[HTML][HTML] Polarizable and non-polarizable force fields: Protein folding, unfolding, and misfolding

AS Kamenik, PH Handle, F Hofer, U Kahler… - The Journal of …, 2020 - pubs.aip.org
Molecular dynamics simulations are an invaluable tool to characterize the dynamic motions
of proteins in atomistic detail. However, the accuracy of models derived from simulations …

Allergenicity and Conformational Diversity of Allergens

CA Seidler, R Zeindl, ML Fernández-Quintero… - Allergies, 2024 - mdpi.com
Allergens are substances that cause abnormal immune responses and can originate from
various sources. IgE-mediated allergies are one of the most common and severe types of …

To stay or not to stay intact as an allergen: the endolysosomal degradation assay used as tool to analyze protein immunogenicity and T cell epitopes

E Öztemiz Topcu, G Gadermaier - Frontiers in Allergy, 2024 - frontiersin.org
Antigen uptake and processing of exogenous proteins is critical for adaptive immunity,
particularly for T helper cell activation. Proteins undergo distinct proteolytic processing in …

Energy penalties enhance flexible receptor docking in a model cavity

AS Kamenik, I Singh, P Lak, TE Balius… - Proceedings of the …, 2021 - National Acad Sciences
Protein flexibility remains a major challenge in library docking because of difficulties in
sampling conformational ensembles with accurate probabilities. Here, we use the model …

pH-dependent structural diversity of profilin allergens determines thermal stability

F Hofer, AL Fischer, AS Kamenik, F Waibl… - Frontiers in …, 2022 - frontiersin.org
The family of profilin allergens is a common class of proteins found in plants, viruses and
various eukaryotes including mammals. Profilins are characterized by an evolutionary …

Structural alterations of antigens at the material interface: An early decision toolbox facilitating safe-by-design nanovaccine development

L Johnson, L Aglas, WT Soh, M Geppert… - International Journal of …, 2021 - mdpi.com
Nanomaterials have found extensive interest in the development of novel vaccines, as
adjuvants and/or carriers in vaccination platforms. Conjugation of protein antigens at the …

pH-induced local unfolding of the Phl p 6 pollen allergen from cpH-MD

F Hofer, AS Kamenik… - Frontiers in Molecular …, 2021 - frontiersin.org
Susceptibility to endosomal degradation is a decisive contribution to a protein's
immunogenicity. It is assumed that the processing kinetics of structured proteins are …