Figure 1: Theoretical/computational approach to calculate two-dimensional (2D) dissociation constants, Kd(2D), from solution measurements, Kd(3D). The equation (upper right) relates 3D to 2D dissociation constants for the trans binding of receptors located on apposed membranes. hMdenotes the range of motion of the EC1 domain (Figure 2) in the monomer (M) hT denotes the range of motion of the EC1 domain in the trans dimer (T). Ω denotes the allowable range of rotational motion of the entire ectodomain when it is attached to the membrane. These three variables are obtained from multiscale simulations that combine atomistic molecular dynamics simulations and coarser-grained simulations where each domain is treated as a rigid object (upper left). The theoretical expression yields Kd(2D), which is transformed into a binding free energy. The calculated trans- and cis-binding free energies are then used in lattice simulations of junction formation (lower left and right). Red and green dots indicate cadherin monomers on apposed cell surfaces, blue dots designate trans dimers, and light yellow denotes the cell-cell contact region. The formation of a blue cluster (lower right) indicates that, when cisinteractions have been strengthened by trans dimerization, a junction has been formed. Whencis interactions are weak, as in our cis mutants, only a few trans dimers are formed (lower left), even though the trans interactions are identical in both cases.
Figure by Yinghao Wu.
Figure 2: Two-dimensional layer seen in cadherin crystal structures reveals atomic-level structure of adherens junctions. The five extracellular cadherin (EC) domains are indicated. The blue and orange layers are shown as protruding between apposed surfaces and bind through the trans(molecules from different surfaces) interface mediated by the swapping of N-terminal β-strands between partner EC1 domains. For clarity, trans interfaces are shown only for the darker-colored molecules, and only a few rows of molecules are shown. The two-dimensional (2D) crystal lattice is formed through both trans and cis (molecules on the same surface) interactions as indicated, producing two linear arrays oriented in nearly perpendiculardirections (arrows) that together produce a 2D layer.
Image by Xiangshu Jin.
Figure 3: Weakening lateral cis interactions disrupts junction formation in liposomes and in transfected cell lines. Left panel: Ordered junctions form between liposomes coated with E-cadherin (Ecad), but aggregation in the liposome-liposome interface is diminished in cis mutants. Right panel: Fluorescently labeled wild-type E-cadherins accumulate at cell-cell interfaces in transfected cell lines but are dispersed throughout the cell surface following transfection with cis mutants.
Adapted from Harrison, O.J., Jin, X., Hong, S., Bahna, F., Ahlsen, G., Brasch, J., Wu, Y., Vendome, J., Felsovalyi, K., Hampton, C.M., Troyanovsky, R.B., Ben-Shaul, A., Frank, J., Troyanovsky, S.M., Shapiro, L., and Honig, B. 2011. Structure 19:244–256.
Figure 4: Protein-protein interaction prediction (PREPPI) using remote structural homology. A single template complex involving ubiquitin (cyan in panels A and B) and ubiquitin-conjugating E2D3 (green in panels A and B) forms the basis of our prediction of two distinct PPIs. A: Interaction between protein kinase C epsilon (PKCε, red in panel A) and serine/threonine-protein kinase D1 (PKD1, purple in panel A). B: Interaction between the von Hippel–Lindau tumor suppressor (VHL, red in panel B) and elongation factor 1-delta (EF1δ, purple in panel B). In both cases there is no sequence relationship between the target and the template proteins. The red structure in panel A and the two purple structures are homology models.
Figure by Qiangfeng Cliff Zhang and Donald Petrey.
Figure 5: Minor groove shape profiles correlate with Hox protein specificity. A: Surface representation of the minor groove region that binds to the N-terminal arm of the Scr (left) and Ubx (right) homeodomains. Surfaces are obtained from crystal structures of Exd-Scr and Exd-Ubx bound to DNA containing the core motif of both proteins. Scr has two narrow sites where Arg3 and Arg5 bind, while Ubx has only a single narrow region where Arg5 binds. The enhanced electrostatic potential in each narrow region is indicated with a red mesh. B: Predicted minor groove width obtained from Monte Carlo simulations plotted along the strongest binding nucleotide sequence for Scr (left) and Ubx (right). Profiles for the 10 strongest binding sequences are shown (bold lines are the averages of the 10). The core motif is highlighted in yellow. C: Heat map characterizing the average minor groove width of all sequences above a relative binding affinity threshold of 0.1 for each Exd-Hox heterodimer. Dark green represents narrow minor groove regions, and white denotes wider minor grooves. D: Dendrogram obtained from clustering of Euclidean distances between average minor groove width of the TGAYNNAY core.
Figure by Peng Liu and Remo Rohs.
