UCSF

The forces and energetic principles that guide molecular structure and dynamics in cellular lipid bilayers are poorly understood, largely due to limited familiarity with physical chemistry outside of water. We strive to enhance our fundamental chemical intuition concerning membrane proteins because their biochemical behavior within lipid membranes governs critical cellular processes and dictates health or disease. Likewise, this intuition paired with the ability manipulate membrane protein structure and function using computational modeling, theoretical calculations, and molecular design are instrumental to the engineering of new therapeutics. The work described here focuses on using protein design and integrative computational approaches to dissect the fundamental biophysical principles underlying protein interactions and folding within the lipid environment, spanning studies of both natural and totally synthetic proteins. Chapter 1 describes the design and experimental characterization of a family of simple synthetic model membrane proteins that rely entirely on the steric packing of lipid-embedded apolar sidechains for their stabilization and folding. This work reveals new fundamental principles governing van der Waals forces for proteins in lipid which should dictate protein structure, function, and evolution. Chapter 2 reports discovery of an evolutionarily conserved interaction motif within the transmembrane (TM) domains of integrin family proteins regulating their biochemical function. This discovery was driven by molecular modeling and all-atom dynamics simulations paired with co-workers’ optical tweezer force spectroscopy experiments. Chapter 3 details the development and application of software to design lipid-soluble peptides that target the transmembrane domains of proteins. We report several molecules that activate integrin α5β1 in human endothelial cell culture, and one with binding specificity for the β1 subunit. Chapter 4 outlines a second campaign with similar software to engineer small synthetic transmembrane proteins that bind and inhibit signal-amplifying erythropoietin receptor (EpoR), a canonical cytokine family receptor. Here, we demonstrate computational design can be used to target membrane-soluble molecules to specifically adopt custom, non-native binding modes to engage targeted regions of protein embedded in lipid. Thus, the efforts described represent leaps in our capacity to compute designer tool molecules entirely from scratch useful for manipulating membrane-spanning regions. These works together define progress in our fundamental biophysical understanding of protein interactions and folding in lipid, as well as our ability to dissect membrane protein structure and function with in silico molecular modeling algorithms and novel chemical biology tools.