This subproject is one of many research subprojects utilizing theresources provided by a Center grant funded by NIH/NCRR. The subproject andinvestigator (PI) may have received primary funding from another NIH source,and thus could be represented in other CRISP entries. The institution listed isfor the Center, which is not necessarily the institution for the investigator.This is a project aimed to understand how proteins fold using both experimental and computational techniques. The latter can guide the search for fast folders and also tructurally consistent mutants. The computational technique we will employ uses statiscal thermodynamics to identify frustrated positions in the protein sequence as well as structurally consistent and less frustrating mutations. This method has been used previously to guide the search for fast folders. In this case, it has been applied to the 20 residue miniprotein, Trp-cage, in an effort to decrease its 4 microsecond folding time further. The experimental techniques we will use include laser induced temperature-jump kinetics experiments (with IR or UV detection) as well as static experiments using fluorescence, infrared spectroscopy, and circular dichroism.We further propose to use computationally assisted peptide design in association with fluorescence correlation spectroscopy (FCS) and fluorescence resonance energy transfer (FRET) based single molecule techniques to design and characterize short peptides that also impede and reverse the polymerization of serpins.
The specific aims are to design and study these peptides both from the theoretical and experimental points of view and to investigate the underlying mechanistic details of depolymerization, thus informing the design of potential therapeutic molecules.
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