Analyzing protein structure and function using ancestral gene reconstruction

Analyzing protein structure and function using ancestral gene reconstruction.

Protein families with functionally diverse members can illuminate the structural determinants of protein function and the process by which protein structure and function evolve. To identify the key amino acid changes that differentiate one family member from another, most studies have taken a horizontal approach, swapping candidate residues between present-day family members. This approach has ...

Synthetic gene technology: applications to ancestral gene reconstruction and structure-function studies of receptors.

Ancestral protein reconstruction: techniques and applications.

Ancestral sequence reconstruction (ASR) is the calculation of ancient protein sequences on the basis of extant ones. It is most powerful in combination with the experimental characterization of the corresponding proteins. Such analyses allow for the study of problems that are otherwise intractable. For example, ASR has been used to characterize ancestral enzymes dating back to the Paleoarchean ...

Algorithms of Ancestral Gene Length Reconstruction

Ancestral sequence reconstruction is a well-known problem in molecular evolution. The problem presented in this study is inspired by sequence reconstruction, but instead of leaf-associated sequences we consider only their lengths. We call this problem ancestral gene length reconstruction. It is a problem of finding an optimal labeling which minimizes the total length's sum of the edges, where b...

Analyzing Protein Structure Using Almost-Delaunay Tetrahedra

Delaunay tessellations and Voronoi diagrams capture proximity relationships among sets of points. When applied to points representing protein atoms or residue positions, they are used to compute molecular surfaces and protein volumes, to define cavities and pockets, to analyze and score packing interactions, and to find structural motifs. Since atom and residue coordinates are known imprecisely...