Proteins interface area

II Figure 1). Adsorption continually occurs around the bubbles to replace protein in areas of the interface where coagulation or stretching of the film is occurring. The actual bubble size in the foam depends upon the rate of protein adsorption as well as upon the ease of film rupture. The protein films on adjacent bubbles come in contact and trap the liquid, preventing it from flowing freely. This restriction is governed by the viscosity of the colloidal solution. The polypeptides of denatured proteins situate to positions where their hydrophobic side chains are directed outward toward each other. Because liquid... 

The binding of the IBD to the HIV-1 IN-CCD is depicted in Fig. 13a showing two IBDs bound to the interface of a single dimer of the CCD, yielding a nearly symmetrical structure [212]. The IBD is composed of a five-helix bundle, consistent with the earlier-described NMR solution structure [209]. Binding to integrase occurs via the al-to-a2 (loop 1) and a4-to-a5 (loop 2) interhelical loops. Loop 1 projects into a crevice at the CCD dimer interface and interacts with both CCD monomers. In contrast, loop 2 interacts exclusively with only one monomer. A total of 1,280 A2 of protein surface area is buried at the IBD-CCD union. It should be noted that an additional 200-300 A2 of buried surface area also comes from the interaction of the IBD with the NTD. 

Table 14-1. Description of the protein-protein complexes used in the parameterization and test sets, in terms of the numbers of atoms and PKs, interface area, and global shape... 

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