Re: CCL:the question about the normal mode analysis

[Richard Gillilan <reg8 - at - cornell.edu>]

bxiong wrote:
 >
 > Dear CCLs:
 > I want to do a normal mode analysis simulation about a protein.
 > 1, I think it can not include the solvent (water). Is it correct?
 Some so-called crystallographic water molecules are bound tightly enough
 to the protein surface that they can be seen in the electron density
 and included in the published pdb file. Do not believe every water molecule
 in a pdb file ... these positions are often highly suspect, but the small
 subset of ones with lowest temperature factor may be real. Also,
 crystallographers
 often do not see (or bother to identify) ions like Na, Cl etc. These are almost
 certainly important. The current view I have seen is that these waters and ions
 have a high turnover rate, but the positions spend most of their time occupied.
 You should take a look at the papers by Faerman and Karplus written a few years
 ago:
    FAERMAN CH, KARPLUS PA
     CONSENSUS PREFERRED HYDRATION SITES IN 6 FKBP12 DRUG COMPLEXES
     PROTEINS 23 (1): 1-11 SEP 1995
    KARPLUS PA, FAERMAN C
     ORDERED WATER IN MACROMOLECULAR STRUCTURE
     CURR OPIN STRUC BIOL 4 (5): 770-776 OCT 1994
 It should be possible to include these in a normal mode simulation.
 Would be interesting to see if they make any difference. Any large-amplitude
 motion of the protein, however, is likely to change the solvent environment
 dramatically. If you do, make sure you use a pdb file that was solved at
 high resolution (better than 2 Ang if possible). Better yet, if the structure
 was phased using signals from the halide ions or similar ... then you really
 know they are real.
 Richard Gillilan
 MacCHESS
 Cornell University