N. Datta-gupta et al., Categorizing reactivity of bacteriorhodopsin cysteine mutants crosslinkingto 4-bromoretinal, BIOC MOL B, 47(5), 1999, pp. 773-780
The structure of bacteriorhodopsin (bR) has been probed by a large number o
f experimental methods. In earlier work distance constraints measured from
the 1BRD Brookhaven structure (1, 2) were used to guide site-directed mutag
enesis/affinity labeling experiments (3-5). In the present study we report
on the use of limited molecular dynamics (MD) investigations of the same bR
/affinity label system. We show here that the chiral center introduced when
4-bromo-all-trans retinal is synthesized produces variable impact on poten
tial crosslinking. Our MD analysis suggests the following ranking of bindin
g site mutants in order of reactivity: R118C> S118C>> S121C> R141C>> S141C>
>> R121C, R138C, S138C. Chirality appears to have limited effect for the M1
18C mutants but shows more dramatic impact for the T121C and S141C mutants.
These results are in excellent agreement with the experimental observation
s and offer encouragement that MD can be a useful component of experimental
design with considerable predictive power.