NMR Dynamic Studies Suggest that Allosteric Activation Regulates Ligand Binding in Chicken Liver Bile Acid-binding Protein

Ragona, Laura; Catalano, Maddalena; Luppi, Marianna; Cicero, Daniel O.; Eliseo, Tommaso; Foote, Jefferson; Fogolari, Federico; Zetta, Lucia; Molinari, Henríette

doi:10.1074/jbc.m513003200

Cited by 52 publications

(144 citation statements)

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“…18 Our NMR dynamic measurements with previously obtained kinetic data 24 suggest that conformational fluctuations have an important role in bile salt-human I-BABP recognition. A conformational transition on a similar time scale has been proposed earlier for several other members of the iLBP family, including the intestinal FABP 16 , cellular retinol binding proteins (CRBP I and II) 17 , and cl-BABP 19 , indicating that it might be a general way of mediating ligand binding in the protein family. 22 To improve our understanding of the role of dynamics in human I-BABP-bile salt recognition, we report here a characterization of the temperature dependence of slow (microsecond to millisecond) and fast (picosecond to nanosecond) backbone motions in the protein through the use of 15 N NMR spin-relaxation analysis.…”

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confidence: 85%

“…Unlike in FABPs, in human I-BABP the two α-helices are well defined in both ligation states and there is no sign of intense motion 18 , raising the possibility of alternative entry/exit mechanisms as it has been suggested for other analogues. [19][20][21][22] The internal binding cavity of I-BABP is unusual in the sense that it contains a large number of hydrophilic side chains that are involved in extensive networks of salt bridges and hydrogen bonds. In fact, NMR spectroscopic and mutagenesis studies have identified two hydrogen-bonding networks as a likely way of energetic communication between the two binding sites.…”

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confidence: 99%

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Temperature Dependence of Backbone Dynamics in Human Ileal Bile Acid-Binding Protein: Implications for the Mechanism of Ligand Binding

2014

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Human ileal bile acid-binding protein (I-BABP), a member of the family of intracellular lipid binding proteins plays a key role in the cellular trafficking and metabolic regulation of bile salts.The protein has two internal and according to a recent study an additional superficial binding site and binds di-and trihydroxy bile salts with positive cooperativity and a high degree of siteselectivity. Previously, in the apo form, we have identified an extensive network of conformational fluctuations on the ms time scale, which cease upon ligation. Additionally, ligand binding at room temperature was found to be accompanied by a slight rigidification of psns backbone flexibility. In the current study, temperature-dependent 15 N NMR spin relaxation measurements were used to gain more insight into the role of dynamics in human I-BABP -bile salt recognition. According to our analysis, residues sensing a conformational exchange in the apo state can be grouped into two clusters with slightly different exchange rates. The entropyenthalpy compensation observed for both clusters suggests a disorder-order transition between a ground and a sparsely populated higher energy state in the absence of ligands. Analysis of the faster, ps-ns motion of 15 N-1 H bond vectors indicates an unusual nonlinear temperaturedependence for both ligation states. Intriguingly, while bile salt binding results in a more uniform response to temperature change throughout the protein, the temperature derivative of the generalized order parameter shows different responses to temperature increase for the two forms of the protein in the investigated temperature range. Analysis of both slow and fast motions in human I-BABP indicates largely different energy landscapes for the apo and holo states suggesting that optimization of binding interactions might be achieved by altering the dynamic behavior of specific segments in the protein. 4Human ileal bile acid binding protein (I-BABP), expressed in the absorptive enterocytes of the distal small intestine has a key role in the enterohepatic circulation of bile salts. 1 In addition to aiding the absorption of lipidlike compounds in the human body 2 , bile salts (Figure 1) are also known as signal molecules, which play important roles in the regulation of metabolic processes.In particular, by binding to the nuclear farnesoid X receptor α (FXR) 3 they provide a negative feedback mechanism for their own synthesis thereby contributing to the maintenance of wholebody cholesterol homeostasis. In addition, by the activation of various mitogen-activated protein kinase pathways and the interaction with the G-protein-coupled receptor TGR5, they participate in the regulation of triglyceride, energy, and glucose metabolism. 4

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confidence: 85%

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Temperature Dependence of Backbone Dynamics in Human Ileal Bile Acid-Binding Protein: Implications for the Mechanism of Ligand Binding

2014

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“…Still, the position of ligands at site 1 is similar in the two homologues, whereas the position of the bile salt at site 2, similarly to cI-BABP, is located substantially closer to the helical region than in the human analogue (not shown). The difference in the position of one of the ligands between the human and chicken homologues might be related to the observation that in the latter the orientation of a-II differs substantially less between the apo [24] and holo [13] states. Also, a-II is substantially less ordered in the cI-BABP complex than in the human analogue.…”

Section: Binding Cavity Of the Ternary Complexmentioning

confidence: 99%

Structural determinants of ligand binding in the ternary complex of human ileal bile acid binding protein with glycocholate and glycochenodeoxycholate obtained from solution NMR

et al. 2016

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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 http://www.rcsb.org/pdb/search/structidSearch.do?structureId=2MM3.

