Using Homology Modeling to Understand the Structural Basis of Specific Interaction of a Plant-Specific AtSar1a-AtSec23a Pair Involved in Protein ER Export

Abstract

Homology modeling allows the prediction of a protein structure based on sequence similarity to a known structure of homologous proteins. In this chapter, we use a plant-specific AtSar1a-Atsec23a pair of proteins as a case study to illustrate how to use homology modeling to understand the specificity of the pairwise interaction between AtSar1a and AtSec23a. The detailed procedures described here are also useful in structure prediction of other protein complexes.

Keywords: Arabidopsis; Homology modeling; Multiple sequence alignment; Protein folding; Structure prediction.