Monte Carlo Methodologies for the Structural Characterization of Globular Proteins

Using MC methods similar to those used to characterize the cavity size distribution in synthetic polymers, new statistical metrics have been defined for the structural characterization of globular proteins.  Some of these metrics include volume, surface area, asymmetry ratio, interior cavity size distribution, and the identification of percolation channels.  Proteins that have been studied include hemoglobin, myoglobin, lysozyme, and aquaporins.  An analysis of cavity statistics provides an efficient method to quantify local properties such as packing density and transport pathways. The average cavity sizes of studied proteins range from 6.0 to 7.0 Å.