What is protein?
My main interest is to know “What is protein?”.
Proteins are very interesting molecules, because they can work systematically under large perturbations caused by surrounding water molecules. A water molecule is not small for proteins, and the number of the water molecules around the proteins is huge. The size of water molecules for protein is like a tennis ball for normal size of puma (180cm, 90kg).
Chemical Function of Individual Proteins
Chemical function of proteins starts with molecular recognition of other molecules, such as small molecules, DNA/RNA and proteins. So, to investigate the molecular recognition is the first step to understand the biochemical function of proteins.
Molecular Recognition with
3.Protein
Protein-protein interaction is a bridge from molecular function to biological functions. We are developing a method to predict complex structures of proteins.
Biological Function of Proteins
Biological functions are realized by interaction networks of proteins. The interaction networks are usually constructed based on experimental PPI information or coexpression of genes. We have developed databases of coexpression networks for Arabidopsis (ATTEDII) and for Human/Mouse (COXPRESdb). We are now trying to develop a method to predict the biological function of proteins based on the analysis of interaction networks.
Structure function Relationship
The reason why protein can work systematically is partly because each protein has its own 3D structures. Thus, I think the first step to know the nature of protein, we should start to understand the relation among sequence-structure-function relationship in proteins.
Protein function can be classified into biochemical function and biological function, or molecular function and cellular function. The former function is realized by a single protein or a single protein complex, and the latter function is achieved through the interaction network of proteins.
