Baker, DavidDiMaio, FrankChen, Zibo2019-02-222019-02-222019-02-222018Chen_washington_0250E_19412.pdfhttp://hdl.handle.net/1773/43306Thesis (Ph.D.)--University of Washington, 2018The binding specificity of DNA molecules is straightforward: adenine binds thymine, and cytosine binds guanine. This simple encoding of specificity enables the binding between two DNA molecules to be modularly and programmatically designed. Proteins do not have such straightforward encoding of binding specificity, but could one design for it? This thesis argues such feature can indeed be designed into proteins. I first show orthogonal heterodimers can be designed modularly and programmably to have DNA-like specificity, followed by showing such principles open the door to algorithmic self-assembly of proteins into 2D lattices.application/pdfen-USCC BY-NC-SABiophysicsComputational biologyStructural biologyBiochemistryBiological chemistryThesis