Jeff Thorne, North Carolina State University

Combining Protein Evolution and Protein Structure

Abstract:
The relationship between phenotype and survival of the genotype is
central to both genetics and evolution.  Protein-coding DNA sequences
are genotype whereas protein tertiary structures are a fundamental
unit of phenotype.

We are studying the impact of protein structure on the evolution of
protein-coding DNA sequences.  In contrast to widely used procedures
that largely model change of genotype as being independent of
phenotype, our approach incorporates phenotype via adoption of
sequence-structure compatibility measures that computational
biologists originally designed for the purpose of protein fold
recognition.  A consequence of our genotype-phenotype models is the
necessity to abandon computational strategies that are conventionally
employed to study molecular evolution.  In addition to protein
structure, there are diverse other aspects of phenotype that are being
predicted in silico by computational biologists.  We emphasize that
these other in silico systems can also be exploited to better
characterize the evolutionary relationship between genotype and
phenotype.