Structure and Dynamics of Biophysical Systems via 2DIR of the Amide-I

This thesis explores the structural dynamics of small molecules and a larger peptide system using Infrared Spectroscopy and Molecular Dynamics (MD) simulations. Ion specific binding of calcium is crucial for many biological functions. For example, calmodulin is an essential protein that undergoes a conformational change upon binding to four calcium ions which then enables binding to numerous targets throughout the body. In addition to playing a vital role in biology, it has been shown that ions are able to modulate the stability of proteins. The Hofmeister series was discovered in 1880 to classify ions based on the strength of their interactions with proteins. This knowledge has produced over a century’s worth of research, yet there remains uncertainty in how ions have such strong influence over proteins. Herein we provide novel spectroscopic and computational evidence to support the presence of an iminium resonance structure stabilized through direct binding of calcium salt with the peptide backbone.

Additionally, this thesis explores fibril formation of cross amyloid peptides. Amyloid fibrils are associated with a multitude of human diseases and infections including Staphylococcus Aureus (S. Aureus), which has the ability to form biofilms. Biofilms are a community of microorganisms irreversibly adhered to surfaces within the body increasing antibiotic resistance and reducing effectiveness of the hosts immune response. Phenol Soluble Modulins (PSMs) play a crucial role in the process of biofilm formation. While most peptides in the PSM family form traditional cross-b fibrils, recent studies have discovered the unique cross-a secondary structure of PSMa3 fibrils. Herein we report on this cross-a amyloid forming peptide using 2DIR spectroscopic methods to reveal cross- a/bpolymorphism upon fibrillation. Aggregation studies track PSMa3 secondary structure elucidating a novel spectroscopic signal unique to cross-a amyloids.