User:Jennifer Taylor/Sandbox 8

You may include any references to papers as in: the use of JSmol in Proteopedia ^[1] or to the article describing Jmol ^[2] to the rescue.

Background

Solution Studies

Structural highlights

Each AphB comprises an N-terminal (DBD) and a C-terminal (RD). The DBD is connected to the RD via the linker helix. AphB subunits are found in two distinct conformations within the tetramer, as determined by the angle between the linker helix and the RD. In the compact form, the RD and linker helix form an angle of 85 degrees, whereas this angle is 150 degrees in the extended form. Interestingly, the LH forms the dimerization interface between one compact and one extended subunit.

The tetramer (chains A, B, C and D) can be described as a dimer of dimers. Each of two identical dimers are composed of a compact (A and C) and extended (B and D) monomer. The compact and extended subunits differ from one another in the angle between the linker helix and the RD, which is 85° in the compact subunits and 150° in the extended subunits (Fig. 1A). The conformational variability in the AphB subunits can be attributed to the flexible loop connecting the linker helix to the regulatory domain.

The tetramer assembles via two distinct dimerization interfaces (Fig. 2A). The N‐terminal dimerization interface (1142 Å2) is primarily made up of an antiparallel coiled‐coil of the two linker helices, held together by hydrophobic, polar and ionic interactions (Fig. 2A, left inset). The C‐terminal dimerization interface (1414 Å2) forms between regulatory domains, which pack against each other in a head‐to‐tail manner (Fig. 2A, right inset). To form the AphB tetramer, each compact subunit interacts with the regulatory domain of one extended subunit and with the linker helix of the other extended subunit (Fig. 2A and B).