DNA Polymerase Beta MOVIES


The enzyme DNA polymerase beta (pol B) fills single nucleotide (nt) gaps in DNA produced by the base excision repair pathway of mammalian cells. Four movies depicting conformational changes of pol B during one turnover of substrate have been constructed using three isomorphous crystallographic structures. To re-run the movie, click on the Reload button on your Netscape window.

MOVIE 1 depicts conformational changes of the THUMB during the catalytic cycle.


MOVIE 2 depicts how thumb conformation affects CATALYTIC ASPARTATE 192.


MOVIE 3 depicts how thumb conformation affects dNTP POSITION.


MOVIE 4 depicts how thumb conformation affects TEMPLATE POSITION.


Polymerase Beta CRYSTAL STRUCTURES

The movies are based on three crystal structures of human DNA polymerase beta, each in a different ligation state: (1) double stranded DNA substrate containing a single nucleotide gap (gap). (2) gap and ddCTP (3) double stranded DNA product containing a nick in the phosphodiester backbone. These crystal structures are depicted in the first, middle, and last frames (respectively) of the movies. All the intervening frames were interpolated by incremental rigid rotations and translations of domains and side chains (using X-plor). No energy terms were used to simulate dynamics of protein motion. There is a more detailed description of the significance of these conformational changes in the following publication:

Sawaya, M.R., Prasad, R., Wilson, S.H., Kraut, J., & Pelletier, H. "Crystal Structures of Human DNA Polymerase Beta Complexed with Gapped and Nicked DNA: Evidence for an Induced Fit Mechanism," (1997) Biochemistry, volume 36, pages 11205-11215.


CONSTRUCTION OF Polymerase Beta MOVIEs

The movies, containing 40 frames each, were assembled using GIFMerge . Images were constructed with the graphics program SETOR written by Stephen Evans (elmo@nrcbsa.bio.nrc.ca) If you dont have Netscape Version 2.0 or better and the image below is static you may download an upgraded version of Netscape here. An ENLARGED version of MOVIE 1 may be viewed with SGI's movieplayer software. To view the movie, click on MOVIE 1. A special thanks goes to Sunny Kim for her help in assembling the movie.

If you have any comments about my movie, please click on my email Michael R. Sawaya (msawaya@ucsd.edu). A screen should pop up (its self explanatory) and there will be buttons for send and cancel. You may also wish to visit my homepage.

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Michael R. Sawaya
Post Graduate Research Chemist 1995-1997