Ligand entry in human ileal bile acid-binding protein is mediated by histidine protonation

Horváth, Gergő; Egyed, Orsolya; Tang, Changguo; Kovács, Mihály; Micsonai, András; Kardos, József; Tőke, Orsolya

doi:10.1038/s41598-019-41180-7

Cited by 3 publications

(15 citation statements)

References 59 publications

(107 reference statements)

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“…Several resonances experience large pH-dependent CSPs, including residues in and around the acidic patch. As the amide backbone chemical shifts are sensitive to changes in electrostatics, hydrogen bonding strength and local conformation, the observed CSPs are indirect reporters of changes in protonation state 33 – 37 , even for residues without a titratable group. Fits of the CSP profiles thus result in a residue-specific, apparent pKa (pKa app ) (Table S4 ).…”

Section: Resultsmentioning

confidence: 99%

Mapping the electrostatic potential of the nucleosome acidic patch

Zhang

Eerland

Horn

et al. 2021

Sci Rep

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The nucleosome surface contains an area with negative electrostatic potential known as the acidic patch, which functions as a binding platform for various proteins to regulate chromatin biology. The dense clustering of acidic residues may impact their effective pKa and thus the electronegativity of the acidic patch, which in turn could influence nucleosome-protein interactions. We here set out to determine the pKa values of residues in and around the acidic patch in the free H2A-H2B dimer using NMR spectroscopy. We present a refined solution structure of the H2A-H2B dimer based on intermolecular distance restraints, displaying a well-defined histone-fold core. We show that the conserved histidines H2B H46 and H106 that line the acidic patch have pKa of 5.9 and 6.5, respectively, and that most acidic patch carboxyl groups have pKa values well below 5.0. For H2A D89 we find strong evidence for an elevated pKa of 5.3. Our data establish that the acidic patch is highly negatively charged at physiological pH, while protonation of H2B H106 and H2B H46 at slightly acidic pH will reduce electronegativity. These results will be valuable to understand the impact of pH changes on nucleosome-protein interactions in vitro, in silico or in vivo.

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Section: Resultsmentioning

confidence: 99%

Mapping the electrostatic potential of the nucleosome acidic patch

Zhang

Eerland

Horn

et al. 2021

Sci Rep

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“…Accordingly, while in the chicken liver analogue the contribution of H98 toward substrate binding is favored by an increase in pH, in the human ileal form it is the opposite. The latter is supported by a pH-dependent analysis of the thermodynamics and kinetics of bile salt binding in hI-BABP showing an increase in the overall binding affinity and the association rate constant of the first binding step below the pK a of H98 [ 65 ]. Importantly, in hI-BABP there are two additional histidines in the C/D-turn as well, which similar to the E/F- and G/H-regions undergoes a conformational change upon ligand binding.…”

Section: Conformational Fluctuations On the Millisecond Timescalementioning

confidence: 97%

“…In the chicken forms (both liver and ileal), such stabilization is contributed by lysine/arginine residues in both the C/D- and the E/F-turns, whereas in the human ileal form by K77 of the E/F-turn only. An additional source of stabilization for the carboxylate group of bile salt at site 2 in hI-BABP may arise through the tautomer equilibrium of H57 in the C/D-turn, whose pK a increases markedly upon ligand binding [ 65 ].…”

Section: Binding Cavity In Babp Complexesmentioning

confidence: 99%

“…The ms-timescale dynamics in both ileal [ 65 ] and liver BABPs [ 56 ] is thought to be associated with the protonation equilibria of histidines, providing a pH-dependent allosteric regulation of a transition between a closed and a more open protein state. In cL-BABP, the observed conformational fluctuation has been related to the tautomer equilibrium of a buried histidine (H98) located near the G/H turn.…”

Section: Conformational Fluctuations On the Millisecond Timescalementioning

confidence: 99%

“…Strikingly, while H98 is conserved in the human ileal analogue as well, there is a significant difference between the two proteins in terms of both the pK a of H98 and its change upon bile salt binding. Unlike in the chicken liver form, where H98 is buried and exhibits a pK a of 4.7 in the apo state, which upon bile salt binding shifts further down [ 40 ], in hI-BABP it is facing the solvent in both ligation states with values of pK a of 6.6 ( apo ) and 7.0 ( holo ) [ 65 ]. Accordingly, while in the chicken liver analogue the contribution of H98 toward substrate binding is favored by an increase in pH, in the human ileal form it is the opposite.…”

Section: Conformational Fluctuations On the Millisecond Timescalementioning

confidence: 99%

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Structural and Dynamic Determinants of Molecular Recognition in Bile Acid-Binding Proteins

Tőke

2022

IJMS

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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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Multiple Timescale Dynamic Analysis of Functionally-Impairing Mutations in Human Ileal Bile Acid-Binding Protein

Horváth

Balterer

Micsonai

et al. 2022

IJMS

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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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Ligand entry in human ileal bile acid-binding protein is mediated by histidine protonation

Cited by 3 publications

References 59 publications

Mapping the electrostatic potential of the nucleosome acidic patch

Mapping the electrostatic potential of the nucleosome acidic patch

Structural and Dynamic Determinants of Molecular Recognition in Bile Acid-Binding Proteins

Multiple Timescale Dynamic Analysis of Functionally-Impairing Mutations in Human Ileal Bile Acid-Binding Protein

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