By using the technology of molecularly imprinted polymer (MIP), we propose to synthesize a protein conformational imprint that also acts as a plastic enzyme, inducing protein structural transitions. The imprint aims at MIP-induced stabilization and / or formation of bound protein secondary structure and the applications associated with analysis and correction of misfolded proteins. The screening of polymeric functional monomers being able to induce the conformational transitions in proteins is investigated in this report. The fluoro-silanes (3-heptafluoroisopropoxy)propalethoxysilane (7F) and 3,3,3-trifluoropropylmethoxysilane (3F) were employed as functional monomers for synthesis of this catalytic protein conformational imprint via sol-gel reactions. 3F was demonstrated superior to 7F for fluoro-modification of tetraethylorthosilicate (TEOS) gel in terms of retaining gel transparency and increasing hydrophobicity while maintaining a uniform distribution of encapsulated protein. Both hydrolyzed 3F and polymerized 3F exhibited strong influences on structure transitions of three template proteins: bovine serum albumin (BSA), beta-lactoglobulin (BLG), and bovine carbonic anhydrase (BCA). The formation of molten globule intermediates that stabilized by increased alpha-helices was induced by the trifluoro-silane in BLG and BCA. Additionally, 3F was effective at a lower concentration than the benchmark fluoro-alcohol 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP), validating the application of 3F as a functional monomer for protein conformational imprinting.