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An experimental approach probing the conformational transitions and energy landscape of antibodies: a glimmer of hope for reviving lost therapeutic candidates using ionic liquid.

ABSTRACT: Understanding protein folding in different environmental conditions is fundamentally important for predicting protein structures and developing innovative antibody formulations. While the thermodynamics and kinetics of folding and unfolding have been extensively studied by computational methods, experimental methods for determining antibody conformational transition pathways are lacking. Motivated to fill this gap, we prepared a series of unique formulations containing a high concentration of a chimeric immunoglobin G4 (IgG4) antibody with different excipients in the presence and absence of the ionic liquid (IL) choline dihydrogen phosphate. We determined the effects of different excipients and IL on protein thermal and structural stability by performing variable temperature circular dichroism and bio-layer interferometry analyses. To further rationalise the observations of conformational changes with temperature, we carried out molecular dynamics simulations on a single antibody binding fragment from IgG4 in the different formulations, at low and high temperatures. We developed a methodology to study the conformational transitions and associated thermodynamics of biomolecules, and we showed IL-induced conformational transitions. We showed that the increased propensity for conformational change was driven by preferential binding of the dihydrogen phosphate anion to the antibody fragment. Finally, we found that a formulation containing IL with sugar, amino acids and surfactant is a promising candidate for stabilising proteins against conformational destabilisation and aggregation. We hope that ultimately, we can help in the quest to understand the molecular basis of the stability of antibodies and protein misfolding phenomena and offer new candidate formulations with the potential to revive lost therapeutic candidates.

SUBMITTER: Shmool TA

PROVIDER: S-EPMC8278930 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:We report an investigation of ordering transitions that are induced in water-dispersed, micrometer-sized droplets of a thermotropic liquid crystal (LC) by the bacterial lipopolysaccharide endotoxin. We reveal that the ordering transitions induced by endotoxin - from a bipolar state of the droplets to a radial state - are strongly dependent on the size of the LC droplets. Specifically, as the diameters of the LC droplets increase from 2 μm to above 10 μm (in phosphate buffered saline with an ionic strength of 90 mM and a pH of 7.2), we measured the percentage of droplets exhibiting a radial configuration in the presence of 100 pg/mL endotoxin to decrease from 98 ± 1 % to 3 ± 2 %. In addition, we measured a decrease in either the ionic strength or pH of the aqueous phase to reduce the percentage of droplets exhibiting a radial configuration in the presence of endotoxin. These results, when interpreted within the context of a simple thermodynamic model that incorporates the contributions of elasticity and surface anchoring to the free energies of the LC droplets, lead us to conclude that (i) the elastic constant K24 plays a central role in determining the size-dependent response of the LC droplets to endotoxin, and (ii) endotoxin-triggered ordering transitions occur only under solution conditions (pH, ionic strength) where the combined contributions of elasticity and surface anchoring to the free energies of the bipolar and radial configurations of the LC droplets are similar in magnitude. Our analysis also suggests that the presence of endotoxin perturbs the free energies of the LC droplets by ~10-17 J/droplet, which is comparable to the standard free energy of self-association of ~103 endotoxin molecules. These results, when combined with prior reports of localization of endotoxin at the center of LC droplets, are consistent with the hypothesis that self-assembly of endotoxin within micrometer-sized LC droplets provides the driving force for the ordering transitions. Overall, these results advance our understanding of ordering transitions triggered by the interactions of analytes with LC droplets and, more broadly, provide guidance to the design of LC droplet systems as the basis of stimuli-responsive soft materials.

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An experimental approach probing the conformational transitions and energy landscape of antibodies: a glimmer of hope for reviving lost therapeutic candidates using ionic liquid.

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