Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics

Chapter 19

Identifying Protein Complexes from Protein–Protein Interaction Networks

JIANXIN WANG, MIN LI, and XIAOQING PENG

19.1 Introduction

Protein complexes are groups of proteins that interact with each other at the same time and place, forming a single multimolecular machine, such as the anaphase promoting complex, RNA splicing and polyadenylation machinery, and protein export and transport complexes. Protein complexes can be classified into obligate and nonobligate types according to whether a protein of a complex can form a stable crystal structure of its own. If it can, (without any other associated protein) in vivo, then a complex formed by such proteins is called a nonobligate protein complex. On the other hand, some proteins can't be found to create a crystal structure independently, but can be found as part of a protein complex that does create a stable crystal structure. Such a protein complex is called an obligate protein complex [1]. Protein complexes also can be divided into two classes: transient protein complexes and permanent complexes. Transient protein complexes form and break down transiently in vivo, whereas permanent complexes don't show such behavior but are typically dissociated by proteolysis [1]. Many protein complexes are well understood, particularly in the model organism Saccharomyces cerevisiae (a strain of yeast, e.g., baker's yeast). For this relatively simple organism, the study of protein complexes is now being performed genomewide, and the elucidation ...