Displaying inter-main chain hydrogen bond patterns in proteins.

Two computer graphics techniques for displaying hydrogen bonds between the main chains of different proteins are described, and illustrated for two thiol proteases. (The X-ray crystallography was performed by Kamphuis et al. in 1984, and by Baker and Dodson in 1980.) One is a three-dimensional model that can be manipulated in space; the hydrogen bonds are represented with the smoothed alpha-carbon plot of the polypeptide chain. In the other type of display, hydrogen bonds are viewed in relation to the one-dimensional sequence. Both types of picture facilitate visualization of hydrogen bond patterns, such that loop motifs, as well as alpha-helices and beta-sheets, can be examined easily. We suggest that such displays are useful as a general means of displaying whole proteins and whole domains because they reveal more information than do conventional simplified pictures of proteins, which focus exclusively on alpha-helices and beta-sheets. These techniques can be implemented on a UNIX-based computer graphics workstation. (UNIX is a trademark of Bell Telephone laboratories.)

One type of gamma-turn, rather than the other gives rise to chain-reversal in proteins.

Gamma-turns may be defined by a hydrogen bond between the carbonyl group of one amino acid residue and the amino group of the acid two residues ahead in the sequence. They occur as two types, inverse gamma-turns and classic gamma-turns (classic gamma-turns are usually called just gamma-turns but we prefer to add the adjective classic to distinguish them from the word gamma-turn, referring collectively to both). Of the two, classic gamma-turns are less common and are considered by all authors to be extreme rarities in proteins. However, we find that a number do occur in a sample of proteins of known three-dimensional structure. One occurs at the edge of the second hypervariable region of the light chain in some immunoglobulins. All classic gamma-turns except one are associated with a reversal in the main chain direction. In most cases, the turn lies at the loop end of a beta-hairpin. By contrast, inverse gamma-turns, although giving rise to a kink in the chain, rarely occur within beta-hairpins and are seldom situated at a position of reversal, by 180 degrees, in chain direction.