Differential effects of SARS-CoV-2 amyloidogenic segments on the aggregation and toxicity of human islet amyloid polypeptide within membrane environments.

Human islet amyloid polypeptide (hIAPP), an intrinsically disordered protein (IDP), plays a significant role in the pathogenesis of type 2 diabetes through its aggregation. Recent studies have suggested that certain viral protein segments exhibit amyloidogenic potential and may influence its amyloid aggregations associated with pathogenesis. However, the potential link between recurrent SARS-CoV-2 infections and the exacerbation of type 2 diabetes remains poorly understood.

Training machine learning potentials for reactive systems: A Colab tutorial on basic models.

In the last several years, there has been a surge in the development of machine learning potential (MLP) models for describing molecular systems. We are interested in a particular area of this field - the training of system-specific MLPs for reactive systems - with the goal of using these MLPs to accelerate free energy simulations of chemical and enzyme reactions. To help new members in our labs become familiar with the basic techniques, we have put together a self-guided Colab tutorial (https://cc-ats.

SARS-COV-2 spike protein fragment eases amyloidogenesis of α-synuclein.

Parkinson's disease is accompanied by the presence of amyloids in the brain that are formed of α-synuclein chains. The correlation between COVID-19 and the onset of Parkinson's disease led to the idea that amyloidogenic segments in SARS-COV-2 proteins can induce aggregation of α-synuclein. Using molecular dynamic simulations, we show that the fragment FKNIDGYFKI of the spike protein, which is unique for SARS-COV-2, preferentially shifts the ensemble of α-synuclein monomer toward rod-like fibril seeding conformations and, at the same time, differentially stabilizes this polymorph over the competing twister-like structure.