Protein Homology Network, data visualization by Alex Adai, Institute for Cellular and Molecular Biology – University of Texas, 2002

“The network summarizes the results of aprox. 92 billion pairwise amino acid sequence alignments between 289,069 proteins from 90 genomes. The final network is composed of 27,325 connected sets summing to 7,940,873 edges. An edge is colored blue if it connectes 2 proteins from the same species, and red if it connects 2 proteins from 2 different species. If that information is not available the edges are colored based on layout hierarchy.”

via Visual Complexity

Caption: “Intercalation induces structural distortions. Left: unchanged DNA strand. Right: DNA strand intercalated at three locations (black areas).”

“In chemistryintercalation is the reversible inclusion of a molecule (or group) between two other molecules (or groups). Examples include DNA intercalation and graphite intercalation compounds.”

From the Wikipedia article on “Intercalation

(img source)

Image 1: B-factor plot for 1AV1 truncated human apolipoprotein A-I


Caption: “B-factor plot of 1AV1, refined at 4 Å using the PMB B-factor patch for isotropic B-factor restraints. Note that even the side-chain b-factors are well-behaved, and that the molecular motions are modeled more accurately by these individual B-factors than they could be by a series of group B-factors.”

What is a B-factor plot? I don’t know, but these folks say: “Blue means helix, red means strand and green means turns and random coil.”

Image 2: Another view of 1AV1 structure

Source and more info:

What is apolipoprotein A1? According to Wikipedia, it’s “the major protein component of high density lipoprotein (HDL) in plasma” i.e. the good cholesterol. It helps clear fats! Good job, apo A-I!