Paper Citing NAMD - Abstract
Foley, Meredith C.; Schlick, Tamar
Simulations of DNA Pol lambda R517 mutants indicate 517's crucial role in ternary complex stability and suggest DNA slippage origin
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130:3967-3977, MAR 26 2008
Unlike some other DNA polymerases, DNA polymerase lambda (pol lambda) utilizes DNA motion and activesite protein residue rearrangements rather than large-scale protein subdomain changes to transition between its active and inactive states. Pol lambda also has an unusual error tendency to generate single-base deletions (also known as frameshift mutations) resulting from DNA template-strand slippage. An understanding of these features requires an atomic-level link between the various structures and motions involved and observed in biochemical functions. Our simulations of pol lambda ternary complexes of various 517 mutants (Lys, Glu, His, Met, and Gin) reveal discrete orientations of the 517 residue with respect to the DNA and associated interactions (mainly electrostatic) that explain the wide range (similar to 3-8 angstrom) of mutant-dependent DNA motion observed (Figure 2 of manuscript): (wild-type < [R517K similar to R517H similar to R517Q] < [R517E similar to R517A similar to R517M]). This motion critically impacts stability of the ternary complex and hence drives/hampers the enzyme's catalytic cycle. In addition to pinpointing a trend for interpreting associated frameshift error rates based on template-strand stability, the close connection between DNA movement and active-site protein residue changes suggests that pol lambda's unique architecture facilitates frameshift errors because small variations in the active-site environment (e.g., orientation of 517) can have large effects on the dynamics of the ternary pol lambda complex.
