Polymorphic cytochrome P450 enzymes (CYPs) and their role in personalized therapy.

The cytochrome P450 (CYP) enzymes are major players in drug metabolism. More than 2,000 mutations have been described, and certain single nucleotide polymorphisms (SNPs) have been shown to have a large impact on CYP activity. Therefore, CYPs play an important role in inter-individual drug response and their genetic variability should be factored into personalized medicine.

SuperTarget and Matador: resources for exploring drug-target relationships.

The molecular basis of drug action is often not well understood. This is partly because the very abundant and diverse information generated in the past decades on drugs is hidden in millions of medical articles or textbooks. Therefore, we developed a one-stop data warehouse, SuperTarget that integrates drug-related information about medical indication areas, adverse drug effects, drug metabolization, pathways and Gene Ontology terms of the target proteins.

X-ray diffraction analysis of crystals containing twofold symmetric nucleosome core particles.

Nucleosome core particles containing a DNA palindrome and purified chicken erythrocyte histone octamer have been reconstituted and crystallized. The dyad symmetry of the palindrome extends the dyad symmetry of the histone octamer to result in a twofold symmetric particle. This ensures that the structure determined by X-ray diffraction will yield a true representation of the DNA strand rather than the twofold averaged structure which would result from using a non-palindromic DNA sequence.

Large-scale production of palindrome DNA fragments.

Our structural studies of nucleosomes necessitated the production of over 100 mg of a 146-bp perfect palindrome DNA for use in the reconstitution of perfectly symmetrical nucleosome core particles for detailed X-ray crystallographic analysis. The propagation of palindromic DNA DNA sequences by bacterial culture is hindered by the instability of these sequences during bacterial replication and recombination. While the loss of some palindrome sequences can be eliminated by the use of sbcB or sbcC mutants of Escherichia coli, not all palindrome-containing plasmids are faithfully maintained by these strains.

Preparative separation of nucleosome core particles containing defined-sequence DNA in multiple translational phases.

The nucleosome core particle is composed of an octamer of core histone proteins and about 146 bp of DNA. When reconstituted from purified histone octamer and defined-sequence, nucleosome positioning DNA fragments, the DNA will bind to the histone core in a number of translational phases with respect to the dyad symmetry axis of the histone octamer. Only one of these phases contains symmetrically bound DNA, and it is this species which is required for crystallization and X-ray diffraction studies.