PROTEINS >>Life & Environment

PERFECTLY STRUCTURED

Proteins control the entire life – if they are folded properly. Incorrectly folded proteins are responsible for serious illnesses such as Alzheimer’s and Parkinson’s disease. Researchers are using supercomputers for the ever more accurate prediction of the spatial structure of key molecules.

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Amino acid chains have a tendency to form into spirals or “beta-pleated sheets” – symbolized with arrows here. However, this is only the secondary structure. How spirals and pleated sheets are winding around each other remains a mystery.

IN A NUTSHELL

 Decoding the three-dimensional structure of proteins is so difficult that researchers have only identified the shape of 0.7 percent of known proteins.  Therefore, and computer scientists are using savvy and computers to shed light on more protein structures.  They are pitting their strength against each other in

N. Speicher/Laguna Design Design N. Speicher/Laguna an international prediction competition.

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PROTEINS

Professor Jens Meiler (left) and his ambitious team of PhD students in Nashville (right): in 2008, they entered an international competition with a new self-developed prediction program.

by Frederik Jötten IT IS MAY 5, 2008, 02:30 pm in problem. But the three-dimensional stops the process and makes sure that the Nashville, Tennessee when the race structure is only known for 0.7 percent repair system is initiated. If the damages begins. Outside the window, the sun of of macromolecules – and this structure is involving the DNA are severe, it the southern state is scorching the the sole decisive factor for whether they activates the self-destruction of the cell. campus. On the can fulfill their function in living However, if p53 is incorrectly folded due inside, in a comfortably air-conditioned creatures. to a mutation, it is no longer able to room full of computers, the competitors monitor the genome. Cells can then wearing jeans and T-shirts are ready to Incorrectly folded proteins cause divide in an uncontrolled way – cancer get started. Nils Wötzel, Julia Köhler, illnesses; this is generally known at least develops. p53 is mutated in 50 percent of Nathan Alexander and Merr Karakas, all since the causes for BSE and the all tumors involving humans. PhD students in their mid-twenties are Creutzfeldt-Jakob disease have been staring at one of the monitors, waiting. identified. The modification of their ROSETTA’S LIMITATIONS Finally, a sequence of letters appears: three-dimensional structure turns Attempts to determine protein structures MFSLRDAKC… An unpronounceable harmless proteins into deadly prions are ongoing around the world, to word composed of 103 letters. It which in turn convert harmless proteins understand the causes of illnesses and to identifies a protein consisting of a chain into the dangerous form. Prion diseases develop new medications. However, 50 with 103 amino acids. This is the starting are rare, but they illustrate the potential percent of all drugs bind to proteins signal of the competition at the end of consequences of structural alterations of integrated in the cell membrane – and for which the young scientists belonging to proteins. Illnesses in which proteins these, it is even more difficult to the group of German structural clump together rather than adopting their determine the three-dimensional shape Jens Meiler are hoping to predict what proper shape are much more common: compared to soluble proteins: the this and more than 100 other proteins the Alzheimer’s and Parkinson’s structure is only known for 0.04 percent. look like. They are joined by 236 other diseases affecting millions of people as competing teams from around the world. they get older are the result of this Jens Meiler’s working group in defective protein folding. Recent studies Nashville is committed to changing this. One of the main challenges of modern suggest that “sick” proteins are refolding The international competition the four is to define the structure of traditional shapes of certain proteins PhD students are participating in is proteins. Proteins control all processes of within the body – similar to prions. called “CASP”. The English life – in plants, animals and humans. abbreviation stands for “Critical Whether it relates to the contraction of And then there are the disorders Assessment of Techniques for Protein our muscles, the digestion of food or our triggered by isolated mutations – genetic Structure Prediction”. The procedure is sense of seeing, hearing and tasting, changes resulting in a non-functional as follows: Researchers who defined a proteins mediate almost all processes in protein. Protein p53 is known as the proteins structure experimentally are living creatures – including pathogens. “master watchman of the genome” for its holding off with the publication of their These days, defining the order of the ability to prevent tumors. If errors in the data. The prediction teams are provided amino acids of proteins is no longer a duplication of the genotype occur, it with the letter sequence, the so-called

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Target 409, a protein from the bacterial cell wall: According to the computer program of Meiler’s team, it could adopt the shapes 1 to 5. Picture 6 illustrates the actual structure in grey along with the details of the best predictions from the Nashville team in color.

amino acid sequence, use the Rosetta’s capabilities are limited”, computer programs to create a says Meiler. “Our program is hypothetical structure – and the designed to overcome these models and reality are compared limitations.” weeks later. At a conference held seven months after the start of the CHANNEL IN THE HEART competition, it will be announced HERG is an example of a membrane which teams were most successful. protein; it occurs in cells of the heart muscle and forms a channel between Jens Meiler already participated in the inside and the outside of the cell. CASP as a post doc. He worked for Potassium ions are flowing out of the inventor of the computer-aided the cell through this channel after prediction tool, the contraction, a requirement for in Seattle for four the heart to be able to pump blood years. While there, he was involved soon again. If the channel does not in the development of the best work properly, it may result in known and thus far most successful prediction program: “Rosetta”. With Rosetta, Meiler won first place in CASP twice. His working group is now participating with a self- developed program for the first time. “For membrane proteins and proteins not resembling any previously known molecules,

PROTEINS

arrhythmia. Numerous drugs, Nils Wötzel starts the program only realized a few of these including some antibiotics and designed to predict the structure. The combinations – namely ones that antipsychotic drugs bind to HERG, supercomputer which fills an entire occur in living creatures in stable thus causing arrhythmia. Therefore, room in the neighboring building and three-dimensional shapes: for every potential drug must now be has a capacity comparable to 2000 example in a basic shape and in investigated first to find out whether traditional PCs starts the calculation. deviating variations created by the it binds to HERG before it can be Preliminary models will be available interaction with other molecules. tested in humans. And this is a in a few days. problem: although HERG is one of CENTURY-OLD DREAM Proteins are part of the most complex the most studied proteins, the Proteins fold as early as during molecules overall. They contain up to determination of its exact structure 100,000 atoms and create the most synthesis. In doing so, they are has been impossible to this day. diverse structures – ranging from the driven by inner energies forcing Algorithms, neuronal networks and tear-resistant construction material them into the most favorable supercomputers are currently being collagen to the variable antibody. energetic status. These forces have used to speed up the search.

