CCL: Questions on the protonations of a HIV-1 protease (1aaq)

 Sent to CCL by: Guosheng Wu [wu_guosheng2002[*]yahoo.com]
 Dear listers,
 I am puzzled in assigning protonation states for some HIV-1 protease complexes,
 and 1aaq(pdb code)
 is a typical complex of many structures.
 > From this structure, one can see all of the 5 oxygen atoms (from Asp 25
 & Asp 125, and ligand OH)
 are very close to each other(2.7~3.1), and almost in the same plane.  Also each
 of the Gly 27 is
 not far away(about 3.3 Angstrom) from the Asp 25, although the angle of H-bond
 is not very good
 (the Xray resolution is 2.5 Angstrom, exp. done in 1992; only one water is
 given, but not close to
 this part).
 Since the OO contact between Asp 25 and Asp 125 is 2.5 Angstrom, which is about
 the distance of OO
 in H5O2+ ion(2.4), one would like to assign a proton between them.  However, it
 seems very
 difficulty to rationalize other polar interactions.
 One possible explanation may have something to do with quantum effect, which may
 lead to some
 modifications over the hybridization of the ligand Oxygen atom, as well as some
 of the C-O-H bond
 angles.  Certainly, some kind of minimizations may be able to help on some
 directions, but it
 seems to me typical current force field would have trouble for this case.
 I wonder if you have done any study on this special complex, or similar cases
 (actually many pdb
 structures are like this one).  I would really appreciate if you could share
 some of your insights
 with me.
 Best regards,
 Guosheng
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