UC San Diego

Computers have held an increasingly important place in chemical and biological research. Non-specialists may presume that computers can perform a small number of specialized techniques, but in reality they may be used on a wide range of biological scales to answer disparate questions in biology and chemistry. This body of work exemplifies that, using scales ranging from coarse grained nodes representing amino acids at the cell scale down to electron density clouds. Specifically, the projects here use elastic network models to investigate basic bacterial biology, Brownian dynamics and molecular dynamics to investigate influenza, and quantum mechanics to investigate tuberculosis. In this work we find that the protein sheets of chimallin in Pseudomonas chlororaphis cells infected with jumbo phage 201phi2-1 display a significant amount of flexibility and have several pores which could transport ions or nucleotides. On a different project we found that glycans can inhibit drug binding to influenza, and that the glycoproteins in influenza can access protein conformations amenable to cellular exocytosis and endocytosis. We also find that the flexibility of these glycoproteins opens new epitopes and drug binding sites that cannot be found from their crystal structures. Finally, we develop force field parameters for cytochrome bd-type quinol oxidase, which is a promising drug target for Mycobacterium tuberculosis and Escherichia coli.