Macromolecular Geometry

Overview

We are interested in the calculation of geometrical quantities associated with macromolecular structures and their motions. These include volumes, surfaces, axes, angles, and distances. Volumes and other quantities related to packing are of particular interest. For instance, one goal is to characterize the special type of atom-to-atom packing that occurs at interfaces, such as those between a protein and water. This analysis is motivated by the work on protein packing begun by Fred Richards a quarter century ago.

Information

Full text of general Scientific American article on water, proteins, simulation, and packing. (1999)
Special Volumes Focus Page (with Pat Fleming of the CSB)
Outline for upcoming article on Protein Geometry (with Fred Richards) (1997)
Seminar on Protein Geometry (1997)
Lecture on Protein Geometry for Bioinformatics Course [html-with-frames] [pdf] (1998)
Information on the calculation of Screw Axes (1997, with "spreadsheet code")
HyperTalk tutorial (1996)
Old HyperTalk tutorial (1995)
Other talks and posters
Information on Liquid Simulation Methods (1992, excerpted from a thesis)

Papers

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.
M Gerstein, A M Lesk, E N Baker, B Anderson, G Norris & C Chothia (1993). "Domain Closure in Lactoferrin: Two Hinges produce a See-saw Motion between Alternative Close-Packed Interfaces," J. Mol. Biol. 234: 357-372.
- [Medline Abstract for 94047086] [Summary Graphic] [ftp directory with many pictures]
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]
M Suzuki & M Gerstein (1995). "The geometry of alpha-helices binding to DNA," Proteins: Structure, Function, Genetics 23: 525-535.
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. 104: 9417-9430.
M Gerstein & C Chothia (1996). "Packing at the Protein-Water Interface" Proc. Natl. Acad. Sci. USA 93: 10167-10172.
- [PubMed 8816770]

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.

Also, there is:

A SERVER for calculating geometric quantities, available in a 'basic' version, which includes accessible surface and volume among other calculations, and an advanced version, which does only volume and surface calculations and has extra parameter choices. (This was set up by Susan Chacko at the NIH.)
Information on the calculation of Screw Axes (1997, with "spreadsheet code")
Extra code and executables for the calculation of H-bonds, Contacts, and Axes. (Only roughly documented at present).

Check out "beta" of version 2.0 of source code release.

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.

Picture Gallery

28 January 2003 / graham@bioinfo.mbb.yale.edu
1 May 1997 / Mark.Gerstein@Yale.edu