Hello again.
The Technical Comments appear in the issue of 21 November, 1986.
The authors refer to the distribution of dihedral angles between two
aromatic residues in globular proteins that appear in Burley and
Petsko, Science 229, 23 (1985). They say that the distribution of
angles is useful only if it differs significantly from a random
distribution. Citing Singh and Thornton, FEBS Lett. 191, 1 (1985),
they say that the random distribution of this angle varies as the sine
of the angle and has a mean value of ~57 degrees. Thus Burley and
Petsko's distribution closely approximates a random distribution.
However, they say it is also necessary to consider the spatial
displacement of the two aromatic rings. Here, two arrangements show
significant deviations from random--the fully stacked arrangement (45
deg. < T <67.5 deg.) is in agreement with recent quantum mechancal
calculations that favor the perpendicular interaction, and in the
partially stacked arrangement the deviation from random (P<60 degrees)
is also consistent with quantum mechanially derived nonbonded
potential calculations.
Further, the cutoff criteria also need to be carefully defined.
Center-to-center distances differ for rings that are in van der Waals
contact. It is preferable for such non-spherical side chains to
define contacting aromatic groups by closest atom-atom distances in
order to arrive at an equal probabillity of contacts around the rings.
In conclusion, they emphasize the importance of taking into
consideration the available 3-dimensional space and expected 'random'
distributions for such side chain interactions. A striking preference
for perpendicular packing of aromatic rings is observed for a small
subgroup in a special spatial displacement. Elsewhere energetic
preferences and constraints imposed by packing of many hydrophobic
residues in the protein core may give a slight preference for either
the perpendicular or the parallel arrangement.
Best of luck with your researchers!
Sincerely,
Richard-ga |