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“…where the differences between the two structures are very small). It is also worth noticing that for one of them, His 98 , an active role, upon protonation and deprotonation, has been assigned in the dynamic behavior of the protein (18). Fig.…”

Section: Structure and Ligand-binding Stoichiometry Of The Wild Typementioning

confidence: 99%

“…Section 1734 solely to indicate this fact. The atomic coordinates and structure factors (code 2QO4,2QO5,and 2QO6) have changes that take place upon ligand binding that have been studied in chicken L-BABP by both x-ray diffraction (11) and NMR spectroscopy that has highlighted the important role of a buried histidine (18). Although L-BABPs have been studied in catfish (Rhandia sapo) (21), lungfish (Lepidosiren paradoxus) (22), Japanese sea perch (Lateolabrax japonicus) (23), gilthead sea bream (Sparus aurata) (24), salmon (Salmo salar L.) (25), shark (Halaelurus bivius) (26), and zebrafish (Danio rerio) (27), there is currently no three-dimensional structure available of an L-BABP belonging to this vertebrate group.…”

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A Single Amino Acid Mutation in Zebrafish (Danio rerio) Liver Bile Acid-binding Protein Can Change the Stoichiometry of Ligand Binding

Capaldi

Guariento²,

Saccomani³

et al. 2007

Journal of Biological Chemistry

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In all of the liver bile acid-binding proteins (L-BABPs) studied so far, it has been found that the stoichiometry of binding is of two cholate molecules per internal binding site. In this paper, we describe the expression, purification, crystallization, and threedimensional structure determination of zebrafish (Danio rerio) L-BABP to 1.5 Å resolution, which is currently the highest available for a protein of this family. Since we have found that in zebrafish, the stoichiometry of binding in the protein cavity is of only one cholate molecule per wild type L-BABP, we examined the role of two crucial amino acids present in the binding site. Using site-directed mutagenesis, we have prepared, crystallized, and determined the three-dimensional structure of co-crystals of two mutants. The mutant G55R has the same stoichiometry of binding as the wild type protein, whereas the C91T mutant changes the stoichiometry of binding from one to two ligand molecules in the cavity and therefore appears to be more similar to the other members of the L-BABP family. Based on the presence or absence of a single disulfide bridge, it can be postulated that fish should bind a single cholate molecule, whereas amphibians and higher vertebrates should bind two. Isothermal titration calorimetry has also revealed the presence in the wild type protein and the G55R mutant of an additional binding site, different from the first and probably located on the surface of the molecule.The liver bile acid-binding proteins, formerly called liver "basic" fatty acid-binding proteins (FABPs), 2 belong to the conserved multigene family of the fatty acid-binding proteins (1-6). Originally, the different members of this family were named according to the tissue from which they were first isolated. More recently, an alternative nomenclature has been proposed, since it is well known that different FABP types can be present in the same tissue (7). In particular, in the liver of several vertebrates, two paralogous groups of FABPs have been described: the liver FABPs and another group that was initially called the liver "basic" FABPs and is currently referred to as the liver bile acid-binding proteins (L-BABPs) (8, 9). The reason for this unusual nomenclature was that the isoelectric point of the first protein of this group that was described, chicken liver BABP, is 9.0, and although it was evident that this protein was different from the canonical liver FABP, its specific ligand was unknown (10). When it was shown that this protein could specifically bind cholic acid, a change in its designation was suggested to avoid confusion (11). The cytosolic bile acid-binding proteins mediate the intracellular movement of bile acids to the membranes across which they exit or enter the cells via membrane-bound transporters (12). The L-BABPs have been shown to be present in birds, amphibians, reptiles, and fish but not in mammals that express the very similar ileal BABPs, formerly called gastrotropins. It is suspected, although not proved, that the function that they perform ...

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NMR Dynamic Studies Suggest that Allosteric Activation Regulates Ligand Binding in Chicken Liver Bile Acid-binding Protein

Cited by 52 publications

References 54 publications

Temperature Dependence of Backbone Dynamics in Human Ileal Bile Acid-Binding Protein: Implications for the Mechanism of Ligand Binding

Temperature Dependence of Backbone Dynamics in Human Ileal Bile Acid-Binding Protein: Implications for the Mechanism of Ligand Binding

Structural determinants of ligand binding in the ternary complex of human ileal bile acid binding protein with glycocholate and glycochenodeoxycholate obtained from solution NMR

A Single Amino Acid Mutation in Zebrafish (Danio rerio) Liver Bile Acid-binding Protein Can Change the Stoichiometry of Ligand Binding

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