1
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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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2
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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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3
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Oddi S, Scipioni L, Totaro A, Angelucci C, Dufrusine B, Sabatucci A, Tortolani D, Coletta I, Alisi MA, Polenzani L, Assfalg M, Caltagirone C, Dainese E, Maccarrone M. The anti-inflammatory agent bindarit acts as a modulator of fatty acid-binding protein 4 in human monocytic cells. Sci Rep 2019; 9:15155. [PMID: 31641194 PMCID: PMC6805920 DOI: 10.1038/s41598-019-51691-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 10/07/2019] [Indexed: 01/11/2023] Open
Abstract
We investigated the cellular and molecular mechanisms by which bindarit, a small indazolic derivative with prominent anti-inflammatory effects, exerts its immunoregulatory activity in lipopolysaccharide (LPS) stimulated human monocytic cells. We found that bindarit differentially regulates the release of interleukin-8 (IL-8) and monocyte chemoattractant protein-1 (MCP-1), enhancing the release of IL-8 and reducing that of MCP-1. These effects specifically required a functional interaction between bindarit and fatty acid binding protein 4 (FABP4), a lipid chaperone that couples intracellular lipid mediators to their biological targets and signaling pathways. We further demonstrated that bindarit can directly interact with FABP4 by increasing its expression and nuclear localization, thus impacting on peroxisome proliferator-activated receptor γ (PPARγ) and LPS-dependent kinase signaling. Taken together, these findings suggest a potential key-role of FABP4 in the immunomodulatory activity of bindarit, and extend the spectrum of its possible therapeutic applications to FABP4 modulation.
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Affiliation(s)
- Sergio Oddi
- Faculty of Veterinary Medicine, University of Teramo, Teramo, 64100, Italy.
- European Center for Brain Research (CERC)/Santa Lucia Foundation IRCCS, Rome, 00143, Italy.
| | - Lucia Scipioni
- European Center for Brain Research (CERC)/Santa Lucia Foundation IRCCS, Rome, 00143, Italy
| | - Antonio Totaro
- European Center for Brain Research (CERC)/Santa Lucia Foundation IRCCS, Rome, 00143, Italy
| | - Clotilde Angelucci
- Faculty of Veterinary Medicine, University of Teramo, Teramo, 64100, Italy
| | - Beatrice Dufrusine
- Faculty of Veterinary Medicine, University of Teramo, Teramo, 64100, Italy
| | | | - Daniel Tortolani
- Faculty of Veterinary Medicine, University of Teramo, Teramo, 64100, Italy
| | - Isabella Coletta
- Angelini RR&D (Research, Regulatory & Development), Angelini S.p.A., Rome, 00181, Italy
| | | | - Lorenzo Polenzani
- Angelini RR&D (Research, Regulatory & Development), Angelini S.p.A., Rome, 00181, Italy
| | - Michael Assfalg
- Department of Biotechnology, University of Verona, Verona, 37129, Italy
| | - Carlo Caltagirone
- European Center for Brain Research (CERC)/Santa Lucia Foundation IRCCS, Rome, 00143, Italy
| | - Enrico Dainese
- Faculty of Veterinary Medicine, University of Teramo, Teramo, 64100, Italy
| | - Mauro Maccarrone
- European Center for Brain Research (CERC)/Santa Lucia Foundation IRCCS, Rome, 00143, Italy.
- Department of Medicine, Campus Bio-Medico University of Rome, Rome, 00128, Italy.
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4
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Pagano K, Paolino M, Fusi S, Zanirato V, Trapella C, Giuliani G, Cappelli A, Zanzoni S, Molinari H, Ragona L, Olivucci M. Bile Acid Binding Protein Functionalization Leads to a Fully Synthetic Rhodopsin Mimic. J Phys Chem Lett 2019; 10:2235-2243. [PMID: 30995409 DOI: 10.1021/acs.jpclett.9b00210] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Rhodopsins are photoreceptive proteins using light to drive a plethora of biological functions such as vision, proton and ion pumping, cation and anion channeling, and gene and enzyme regulation. Here we combine organic synthesis, NMR structural studies, and photochemical characterization to show that it is possible to prepare a fully synthetic mimic of rhodopsin photoreceptors. More specifically, we conjugate a bile acid binding protein with a synthetic mimic of the rhodopsin protonated Schiff base chromophore to achieve a covalent complex featuring an unnatural protein host, photoswitch, and photoswitch-protein linkage with a reverse orientation. We show that, in spite of its molecular-level diversity, light irradiation of the prepared mimic fuels a photochromic cycle driven by sequential photochemical and thermal Z/E isomerizations reminiscent of the photocycles of microbial rhodopsins.
