MAT Program Fall 2011 Seminar Series
WHERE DO PROTEINS FIT IN THE STRUCTURAL CLASSIFICATION OF
Osman Burak Okan
Department of Materials Science and Engineering,
Rensselaer Polytechnic Institute, Troy, NY, USA
In this work, we use Bond Orientational Order Parameters (BOOP)  as the universal
descriptors of local packing in proteins. To classify proteins as a distinct family, this local
view is combined with a global one which is portrayed by translational order parameters and
the free volume distribution.
Our findings indicate that the organization of first coordination shells carries strong signatures
of close packed crystalline order in BOOP space. We also show that proteins exhibit no
icosahedral bond orientational order in heavy atom and residue level packing. Close
packedness is characterized by the space filling ratio of 0.74048 and is achieved through
stacking of hexagonal arrays. Depending on stacking order, this creates Face Centered
Cubic(FCC) and Hexagonal Close Packed(HCP) crystals as well as an infinite variety of
FCC-HCP mixtures. Using radial distribution formalism, we show that protein-crystal
correspondence is strictly local and it extends up-to second nearest neighbors. Due to local
correspondence, arbitrarily stacked systems capture protein properties as accurate as ideal
In passing from bulk crystals to proteins we propose a robust route which randomly
distributes free volume pockets in a close packed lattice. Remarkably, our results indicate that
such protein-like structures automatically possess a power-law distribution of free volume.
This is in contrast with Cohen-Turnbull theory of dense liquids and glasses. We conclude
that proteins constitute a unique disordered phase with no icosahedral order.
1. Steinhardt, P.J., D.R. Nelson, and M. Ronchetti, Bond-orientational order in liquids
and glasses. Physical Review B, 1983. 28(2): p. 784.
2. Cohen, M.H. and D. Turnbull, Molecular Transport in Liquids and Glasses. Vol. 31.
1959: AIP. 1164-1169.
Wednesday, 4 January 2012, 13.40
*MALDI-MS stands for Matrix Assisted Laser Desorption Ionization Mass Spectroscopy: a workhorse method in proteomics and biochemistry.