37134 Verona, Italy.
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Drakou CE, Tsitsanou KE, Potamitis C, Fessas D, Zervou M, Zographos SE. The crystal structure of the AgamOBP1•Icaridin complex reveals alternative binding modes and stereo-selective repellent recognition. Cell Mol Life Sci 2017; 74:319-338. [PMID: 27535661 PMCID: PMC11107575 DOI: 10.1007/s00018-016-2335-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 07/27/2016] [Accepted: 08/09/2016] [Indexed: 10/21/2022]
Abstract
Anopheles gambiae Odorant Binding Protein 1 in complex with the most widely used insect repellent DEET, was the first reported crystal structure of an olfactory macromolecule with a repellent, and paved the way for OBP1-structure-based approaches for discovery of new host-seeking disruptors. In this work, we performed STD-NMR experiments to directly monitor and verify the formation of a complex between AgamOBP1 and Icaridin, an efficient DEET alternative. Furthermore, Isothermal Titration Calorimetry experiments provided evidence for two Icaridin-binding sites with different affinities (Kd = 0.034 and 0.714 mM) and thermodynamic profiles of ligand binding. To elucidate the binding mode of Icaridin, the crystal structure of AgamOBP1•Icaridin complex was determined at 1.75 Å resolution. We found that Icaridin binds to the DEET-binding site in two distinct orientations and also to a novel binding site located at the C-terminal region. Importantly, only the most active 1R,2S-isomer of Icaridin's equimolar diastereoisomeric mixture binds to the AgamOBP1 crystal, providing structural evidence for the possible contribution of OBP1 to the stereoselectivity of Icaridin perception in mosquitoes. Structural analysis revealed two ensembles of conformations differing mainly in spatial arrangement of their sec-butyl moieties. Moreover, structural comparison with DEET indicates a common recognition mechanism for these structurally related repellents. Ligand interactions with both sites and binding modes were further confirmed by 2D 1H-15N HSQC NMR spectroscopy. The identification of a novel repellent-binding site in AgamOBP1 and the observed structural conservation and stereoselectivity of its DEET/Icaridin-binding sites open new perspectives for the OBP1-structure-based discovery of next-generation insect repellents.
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Affiliation(s)
- Christina E Drakou
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 11635, Athens, Greece
| | - Katerina E Tsitsanou
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 11635, Athens, Greece
| | - Constantinos Potamitis
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 11635, Athens, Greece
| | - Dimitrios Fessas
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Via Celoria 2, 20133, Milan, Italy
| | - Maria Zervou
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 11635, Athens, Greece
| | - Spyros E Zographos
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 11635, Athens, Greece.
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Siow HL, Choi SB, Gan CY. Structure–activity studies of protease activating, lipase inhibiting, bile acid binding and cholesterol-lowering effects of pre-screened cumin seed bioactive peptides. J Funct Foods 2016. [DOI: 10.1016/j.jff.2016.10.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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Hendrick AG, Müller I, Willems H, Leonard PM, Irving S, Davenport R, Ito T, Reeves J, Wright S, Allen V, Wilkinson S, Heffron H, Bazin R, Turney J, Mitchell PJ. Identification and Investigation of Novel Binding Fragments in the Fatty Acid Binding Protein 6 (FABP6). J Med Chem 2016; 59:8094-102. [PMID: 27500412 DOI: 10.1021/acs.jmedchem.6b00869] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Fatty acid binding protein 6 (FABP6) is a potential drug discovery target, which, if inhibited, may have a therapeutic benefit for the treatment of diabetes. Currently, there are no published inhibitors of FABP6, and with the target believed to be amenable to fragment-based drug discovery, a structurally enabled program was initiated. This program successfully identified fragment hits using the surface plasmon resonance (SPR) platform. Several hits were validated with SAR and were found to be displaced by the natural ligand taurocholate. We report the first crystal structure of human FABP6 in the unbound form, in complex with cholate, and with one of the key fragments.