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Affiliation(s)
- Katiuscia Pagano
- Istituto per lo Studio delle Macromolecole, CNR , Via A. Corti 12 , 20133 Milano , Italy
| | - Marco Paolino
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018-2022) , Università degli Studi di Siena , Via Aldo Moro 2 , 53100 Siena , Italy
| | - Stefania Fusi
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018-2022) , Università degli Studi di Siena , Via Aldo Moro 2 , 53100 Siena , Italy
| | | | | | - Germano Giuliani
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018-2022) , Università degli Studi di Siena , Via Aldo Moro 2 , 53100 Siena , Italy
| | - Andrea Cappelli
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018-2022) , Università degli Studi di Siena , Via Aldo Moro 2 , 53100 Siena , Italy
| | - Serena Zanzoni
- Centro Piattaforme Tecnologiche , Università di Verona , Strada Le Grazie , 37134 Verona , Italy
| | - Henriette Molinari
- Istituto per lo Studio delle Macromolecole, CNR , Via A. Corti 12 , 20133 Milano , Italy
| | - Laura Ragona
- Istituto per lo Studio delle Macromolecole, CNR , Via A. Corti 12 , 20133 Milano , Italy
| | - Massimo Olivucci
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018-2022) , Università degli Studi di Siena , Via Aldo Moro 2 , 53100 Siena , Italy
- Chemistry Department , Bowling Green State University , Bowling Green , Ohio 43403 , United States
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5
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Horváth G, Egyed O, Tang C, Kovács M, Micsonai A, Kardos J, Toke O. Ligand entry in human ileal bile acid-binding protein is mediated by histidine protonation. Sci Rep 2019; 9:4825. [PMID: 30886237 PMCID: PMC6423008 DOI: 10.1038/s41598-019-41180-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 02/28/2019] [Indexed: 01/07/2023] Open
Abstract
Human ileal bile acid-binding protein (hI-BABP) has a key role in the intracellular transport of bile salts. To explore the role of histidine protonation in the binding process, the pH-dependence of bile salt binding and internal dynamics in hI-BABP was investigated using NMR spectroscopy and biophysical tools. Thermodynamic and kinetic measurements show an increase in the overall binding affinity and the association rate constant of the first binding step below the pKa of the histidines, suggesting that ligand binding is favoured by the protonated state. The overlap between residues exhibiting a high sensitivity to pH in their backbone amide chemical shifts and protein regions undergoing a global ms conformational exchange indicate a connection between the two processes. According to 15N NMR relaxation dispersion analysis, the slow motion is most pronounced at and above the pKa of the histidines. In agreement with the NMR measurements, MD simulations show a stabilization of the protein by histidine protonation. Hydrogen-bonding and van der Waals interactions mediating the flow of information between the C/D- and G/H-turn regions hosting the three histidines, suggest a complex way of pH-governed allosteric regulation of ligand entry involving a transition between a closed and a more open protein state.
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Affiliation(s)
- Gergő Horváth
- Laboratory for NMR Spectroscopy, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 2 Magyar tudósok körútja, H-1117, Budapest, Hungary
| | - Orsolya Egyed
- Laboratory for NMR Spectroscopy, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 2 Magyar tudósok körútja, H-1117, Budapest, Hungary
| | - Changguo Tang
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, Missouri, 63110, USA
| | - Mihály Kovács
- Department of Biochemistry, ELTE-MTA "Momentum" Motor Enzymology Research Group, Eötvös Loránd University, Pázmány Péter sétány 1/C, H-1117, Budapest, Hungary
| | - András Micsonai
- Department of Biochemistry, MTA-ELTE NAP B Neuroimmunology Research Group, Institute of Biology, Eötvös Loránd University, Pázmány Péter sétány 1/C, H-1117, Budapest, Hungary
| | - József Kardos
- Department of Biochemistry, MTA-ELTE NAP B Neuroimmunology Research Group, Institute of Biology, Eötvös Loránd University, Pázmány Péter sétány 1/C, H-1117, Budapest, Hungary
| | - Orsolya Toke
- Laboratory for NMR Spectroscopy, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 2 Magyar tudósok körútja, H-1117, Budapest, Hungary.
