End-to-end vs interior loop formation kinetics in unfolded polypeptide chains

The conformational search for favorable intramolecular interactions during protein folding is limited by intrachain diffusion processes. Recent studies on the dynamics of loop formation in unfolded polypeptide chains have focused on loops involving residues near the chain ends. During protein folding, however, most contacts are formed between residues in the interior of the chain. We compared the kinetics of end-to-end loop formation (type I loops) to the formation of end-to-interior (type II loops) and interior-to-interior loops (type III loops) using triplet-triplet energy transfer from xanthone to naphthylalanine. The results show that formation of type II and type III loops is slower compared to type I loops of the same size and amino acid sequence. The rate constant for type II loop formation decreases with increasing overall chain dimensions up to a limiting value, at which loop formation is about 2.5-fold slower for type II loops compared to type I loops. Comparing type II loops of different loop size and amino acid sequence shows that the ratio of loop dimension over total chain dimension determines the rate constant for loop formation. Formation of type III loops is 1.7-fold slower than formation of type II loops, indicating that local chain motions are strongly coupled to motions of other chain segments which leads to faster dynamics toward the chain ends. Our results show that differences in the kinetics of formation of type I, type II, and type III loops are mainly caused by differences in internal flexibility at the different positions in the polypeptide chain. Interactions of the polypeptide chain with the solvent contribute to the kinetics of loop formation, which are strongly viscosity-dependent. However, the observed differences in the kinetics of formation of type I, type II, and type III loops are not due to the increased number of peptide-solvent interactions in type II and type III loops compared to type I loops as indicated by identical viscosity dependencies for the kinetics of formation of the different types of loops.