11
Protein Volumes
- Why Calculate?
- Measuring packing efficiency is equivalent to quantifying
Lennard-Jones energy (U = A/r^12 - B/r^6). L-J interactions, which
are also known as Van der Waals (VDW) interactions, are the most basic
type of interaction in molecular systems.
- It is observed that protein interiors are tightly packed, fitting
together like a jig-saw puzzle. This essentially implies that VDW
interactions are very important in structuring the protein interior.
- Because of tight packing the various types of protein residues and
atoms occupy well-defined amounts of space.
- Tight packing is a driving force in ligand binding and is
essential in the specificity of various recognition processes
(e.g. antibodies and antigens)
- Protein packing is interesting because other substances have very
different types of packing. For instance, water structure is dominated
by H-bonding rather than tight packing.
Talk on Surfaces and Volumes /
(C) Mark Gerstein (mbg@hyper.stanford.edu) /
May 1996