In 1961, he took a post-doctoral fellowship at the California Institute of Technology, working with George S. Hammond, who was an organic photo-chemist.
Early in his career, Knowles studied α-chymotrypsin[17] and pepsin,[3] which are nonspecific proteases, meaning they accept a broad range of substrates.
In 1972, Knowles developed a method for photo-affinity labelling, enabling the formation of a covalent bond between a protein and a ligand under the control of light.
[18] Knowles then began seminal studies on the glycolytic enzyme triosephosphate isomerase (TIM).
[19] His profile showed that TIM was a "perfect" enzyme in that catalysis is limited only by the rate of diffusion.
Later, Knowles applied similar methods to proline racemase,[20] developing an elegant method to discern whether a reaction proceeds via a stepwise or concerted manner and discovering the consequences of "oversaturation", a situation in which the interconversion of unliganded forms of the enzyme limit catalysis.
He held honorary degrees from the University of Edinburgh and the Eidgenössische Technische Hochschule in Zürich.