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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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Horváth G, Biczók L, Majer Z, Kovács M, Micsonai A, Kardos J, Toke O. Structural insight into a partially unfolded state preceding aggregation in an intracellular lipid-binding protein. FEBS J 2017; 284:3637-3661. [DOI: 10.1111/febs.14264] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 08/15/2017] [Accepted: 09/05/2017] [Indexed: 12/15/2022]
Affiliation(s)
- Gergő Horváth
- Laboratory for NMR Spectroscopy; Research Centre for Natural Sciences; Hungarian Academy of Sciences; Budapest Hungary
| | - László Biczók
- Institute of Materials and Environmental Chemistry; Research Centre for Natural Sciences; Hungarian Academy of Sciences; Budapest Hungary
| | - Zsuzsa Majer
- Institute of Chemistry; Eötvös Loránd University; Budapest Hungary
| | - Mihály Kovács
- Department of Biochemistry; ELTE-MTA ‘Momentum’ Motor Enzymology Research Group; Eötvös Loránd University; Budapest Hungary
| | - András Micsonai
- Department of Biochemistry; MTA-ELTE NAP B Neuroimmunology Research Group; Institute of Biology; Eötvös Loránd University; Budapest Hungary
| | - József Kardos
- Department of Biochemistry; MTA-ELTE NAP B Neuroimmunology Research Group; Institute of Biology; Eötvös Loránd University; Budapest Hungary
| | - Orsolya Toke
- Laboratory for NMR Spectroscopy; Research Centre for Natural Sciences; Hungarian Academy of Sciences; Budapest Hungary
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Curto LM, Angelani CR, Delfino JM. Intervening in the β-barrel structure of lipid binding proteins: consequences on folding, ligand-binding and aggregation propensity. Prostaglandins Leukot Essent Fatty Acids 2015; 93:37-43. [PMID: 25242388 DOI: 10.1016/j.plefa.2014.08.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 07/26/2014] [Accepted: 08/01/2014] [Indexed: 02/02/2023]
Abstract
Natural β-folds manage to fold up successfully. By contrast, attempts to dissect fragments or peptides from well folded β-sheet proteins have met with insurmountable difficulties. Here we briefly review selected successful cases of intervention on the well-known scaffold of intestinal fatty acid binding protein (IFABP). Lessons from these examples might set guidelines along the design of proteins belonging to this class. Impact of modifications on topology, binding and aggregation is highlighted. With the aid of abridged variants of IFABP we focus on key structural features responsible for the assembly into oligomeric forms or aggregates.
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Affiliation(s)
- L M Curto
- Department of Biological Chemistry and Institute of Biochemistry and Biophysics (IQUIFIB), School of Pharmacy and Biochemistry, University of Buenos Aires, Junín 956, C1113AAD Buenos Aires, Argentina
| | - C R Angelani
- Department of Biological Chemistry and Institute of Biochemistry and Biophysics (IQUIFIB), School of Pharmacy and Biochemistry, University of Buenos Aires, Junín 956, C1113AAD Buenos Aires, Argentina
| | - J M Delfino
- Department of Biological Chemistry and Institute of Biochemistry and Biophysics (IQUIFIB), School of Pharmacy and Biochemistry, University of Buenos Aires, Junín 956, C1113AAD Buenos Aires, Argentina.
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4
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Ab initio calculations of cooperativity effects on chalcogen bonding: linear clusters of (OCS)2–8 and (OCSe)2–8. Struct Chem 2014. [DOI: 10.1007/s11224-014-0477-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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5
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Vega S, Neira JL, Marcuello C, Lostao A, Abian O, Velazquez-Campoy A. NS3 protease from hepatitis C virus: biophysical studies on an intrinsically disordered protein domain. Int J Mol Sci 2013; 14:13282-306. [PMID: 23803659 PMCID: PMC3742187 DOI: 10.3390/ijms140713282] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 06/04/2013] [Accepted: 06/13/2013] [Indexed: 12/14/2022] Open
Abstract
The nonstructural protein 3 (NS3) from the hepatitis C virus (HCV) is responsible for processing the non-structural region of the viral precursor polyprotein in infected hepatic cells. NS3 protease activity, located at the N-terminal domain, is a zinc-dependent serine protease. A zinc ion, required for the hydrolytic activity, has been considered as a structural metal ion essential for the structural integrity of the protein. In addition, NS3 interacts with another cofactor, NS4A, an accessory viral protein that induces a conformational change enhancing the hydrolytic activity. Biophysical studies on the isolated protease domain, whose behavior is similar to that of the full-length protein (e.g., catalytic activity, allosteric mechanism and susceptibility to inhibitors), suggest that a considerable global conformational change in the protein is coupled to zinc binding. Zinc binding to NS3 protease can be considered as a folding event, an extreme case of induced-fit binding. Therefore, NS3 protease is an intrinsically (partially) disordered protein with a complex conformational landscape due to its inherent plasticity and to the interaction with its different effectors. Here we summarize the results from a detailed biophysical characterization of this enzyme and present new experimental data.