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Affiliation(s)
- Alan G Hendrick
- Takeda Cambridge , 418 Cambridge Science Park, Cambridge CB4 0PZ, United Kingdom
| | - Ilka Müller
- Charles River , Chesterford Research Park, Saffron Walden, Essex CB10 1XL, United Kingdom
| | - Henriëtte Willems
- Takeda Cambridge , 418 Cambridge Science Park, Cambridge CB4 0PZ, United Kingdom
| | - Philip M Leonard
- Charles River , Chesterford Research Park, Saffron Walden, Essex CB10 1XL, United Kingdom
| | - Steve Irving
- Charles River , Ingram Building, Parkwood Road, Canterbury, Kent CT2 7NH, United Kingdom
| | - Richard Davenport
- Takeda Cambridge , 418 Cambridge Science Park, Cambridge CB4 0PZ, United Kingdom
| | - Takashi Ito
- Biomolecular Research Laboratories, Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome, Fujisawa 251-8555, Japan
| | - Jenny Reeves
- Takeda Cambridge , 418 Cambridge Science Park, Cambridge CB4 0PZ, United Kingdom
| | - Susanne Wright
- Takeda Cambridge , 418 Cambridge Science Park, Cambridge CB4 0PZ, United Kingdom
| | - Vivienne Allen
- Charles River , Chesterford Research Park, Saffron Walden, Essex CB10 1XL, United Kingdom
| | - Stephen Wilkinson
- Charles River , Chesterford Research Park, Saffron Walden, Essex CB10 1XL, United Kingdom
| | - Helen Heffron
- Takeda Cambridge , 418 Cambridge Science Park, Cambridge CB4 0PZ, United Kingdom
| | - Richard Bazin
- Charles River , Ingram Building, Parkwood Road, Canterbury, Kent CT2 7NH, United Kingdom
| | - Jennifer Turney
- Charles River , Chesterford Research Park, Saffron Walden, Essex CB10 1XL, United Kingdom
| | - Philip J Mitchell
- Takeda Cambridge , 418 Cambridge Science Park, Cambridge CB4 0PZ, United Kingdom
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Lee CW, Kim JE, Do H, Kim RO, Lee SG, Park HH, Chang JH, Yim JH, Park H, Kim IC, Lee JH. Structural basis for the ligand-binding specificity of fatty acid-binding proteins (pFABP4 and pFABP5) in gentoo penguin. Biochem Biophys Res Commun 2015. [PMID: 26206084 DOI: 10.1016/j.bbrc.2015.07.087] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Fatty acid-binding proteins (FABPs) are involved in transporting hydrophobic fatty acids between various aqueous compartments of the cell by directly binding ligands inside their β-barrel cavities. Here, we report the crystal structures of ligand-unbound pFABP4, linoleate-bound pFABP4, and palmitate-bound pFABP5, obtained from gentoo penguin (Pygoscelis papua), at a resolution of 2.1 Å, 2.2 Å, and 2.3 Å, respectively. The pFABP4 and pFABP5 proteins have a canonical β-barrel structure with two short α-helices that form a cap region and fatty acid ligand binding sites in the hydrophobic cavity within the β-barrel structure. Linoleate-bound pFABP4 and palmitate-bound pFABP5 possess different ligand-binding modes and a unique ligand-binding pocket due to several sequence dissimilarities (A76/L78, T30/M32, underlining indicates pFABP4 residues) between the two proteins. Structural comparison revealed significantly different conformational changes in the β3-β4 loop region (residues 57-62) as well as the flipped Phe60 residue of pFABP5 than that in pFABP4 (the corresponding residue is Phe58). A ligand-binding study using fluorophore displacement assays shows that pFABP4 has a relatively strong affinity for linoleate as compared to pFABP5. In contrast, pFABP5 exhibits higher affinity for palmitate than that for pFABP4. In conclusion, our high-resolution structures and ligand-binding studies provide useful insights into the ligand-binding preferences of pFABPs based on key protein-ligand interactions.
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Affiliation(s)
- Chang Woo Lee
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon 406-840, Republic of Korea
| | - Jung Eun Kim
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, Republic of Korea; Department of Pharmacy, Graduate School, Sungkyunkwan University, Suwon 440-746, Republic of Korea
| | - Hackwon Do
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, Republic of Korea
| | - Ryeo-Ok Kim
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, Republic of Korea
| | - Sung Gu Lee
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon 406-840, Republic of Korea
| | - Hyun Ho Park
- Department of Biochemistry, School of Biotechnology and Graduate School of Biochemistry, Yeungnam University, Gyeongsan, Republic of Korea
| | - Jeong Ho Chang
- Department of Biology Education, Kyungpook National University, Daegu 702-701, Republic of Korea
| | - Joung Han Yim
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, Republic of Korea
| | - Hyun Park
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon 406-840, Republic of Korea
| | - Il-Chan Kim
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, Republic of Korea.
| | - Jun Hyuck Lee
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon 406-840, Republic of Korea.
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All-Purpose Containers? Lipid-Binding Protein - Drug Interactions. PLoS One 2015; 10:e0132096. [PMID: 26167932 PMCID: PMC4500398 DOI: 10.1371/journal.pone.0132096] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 06/10/2015] [Indexed: 01/30/2023] Open
Abstract
The combined use of in vitro (19F-NMR) and in silico (molecular docking) procedures demonstrates the affinity of a number of human calycins (lipid-binding proteins from ileum, liver, heart, adipose tissue and epidermis, and retinol-binding protein from intestine) for different drugs (mainly steroids and vastatins). Comparative evaluations on the complexes outline some of the features relevant for interaction (non-polar character of the drugs; amino acids and water molecules in the protein calyx most often involved in binding). Dissociation constants (Ki) for drugs typically lie in the same range as Ki for natural ligands; in most instances (different proteins and docking conditions), vastatins are the strongest interactors, with atorvastatin ranking top in half of the cases. The affinity of some calycins for some of the vastatins is in the order of magnitude of the drug Cmax after systemic administration in humans. The possible biological implications of this feature are discussed in connection with drug delivery parameters (route of administration, binding to carrier proteins, distribution to, and accumulation in, human tissues).
