Malignant cancer cells not only proliferate faster than most body cells. They are also more dependent on the most important cellular garbage disposal unit, the proteasome, which degrades defective proteins. Therapies for some types of cancer exploit this dependence: Patients are treated with inhibitors, which block the proteasome. The ensuing pile-up of junk overwhelms the cancer cell, ultimately killing it. Scientists have now succeeded in determining the human proteasome’s 3D structure in unprecedented detail and have deciphered the mechanism by which inhibitors block the proteasome. Their results will pave the way to develop more effective proteasome inhibitors for cancer therapy.
In order to understand how cellular machines such as the proteasome work, it is essential to determine their three-dimensional structure in detail. With its more than 50000 atoms, the barrel-shaped proteasome, however, is a true challenge for structural biologists.
A group of scientists led by Ashwin Chari at the Max Planck Institute (MPI) for Biophysical Chemistry in Göttingen and Gleb Bourenkov at EMBL have now managed to determine the three-dimensional structure of the human proteasome at an unprecedented resolution of 1.8 Ångström – enabling them to pinpoint the position of single atoms in the garbage disposal unit.
In a next step, the researchers solved the structure of the proteasome bound to four different inhibitors that are either already used in the clinic or are currently undergoing clinical trials. “The substantial improvement in resolution compared to previous proteasome structures has allowed us to establish the exact chemical mechanism by which inhibitors block the proteasome.
This knowledge makes it possible to optimize inhibitor design and efficacy – since only inhibitors tailored to the proteasome shut it down completely,” says Chari, project group leader in the Department of Structural Dynamics headed by Holger Stark at the MPI for Biophysical Chemistry.
The scientists discovered an important detail in the proteasome’s active site. The active site is what enables the proteasome to degrade the cell’s junk, and it is what the inhibitor drugs bind to in order to shut off that activity. In contrast to the common perception, a 7-ring structure is formed by the chemical reaction of inhibitor and proteasome active site, which contains an additional so-called methylene group.
This has far-reaching consequences for the inhibitor’s efficacy and chemical mechanism, the researchers explain. “Even though a methylene group just comprises one carbon atom and its two associated protons amidst the more than 50000 atoms of the proteasome, it decisively influences which chemical features make the inhibitor most effective in blocking the proteasome,” says Thomas Schneider, who leads a group at EMBL.
“This has to be taken into account when developing new inhibitors and searching for new drug candidates,” adds Holger Stark. The researchers have already filed a patent application for the chemical procedure to design such inhibitors. “Clinical applications are always preceded by knowledge about targets – therefore, the details, where every atom counts, make all the difference,” Bourenkov states.
Huge effort reveals a small difference
The project’s success is the result of fantastic teamwork, as Max Planck researcher Chari emphasizes: “A group of scientists, all experts in their respective fields, contributed their specialized knowledge, expertise, and complemented each other perfectly.” Structural biologists, physicists, enzymologists, and biochemists of the MPI for Biophysical Chemistry, EMBL, and the University of Göttingen developed several innovative procedures.
To determine a molecule’s structure using X-ray crystallography, scientists grow crystals of that molecule, then shine a powerful beam of X-ray light on the crystal. Based on how the X-rays scatter after hitting the crystal, researchers can deduce the molecule’s 3D structure. Fabian Henneberg and Jil Schrader, junior scientists in Stark’s department and first authors of the report now published in Science, used a new method to purify proteasomes and grow the high-quality crystals that made it possible to solve its 3D structure in such detail.
The scientists have filed for a second patent application based on the purification and crystallization procedure employed in this work. “The pipeline we use to purify and crystallize the proteasome with and without inhibitors is also suitable to discover new proteasome inhibitors – in an industrial setting, screening several hundred compounds per week could be feasible,” Chari predicts.
However, the crystals were only one element of the project’s success. The second were the cutting-edge instruments developed by the EMBL research facility on the Deutsches Elektronen Synchrotron (DESY) campus in Hamburg. “The DESY light source generates X-rays of exceptional quality. With the help of powerful X-ray optics, we were able to tailor X-rays to perfectly suit the crystallized proteasome. Only this made it possible to determine the proteasome structure in unprecedented detail,” concludes Bourenkov.
The X-ray optics used in this work were installed in DESY’s PETRA III hall in 2015 thanks to funding from the German Federal Ministry for Education and Research´s (BMBF) RÅC support scheme.
Schrader J, Henneberg F, Mata R, Tittmann K, Schneider TR, Stark H, Bourenkov G, Chari A: The inhibition mechanism of human 20S proteasomes enables next-generation inhibitor design. Science, August 5, 2016, doi:10.1126/science.aaf8993
Dr. Ashwin Chari, Department of Structural Dynamics,
Max Planck Institute for Biophysical Chemistry, Göttingen
Phone: +49 551 201-1654
Dr. Gleb Bourenkov
Phone: +49 40 89902-120
Dr. Carmen Rotte, Press and Public Relations
Max Planck Institute for Biophysical Chemistry, Göttingen
Phone: +49 551 201-1304
Sonia Furtado Neves, Press Office
Phone: +49 6221 387 8263
E-mail: firstname.lastname@example.org, email@example.com
http://www.mpibpc.mpg.de/15429219/pr_1628 - Original press release
http://www.mpibpc.mpg.de/stark – Webpage of the Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Göttingen
http://www.embl-hamburg.de/research/unit/schneider – Webpage of the Schneider group, EMBL, Hamburg
Dr. Carmen Rotte | Max-Planck-Institut für biophysikalische Chemie
How do muscles know what time it is?
21.08.2018 | Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt
A novel synthetic antibody enables conditional “protein knockdown” in vertebrates
20.08.2018 | Technische Universität Dresden
There are currently great hopes for solid-state batteries. They contain no liquid parts that could leak or catch fire. For this reason, they do not require cooling and are considered to be much safer, more reliable, and longer lasting than traditional lithium-ion batteries. Jülich scientists have now introduced a new concept that allows currents up to ten times greater during charging and discharging than previously described in the literature. The improvement was achieved by a “clever” choice of materials with a focus on consistently good compatibility. All components were made from phosphate compounds, which are well matched both chemically and mechanically.
The low current is considered one of the biggest hurdles in the development of solid-state batteries. It is the reason why the batteries take a relatively long...
New design tool automatically creates nanostructure 3D-print templates for user-given colors
Scientists present work at prestigious SIGGRAPH conference
Most of the objects we see are colored by pigments, but using pigments has disadvantages: such colors can fade, industrial pigments are often toxic, and...
Scientists at the University of California, Los Angeles present new research on a curious cosmic phenomenon known as "whistlers" -- very low frequency packets...
Scientists develop first tool to use machine learning methods to compute flow around interactively designable 3D objects. Tool will be presented at this year’s prestigious SIGGRAPH conference.
When engineers or designers want to test the aerodynamic properties of the newly designed shape of a car, airplane, or other object, they would normally model...
Researchers from TU Graz and their industry partners have unveiled a world first: the prototype of a robot-controlled, high-speed combined charging system (CCS) for electric vehicles that enables series charging of cars in various parking positions.
Global demand for electric vehicles is forecast to rise sharply: by 2025, the number of new vehicle registrations is expected to reach 25 million per year....
17.08.2018 | Event News
08.08.2018 | Event News
27.07.2018 | Event News
21.08.2018 | Materials Sciences
20.08.2018 | Information Technology
20.08.2018 | Life Sciences