Statistical analysis of 15 dimensions in the crystallization space for protein-DNA complexes.
Solving the three dimensional structure of a protein-DNA complex is a prerequisite to understand, at the atomic level, the interactions between DNA-binding proteins and their target DNA sequences. Arranging these complexes into an ordered and repetitive network (a crystal, suitable for X-Ray analysis) is a time-limiting empirical step. Although it has been suggested that the crystallization space for protein-DNA complexes is probably smaller than that of non-complexed proteins, a study presenting a detailed and updated analysis of this space is still missing. Here, we analyze the successful crystallization conditions of several hundred protein-DNA complexes and present a bias-free statistical analysis of 15 crystallization parameters that include concentration, temperature, pH, precipitants, salts, divalent cations and polyamines. Our analysis shows that some crystallization parameters are interestingly restricted into narrow intervals. These restrictions could be very helpful in the design of sparse-matrix crystallization screens that target exclusively protein-DNA complexes.
Saïda
Fakhri
F
Center for Molecular Genetics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0634, USA. fsaida@biomail.ucsd.edu
D002021:Buffers; D002413:Cations, Divalent / Q000737:chemistry; D003460:Crystallization; D004247:DNA / Q000737:chemistry*; D005990:Glycerol / Q000737:chemistry; D006863:Hydrogen-Ion Concentration; D046911:Macromolecular Substances; D009690:Nucleic Acid Conformation; D011073:Polyamines / Q000737:chemistry; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012492:Salts / Q000737:chemistry; D013696:Temperature; D013816:Thermodynamics
D002021:Buffers; D002413:Cations, Divalent; D046911:Macromolecular Substances; D011073:Polyamines; D011506:Proteins; D012492:Salts; D004247:DNA; D005990:Glycerol