Genetic interaction mapping informs integrative structure determination of protein complexes

Determining structures of protein complexes is crucial for understanding cellular functions. Here, we describe an integrative structure determination approach that relies on in vivo measurements of genetic interactions. We construct phenotypic profiles for point mutations crossed against gene deletions or exposed to environmental perturbations, followed by converting similarities between two profiles into an upper bound on the distance between the mutated residues. We determine the structure of the yeast histone H3-H4 complex based on similar to 500,000 genetic interactions of 350 mutants. We then apply the method to subunits Rpb1-Rpb2 of yeast RNA polymerase II and subunits RpoB-RpoC of bacterial RNA polymerase. The accuracy is comparable to that based on chemical cross-links; using restraints from both genetic interactions and cross-links further improves model accuracy and precision. The approach provides an efficient means to augment integrative structure determination with in vivo observations

DEAR1 Is a Dominant Regulator of Acinar Morphogenesis and an Independent Predictor of Local Recurrence-Free Survival in Early-Onset Breast Cancer

Ann Killary and colleagues describe a new gene that is genetically altered in breast tumors, and that may provide a new breast cancer prognostic marker

Effect of hypoxia on the peritoneal macrophages.

<p>(A) HIF-1α/β-actin ratios. Inset figure represents one of western blotting experiments. (B) TNF-α levels. Inset figure shows the distance between the biomaterial and cultured cells to generate two hypoxic levels, 0.84% and 2.21%. Data are presented as mean ± SD (n = 4-6/group); ^*P<0.05 vs. the control group; ^#P<0.05 vs. the matrix group; ^%P<0.05 vs. “0.84% O₂” group.</p

Effect of glucose oxidase to catalase ratio in biomaterial.

<p>(A) Hydrogen peroxide concentration after 24 hours incubation. The ratio of glucose oxidase to catalase was adjusted to 1:0, 1:1, 1:5, 1:10 and 1:50. (B) D-glucose concentration after 4, 12, 24 and 48 hours incubation. Glucose oxidase coating density was adjusted to 1.5 U/ cm², 3 U/ cm², and 15 U/ cm². The biomaterial with glucose oxidase to catalase ratio of 1:50 and glucose oxidase coating density of 1.5 U/cm² has negligible hydrogen peroxide production and D-glucose consumption. Data are presented as mean ± SD (n = 8-10/group).</p