Exploring the relationship between secondary structure and native topology in protein domains

Since the introduction of Pauling's groundbreaking model, numerous experiments have shown that hydrogen-bonded secondary structure is an important factor in protein folding. Under folding conditions, the linear polypeptide chain can form marginally stable elements of secondary structure on a rapid time scale. Such elements, which are in dynamic equilibrium with their respective coil states, interact with one another, further organizing and stabilizing the protein. We hypothesize that this latter step is rate limiting in the folding of a protein domain. To validate this idea, I tested whether the logarithm of the folding rate constant is linearly correlated with a protein's secondary structure content. The observed, large correlation coefficient is consistent with our hypothesis and underscores the importance of secondary structure elements in organizing the folding process.; Przytycka and Rose proposed that the sequence of secondary structure elements is sufficient to capture a protein's native conformation, and they tested this proposal for a large collection of representative protein domains by showing that the hierarchic tree derived by aligning secondary structure sequences is almost identical to the one derived by direct three-dimensional structure comparison.; To extend this idea, I developed a dynamic programming algorithm to compare domain structures by aligning mesostate sequences, where a mesostate is a coarse-grained representation of a backbone torsion angle. Comparison of the performance of this algorithm against several existing fold recognition algorithms further supports the proposition that the sequence of secondary structure elements determines the protein's three-dimensional conformation.; To retrieve the information about native conformation that is implicit in the mesostate sequence, I developed a fragment replacement Monte-Carlo algorithm that uses only this information to generate tertiary structure. Specifically, a crude potential including only hydrogen bonding, steric exclusion, and spatial confinement was sufficient to regenerate native-like backbone topology from the coarse-grained torsion angle restraints imposed by the native mesostate sequence.; This dissertation is divided into three major parts, each of which corresponds to one of the three topics mentioned above. Together, these three inter-related approaches highlight the central role that secondary structure plays in the protein folding process.