Subject: hydrodynamic properties from structures?

From: Bruce Allan Palfey <[email-masked]>
Date: Thu, 9 Dec 1999 23:17:26 -0500 (EST)

Thank you Rick Venable and Mike Gilson for providing answers (included
below) to my recent question.

Bruce

Original Question:

In the "old" days of biophysics, when 3-D structures were still fairly
hard to come by, people would get very rough ideas of the shape of
proteins from hydrodynamic experiments like analytical ultracentrifugation
or viscosity measurements.  I was wondering if things have now come full
circle:  Given a protein structure from crystallography or NMR, are there
any programs that will calculate the frictional coefficient or shape
parameters used in hydrodynamic analyses?

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There are several programs; we've developed one named HI in our own lab
based on bead models published years ago by Bloomfield and Garcia de la
Torre.  Another is HYDRO from Garcia de la Torre's lab.  While original
work was done using a small number of beads, e.g. 8 beads for a protein
subunit, computer power advances allowed us to move to atomic detail.
We've found that a solvation shell is needed to reproduce experimental
data at that level of detail.  We've applied our program to NMR studies
of proteins.  I'm aware of at least one other approach as well.

Refs, program pointers available on request.

--
Rick Venable                  =====\     |=|    "Eschew Obfuscation"
FDA/CBER Biophysics Lab       |____/     |=|
Bethesda, MD  U.S.A.          |   \    / |=|  ( Not an official statement
or
[email-masked]          |    \  /  |=|    position of the FDA; for
that,
http://www.erols.com/rvenable       \/   |=|    see   http://www.fda.gov
)

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Yes, there are such programs.  See references from J. Antosiewicz and
also Garcia-Torres.

Best regards,

Mike Gilson

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