Recent Developments in Structural Proteomics: From Protein Identifications and Structure Determinations to Protein-Protein Interactions

The human genome project has opened novel scientific avenues such as structural proteomics. The major challenge in structural proteomics is to predict protein structure-function relationships, including the identification of those proteins whose structures are partially or fully unknown. The use of two-dimensional gel electrophoresis and mass spectrometry methods to identify proteins strongly aids our understanding of biological regulatory networks that govern protein expressions. After identifying proteins, the crucial step is to determine their functions and structures. Recent developments of many high-throughput methodologies and technologies have enabled novel data to be generated with efficiency and speed. Protein structures are typically determined by experimental approaches such as X-ray crystallography or NMR spectroscopy. However, the knowledge of three-dimensional space by these techniques are still limited. Thus, computational methods such as comparative approaches and molecular dynamics simulations are intensively used as alternative tools to predict the three-dimensional structures and dynamic behaviors of proteins. This review summarizes recent advances in high-throughput structural proteomics that involve instrumentation methods such as two-dimensional gel electrophoresis, mass spectrometry, X-ray crystallography, and NMR spectroscopy, and computational methods such as comparative approaches and molecular dynamics simulations. New insights into proteinprotein interactions and relationships between structure and protein-protein interactions will also be presented.