| Abstract: | Tertiary structure of globular proteins has traditionally been analyzed in terms of the organization of secondary structure elements. This paper presents a method for systematically identifying different topological features of the convolutions of the backbone. We define a loop as a segment of chain whose end residues are in contact. We find some loops which are threaded by another segment of chain passing through the loop or actually linked with another loop. Fifty-six loop threadings were found among the 20 proteins studied, all of them occurring in a subset of seven proteins. In our sample, threadings and linkings were generally found if and only if the protein has more than 200 residues. To account for the existence of these topological features, despite their apparent entropic unfavorability, we have proposed a number of kinetic mechanisms by which they may form without a thread actually passing through a loop. We have found that almost all loop threadings possess structural features that would make one of these mechanisms plausible. |