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6
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Horváth G, Bencsura Á, Simon Á, Tochtrop GP, DeKoster GT, Covey DF, Cistola DP, Toke O. Structural determinants of ligand binding in the ternary complex of human ileal bile acid binding protein with glycocholate and glycochenodeoxycholate obtained from solution NMR. FEBS J 2016; 283:541-55. [PMID: 26613247 DOI: 10.1111/febs.13610] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 11/03/2015] [Accepted: 11/24/2015] [Indexed: 01/13/2023]
Abstract
UNLABELLED Besides aiding digestion, bile salts are important signal molecules exhibiting a regulatory role in metabolic processes. Human ileal bile acid binding protein (I-BABP) is an intracellular carrier of bile salts in the epithelial cells of the distal small intestine and has a key role in the enterohepatic circulation of bile salts. Positive binding cooperativity combined with site selectivity of glycocholate and glycochenodeoxycholate, the two most abundant bile salts in the human body, make human I-BABP a unique member of the family of intracellular lipid binding proteins. Solution NMR structure of the ternary complex of human I-BABP with glycocholate and glycochenodeoxycholate reveals an extensive network of hydrogen bonds and hydrophobic interactions stabilizing the bound bile salts. Conformational changes accompanying bile salt binding affects four major regions in the protein including the C/D, E/F and G/H loops as well as the helical segment. Most of these protein regions coincide with a previously described network of millisecond time scale fluctuations in the apo protein, a motion absent in the bound state. Comparison of the heterotypic doubly ligated complex with the unligated form provides further evidence of a conformation selection mechanism of ligand entry. Structural and dynamic aspects of human I-BABP-bile salt interaction are discussed and compared with characteristics of ligand binding in other members of the intracellular lipid binding protein family. PROTEIN DATA BANK ACCESSION NUMBERS The coordinates of the 10 lowest energy structures of the human I-BABP : GCDA : GCA complex as well as the distance restraints used to calculate the final ensemble have been deposited in the Brookhaven Protein Data Bank with accession number 2MM3.
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Affiliation(s)
- Gergő Horváth
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Ákos Bencsura
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Ágnes Simon
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Gregory P Tochtrop
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA.,Department of Molecular Biology and Pharmacology, Washington University School of Medicine, St Louis, MO, USA
| | - Gregory T DeKoster
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA
| | - Douglas F Covey
- Department of Molecular Biology and Pharmacology, Washington University School of Medicine, St Louis, MO, USA
| | - David P Cistola
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA
| | - Orsolya Toke
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
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7
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Tomaselli S, Pagano K, Boulton S, Zanzoni S, Melacini G, Molinari H, Ragona L. Lipid binding protein response to a bile acid library: a combined NMR and statistical approach. FEBS J 2015; 282:4094-113. [PMID: 26260520 DOI: 10.1111/febs.13405] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 07/20/2015] [Accepted: 08/06/2015] [Indexed: 01/23/2023]
Abstract
Primary bile acids, differing in hydroxylation pattern, are synthesized from cholesterol in the liver and, once formed, can undergo extensive enzyme-catalysed glycine/taurine conjugation, giving rise to a complex mixture, the bile acid pool. Composition and concentration of the bile acid pool may be altered in diseases, posing a general question on the response of the carrier (bile acid binding protein) to the binding of ligands with different hydrophobic and steric profiles. A collection of NMR experiments (H/D exchange, HET-SOFAST, ePHOGSY NOESY/ROESY and (15) N relaxation measurements) was thus performed on apo and five different holo proteins, to monitor the binding pocket accessibility and dynamics. The ensemble of obtained data could be rationalized by a statistical approach, based on chemical shift covariance analysis, in terms of residue-specific correlations and collective protein response to ligand binding. The results indicate that the same residues are influenced by diverse chemical stresses: ligand binding always induces silencing of motions at the protein portal with a concomitant conformational rearrangement of a network of residues, located at the protein anti-portal region. This network of amino acids, which do not belong to the binding site, forms a contiguous surface, sensing the presence of the bound lipids, with a signalling role in switching protein-membrane interactions on and off.
