Pierre Tuffery | PubMed Health

PubMed2005

Improved greedy algorithm for protein structure reconstruction.

This article concerns the development of an improved greedy algorithm for protein structure reconstruction. Our stochastic greedy algorithm, which attempts to locate the ground state of an approximate energy function, exploits the fact that protein structures consist of overlapping structural building blocks that are not independent. Application of this approach to a series of 16 proteins with 50-250 amino acids leads to predicted models deviating from the experimental structures by 0.5 A RMSD using an RMSD-based energy function and within 1.5 to 4.8 A RMSD using a Go-based energy function. The Go-based results are significant because they illustrate the strength of combining structural fragments and stochastic greedy algorithms in capturing the native structures of proteins stabilized by long-range interactions separated by more than 30 amino acids. These results clearly open the door to less computationally demanding solutions to predict structures from sequences.

Algorithms↗

PubMed2003

A triple-mutated allele of granzyme B incapable of inducing apoptosis.

Granzyme B (GzmB) is a serine protease involved in many pathologies, including viral infections, autoimmunity, transplant rejection, and antitumor immunity. To measure the extent of genetic variation in GzmB, we screened the GzmB gene for polymorphisms and defined a frequently represented triple-mutated GzmB allele. In this variant, three amino acids of the mature protein Q(48)P(88)Y(245) are mutated to R(48)A(88)H(245). In CD8(+) cytotoxic T lymphocytes, GzmB was expressed at similar levels in QPY homozygous, QPY/RAH heterozygous, and RAH homozygous individuals, demonstrating that RAH GzmB is a stable protein. Active RAH GzmB expressed in glioblastoma cell lines displayed proteolytic activity, but in contrast to QPY GzmB, it did not accumulate in the nucleus and was unable to induce Bid cleavage, cytochrome c release, or apoptosis. Molecular modeling showed that the three amino acid substitutions clustered near the C-terminal alpha-helix of the protein, indicating that this region of the protein may be involved in the intracellular targeting of GzmB. The triple-mutated GzmB allele that we describe appears to be incapable of inducing apoptosis in tumor cell lines, and its presence could, therefore, influence both the prognosis of cancer patients and the success rates of antitumor cellular immunotherapy.

Alleles↗