Molecular modelling and design of analogues of the peptide hormone urotensin II.

The X-ray crystallography of papain (lower diagram) was carried out by Kamphuis er a/ . [5] and that for actinidin (upper diagram) was by Baker & Dodson [6] . Both studies were at high resolution. Hydrogen bonds are defined by the method of Baker & Hubbard [7]. The sequence is given as the standard one-letter code. Hydrogen bonds are drawn in a pipe-like representation. Where NH and C O groups of a pair of amino acids are bonded, a single thick line is drawn; this is characteristic of antiparallel /?sheet. The letter for each amino acid is surrounded by a small box. The left-hand side of the box corresponds to the NH part and the right-hand side to the C O part. Hydrogen bonds are drawn at one side or the other of the box to represent NH or CO groups, except for the paired bonds mentioned above, which are drawn in the middle. Groups of bonds that form parallel /?-sheet are displayed by means of a hollow rectangular box; one is seen at the bottom of both diagrams in Fig. 1. Programs are written in C on a UNIX-based computer graphics workstation with a window management system, the Whitechapel CG-1. Fig. 1 is a photograph of the screen, which is in colour, but is reproduced in black and white.