Protein breakdown: X-ray clues in disease

Protein machines

Modelling human TPPII
(Credit: Rockel/MPIB).

X-ray crystallography has been used to investigate the protein machinery that medical researchers say goes awry in uncontrolled or inaccurate degradation of cellular proteins. The research offers new clues on how cancer or Alzheimer's disease might develop.

All kinds of disease conditions can arise when degradation of cellular proteins goes awry and these biomolecules are broken down in an uncontrolled manner. Now, researchers at the Max Planck Institute of Biochemistry (MPIB) in Martinsried near Munich, Germany, have used X-ray crystallography and other techniques to reveal the structure and operating mechanism of an important component of the degradation machinery in humans, the enzyme tripeptidyl peptidase II (TPPII).

"Decoding the structure of TPPII is a crucial milestone towards understanding the complex activation and control of protein degradation", explains MPIB scientist Beate Rockel. Rockel and colleagues have no published details in the journal Structure.

The normal process of protein degradation when the biomolecules has been damaged or misfolded usually involves entirely unfolding the long chain of amino acids so that it can be cleaved into smaller digestible peptide snippets. TPPII is one of the enzymes involved in the chopping up of these peptide snippets into even smaller pieces so that their components might be recycled within the cell. TPPII is a large enzyme complex comprising 32 to 40 identical subunits, none of which shows any activity alone. The complex is functional only when subunits entwine. Team member Anne-Marie Schönegge points out that the enzyme complex is about one hundred times larger than most other protein-degrading enzymes. "TPPII is a real giant amongst cellular proteins", she says. "Solving the structure of such a colossus is a difficult task."

International structure

Working with colleagues at the Lawrence Berkeley National Laboratory in Berkeley, the MPIB team has solved the atomic structure of the TPPII-subunit from the fruit fly and then taken this data as the basis of a model of human TPPII-subunit. Cryoelectron microscopy and single-particle reconstruction also allowed the team to reveal the structure of complete and active TPPII-complexes for both fruit fly and human at medium resolution.

However, by combining the structure of the complete complexes with the more detailed atomic resolution models derived from the X-ray work, they could obtain details of the human TPPII to show that the subunits enclose a cavity system which traverses the whole TPPII complex and encloses catalytic centre of the enzyme complex. The team could then identify the substrate entry point and the active regions by fitting the structures of the inactive subunits into the active structure.

"Insights into the TPPII structure could contribute to the development of new drugs in the future, since there are indications that TPPII may be involved in diseases such as muscle wasting, adiposis and cancer," Rockel says.