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Affiliation(s)
- Sonia Vega
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit BIFI-IQFR (CSIC), University of Zaragoza, Zaragoza 50018, Spain; E-Mails: (S.V.); (J.L.N.)
| | - Jose L. Neira
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit BIFI-IQFR (CSIC), University of Zaragoza, Zaragoza 50018, Spain; E-Mails: (S.V.); (J.L.N.)
- Institute of Molecular and Cell Biology, Miguel Hernandez University, Elche (Alicante) 03202, Spain
| | - Carlos Marcuello
- Advanced Microscopy Laboratory (LMA), Institute of Nanoscience of Aragon (INA), University of Zaragoza, Zaragoza 50018, Spain; E-Mails: (C.M.); (A.L.)
| | - Anabel Lostao
- Advanced Microscopy Laboratory (LMA), Institute of Nanoscience of Aragon (INA), University of Zaragoza, Zaragoza 50018, Spain; E-Mails: (C.M.); (A.L.)
- ARAID Foundation, Government of Aragon, Zaragoza 50018, Spain
| | - Olga Abian
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit BIFI-IQFR (CSIC), University of Zaragoza, Zaragoza 50018, Spain; E-Mails: (S.V.); (J.L.N.)
- IIS Aragon–Aragon Health Science Institute (I+CS), Zaragoza 50009, Spain
- Network Biomedical Research Center on Hepatic and Digestive Diseases (CIBERehd), Barcelona 08036, Spain
- Authors to whom correspondence should be addressed; E-Mails: (O.A.); (A.V.-C.); Tel.: +34-976-761-000 (ext. 5417) (O.A.); +34-976-762-996 (A.V.-C.); Fax: +34-976-762-990 (O.A. & A.V.-C.)
| | - Adrian Velazquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit BIFI-IQFR (CSIC), University of Zaragoza, Zaragoza 50018, Spain; E-Mails: (S.V.); (J.L.N.)
- ARAID Foundation, Government of Aragon, Zaragoza 50018, Spain
- Department of Biochemistry and Cellular and Molecular Biology, Faculty of Sciences, University of Zaragoza, Zaragoza 50009, Spain
- Authors to whom correspondence should be addressed; E-Mails: (O.A.); (A.V.-C.); Tel.: +34-976-761-000 (ext. 5417) (O.A.); +34-976-762-996 (A.V.-C.); Fax: +34-976-762-990 (O.A. & A.V.-C.)
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6
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Esrafili MD. A theoretical investigation of the characteristics of hydrogen/halogen bonding interactions in dibromo-nitroaniline. J Mol Model 2012; 19:1417-27. [DOI: 10.1007/s00894-012-1691-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 11/12/2012] [Indexed: 10/27/2022]
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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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8
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Basehore HK, Ropson IJ. Residual interactions in unfolded bile acid-binding protein by 19F NMR. Protein Sci 2011; 20:327-35. [PMID: 21280124 DOI: 10.1002/pro.563] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The folding initiation mechanism of human bile acid-binding protein (BABP) has been examined by (19) F NMR. Equilibrium unfolding studies of BABP labeled with fluorine at all eight of its phenylalanine residues showed that at least two sites experience changes in solvent exposure at high denaturant concentrations. Peak assignments were made by site-specific 4FPhe incorporation. The resonances for proteins specifically labeled at Phe17, Phe47, and Phe63 showed changes in chemical shift at denaturant concentrations at which the remaining five phenylalanine residues appear to be fully solvent-exposed. Phe17 is a helical residue that was not expected to participate in a folding initiation site. Phe47 and Phe63 form part of a hydrophobic core region that may be conserved as a site for folding initiation in the intracellular lipid-binding protein family.
