User:Karsten Theis/PolB movies
From Proteopedia
This was adapted from https://web.archive.org/web/20020209033739/http://chem-faculty.ucsd.edu/kraut/bpol.html as a way to introduce archieved movies from Michael Sawaya made for a 1997 paper.
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)
