Domain-mediated interactions for protein subfamily identification

Within a protein family, proteins with the same domain often exhibit different cellular functions, despite the shared evolutionary history and molecular function of the domain. We hypothesized that domain-mediated interactions (DMIs) may categorize a protein family into subfamilies because the diversified functions of a single domain often depend on interacting partners of domains. Here we systematically identified DMI subfamilies, in which proteins share domains with DMI partners, as well as with various functional and physical interaction networks in individual species. In humans, DMI subfamily members are associated with similar diseases, including cancers, and are frequently co-associated with the same diseases. DMI information relates to the functional and evolutionary subdivisions of human kinases. In yeast, DMI subfamilies contain proteins with similar phenotypic outcomes from specific chemical treatments. Therefore, the systematic investigation here provides insights into the diverse functions of subfamilies derived from a protein family with a link-centric approach and suggests a useful resource for annotating the functions and phenotypic outcomes of proteins.11Ysciescopu

Evolution of the Protein Interaction Network of Budding Yeast: Role of the Protein Family Compatibility Constraint

Understanding of how protein interaction networks (PIN) of living organisms have evolved or are organized can be the first stepping stone in unveiling how life works on a fundamental ground. Here we introduce a hybrid network model composed of the yeast PIN and the protein family interaction network. The essential ingredient of the model includes the protein family identity and its robustness under evolution, as well as the three previously proposed ones: gene duplication, divergence, and mutation. We investigate diverse structural properties of our model with parameter values relevant to yeast, finding that the model successfully reproduces the empirical data.Comment: 5 pages, 5 figures, 1 table. Title changed. Final version published in JKP

Inclusive angular distribution of alpha and Li fragments produced in the Fe-C and Fe-Pb collisions at 1.88 GeV/u

The LS (laboratory system) emission angles theta for 2188 and 298 Li fragments, produced inclusively in relativistic Fe-C and Fe-Pb collisions, have been measured in reference to incident Fe-ion beam tracks nearby in nuclear emulsion. An empirical differential frequency formula, dN(cot theta) = exp (a + b cot theta)d(cot theta) is obtained with the constant b approx. = -0.026 at 1.88 GeV/u, which seems to be independent on the kinds of target nucleus as well as on the kinds of projectile fragments

Betweenness centrality correlation in social networks

Scale-free (SF) networks exhibiting a power-law degree distribution can be grouped into the assortative, dissortative and neutral networks according to the behavior of the degree-degree correlation coefficient. Here we investigate the betweenness centrality (BC) correlation for each type of SF networks. While the BC-BC correlation coefficients behave similarly to the degree-degree correlation coefficients for the dissortative and neutral networks, the BC correlation is nontrivial for the assortative ones found mainly in social networks. The mean BC of neighbors of a vertex with BC $g_i$ is almost independent of $g_i$, implying that each person is surrounded by almost the same influential environments of people no matter how influential the person is.Comment: 4 pages, 4 figures, 1 tabl