American Physical Society Meeting, Minneapolis, March 20-24, 2000

Computer Modeling of the Earliest Cellular Structures and Functions

Andrew Pohorille^1,2, Christophe Chipot^1,3 and Karl Schweighofer^1,2

¹ NASA Center for Computational Astrobiology  ² Department of Pharmaceutical Chemistry, University of California, San Francisco  ³ Laboratoire de Chimie Théorique, CNRS, Nancy, France

In the absence of extinct or extant record of protocells (the earliest ancestors of contemporary cells), the most direct way to test our understanding of the origin of cellular life is to construct laboratory models of protocells. Such efforts are currently underway in the NASA Astrobiology Program. They are accompanied by computational studies aimed at explaining self-organization of simple molecules into ordered structures and developing designs for molecules that perform protocellular functions. Many of these functions, such as import of nutrients, capture and storage of energy, and response to changes in the environment are carried out by proteins bound to membranes.

We will discuss a series of large-scale, molecular-level computer simulations which demonstrate (a) how small proteins (peptides) organize themselves into ordered structures at water-membrane interfaces and insert into membranes, (b) how these peptides aggregate to form membrane-spanning structures (e.g. channels), and (c) by what mechanisms such aggregates perform essential protocellular functions, such as proton transport of protons across cell walls, a key step in cellular bioenergetics.

The simulations were performed using the molecular dynamics method, in which Newton's equations of motion for each atom in the system are solved iteratively. The problems of interest required simulations on multi-nanosecond time scales, which corresponded to 10⁶-10⁸ time steps.