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Affiliation(s)
- Simona Tomaselli
- NMR Laboratory, Istituto per lo Studio delle Macromolecole (ISMAC), Milano, Italy
| | - Katiuscia Pagano
- NMR Laboratory, Istituto per lo Studio delle Macromolecole (ISMAC), Milano, Italy
| | - Stephen Boulton
- Departments of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | | | - Giuseppe Melacini
- Departments of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada.,Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Canada
| | - Henriette Molinari
- NMR Laboratory, Istituto per lo Studio delle Macromolecole (ISMAC), Milano, Italy
| | - Laura Ragona
- NMR Laboratory, Istituto per lo Studio delle Macromolecole (ISMAC), Milano, Italy
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8
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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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9
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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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10
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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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11
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Ceccon A, D'Onofrio M, Zanzoni S, Longo DL, Aime S, Molinari H, Assfalg M. NMR investigation of the equilibrium partitioning of a water-soluble bile salt protein carrier to phospholipid vesicles. Proteins 2013; 81:1776-91. [DOI: 10.1002/prot.24329] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2013] [Revised: 04/29/2013] [Accepted: 05/09/2013] [Indexed: 11/07/2022]
Affiliation(s)
- Alberto Ceccon
- Department of Biotechnology; University of Verona; 37134 Verona Italy
| | | | - Serena Zanzoni
- Department of Biotechnology; University of Verona; 37134 Verona Italy
| | - Dario Livio Longo
- Department of Molecular Biotechnologies and Health Sciences; Molecular Imaging Center, University of Torino; 10126 Torino Italy
| | - Silvio Aime
- Department of Molecular Biotechnologies and Health Sciences; Molecular Imaging Center, University of Torino; 10126 Torino Italy
| | | | - Michael Assfalg
- Department of Biotechnology; University of Verona; 37134 Verona Italy
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12
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Favretto F, Assfalg M, Gallo M, Cicero DO, D'Onofrio M, Molinari H. Ligand Binding Promiscuity of Human Liver Fatty Acid Binding Protein: Structural and Dynamic Insights from an Interaction Study with Glycocholate and Oleate. Chembiochem 2013; 14:1807-19. [DOI: 10.1002/cbic.201300156] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Indexed: 11/09/2022]
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13
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D'Onofrio M, Gianolio E, Ceccon A, Arena F, Zanzoni S, Fushman D, Aime S, Molinari H, Assfalg M. High Relaxivity Supramolecular Adducts Between Human-Liver Fatty-Acid-Binding Protein and Amphiphilic GdIII Complexes: Structural Basis for the Design of Intracellular Targeting MRI Probes. Chemistry 2012; 18:9919-28. [DOI: 10.1002/chem.201103778] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Revised: 05/08/2012] [Indexed: 01/14/2023]
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14
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Eberini I, Sensi C, Bovi M, Molinari H, Galliano M, Bonomi F, Iametti S, Gianazza E. Wards in the keyway: amino acids with anomalous pK(a)s in calycins. Amino Acids 2012; 43:2457-68. [PMID: 22643844 DOI: 10.1007/s00726-012-1324-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Accepted: 05/15/2012] [Indexed: 11/24/2022]
Abstract
As a follow-up to our recent analysis of the electrostatics of bovine β-lactoglobulin (Eberini et al. in Amino Acids 42:2019-2030, 2011), we investigated whether the occurrence in the native structure of calycins-the superfamily to which β-lactoglobulin belongs-of amino acids with anomalous pK (a)s is an infrequent or, on the contrary, a common occurrence, and whether or not a general pattern may be recognized. To this aim, we randomly selected four calycins we had either purified from natural sources or prepared with recombinant DNA technologies during our previous and current structural and functional studies on this family. Their pIs vary over several pH units and their known functions are as diverse as carriers, enzymes, immunomodulators and/or extracellular chaperones. In our survey, we used both in silico prediction methods and in vitro procedures, such as isoelectric focusing, electrophoretic titration curves and spectroscopic techniques. By comparing the results under native conditions (no exposure of the proteins to chaotropic agents) to those after protein unfolding (in the presence of 8 M urea), a shift is observed in the pK (a) of at least one amino acid per protein, which results in a measurable change in pI. Three types of amino acids are involved: Cys, Glu, and His, their position varies along the calycin sequence. Although no common mechanism may thus be recognized, we hypothesize that the 'normalization' of anomalous pK (a)s may be the phenomenon that accompanies, and favors, structural rearrangements such as those involved in ligand binding by these proteins. An interesting, if anecdotal, validation to this view comes from the behavior of human retinol binding protein, for which the pI of the folded and liganded protein is intermediate between those of the folded and unliganded and of the unfolded protein forms. Likewise, both solid (from crystallography) and solution state (from CD spectroscopy) data confirm that the protein undergoes structural rearrangement upon retinol binding.
