Knob-socket Investigation of Stability and Specificity in Alpha-helical Secondary and Quaternary Packing Structure
Date of Award
Doctor of Philosophy (Ph.D.)
Pharmaceutical and Chemical Sciences
Jerry W. Tsai
First Committee Member
C. Michael McCallum
Second Committee Member
Joseph S. Harrison
Third Committee Member
Craig A. Vierra
The novel knob-socket (KS) model provides a construct to interpret and analyze the direct contributions of amino acid residues to the stability in α-helical protein structures. Based on residue preferences derived from a set of protein structures, the KS construct characterizes intra- and inter-helical packing into regular patterns of simple motifs. The KS model was used in the de novo design of an α-helical homodimer, KSα1.1. Using site-directed mutagenesis, KSα1.1 point mutants were designed to selectively increase and decrease stability by relating KS propensities with changes to α-helical structure. This study suggests that the sockets from the KS Model can be used as a measure of α-helical structure and stability.
The KS model was also used to investigate coiled-coil specificity in bZIP proteins. Identifying and characterizing the interactions that determine the dimerization specificity between bZIP proteins is a crucial factor in better understanding disease formation and proliferation, as well as developing drugs or therapeutics to combat these diseases. Knob-Socket mapping methods identified Asn residues at a positions within the helices, and were determined to be crucial factors in coiled-coil specificity. Site-directed mutagenesis was conducted to investigate the role of the Asn residues, as well as the role played by the neighboring residues at the g and b positions. The results indicate that the Asn at the a position defines coiled-coil specificity, and that the Knob-Socket model can be used to determine bZIP protein quaternary interactions.
Rabara, Taylor Renee. (2019). Knob-socket Investigation of Stability and Specificity in Alpha-helical Secondary and Quaternary Packing Structure. University of the Pacific, Dissertation. https://scholarlycommons.pacific.edu/uop_etds/3633