AMINO ACID STRUCTURAL CODE APPLIED TO PROTEIN STRUCTURE PREDICTION AND DESIGN
Introduction/Abstract
The close packing in the protein structure results from the interaction of amino acid side chains distant in sequence position.
Purpose
In an exhaustive analysis of packing in the Protein Data Bank, the knob-socket tetrahedral construct was identified as a fundamental principle underlying the packing in protein structure.
Method
Application of this knob-socket principle to the classification of protein structure reveals distinct amino acid preferences for specific knob-socket arrangements in protein packing. These preferences define a discrete amino acid code for the relative spatial arrangement of protein residues in secondary and tertiary structure.
Results
Amino acid composition of 3-residue sockets specifies secondary structure, while interaction of the 3-residue socket with a fourth residue indicates tertiary packing. This code for amino acid structure was applied in protein structure prediction and protein structure design to test its practicality and accuracy. In a completely new approach to structure prediction, secondary structure elements were precisely packed using the aforementioned amino acid patterns in an essentially hand building process. This was accomplished for 54 targets from the 10th Critical Assessment of Structure Prediction experiment and our resulting predictions are evaluated for contributions and limitations. For protein design, the knob-socket principle was used to construct a specific protein fold. Preliminary experimental results from CD and NMR are shown of the protein design.
Significance
This approach represents a novel and significant advancement in the understanding of protein structure for prediction and design.
Location
DeRosa University Center, Stockton campus, University of the Pacific
Format
Poster Presentation
AMINO ACID STRUCTURAL CODE APPLIED TO PROTEIN STRUCTURE PREDICTION AND DESIGN
DeRosa University Center, Stockton campus, University of the Pacific
The close packing in the protein structure results from the interaction of amino acid side chains distant in sequence position.