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Favretto F, Ceccon A, Zanzoni S, D'Onofrio M, Ragona L, Molinari H, Assfalg M. The unique ligand binding features of subfamily-II iLBPs with respect to bile salts and related drugs. Prostaglandins Leukot Essent Fatty Acids 2015; 95:1-10. [PMID: 25468388 DOI: 10.1016/j.plefa.2014.10.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 10/20/2014] [Indexed: 11/28/2022]
Abstract
Intracellular lipid binding proteins (iLBPs) are a family of evolutionarily related small cytoplasmic proteins implicated in the transcellular transport of lipophilic ligands. Subfamily-II iLBPs include the liver fatty acid binding protein (L-FABP), and the ileal and the liver and ileal bile acid binding proteins (L-BABP and I-BABP). Atomic-level investigations during the past 15-20 years have delivered relevant information on bile acid binding by this protein group, revealing unique features including binding cooperativity, promiscuity, and site selectivity. Using NMR spectroscopy and other biophysical techniques, our laboratories have contributed to an understanding of the molecular determinants of some of these properties and their generality among proteins from different animal species. We focused especially on formation of heterotypic complexes, considering the mixed compositions of physiological bile acid pools. Experiments performed with synthetic bile acid derivatives showed that iLBPs could act as targets for cell-specific contrast agents and, more generally, as effective carriers of amphiphilic drugs. This review collects the major findings related to bile salt interactions with iLBPs aiming to provide keys for a deeper understanding of protein-mediated intracellular bile salt trafficking.
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Affiliation(s)
- Filippo Favretto
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, Verona 37134, Italy
| | - Alberto Ceccon
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, Verona 37134, Italy
| | - Serena Zanzoni
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, Verona 37134, Italy
| | - Mariapina D'Onofrio
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, Verona 37134, Italy
| | - Laura Ragona
- Institute for Macromolecular Studies, National Research Council, Via Bassini 15, Milan 20133, Italy
| | - Henriette Molinari
- Institute for Macromolecular Studies, National Research Council, Via Bassini 15, Milan 20133, Italy
| | - Michael Assfalg
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, Verona 37134, Italy.
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15
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Favretto F, Santambrogio C, D'Onofrio M, Molinari H, Grandori R, Assfalg M. Bile salt recognition by human liver fatty acid binding protein. FEBS J 2015; 282:1271-88. [PMID: 25639618 DOI: 10.1111/febs.13218] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 12/22/2014] [Accepted: 01/26/2015] [Indexed: 12/24/2022]
Abstract
Fatty acid binding proteins (FABPs) act as intracellular carriers of lipid molecules, and play a role in global metabolism regulation. Liver FABP (L-FABP) is prominent among FABPs for its wide ligand repertoire, which includes long-chain fatty acids as well as bile acids (BAs). In this work, we performed a detailed molecular- and atomic-level analysis of the interactions established by human L-FABP with nine BAs to understand the binding specificity for this important class of cholesterol-derived metabolites. Protein-ligand complex formation was monitored using heteronuclear NMR, steady-state fluorescence spectroscopy, and mass spectrometry. BAs were found to interact with L-FABP with dissociation constants in the narrow range of 0.6-7 μm; however, the diverse substitution patterns of the sterol nucleus and the presence of side-chain conjugation resulted in complexes endowed with various degrees of conformational heterogeneity. Trihydroxylated BAs formed monomeric complexes in which single ligand molecules occupied similar internal binding sites, based on chemical-shift perturbation data. Analysis of NMR line shapes upon progressive addition of taurocholate indicated that the binding mechanism departed from a simple binary association equilibrium, and instead involved intermediates along the binding path. The co-linear chemical shift behavior observed for L-FABP complexes with cholate derivatives added insight into conformational dynamics in the presence of ligands. The observed spectroscopic features of L-FABP/BA complexes, discussed in relation to ligand chemistry, suggest possible molecular determinants of recognition, with implications regarding intracellular BA transport. Our findings suggest that human L-FABP is a poorly selective, universal BA binder.
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16
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Dawson PA, Karpen SJ. Intestinal transport and metabolism of bile acids. J Lipid Res 2014; 56:1085-99. [PMID: 25210150 DOI: 10.1194/jlr.r054114] [Citation(s) in RCA: 336] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Indexed: 12/17/2022] Open
Abstract
In addition to their classical roles as detergents to aid in the process of digestion, bile acids have been identified as important signaling molecules that function through various nuclear and G protein-coupled receptors to regulate a myriad of cellular and molecular functions across both metabolic and nonmetabolic pathways. Signaling via these pathways will vary depending on the tissue and the concentration and chemical structure of the bile acid species. Important determinants of the size and composition of the bile acid pool are their efficient enterohepatic recirculation, their host and microbial metabolism, and the homeostatic feedback mechanisms connecting hepatocytes, enterocytes, and the luminal microbiota. This review focuses on the mammalian intestine, discussing the physiology of bile acid transport, the metabolism of bile acids in the gut, and new developments in our understanding of how intestinal metabolism, particularly by the gut microbiota, affects bile acid signaling.
