Framework model for DNA polymerases.
Biochemistry
; 44(18): 6877-88, 2005 May 10.
Article
in En
| MEDLINE
| ID: mdl-15865433
ABSTRACT
DNA polymerases are complex machines with both chemical and mechanical functions. Recent crystal structures, ensemble kinetics, and single-molecule investigations have helped to elucidate the main properties of several DNA polymerases, all of which share common structural elements and a common basic mechanism, despite wide variations in amino acid sequence. The framework model is intended to aid in the understanding of these common features (and differences). It defines a class of models that automatically incorporates most of what is known about DNA polymerases within a single theoretical structure so that it is easier to make comparisons between them and to generate detailed models for specific polymerases. The framework model has three main elements (1) a set of four key variables that describe the important motions within the protein-DNA-nucleotide complex, (2) a complete set of conformational states for the protein-DNA-nucleotide system, and (3) an approximate potential energy surface that controls the motions and transition rates between states. As an example application, we use the general framework ideas to build a detailed model for the HIV reverse transcriptase that is consistent with existing data, and predicts force-velocity curves and stepping-statistics histograms that can be directly compared to experiment.
Search on Google
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Computer Simulation
/
Models, Molecular
/
DNA-Directed DNA Polymerase
/
Models, Chemical
Type of study:
Prognostic_studies
Limits:
Animals
/
Humans
Language:
En
Journal:
Biochemistry
Year:
2005
Document type:
Article
Affiliation country:
United States