Protein Packing


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


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.
- [Abstract] [ftp directory with manuscript] [ Talk Abstract]
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.
- [Abstract]
M Gerstein & R M Lynden-Bell (1993). "What is the natural boundary for a protein in solution?" J. Mol. Biol. 230: 641-650.
Y Harpaz, M Gerstein & C Chothia (1994). "Volume Changes on Protein Folding," Structure 2: 641-649.
- [Medline Abstract for 95006332]
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.
- [ftp directory with manuscript, talks, programs & data]
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).
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.


More pictures in an ftp archive.
1 May 1996