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Affiliation(s)
- Paul A Dawson
- Department of Pediatrics, Division of Gastroenterology, Hepatology, and Nutrition, Emory University, Atlanta, GA 30322
| | - Saul J Karpen
- Department of Pediatrics, Division of Gastroenterology, Hepatology, and Nutrition, Emory University, Atlanta, GA 30322
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17
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Gioiello A, Venturoni F, Tamimi S, Custodi C, Pellicciari R, Macchiarulo A. Conformational properties of cholic acid, a lead compound at the crossroads of bile acid inspired drug discovery. MEDCHEMCOMM 2014. [DOI: 10.1039/c4md00024b] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
DFT and NMR spectroscopy studies unveil three major minima conformations of cholic acid that may affect its biological properties.
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Affiliation(s)
- Antimo Gioiello
- Dipartimento di Chimica e Tecnologia del Farmaco
- Università degli Studi di Perugia
- 06123 Perugia, Italy
| | - Francesco Venturoni
- Dipartimento di Chimica e Tecnologia del Farmaco
- Università degli Studi di Perugia
- 06123 Perugia, Italy
| | - Sara Tamimi
- Dipartimento di Chimica e Tecnologia del Farmaco
- Università degli Studi di Perugia
- 06123 Perugia, Italy
| | - Chiara Custodi
- Dipartimento di Chimica e Tecnologia del Farmaco
- Università degli Studi di Perugia
- 06123 Perugia, Italy
| | - Roberto Pellicciari
- Dipartimento di Chimica e Tecnologia del Farmaco
- Università degli Studi di Perugia
- 06123 Perugia, Italy
- TES Pharma S.r.l
- Perugia, Italy
| | - Antonio Macchiarulo
- Dipartimento di Chimica e Tecnologia del Farmaco
- Università degli Studi di Perugia
- 06123 Perugia, Italy
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18
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Ruskamo S, Yadav RP, Sharma S, Lehtimäki M, Laulumaa S, Aggarwal S, Simons M, Bürck J, Ulrich AS, Juffer AH, Kursula I, Kursula P. Atomic resolution view into the structure-function relationships of the human myelin peripheral membrane protein P2. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:165-76. [PMID: 24419389 PMCID: PMC3919267 DOI: 10.1107/s1399004713027910] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 10/11/2013] [Indexed: 01/03/2023]
Abstract
P2 is a fatty acid-binding protein expressed in vertebrate peripheral nerve myelin, where it may function in bilayer stacking and lipid transport. P2 binds to phospholipid membranes through its positively charged surface and a hydrophobic tip, and accommodates fatty acids inside its barrel structure. The structure of human P2 refined at the ultrahigh resolution of 0.93 Å allows detailed structural analyses, including the full organization of an internal hydrogen-bonding network. The orientation of the bound fatty-acid carboxyl group is linked to the protonation states of two coordinating arginine residues. An anion-binding site in the portal region is suggested to be relevant for membrane interactions and conformational changes. When bound to membrane multilayers, P2 has a preferred orientation and is stabilized, and the repeat distance indicates a single layer of P2 between membranes. Simulations show the formation of a double bilayer in the presence of P2, and in cultured cells wild-type P2 induces membrane-domain formation. Here, the most accurate structural and functional view to date on P2, a major component of peripheral nerve myelin, is presented, showing how it can interact with two membranes simultaneously while going through conformational changes at its portal region enabling ligand transfer.
