The Greek key motif: extraction, classification and analysis

Abstract

The Greek key is a very common structural motif in proteins. It has been traditionally defined as four beta-strands with '+3,-1,-1' topology. This definition encompasses motifs with several different three-dimensional structures. We have classified Greek keys, based on their hydrogen bonding patterns, into three groups with similar three-dimensional structures. All examples of Greek keys in each of these classes have been automatically extracted using a set of programs. Analysis of these examples shows the variability of secondary structure segment length and sequences of Greek keys even within one class. This variability suggests that no single folding pathway is likely to fit all Greek key structures.