The Use of Tertiary Templates in the Analysis of Favorable Helix-Helix
 Packing Sites

 J. W. Ponder and F. M. Richards

 J. Cellular Biochem., 13A, 59 (1989)

 Abstract:

 The ability of two helical amino acid sequences to pack together has
 been investigated using our recently developed protein tertiary template
 algorithm. A helix interaction site is defined as a central residue and
 four of its nearest neighbors from the same face of a helix (residues i,
 i+/-3 and i+/-4). Given two such interaction sites, we have performed
 packing computations to determine the allowed sequences consistent with
 the usual helix-helix geometries. When starting from a known sequence,
 these methods can be used to find pairs of interaction sites which mesh
 to form favorable packing arrangements. All ten residues in the pair of
 sites are subjected to a tree search to identify allowed side chain
 rotamer combinations consistent with the known sequence. At present, we
 have results on some simple model systems and are starting to apply the
 techniques to members of the globin family. In the latter systems, lists
 of favorable pairs of sites can be combined with other geometrical
 constraints to provide a low resolution tertiary structure. In this
 sense the current work in an extension of earlier helix packing algorithms
 of Richmond and Richards. Implications of these modeling techniques for
 analysis of helix-helix packing in membrane proteins is discussed.