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Affiliation(s)
- Salla Ruskamo
- Department of Biochemistry, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Ravi P. Yadav
- Molecular Biology Unit, Institute of Medical Sciences (IMS), Banaras Hindu University, Varanasi, India
- Centre for Structural Systems Biology, Helmholtz Centre for Infection Research (CSSB-HZI), German Electron Synchrotron (DESY), Hamburg, Germany
| | - Satyan Sharma
- Department of Biochemistry, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Mari Lehtimäki
- Department of Biochemistry, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Saara Laulumaa
- Department of Biochemistry, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Centre for Structural Systems Biology, Helmholtz Centre for Infection Research (CSSB-HZI), German Electron Synchrotron (DESY), Hamburg, Germany
| | - Shweta Aggarwal
- Max Planck Institute for Experimental Medicine, Göttingen, Germany
| | - Mikael Simons
- Max Planck Institute for Experimental Medicine, Göttingen, Germany
| | - Jochen Bürck
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute for Technology (KIT), Karlsruhe, Germany
| | - Anne S. Ulrich
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute for Technology (KIT), Karlsruhe, Germany
| | - André H. Juffer
- Department of Biochemistry, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Inari Kursula
- Department of Biochemistry, University of Oulu, Oulu, Finland
- Centre for Structural Systems Biology, Helmholtz Centre for Infection Research (CSSB-HZI), German Electron Synchrotron (DESY), Hamburg, Germany
| | - Petri Kursula
- Department of Biochemistry, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Centre for Structural Systems Biology, Helmholtz Centre for Infection Research (CSSB-HZI), German Electron Synchrotron (DESY), Hamburg, Germany
- Department of Chemistry, University of Hamburg, Hamburg, Germany
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19
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Pagano K, Tomaselli S, Zanzoni S, Assfalg M, Molinari H, Ragona L. Bile acid binding protein: a versatile host of small hydrophobic ligands for applications in the fields of MRI contrast agents and bio-nanomaterials. Comput Struct Biotechnol J 2013; 6:e201303021. [PMID: 24688729 PMCID: PMC3962148 DOI: 10.5936/csbj.201303021] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 11/19/2013] [Accepted: 11/22/2013] [Indexed: 01/02/2023] Open
Abstract
During the last decade a growing amount of evidence has been obtained, supporting the role of the beta-clamshell family of intracellular lipid binding proteins (iLBPs) not only in the translocation of lipophilic molecules but also in lipid mediated signalling and metabolism. Given the central role of lipids in physiological processes, it is essential to have detailed knowledge on their interactions with cognate binding proteins. Structural and dynamical aspects of the binding mechanisms have been widely investigated by means of NMR spectroscopy, docking and molecular dynamics simulation approaches. iLBPs share a stable beta-barrel fold, delimiting an internal cavity capable of promiscuous ligand binding and display significant flexibility at the putative ligand portal. These features make this class of proteins good scaffolds to build host-guest systems for applications in nanomedicine and nanomaterials.
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Affiliation(s)
- Katiuscia Pagano
- Istituto per lo Studio delle Macromolecole, CNR, via Bassini 15, 20133 Milano, Italy
| | - Simona Tomaselli
- Istituto per lo Studio delle Macromolecole, CNR, via Bassini 15, 20133 Milano, Italy
| | - Serena Zanzoni
- Dipartimento di Biotecnologie, Università degli Studi di Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Michael Assfalg
- Dipartimento di Biotecnologie, Università degli Studi di Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Henriette Molinari
- Istituto per lo Studio delle Macromolecole, CNR, via Bassini 15, 20133 Milano, Italy
| | - Laura Ragona
- Istituto per lo Studio delle Macromolecole, CNR, via Bassini 15, 20133 Milano, Italy
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20
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Parmar MB, Wright JM. Comparative genomic organization and tissue-specific transcription of the duplicated fabp7 and fabp10 genes in teleost fishes. Genome 2013; 56:691-701. [DOI: 10.1139/gen-2013-0172] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A whole-genome duplication (WGD) early in the teleost fish lineage makes fish ideal organisms to study the fate of duplicated genes and underlying evolutionary trajectories that have led to the retention of ohnologous gene duplicates in fish genomes. Here, we compare the genomic organization and tissue-specific transcription of the ohnologous fabp7 and fabp10 genes in medaka, three-spined stickleback, and spotted green pufferfish to the well-studied duplicated fabp7 and fabp10 genes of zebrafish. Teleost fabp7 and fabp10 genes contain four exons interrupted by three introns. Polypeptide sequences of Fabp7 and Fabp10 show the highest sequence identity and similarity with their orthologs from vertebrates. Orthology was evident as the ohnologous Fabp7 and Fabp10 polypeptides of teleost fishes each formed distinct clades and clustered together with their orthologs from other vertebrates in a phylogenetic tree. Furthermore, ohnologous teleost fabp7 and fabp10 genes exhibit conserved gene synteny with human FABP7 and chicken FABP10, respectively, which provides compelling evidence that the duplicated fabp7 and fabp10 genes of teleost fishes most likely arose from the well-documented WGD. The tissue-specific distribution of fabp7a, fabp7b, fabp10a, and fabp10b transcripts provides evidence of diverged spatial transcriptional regulation between ohnologous gene duplicates of fabp7 and fabp10 in teleost fishes.