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Affiliation(s)
- H Kenney Basehore
- Department of Biochemistry and Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17022, USA
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9
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Zhuang Z, Jewett AI, Kuttimalai S, Bellesia G, Gnanakaran S, Shea JE. Assisted peptide folding by surface pattern recognition. Biophys J 2011; 100:1306-15. [PMID: 21354404 DOI: 10.1016/j.bpj.2010.12.3735] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2010] [Revised: 12/09/2010] [Accepted: 12/21/2010] [Indexed: 10/18/2022] Open
Abstract
Natively disordered proteins belong to a unique class of biomolecules whose function is related to their flexibility and their ability to adopt desired conformations upon binding to substrates. In some cases these proteins can bind multiple partners, which can lead to distinct structures and promiscuity in functions. In other words, the capacity to recognize molecular patterns on the substrate is often essential for the folding and function of intrinsically disordered proteins. Biomolecular pattern recognition is extremely relevant both in vivo (e.g., for oligomerization, immune response, induced folding, substrate binding, and molecular switches) and in vitro (e.g., for biosensing, catalysis, chromatography, and implantation). Here, we use a minimalist computational model system to investigate how polar/nonpolar patterns on a surface can induce the folding of an otherwise unstructured peptide. We show that a model peptide that exists in the bulk as a molten globular state consisting of many interconverting structures can fold into either a helix-coil-helix or an extended helix structure in the presence of a complementary designed patterned surface at low hydrophobicity (3.7%) or a uniform surface at high hydrophobicity (50%). However, we find that a carefully chosen surface pattern can bind to and catalyze the folding of a natively unfolded protein much more readily or effectively than a surface with a noncomplementary or uniform distribution of hydrophobic residues.
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Affiliation(s)
- Zhuoyun Zhuang
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, USA
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10
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Abian O, Vega S, Neira JL, Velazquez-Campoy A. Conformational stability of hepatitis C virus NS3 protease. Biophys J 2011; 99:3811-20. [PMID: 21112306 DOI: 10.1016/j.bpj.2010.10.037] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Revised: 10/22/2010] [Accepted: 10/26/2010] [Indexed: 11/17/2022] Open
Abstract
The hepatitis C virus NS3 protease is responsible for the processing of the nonstructural region of viral precursor polyprotein in infected hepatic cells. NS3 has been considered a target for drug discovery for a long time. NS3 is a zinc-dependent serine protease. However, the zinc ion is not involved in the catalytic mechanism, because it is bound far away from the active site. Thus, zinc is essential for the structural integrity of the protein and it is considered to have a structural role. The first thermodynamic study on the conformational equilibrium and stability of NS3 and the effect of zinc on such equilibrium is presented here. In agreement with a previous calorimetric study on the binding of zinc to NS3, the global unfolding heat capacity is dominated by the zinc dissociation step, suggesting that the binding of zinc induces a significant structural rearrangement of the protein. In addition, contrary to other homologous zinc-dependent proteases, the zinc-free NS3 protease is not completely unstructured. It is apparent that the conformational landscape of hepatitis C virus NS3 protease is fairly complex due to its intrinsic plasticity, and to the interactions with its different effectors (zinc and the accessory viral protein NS4A) and their modulation of the population of the different conformational states.
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Affiliation(s)
- Olga Abian
- Institute of Biocomputation and Physics of Complex Systems, Universidad de Zaragoza, Zaragoza, Spain.
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11
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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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12
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Oh KJ, Cash KJ, Plaxco KW. Beyond molecular beacons: optical sensors based on the binding-induced folding of proteins and polypeptides. Chemistry 2009; 15:2244-51. [PMID: 19191230 DOI: 10.1002/chem.200701748] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Many polypeptides and small proteins can be readily engineered such that they only fold upon binding a specific target ligand. This approach couples target recognition with a considerable change in polymer structure and dynamics. Recent years have seen the development of a number of biosensors that couple these large changes to readily measurable optical (fluorescent) outputs. These sensors afford the detection of a wide variety of macromolecular targets including proteins, polypeptides, and nucleic acids. Here we describe the design of such biosensors, from the first iterations as protein engineering experiments, to the development of biosensors targeting a range of protein and nucleic acid targets.
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Affiliation(s)
- Kenneth J Oh
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, USA
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13
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Milanesi L, Jelinska C, Hunter CA, Hounslow AM, Staniforth RA, Waltho JP. A Method for the Reversible Trapping of Proteins in Non-Native Conformations. Biochemistry 2008; 47:13620-34. [DOI: 10.1021/bi801362f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lilia Milanesi
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, U.K., Centre for Chemical Biology, Krebs Institute for Biomolecular Science, Department of Chemistry, The University of Sheffield, Sheffield S3 7HF, U.K., and Faculty of Life Sciences and Manchester Interdisciplinary Biocentre, The University of Manchester, Manchester M1 7DN, U.K
| | - Clare Jelinska
