Biology subjects

Gan, S. K.-E.

Publications and source records attributed to Gan, S. K.-E..

5 recordsLinked to original sources

bioRxiv2026

Ara h 2 and FcϵRIα binding elicit state-dependent allostery in IgE

Background: Peanuts are among the most prevalent food allergens responsible for anaphylaxis, particularly in children. Allergic responses may be mitigated by disrupting molecular interactions between immunoglobulin-E (IgE) and its binding partners: peanut allergen (Ara h 2) and IgE receptors (Fc{epsilon}RI). However, the structural dynamics of IgE upon engaging these factors are not yet fully elucidated. Objective: To characterize how Ara h 2 and/or Fc{epsilon}RI binding influence IgE flexibility and its interdomain communications. Methods: The structural dynamics of full-length IgE in various unbound and bound states were examined by combining molecular dynamics (MD) simulations with cross linking mass spectrometry (XLMS). Causal relationship between IgE domains were characterized to infer allosteric communication pathways, which were assessed through hydrogen-deuterium exchange mass spectrometry (HDX-MS). Results: Non canonical bent IgE conformations were identified. We demonstrate that Fc{epsilon}RI binding immobilizes IgE predominantly by stabilizing and restricting Fc flexibility, whereas Ara h 2 binding induces specific conformational changes within the Fc{epsilon}RI-binding region. Our results further suggest that the C{epsilon} domains retain sufficient freedom to enable causal dynamics by the Fabs in a binding-dependent manner, thereby modulating the receptor engagement potential of IgE. Notably, concurrent binding of Ara h 2 and Fc{varepsilon}RI to IgE shifts the allosteric communication between the Fabs and Fc regions from the C{epsilon}3 to C{epsilon}4 domain. Conclusion: Our findings provide new insights into the dynamic regulation of IgE and its role in allergic responses. This could serve as a structural framework for understanding IgE signaling in peanut allergy and suggest potential targets for therapeutic interventions

immunology↗

bioRxiv2021

Augmenting Whole Recombinant Antibody Production in HEK293E Cells: Optimizing Transfection and Culture Parameters

BackgroundOptimising recombinant antibody production is important for cost-effective therapeutics and diagnostics. With impact on commercialisation, higher productivity beyond laboratory scales is highly sought, where efficient production can also accelerate antibody characterisations and investigations. MethodsInvestigating HEK293E cells for mammalian antibody production, various transfection and culture parameters were systematically analysed for antibody light chain production before evaluating them for whole antibody production. Transfection parameters investigated include seeding cell density, the concentration of the transfection reagent and DNA, complexation time, temperature, and volume, as well as culture parameters such as medium replacement, serum deprivation, use of cell maintenance antibiotic, incubation temperature, medium volume, post-transfection harvest day and common nutrient supplements. ResultsUsing 2 mL adherent HEK293E cell culture transfections with 25 kDa linear Polyethylenimine in the most optimised parameters, we demonstrated a ~2-fold production increase for light chain alone and for whole antibody production reaching 536 and 49 g respectively in a cost-effective manner. With the addition of peptone, {kappa} light chain increased by ~4-fold to 1032 g while whole antibody increased to a lesser extent by ~2.5-fold to 51 g, with benefits potentially for antibodies limited by their light chains in production. ConclusionsOur optimised findings show promise for a more efficient and convenient antibody production method through transfection and culture optimisations that can be incorporated to scale up processes and with potential transferability to other mammalian-based recombinant protein production using HEK293E cells. Statement of SignificanceRecombinant antibody production is crucial for antibody research and development. Systematically investigating transfection and culture parameters such as PEI/DNA concentrations, complexation time, volume, and temperature, supplements, etc., we demonstrated a ~4-fold light chain alone production increase to 1032 g and a 2.5-fold whole antibody production increase to 51 g from 2 mL transfections.