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Affiliation(s)
- Manoj B. Parmar
- Department of Biology, Dalhousie University, 1355 Oxford Street, P.O. Box 15000, Halifax, NS B3H 4R2, Canada
| | - Jonathan M. Wright
- Department of Biology, Dalhousie University, 1355 Oxford Street, P.O. Box 15000, Halifax, NS B3H 4R2, Canada
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21
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Turpin ER, Fang HJ, Thomas NR, Hirst JD. Cooperativity and site selectivity in the ileal lipid binding protein. Biochemistry 2013; 52:4723-33. [PMID: 23758264 DOI: 10.1021/bi400192w] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The ileal lipid binding protein (ILBP or I-BABP) binds bile salts with positive cooperativity and has unusual site selectivity, whereby cholic acid binds preferentially in one site and chenodeoxycholic in another, despite both sites having an affinity for both ligands and the ligands only differing by a single hydroxyl group. Previous studies of the human variant have assumed that the ligand/protein binding ratio is 2:1, but we show, using electrospray ionization mass spectroscopy, that human ILBP binds bile acids with a 3:1 ratio, even at low protein and ligand concentrations. Docking calculations and molecular dynamics (MD) simulations identify an allosterically active binding site on the protein exterior that induces a change from a closed conformation to an open one, characterized by a movement of one of the α-helices by ~10° with respect to the β-clam shell. Additional independent MD simulations of several hundred nanoseconds implicate the change between conformations in the mechanisms of both cooperativity and ligand site selectivity.
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Affiliation(s)
- Eleanor R Turpin
- School of Chemistry, University of Nottingham , University Park, Nottingham NG7 2RD, United Kingdom
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22
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Transport and biological activities of bile acids. Int J Biochem Cell Biol 2013; 45:1389-98. [PMID: 23603607 DOI: 10.1016/j.biocel.2013.04.012] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2013] [Revised: 03/30/2013] [Accepted: 04/09/2013] [Indexed: 12/29/2022]
Abstract
Bile acids have emerged as important biological molecules that support the solubilization of various lipids and lipid-soluble compounds in the gut, and the regulation of gene expression and cellular function. Bile acids are synthesized from cholesterol in the liver and eventually released into the small intestine. The majority of bile acids are recovered in the distal end of the small intestine and then returned to the liver for reuse. The components of the mechanism responsible for the recycling of bile acids within the enterohepatic circulation have been identified whereas the mechanism for intracellular transport is less understood. Recently, the ileal lipid binding protein (ILBP; human gene symbol FABP6) was shown to be needed for the efficient transport of bile acids from the apical side to the basolateral side of enterocytes in the distal intestine. This review presents an overview of the transport of bile acids between the liver and the gut as well as within hepatocytes and enterocytes. A variety of pathologies is associated with the malfunction of the bile acid transport system.
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23
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Zanzoni S, D’Onofrio M, Molinari H, Assfalg M. Recombinant proteins incorporating short non-native extensions may display increased aggregation propensity as detected by high resolution NMR spectroscopy. Biochem Biophys Res Commun 2012; 427:677-81. [DOI: 10.1016/j.bbrc.2012.09.121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2012] [Accepted: 09/23/2012] [Indexed: 10/27/2022]
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24
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Ghai R, Falconer RJ, Collins BM. Applications of isothermal titration calorimetry in pure and applied research--survey of the literature from 2010. J Mol Recognit 2012; 25:32-52. [PMID: 22213449 DOI: 10.1002/jmr.1167] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Isothermal titration calorimetry (ITC) is a biophysical technique for measuring the formation and dissociation of molecular complexes and has become an invaluable tool in many branches of science from cell biology to food chemistry. By measuring the heat absorbed or released during bond formation, ITC provides accurate, rapid, and label-free measurement of the thermodynamics of molecular interactions. In this review, we survey the recent literature reporting the use of ITC and have highlighted a number of interesting studies that provide a flavour of the diverse systems to which ITC can be applied. These include measurements of protein-protein and protein-membrane interactions required for macromolecular assembly, analysis of enzyme kinetics, experimental validation of molecular dynamics simulations, and even in manufacturing applications such as food science. Some highlights include studies of the biological complex formed by Staphylococcus aureus enterotoxin C3 and the murine T-cell receptor, the mechanism of membrane association of the Parkinson's disease-associated protein α-synuclein, and the role of non-specific tannin-protein interactions in the quality of different beverages. Recent developments in automation are overcoming limitations on throughput imposed by previous manual procedures and promise to greatly extend usefulness of ITC in the future. We also attempt to impart some practical advice for getting the most out of ITC data for those researchers less familiar with the method.
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Affiliation(s)
- Rajesh Ghai
- Institute for Molecular Bioscience (IMB), University of Queensland, St. Lucia, Queensland, 4072, Australia
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25
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Tripsianes K, Madl T, Machyna M, Fessas D, Englbrecht C, Fischer U, Neugebauer KM, Sattler M. Structural basis for dimethylarginine recognition by the Tudor domains of human SMN and SPF30 proteins. Nat Struct Mol Biol 2011; 18:1414-20. [PMID: 22101937 DOI: 10.1038/nsmb.2185] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Accepted: 10/14/2011] [Indexed: 11/09/2022]
Abstract
Arginine dimethylation plays critical roles in the assembly of ribonucleoprotein complexes in pre-mRNA splicing and piRNA pathways. We report solution structures of SMN and SPF30 Tudor domains bound to symmetric and asymmetric dimethylated arginine (DMA) that is inherent in the RNP complexes. An aromatic cage in the Tudor domain mediates dimethylarginine recognition by electrostatic stabilization through cation-π interactions. Distinct from extended Tudor domains, dimethylarginine binding by the SMN and SPF30 Tudor domains is independent of proximal residues in the ligand. Yet, enhanced micromolar affinities are obtained by external cooperativity when multiple methylation marks are presented in arginine- and glycine-rich peptide ligands. A hydrogen bond network in the SMN Tudor domain, including Glu134 and a tyrosine hydroxyl of the aromatic cage, enhances cation-π interactions and is impaired by a mutation causing an E134K substitution associated with spinal muscular atrophy. Our structural analysis enables the design of an optimized binding pocket and the prediction of DMA binding properties of Tudor domains.
