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Updated 4th, Jan., 2010

Interfaces of Proteins in Interactions

About 70% of cell weight is water, 26% is macromolecules like proteins and DNA, and 4% is lipids and ions. Cells are densely packed with proteins. Proteins in tight interactions maintain cell structure and proteins switch their interaction partners in response to the signal from the environment. Protein interactions are the essence of their roles in cells. Researchers for elucidating the structural detail of protein-protein interactions is, therefore, performed worldwide.

In molecular biology textbook, proteins are described by circles and squares, and protein interactions are depicted by putting the two circles side by side. Anyone knows that protein structure is completely different from a simple circle and square. But we still tend to imagine the proteins in interaction based on these diagrams. An interface of two circles is just a point and an interface of two squares is just a line (of two cubes is just wide flat faces). Are the real interfaces wide and flat? What is the atomic detail of protein-protein interfaces?

Many researchers have similar questions in mind and have studied the interfaces of their favorite protein complex. It is now known that there are many modes in protein-protein interfaces. The qualitative knowledge of the interface structures is based on different measurements and we do not have the general view of the interfaces. Dr. Steven Hayward at UEA in England and this research group started to gather coordinates of protein complexes and characterize the common features of the interfaces. The results are all gathered and presented in DACSIS.

A protein generally forms a globular structure by itself. But protein-protein interfaces are revealed not always to be flat. We found many cases that a part of the polypeptide chains from one or both of the proteins in the interface is unwound and protrudes into the other proteins. A left graphics shows an enzyme in a cell working in complex of white and grey proteins. The enzyme is known to work in this form in cells. The segment of grey protein protruding into the white protein is in red and the segment of white protein protruding into the grey protein is in yellow. Other parts of the interfaces of white and grey proteins are clearly separated. About 1/3 of the interfaces are interwound in DACSIS database.

Imagine the behavior of the protruding segments in interfaces, when the protein exists alone. The composition of amino acid residues in the protruding segments tells that the segment is floppy compared with, for example, a segment in internal part of the protein. The segment may be floppy when the protein exist alone and grab the partner protein when the protein bumps into the partner (just like handshake). This group starts to perform computer simulation to show whether the speculation can be experimentally warranted.

Kei Yura, Steven Hayward (2009) The interwinding nature of protein-protein interfaces and its implication for protein complex formation. Bioinformatics, 25(23), 3108-3113.