I am interested in doing large scale simulations of biological
systems, specifically, part of a virus capsid.
Some background: I am a grad student in the physics department at
the University of Illinois working under Klaus Schulten in the
Theoretical Biophysics group at the Beckman Institute. Part of the
group does molecular dynamics simulations. Some of the systems people
here have worked on are bacteriorhodopsin, membranes, and the
glucocorticoid receptor. There is experience in the group in writing
molecular dynamics code. The experience will be used to write a new
md program which is designed to be inherently parallel for use on a
workstation cluster and compatible with the X-Plor format and the
CHARMm Hamiltonian. This will help make large simulations take
I've taken an interest in picornavirus structure. I've done a bit
of background reading (which took a while because my background is in
physics and computer science) and become interested in studying the
hydrophobic pocket in the VP1 protein.
From what I've read, there are two likely viruses with which I would
work; rhino (14 and 1a), and poliovirus (type 1 (mahoney)). There are
more picornaviruses whose structure has been resolved, but I just
haven't read enough to understand the questions associated with them,
There is a lot of research on the WIN class of antiviral drugs, but
I haven't seen anything in the way of simulation work related to them.
(I figure that such work exists, but I just haven't found it.) In
addition, I read one paper by Hogle which talks about sphingosine (or
rather; a region of extra electron density which can be fit with a
sphingosine but whose composition has not been determined by chemical
means) in the hydrophobic pocket of polio. That paper was some five
years old and I figure that much research has been done since then,
but that I just don't know where to look.
The simplest research for me to do is to examine the strucural
dynamics of the poliovirus with and without a sphingosine in one of
the pockets. That would take a couple of months of computer time, and
I would have data. However, I wouldn't know how to interpret that
data nor even know if such information would be useful.
Hence, what I'm asking you all is for some pointers on current
research in picornaviruses with an emphasis on the hydrophobic pocket
of either polio or rhino. In addition, I would like to know if anyone
has done dynamical simulation work on virus structures. Any such and
related work would be much appreciated.
dalke at ks.uiuc.edu