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26
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Zanzoni S, Assfalg M, Giorgetti A, D'Onofrio M, Molinari H. Structural requirements for cooperativity in ileal bile acid-binding proteins. J Biol Chem 2011; 286:39307-17. [PMID: 21917914 PMCID: PMC3234755 DOI: 10.1074/jbc.m111.261099] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Ileal bile acid-binding proteins (I-BABP), belonging to the family of intracellular lipid-binding proteins, control bile acid trafficking in enterocytes and participate in regulating the homeostasis of these cholesterol-derived metabolites. I-BABP orthologues share the same structural fold and are able to host up to two ligands in their large internal cavities. However variations in the primary sequences determine differences in binding properties such as the degree of binding cooperativity. To investigate the molecular requirements for cooperativity we adopted a gain-of-function approach, exploring the possibility to turn the noncooperative chicken I-BABP (cI-BABP) into a cooperative mutant protein. To this aim we first solved the solution structure of cI-BABP in complex with two molecules of the physiological ligand glycochenodeoxycholate. A comparative structural analysis with closely related members of the same protein family provided the basis to design a double mutant (H99Q/A101S cI-BABP) capable of establishing a cooperative binding mechanism. Molecular dynamics simulation studies of the wild type and mutant complexes and essential dynamics analysis of the trajectories supported the role of the identified amino acid residues as hot spot mediators of communication between binding sites. The emerging picture is consistent with a binding mechanism that can be described as an extended conformational selection model.
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Affiliation(s)
- Serena Zanzoni
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
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27
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Smathers RL, Petersen DR. The human fatty acid-binding protein family: evolutionary divergences and functions. Hum Genomics 2011; 5:170-91. [PMID: 21504868 PMCID: PMC3500171 DOI: 10.1186/1479-7364-5-3-170] [Citation(s) in RCA: 310] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Fatty acid-binding proteins (FABPs) are members of the intracellular lipid-binding protein (iLBP) family and are involved in reversibly binding intracellular hydrophobic ligands and trafficking them throughout cellular compartments, including the peroxisomes, mitochondria, endoplasmic reticulum and nucleus. FABPs are small, structurally conserved cytosolic proteins consisting of a water-filled, interior-binding pocket surrounded by ten anti-parallel beta sheets, forming a beta barrel. At the superior surface, two alpha-helices cap the pocket and are thought to regulate binding. FABPs have broad specificity, including the ability to bind long-chain (C16-C20) fatty acids, eicosanoids, bile salts and peroxisome proliferators. FABPs demonstrate strong evolutionary conservation and are present in a spectrum of species including Drosophila melanogaster, Caenorhabditis elegans, mouse and human. The human genome consists of nine putatively functional protein-coding FABP genes. The most recently identified family member, FABP12, has been less studied.
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Affiliation(s)
- Rebecca L Smathers
- Molecular Toxicology and Environmental Health Sciences Program, Department of Pharmaceutical Sciences, University of Colorado Denver, Aurora, CO 80045, USA
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28
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Freiburger LA, Mittermaier AK, Auclair K. Collecting variable-concentration isothermal titration calorimetry datasets in order to determine binding mechanisms. J Vis Exp 2011:2529. [PMID: 21505408 DOI: 10.3791/2529] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Isothermal titration calorimetry (ITC) is commonly used to determine the thermodynamic parameters associated with the binding of a ligand to a host macromolecule. ITC has some advantages over common spectroscopic approaches for studying host/ligand interactions. For example, the heat released or absorbed when the two components interact is directly measured and does not require any exogenous reporters. Thus the binding enthalpy and the association constant (Ka) are directly obtained from ITC data, and can be used to compute the entropic contribution. Moreover, the shape of the isotherm is dependent on the c-value and the mechanistic model involved. The c-value is defined as c = n[P]tKa, where [P]t is the protein concentration, and n is the number of ligand binding sites within the host. In many cases, multiple binding sites for a given ligand are non-equivalent and ITC allows the characterization of the thermodynamic binding parameters for each individual binding site. This however requires that the correct binding model be used. This choice can be problematic if different models can fit the same experimental data. We have previously shown that this problem can be circumvented by performing experiments at several c-values. The multiple isotherms obtained at different c-values are fit simultaneously to separate models. The correct model is next identified based on the goodness of fit across the entire variable-c dataset. This process is applied here to the aminoglycoside resistance-causing enzyme aminoglycoside N-6'-acetyltransferase-Ii (AAC(6')-Ii). Although our methodology is applicable to any system, the necessity of this strategy is better demonstrated with a macromolecule-ligand system showing allostery or cooperativity, and when different binding models provide essentially identical fits to the same data. To our knowledge, there are no such systems commercially available. AAC(6')-Ii, is a homo-dimer containing two active sites, showing cooperativity between the two subunits. However ITC data obtained at a single c-value can be fit equally well to at least two different models a two-sets-of-sites independent model and a two-site sequential (cooperative) model. Through varying the c-value as explained above, it was established that the correct binding model for AAC(6')-Ii is a two-site sequential binding model. Herein, we describe the steps that must be taken when performing ITC experiments in order to obtain datasets suitable for variable-c analyses.
