AUTO-MUTE 2.0: A Portable Framework with Enhanced Capabilities for Predicting Protein Functional Consequences upon Mutation

Figure 1

Delaunay tessellation of the HIV-1 reverse transcriptase enzyme (PDB ID: 1rtjA). Initially, the protein is represented as a discrete set of points in 3D space, corresponding to the C-alpha atomic coordinates of every amino acid residue in the structure. A 3D tetrahedral tiling is then obtained by using these C-alpha points to serve as vertices. The complete tessellation yields hundreds of solid tetrahedra that are packed against one another in the form of a convex hull, filling the space otherwise occupied by the protein structure. Shown here is the modified tessellation obtained by removing all edges longer than 12 Å, which reveals clefts and pockets on the protein surface and ensures that each tetrahedron identifies a quadruplet of interacting amino acid residues at its four vertices via their C-alpha coordinates. Each C-alpha point is typically shared as a vertex by several tetrahedra as a result of their packed arrangement; hence, each amino acid may simultaneously participate in a number of distinct nearest neighbor residue quadruplets.