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, U.K., Centre for Chemical Biology, Krebs Institute for Biomolecular Science, Department of Chemistry, The University of Sheffield, Sheffield S3 7HF, U.K., and Faculty of Life Sciences and Manchester Interdisciplinary Biocentre, The University of Manchester, Manchester M1 7DN, U.K
| | - Christopher A. Hunter
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, U.K., Centre for Chemical Biology, Krebs Institute for Biomolecular Science, Department of Chemistry, The University of Sheffield, Sheffield S3 7HF, U.K., and Faculty of Life Sciences and Manchester Interdisciplinary Biocentre, The University of Manchester, Manchester M1 7DN, U.K
| | - Andrea M. Hounslow
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, U.K., Centre for Chemical Biology, Krebs Institute for Biomolecular Science, Department of Chemistry, The University of Sheffield, Sheffield S3 7HF, U.K., and Faculty of Life Sciences and Manchester Interdisciplinary Biocentre, The University of Manchester, Manchester M1 7DN, U.K
| | - Rosemary A. Staniforth
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, U.K., Centre for Chemical Biology, Krebs Institute for Biomolecular Science, Department of Chemistry, The University of Sheffield, Sheffield S3 7HF, U.K., and Faculty of Life Sciences and Manchester Interdisciplinary Biocentre, The University of Manchester, Manchester M1 7DN, U.K
| | - Jonathan P. Waltho
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, U.K., Centre for Chemical Biology, Krebs Institute for Biomolecular Science, Department of Chemistry, The University of Sheffield, Sheffield S3 7HF, U.K., and Faculty of Life Sciences and Manchester Interdisciplinary Biocentre, The University of Manchester, Manchester M1 7DN, U.K
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The X-ray structure of zebrafish (Danio rerio) ileal bile acid-binding protein reveals the presence of binding sites on the surface of the protein molecule. J Mol Biol 2008; 385:99-116. [PMID: 18952094 DOI: 10.1016/j.jmb.2008.10.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2008] [Revised: 09/24/2008] [Accepted: 10/01/2008] [Indexed: 02/05/2023]
Abstract
The ileal bile acid-binding proteins (I-BABPs), also called ileal lipid-binding proteins or gastrotropins, belong to the family of the fatty acid-binding proteins and play an important role in the solubilization and transport of bile acids in the enterocyte. This article describes the expression, purification, crystallization, and three-dimensional structure determination of zebrafish (Danio rerio) I-BABP both in its apo form and bound to cholic acid. This is the first X-ray structure of an I-BABP. The structure of the apoprotein was determined to a resolution of 1.6 A, and two different monoclinic crystal forms of the holoprotein were solved and refined to 2.2 A resolution. Three protein molecules are present in the asymmetric unit of one of the co-crystal forms and two in the other, and therefore, the results of this study refer to observations made on five different protein molecules in the crystalline state. In every case, two cholate ligands were found bound in approximately the same position in the internal cavity of the protein molecules, but an unexpected result is the presence of clear and unambiguous electron density for several cholate molecules bound on hydrophobic patches on the surface of all the five independent protein molecules examined. Isothermal titration calorimetry was used for the thermodynamic characterization of the binding mechanism and has yielded results that are consistent with the X-ray data. Ligand binding is described in detail, and the conformational changes undergone by the protein molecule in the apo-to-holo transition are examined by superposition of the apo- and holoprotein models. The structure of the holoprotein is also compared with that of the liver BABP from the same species and those of other I-BABPs determined by NMR.
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15
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Kouvatsos N, Thurston V, Ball K, Oldham NJ, Thomas NR, Searle MS. Bile Acid Interactions with Rabbit Ileal Lipid Binding Protein and an Engineered Helixless Variant Reveal Novel Ligand Binding Properties of a Versatile β-Clam Shell Protein Scaffold. J Mol Biol 2007; 371:1365-77. [PMID: 17618650 DOI: 10.1016/j.jmb.2007.06.024] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2007] [Revised: 06/07/2007] [Accepted: 06/11/2007] [Indexed: 11/25/2022]
Abstract
The intracellular ileal lipid binding proteins (ILBPs) are involved in the transport and enterohepatic circulation of bile acids. ILBPs from different species show high sequence and structural homology and have been shown to bind multiple bile acid ligands with differing degrees of selectivity and positive co-operativity. Human ILBP binds bile acid derivatives in a well-characterised 2:1 ligand:protein complex, however, we show that the highly homologous rabbit ILBP (82% sequence identity) with seven conservative substitutions preferentially binds multiple conjugated deoxycholate ligands in a novel 3:1 binding mode essentially within the same beta-clam shell structure. We have extended these studies to investigate the role of the alpha-helical capping motif (residues 9-35) in controlling the dimensions of the binding cavity and ligand uptake. Substituting the alpha-helical motif (residues 9-35) with a short Gly-Gly-Ser-Gly linker dramatically affects the protein stability such that under physiological conditions the mutant (Deltaalpha-ILBP) is highly disordered. However, we show that the inability of the mutant to adopt a stable three-dimensional structure under these conditions is no barrier to binding ligands with near-native affinity. These structural modifications not only demonstrate the possibility of strong coupling between ligand binding and protein folding, but result in changes in bile acid selectivity and binding stoichiometry, which we characterise in detail using isothermal calorimetry and mass spectrometry.
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Affiliation(s)
- Nikolaos Kouvatsos
- Centre for Biomolecular Sciences, School of Chemistry, University Park, Nottingham NG7 2RD, UK
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