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29
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Falconer RJ, Collins BM. Survey of the year 2009: applications of isothermal titration calorimetry. J Mol Recognit 2010; 24:1-16. [DOI: 10.1002/jmr.1073] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Sorg JA, Sonenshein AL. Inhibiting the initiation of Clostridium difficile spore germination using analogs of chenodeoxycholic acid, a bile acid. J Bacteriol 2010; 192:4983-90. [PMID: 20675492 PMCID: PMC2944524 DOI: 10.1128/jb.00610-10] [Citation(s) in RCA: 244] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2010] [Accepted: 07/19/2010] [Indexed: 12/26/2022] Open
Abstract
To cause disease, Clostridium difficile spores must germinate in the host gastrointestinal tract. Germination is initiated upon exposure to glycine and certain bile acids, e.g., taurocholate. Chenodeoxycholate, another bile acid, inhibits taurocholate-mediated germination. By applying Michaelis-Menten kinetic analysis to C. difficile spore germination, we found that chenodeoxycholate is a competitive inhibitor of taurocholate-mediated germination and appears to interact with the spores with greater apparent affinity than does taurocholate. We also report that several analogs of chenodeoxycholate are even more effective inhibitors. Some of these compounds resist 7α-dehydroxylation by Clostridium scindens, a core member of the normal human colonic microbiota, suggesting that they are more stable than chenodeoxycholate in the colonic environment.
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Affiliation(s)
- Joseph A. Sorg
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts
| | - Abraham L. Sonenshein
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts
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Freiburger LA, Auclair K, Mittermaier AK. Elucidating protein binding mechanisms by variable-c ITC. Chembiochem 2010; 10:2871-3. [PMID: 19856370 DOI: 10.1002/cbic.200900614] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Lee A Freiburger
- Department of Chemistry, McGill University, Montréal, Québec, Canada
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Chicken ileal bile-acid-binding protein: a promising target of investigation to understand binding co-operativity across the protein family. Biochem J 2009; 425:413-24. [PMID: 19874274 DOI: 10.1042/bj20091209] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Protein-bile acid interactions are crucial microscopic events at the basis of both physiological and pathological biochemical pathways. BABPs (bile-acid-binding proteins) are intracellular transporters able to bind ligands with different stoichiometry, selectivity and co-operativity. The molecular determinants and energetics of interaction are the observables that connect the microscopic to the macroscopic frameworks. The present paper addresses the study and proposes a mechanism for the multi-site interaction of bile acids with chicken I-BABP (ileal BABP) with the aim of elucidating the determinants of ligand binding in comparison with homologous proteins from different species and tissues. A thermodynamic binding model describing two independent consecutive binding sites is derived from isothermal titration calorimetry experiments and validated on the basis of both protein-observed and ligand-observed NMR titration data. It emerges that a singly bound protein is relatively abundant at low ligand/protein molar ratios assessing the absence of strong co-operativity. Both the measured energetics of binding and the distributed protein chemical-shift perturbations are in agreement with a first binding event triggering a global structural rearrangement. The enthalpic and entropic contributions associated with binding of the first ligand indicate that the interaction increases stability and order of the bound protein. The results described in the present study point to the presence of a protein scaffold which is able to establish long-range communication networks, but does not manifest positive-binding co-operativity, as observed for the human protein. We consider chicken I-BABP a suitable model to address the molecular basis for a gain-of-function on going from non-mammalian to mammalian species.
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Rea AM, Thurston V, Searle MS. Mechanism of Ligand-Induced Folding of a Natively Unfolded Helixless Variant of Rabbit I-BABP. Biochemistry 2009; 48:7556-64. [DOI: 10.1021/bi900805s] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anita M. Rea
- School of Chemistry, Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Victoria Thurston
- School of Chemistry, Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Mark S. Searle
- School of Chemistry, Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham NG7 2RD, U.K
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