Multi-body interactions within the graph of protein structure.
We construct a graphical representation of protein structure based on the 3D C-alpha carbon point set, using the Delaunay tessellation to define interacting quadruples of amino acid residues. The tessellation is filtered by two criteria: interaction distance less than 9.5 angstroms and circumsphere radius less than 8.0 angstroms using dataset of 608 protein structures of low mutual sequence identity and a likelihood ratio test, we show that 3-body and 4-body interactions are indeed significant. We identify particular significant three-body interactions by first reducing the dataset to interacting triples, and classifying amino acid residues in a reduced alphabet. Although cystein was previously shown to be a dominant source of 3-body interactions, we now identify additional significant 3-body interactions of charged, hydrophobic and small residues.
Munson
P J
PJ
Analytical Biostatistics Section, LSB, DCRT National Institutes of Health, Bethesda, MD 20892-5626, USA. munson@helix.nih.gov
Singh
R K
RK
D000465:Algorithms; D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry; D003545:Cysteine / Q000737:chemistry; D016208:Databases, Factual; D016013:Likelihood Functions; D016014:Linear Models; D008956:Models, Chemical; D008969:Molecular Sequence Data; D011487:Protein Conformation; D017510:Protein Folding; D012984:Software; D013816:Thermodynamics
D000596:Amino Acids; D003545:Cysteine