molecular biology↗

bioRxiv2020

Molecular insight into Nickel(II) binding by Her2-specific IgE: a possible mechanistic insight into the pathogenesis of Type I nickel hypersensitivity

Nickel (Ni) allergy has been reported in contact dermatitis Type IV (Ni-specific T cells mediated) and asthmatic Type I (IgE-mediated) hypersensitivities. Associations between the two hypersensitivities have been found in some patients, but the underlying mechanisms remain enigmatic. Using Her2-specific IgEs as models, we found additional binding to Ni-NTA without observable changes in binding to Her2 and that glutamine, together with the canonical Ni2+-binding histidine, could form Ni2+ binding signatures. This mechanism may underlie Type I hypersensitivity in the selection of anti-Ni2+ IgEs. This mechanism may also underlie Type IV hypersensitivity and the interaction of immunoglobulin proteins with other heavy metal ions. Our findings shed light to how Ni hypersensitivities can occur and how they can be avoided in therapeutics design, or even incorporated for biotechnological purification purposes.

immunology↗

bioRxiv2019

The structural basis for distinct binding avidity of Pertuzumab and Trastuzumab IgM towards HER2

Harnessing the therapeutic potential of immunoglobulin M (IgM) is of considerable interest in immunotherapy due to its complement-activating and cell-agglutinating abilities. Pertuzumab and Trastuzumab are monoclonal antibody drugs used in therapy for patients with human epidermal growth factor receptor 2 (HER2)-positive breast cancer but exhibit significantly different binding affinities as IgM when compared to the original IgG1 form. While the affinity of Pertuzumab IgM to the HER2 extracellular domain is about one order of magnitude higher than IgG1 in experiments, it was recently reported that Trastuzumab IgM and IgG have similar equilibrium dissociation constants to one another. We now perform an integrative multiscale simulation study in order to understand the structural basis for the differences in behavior between the two antibodies, based on complete antibody assemblies. We show that Pertuzumab IgM is able to utilize all of its V-regions to engage HER2 in a more stable mode than Trastuzumab IgM due to steric clashes between the large globular HER2 domains when bound to Trastuzumab. This is subsequently validated by confirming that Pertuzumab IgM inhibits proliferation in HER2 over-expressing live cells more effectively than its IgG1 counterpart. Given the widespread clinical use of Trastuzumab and Pertuzumab, elucidating the molecular details of antibody-antigen interaction may help guide the choice of epitopes for future design and selection of improved therapeutic antibody isotypes.

immunology↗

bioRxiv2019

Predicting mutations in HIV-1 Gag: Insights from in silico and an in vitro BSL2 platform on thermostability and allosteric effects

While drug resistant mutations in HIV-1 is largely credited to its error prone HIV-1 RT, host proteins such as deaminases may also play a role generating mutations. Many HIV-1 RT mutational in vitro studies utilize reporter genes (LacZ) as template, leaving out the possible contribution of HIV codon usage and gene-specific effects. To address this gap, we studied HIV-1 RT mutation rates and bias on its own Gag, protease, and RT p66 genes in an in-vitro selection pressure free system. We found rare clinical mutations with a general avoidance of crucial functional sites in the background mutations rates for Gag, protease and RT p66 at 4.71 x 10-5, 6.03 x 10-5, and 7.09 x 10-5 mutations/bp respectively. Gag and p66 genes showed a large number of A to G hypermutations likely due to cellular adenosine deaminases. Comparisons with silently mutated p66 sequences showed an increase in mutation rates (1.88 x 10-4 mutations/bp) and that A to G mutations occurred in regions reminiscent of ADAR neighbour preferences. Mutational free energies by the A to G mutations revealed an avoidance of destabilizing effects with the natural p66 gene codon usage providing barriers to ADAR effects. Our study demonstrates the importance of studying mutation emergence in HIV genes to understand how fast drug resistance can emerge, sometimes with contributions of host deaminases, providing transferable applications to how new viral diseases and drug resistances can emerge.

microbiology↗