Bayesian analysis of isothermal titration calorimetry for binding thermodynamics

Nguyen, Trung Hai; Rustenburg, Ariën S.; Krimmer, S.G.; He-xi, Zhang; Clark, John D.; Novick, Paul; Branson, Kristin; Pande, Vijay S.; Chodera, John D.; Minh, David D. L.

doi:10.1371/journal.pone.0203224

“…The understanding of Aβ self-assembly would be further illuminated. Several approaches were developed to determine the binding affinity between the two molecules. − Here, the umbrella sampling (US) method was employed to estimate the disassociation energy barrier referring to a previous study . The free energy Δ G over US simulations along reaction coordinate ξ was determined employing the weight histogram analysis method (WHAM) .…”

Section: Results and Discussionmentioning

confidence: 99%

C-Terminal Plays as the Possible Nucleation of the Self-Aggregation of the S-Shape Aβ_11–42 Tetramer in Solution: Intensive MD Study

Tùng

¹

,

Derreumaux

²

,

Vu

³

et al. 2019

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Amyloid beta (Aβ) peptides are characterized as the major factors associated with neuron death in Alzheimer’s disease, which is listed as the most common form of neurodegeneration. Disordered Aβ peptides are released from proteolysis of the amyloid precursor protein. The Aβ self-assembly process roughly takes place via five steps: disordered forms → oligomers → photofibrils → mature fibrils → plaques. Although Aβ fibrils are often observed in patient brains, oligomers were recently indicated to be major neurotoxic elements. In this work, the neurotoxic compound S-shape Aβ 11–42 tetramer (S4Aβ 11–42 ) was investigated over 10 μs of unbiased MD simulations. In particular, the S4Aβ 11–42 oligomer adopted a high dynamics structure, resulting in unsuccessful determination of their structures in experiments. The C-terminal was suggested as the possible nucleation of the Aβ 42 aggregation. The sequences 27–35 and 39–40 formed rich β-content, whereas other residues mostly adopted coil structures. The mean value of the β-content over the equilibrium interval is ∼42 ± 3%. Furthermore, the dissociation free energy of the S4Aβ 11–42 peptide was predicted using a biased sampling method. The obtained free energy is Δ G US = −58.44 kcal/mol which is roughly the same level as the corresponding value of the U-shape Aβ 17-42 peptide. We anticipate that the obtained S4Aβ 11–42 structures could be used as targets for AD inhibitor screening over the in silico study.

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“…S28 assuming different stoichiometric binding models as described in the Supporting Material. The Bayesian approach used to fit the ITC data was based on Nguyen and co-workers (2018) (22). Fits to the Hill model considered the dissociation constant, K d , the Hill coefficient (n Hill ), and the molar binding enthalpy (∆H bind ) as free parameters, while fits to the stepwise model treated 4 , and ∆H bind as free parameters.…”

Section: Calorimetrymentioning

confidence: 99%

CALX-CBD1 Ca2+-Binding Cooperativity Studied by NMR Spectroscopy and ITC with Bayesian Statistics

Cardoso

¹

,

Rivera

²

,

Vitale

³

et al. 2020

Biophysical Journal

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The Na + /Ca 2+ exchanger of Drosophila melanogaster, CALX, is the main Ca 2+ -extrusion mechanism in olfactory sensory neurons and photoreceptor cells. Na + /Ca 2+ exchangers have two Ca 2+ sensor domains, CBD1 and CBD2. In contrast to the mammalian homologues, CALX is inhibited by Ca 2+ -binding to CALX-CBD1, while CALX-CBD2 does not bind Ca 2+ at physiological concentrations. CALX-CBD1 consists of a β-sandwich and displays four Ca 2+ binding sites at the tip of the domain. In this study, we used NMR spectroscopy and isothermal titration calorimetry (ITC) to investigate the cooperativity of Ca 2+ -binding to CALX-CBD1. We observed that this domain binds Ca 2+ in the slow exchange regime at the NMR chemical shift time scale. Ca 2+ -binding restricts the dynamics in the Ca 2+ -binding region. Experiments of 15 N CEST and 15 N R 2 dispersion allowed the determination of Ca 2+ dissociation rates (≈ 20 s −1 ). NMR titration curves of residues in the Ca 2+ -binding region were sigmoidal due to the contribution of chemical exchange to transverse magnetization relaxation rates, R 2 . Hence, a novel approach to analyze NMR titration curves was proposed. Ca 2+ -binding cooperativity was examined assuming two different stoichiometric binding models and using a Bayesian approach for data analysis. Fittings of NMR and ITC binding curves to the Hill model yielded n Hill = 2.9 − 3.1, near maximum cooperativity (n Hill = 4). By assuming a stepwise model to interpret the ITC data, we found that the probability of binding from 2 up to 4 Ca 2+ is at least three orders of magnitude higher than that of binding a single Ca 2+ . Hence, four Ca 2+ ions bind almost simultaneously to CALX-CBD1. Cooperative Ca 2+ -binding is key to enable this exchanger to efficiently respond to changes in the intracellular Ca 2+ -concentration in sensory neuronal cells. SIGNIFICANCE CALX-CBD1 is the Ca 2+ -sensor domain of the Na + /Ca 2+ exchanger of Drosophila melanogaster. It consists of a β-sandwich, and contains four Ca 2+ binding sites at the distal loops. In this study, we examined the cooperative binding of four Ca 2+ ions to CALX-CBD1 using NMR spectroscopy and isothermal titration calorimetry (ITC) experiments. NMR and ITC data were analyzed using the framework of the binding polynomial formalism and Bayesian statistics. A novel approach to analyze NMR titration data in the slow exchange regime was proposed. These results support the view that CALX-CBD1 binds four Ca 2+ with high cooperativity. The significant ligand binding cooperativity exhibited by this domain is determinant for the efficient allosteric regulation of this exchanger by intracellular Ca 2+ .

