High-Throughput Reconstruction of Ancestral Protein Sequence, Structure, and Molecular Function.

High-Throughput Reconstruction of Ancestral Protein Sequence, Structure, and Molecular Function. Methods Mol Biol. 2019;1851:135-170 Authors: Aadland K, Pugh C, Kolaczkowski B Abstract Ancestral protein sequence reconstruction is a powerful technique for explicitly testing hypotheses about the evolution of molecular function, allowing researchers to meticulously dissect how historical changes in protein sequence impacted functional repertoire by altering the protein's 3D structure. These techniques have provided concrete, experimentally validated insights into ancient evolutionary processes and help illuminate the complex relationship between protein sequence, structure, and function. Inferring the protein family phylogenies on which ancestral sequence reconstruction depends and reconstructing the sequences, themselves, are amenable to high-throughput computational analysis. However, determining the structures of ancestral-reconstructed proteins and characterizing their functions typically rely on time-consuming and expensive laboratory analyses, limiting most current studies to examining a relatively small number of specific hypotheses. For this reason, we have little detailed, unbiased information about how molecular function evolves across large protein family phylogenies. Here we describe a generalized protocol that integrates ancestral sequence reconstruction with structural homology modeling and structure-based molecular affini...
Source: Mol Biol Cell - Category: Molecular Biology Authors: Tags: Methods Mol Biol Source Type: research