Protein Packing
Overview
We are generally interested in protein packing and volumes. We used
molecular simulation and Voronoi volume calculations to try and
understand the special type of atom-to-atom packing that occurs at the
interface between a protein and water. This work derives from the work
on protein packing begun by Fred
Richards at Yale.
Information on the Calculation of Volumes and Surfaces
Papers
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M Gerstein (1992). "A Resolution-Sensitive Procedure for
Comparing Protein Surfaces and its Application to the Comparison of
Antigen-Combining Sites," Acta Cryst. A48: 271-276.
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[Abstract] [ftp directory with
manuscript] [
Talk Abstract]
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M Gerstein & R M Lynden-Bell (1993). "Simulation of Water
around a Model Protein Helix. 2. The Relative Contributions of
Packing, Hydrophobicity, and Hydrogen Bonding," J. Phys. Chem.
97: 2991-2999.
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[Abstract]
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M Gerstein & R M Lynden-Bell (1993). "What is the natural boundary
for a protein in solution?" J. Mol. Biol. 230: 641-650.
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Y Harpaz, M Gerstein & C Chothia (1994). "Volume Changes
on Protein Folding," Structure 2: 641-649.
- - [Medline Abstract for 95006332]
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M Gerstein, J Tsai & M Levitt (1995). "The volume of atoms
on the protein surface: Calculated from simulation, using Voronoi
polyhedra," J. Mol. Biol. 249: 955-966.
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[ftp
directory with manuscript, talks, programs & data]
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J Tsai, M Gerstein & M Levitt (1996). "Keeping the Shape but
Changing the Charges: A Simulation Study of Urea and its
Iso-steric Analogues," J. Chem. Phys. (in press).
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M Gerstein & C Chothia (1996). "Packing at the Protein-Water Interface"
Proc. Natl. Acad. Sci. USA 93: 10167-10172.
Source Code
A library of C source code is available. It contains programs for
calculating volumes (using the Voronoi method), surfaces contacts, and
other parameters relevant to the protein surface. It also contains
code for doing a least-squares fit of two structures and for
calculating geometrical parameters such as helix axes.
Standard volumes
A file giving statistics on the
volumes for buried core atoms in a database of 119 structures. These
reference atomic volumes can be compared to the volumes calculated
with the volume program (above) to see how well-packed a given atom
is.
Pictures
More pictures in an
ftp archive.
1 May 1996