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Affiliation(s)
- Ivano Eberini
- Gruppo di Studio per la Proteomica e la Struttura delle Proteine, Dipartimento di Scienze Farmacologiche, Università degli Studi di Milano, via Giuseppe Balzaretti 9, 20133, Milan, Italy
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15
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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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16
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Cogliati C, Ragona L, D'Onofrio M, Günther U, Whittaker S, Ludwig C, Tomaselli S, Assfalg M, Molinari H. Site-Specific Investigation of the Steady-State Kinetics and Dynamics of the Multistep Binding of Bile Acid Molecules to a Lipid Carrier Protein. Chemistry 2010; 16:11300-10. [DOI: 10.1002/chem.201000498] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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17
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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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18
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Pedò M, Löhr F, D'Onofrio M, Assfalg M, Dötsch V, Molinari H. NMR studies reveal the role of biomembranes in modulating ligand binding and release by intracellular bile acid binding proteins. J Mol Biol 2009; 394:852-63. [PMID: 19836400 DOI: 10.1016/j.jmb.2009.10.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Revised: 10/05/2009] [Accepted: 10/08/2009] [Indexed: 10/20/2022]
Abstract
Bile acid molecules are transferred vectorially between basolateral and apical membranes of hepatocytes and enterocytes in the context of the enterohepatic circulation, a process regulating whole body lipid homeostasis. This work addresses the role of the cytosolic lipid binding proteins in the intracellular transfer of bile acids between different membrane compartments. We present nuclear magnetic resonance (NMR) data describing the ternary system composed of the bile acid binding protein, bile acids, and membrane mimetic systems, such as anionic liposomes. This work provides evidence that the investigated liver bile acid binding protein undergoes association with the anionic membrane and binding-induced partial unfolding. The addition of the physiological ligand to the protein-liposome mixture is capable of modulating this interaction, shifting the equilibrium towards the free folded holo protein. An ensemble of NMR titration experiments, based on nitrogen-15 protein and ligand observation, confirm that the membrane and the ligand establish competing binding equilibria, modulating the cytoplasmic permeability of bile acids. These results support a mechanism of ligand binding and release controlled by the onset of a bile salt concentration gradient within the polarized cell. The location of a specific protein region interacting with liposomes is highlighted.
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Affiliation(s)
- Massimo Pedò
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
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19
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Cogliati C, Tomaselli S, Assfalg M, Pedò M, Ferranti P, Zetta L, Molinari H, Ragona L. Disulfide bridge regulates ligand-binding site selectivity in liver bile acid-binding proteins. FEBS J 2009; 276:6011-23. [PMID: 19754879 DOI: 10.1111/j.1742-4658.2009.07309.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bile acid-binding proteins (BABPs) are cytosolic lipid chaperones that play central roles in driving bile flow, as well as in the adaptation to various pathological conditions, contributing to the maintenance of bile acid homeostasis and functional distribution within the cell. Understanding the mode of binding of bile acids with their cytoplasmic transporters is a key issue in providing a model for the mechanism of their transfer from the cytoplasm to the nucleus, for delivery to nuclear receptors. A number of factors have been shown to modulate bile salt selectivity, stoichiometry, and affinity of binding to BABPs, e.g. chemistry of the ligand, protein plasticity and, possibly, the formation of disulfide bridges. Here, the effects of the presence of a naturally occurring disulfide bridge on liver BABP ligand-binding properties and backbone dynamics have been investigated by NMR. Interestingly, the disulfide bridge does not modify the protein-binding stoichiometry, but has a key role in modulating recognition at both sites, inducing site selectivity for glycocholic and glycochenodeoxycholic acid. Protein conformational changes following the introduction of a disulfide bridge are small and located around the inner binding site, whereas significant changes in backbone motions are observed for several residues distributed over the entire protein, both in the apo form and in the holo form. Site selectivity appears, therefore, to be dependent on protein mobility rather than being governed by steric factors. The detected properties further establish a parallelism with the behaviour of human ileal BABP, substantiating the proposal that BABPs have parallel functions in hepatocytes and enterocytes.
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Affiliation(s)
- Clelia Cogliati
- Laboratorio NMR, Istituto per lo Studio delle Macromolecole, CNR, Milan, Italy
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