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“…Fits to the Hill model considered the dissociation constant, K d , the Hill coefficient (n Hill ), and the molar binding enthalpy (∆H bind ) as free parameters, while fits to the stepwise model treated 4 , and ∆H bind as free parameters. As proposed by Nguyen and co-workers (2018) (22), we included a set of nuisance parameters involved in the theory, among which are the ligand concentration in the syringe [L] o , the protein concentration in the cell [P] tot , the heat offset Q o and the Gaussian error of the ITC data, σ, for each ITC curve. The latter was considered the same for all data points.…”

Section: Calorimetrymentioning

confidence: 99%

CALX-CBD1 Ca²⁺-binding cooperativity studied by NMR spectroscopy and ITC with Bayesian statistics

Cardoso

¹

,

Rivera

²

,

Vitale

³

et al. 2019

Preprint

View full text Add to dashboard Cite

The Na + /Ca 2+ exchanger of Drosophila melanogaster, CALX, is the main Ca 2+ -extrusion mechanism in olfactory sensory neurons and photoreceptor cells. Na + /Ca 2+ exchangers have two Ca 2+ sensor domains, CBD1 and CBD2. In contrast to the mammalian homologues, CALX is inhibited by Ca 2+ -binding to CALX-CBD1, while CALX-CBD2 does not bind Ca 2+ at physiological concentrations. CALX-CBD1 consists of a β-sandwich and displays four Ca 2+ binding sites at the tip of the domain. In this study, we used NMR spectroscopy and isothermal titration calorimetry (ITC) to investigate the cooperativity of Ca 2+ -binding to CALX-CBD1. We observed that this domain binds Ca 2+ in the slow exchange regime at the NMR chemical shift time scale. Ca 2+ -binding restricts the dynamics in the Ca 2+ -binding region. Experiments of 15 N CEST and 15 N R 2 dispersion allowed the determination of Ca 2+ dissociation rates (≈ 20 s −1 ). NMR titration curves of residues in the Ca 2+ -binding region were sigmoidal due to the contribution of chemical exchange to transverse magnetization relaxation rates, R 2 . Hence, a novel approach to analyze NMR titration curves was proposed. Ca 2+ -binding cooperativity was examined assuming two different stoichiometric binding models and using a Bayesian approach for data analysis. Fittings of NMR and ITC binding curves to the Hill model yielded n Hill = 2.9 − 3.1, near maximum cooperativity (n Hill = 4). By assuming a stepwise model to interpret the ITC data, we found that the probability of binding from 2 up to 4 Ca 2+ is at least three orders of magnitude higher than that of binding a single Ca 2+ . Hence, four Ca 2+ ions bind almost simultaneously to CALX-CBD1. Cooperative Ca 2+ -binding is key to enable this exchanger to efficiently respond to changes in the intracellular Ca 2+ -concentration in sensory neuronal cells. SIGNIFICANCE CALX-CBD1 is the Ca 2+ -sensor domain of the Na + /Ca 2+ exchanger of Drosophila melanogaster. It consists of a β-sandwich, and contains four Ca 2+ binding sites at the distal loops. In this study, we examined the cooperative binding of four Ca 2+ ions to CALX-CBD1 using NMR spectroscopy and isothermal titration calorimetry (ITC) experiments. NMR and ITC data were analyzed using the framework of the binding polynomial formalism and Bayesian statistics. A novel approach to analyze NMR titration data in the slow exchange regime was proposed. These results support the view that CALX-CBD1 binds four Ca 2+ with high cooperativity. The significant ligand binding cooperativity exhibited by this domain is determinant for the efficient allosteric regulation of this exchanger by intracellular Ca 2+ .

show abstract

Bayesian analysis of isothermal titration calorimetry for binding thermodynamics

Cited by 29 publications

References 41 publications

C-Terminal Plays as the Possible Nucleation of the Self-Aggregation of the S-Shape Aβ_11–42 Tetramer in Solution: Intensive MD Study

C-Terminal Plays as the Possible Nucleation of the Self-Aggregation of the S-Shape Aβ_11–42 Tetramer in Solution: Intensive MD Study

CALX-CBD1 Ca2+-Binding Cooperativity Studied by NMR Spectroscopy and ITC with Bayesian Statistics

CALX-CBD1 Ca²⁺-binding cooperativity studied by NMR spectroscopy and ITC with Bayesian statistics

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Bayesian analysis of isothermal titration calorimetry for binding thermodynamics

Cited by 29 publications

References 41 publications

C-Terminal Plays as the Possible Nucleation of the Self-Aggregation of the S-Shape Aβ11–42 Tetramer in Solution: Intensive MD Study

C-Terminal Plays as the Possible Nucleation of the Self-Aggregation of the S-Shape Aβ11–42 Tetramer in Solution: Intensive MD Study

CALX-CBD1 Ca2+-Binding Cooperativity Studied by NMR Spectroscopy and ITC with Bayesian Statistics

CALX-CBD1 Ca2+-binding cooperativity studied by NMR spectroscopy and ITC with Bayesian statistics

Contact Info

Product

Resources

About

C-Terminal Plays as the Possible Nucleation of the Self-Aggregation of the S-Shape Aβ_11–42 Tetramer in Solution: Intensive MD Study

C-Terminal Plays as the Possible Nucleation of the Self-Aggregation of the S-Shape Aβ_11–42 Tetramer in Solution: Intensive MD Study

CALX-CBD1 Ca²⁺-binding cooperativity studied by NMR spectroscopy and ITC with Bayesian statistics