This is how biologists determine the real 3D structure of a protein: they allow crystals to form (left), bombard such a crystal with X-rays in a diffractometer (center) and determine the structure from the diffraction pattern (right).

The 8th round of the CASP The structural formulas of the 20 one thing in common: they are competition also includes a protein amino acids from which organisms already present in the amino acid which is involved in the structure of establish proteins are written with sequence. Therefore, researchers bacterial cell walls and plays a key marker on a board hanging on the have been dreaming for centuries to role in the resistance against wall next to the computer. All of predict the structure of a protein antibiotics. Many antibiotics, them have an identical part – and a solely based on the sequence of the including penicillin, bind to this so-called residue which makes them amino acids. But in spite of years of protein, thus inhibiting its function different. intensive research, computer models and preventing the pathogens from are only approximations so far. propagating. However, for the The length of an average protein is Individual atoms within a protein researchers in Nashville, this is 300 amino acids, in other words, have an estimated diameter of one simply “target” number 409. CASP there are 20 to the power of 300 angstrom (1.0 x 10-10 meter). On is not about the function of certain possible combinations. This figure is average, the best estimates are off by proteins, but rather about the basic so large that the number of atoms in up to 5 angstroms, moderate principles of protein folding and the entire universe would not suffice estimates by 10 and poor ones by 20 how they can be computer- to create only a single sample of and more. simulated. each molecule. Nevertheless, nature

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the structure of Diacylglycerol kinase, Seven months later, in December 2008, one of the important metabolic enzymes the results are presented. The computer sitting in the cell membrane, in the simulations of target 409 from all the Journal Science in June 2009. The participating groups greatly deviate from difficulties involved in the determination the real structure. Once again it becomes

of protein structures illustrate the scope blatantly obvious that it is still a long of efforts that could be saved if a reliable way until the nature of protein folding prediction by means of the computer can be predicted by computers. The best These days, mainly two methods are were possible. simulations are off by 3.1 angstroms, the used for the experimental one from the Meiler group is off by 13.5. determination of protein structures. RED SPIRALS AND GREEN In terms of this protein, this means rank They are the nuclear magnetic ARROWS 75 of 129 groups who worked on this resonance spectroscopy and the by Nashville, three weeks after the start of target. There are other molecules, for far most commonly used structural the competition: discussion between the which the researchers from Nashville researchers in front of a monitor. The scored better: for target 396, they are X-ray analysis. For the latter, a letter sequence turned into three- only off by 4 angstroms. Overall, the protein crystal is first produced. X- dimensional structures. The group researchers from Nashville are ranked in ray light is sent through the crystal compiled ten different predictions of the middle. Disappointed? “No. We and the structure can be calculated target 409 using a variety of methods. participated for the first time in the based on the diffraction pattern. Yet The researchers are now discussing competition with our new program. It is many proteins, particularly ones which ones to submit. A bundle of red not yet mature. Next time, we will do sitting in membranes have not spirals and green arrows first appears on better”, says Wötzel. CASP 9, the new formed any crystals to this day. the monitor. They represent the so-called competition will start on May 3, 2010. Nuclear magnetic resonance secondary structures of the protein. Before the amino acid chain folds into its spectroscopy can be used for those. spatial structure, it either winds into an FREDERIK JÖTTEN is a biologist and free- However, this is a very tedious alpha helix similar to a spiral staircase lance journalist. While pursuing his studies, procedure as illustrated by a recent (in the computer simulation: a spiral) or he attempted in vain to isolate a protein of the example: a worldwide cooperation forms a surface, the beta-pleated sheet malaria pathogen. of researchers needed 13 years, until (arrow). It looks very confusing on the MORE ABOUT THE TOPIC they were finally able to publish monitor. “This will be difficult, but we will try”, says Nils Wötzel. With 103 READING MATERIAL amino acids, the molecule is not very big Dietmar Zimmer indeed, but it consists of many pleated JENSEITS DER GENE sheets which are much more difficult to Proteine – Schlüssel zum Verständnis des simulate than helices. Lebens (BEYOND GENES Proteins – the key to understanding life) The doctoral candidate turns the protein Klett Cotta, Stuttgart, 2005, € 19.50 (available on the monitor and opens a second from second hand bookshops only) prediction. It looks slightly different than the first one. The second prediction John W. Moore and Tina Blasche shows a pleated sheet in the location BIOCHEMIE FÜR DUMMIES where the first one shows a helix. Three (BIOCHEMISTRY FOR DUMMIES) thoughtful faces are reflected on the Wiley-VCH, Weinheim 2009, € 19.95 monitor. “We have to decide which Vivienne Baillie Gerritsen models we want to submit”, urges TALES FROM A SMALL WORLD Nathan Alexander. Five models per day Swiss Institute of Bioinformatics 2009 are eligible to participate in the Available from www.proteinspotlight.org competition. “This one most resembles a A protein is introduced in popular science protein”, says Julia Köhler, pointing to terms every month on this website. The book one of the colorful tufts. “In this model, contains a collection of texts from this series. the helix is not protruding as much as in the other model.” The group decides to INTERNET Learn how lay persons can get involved in the submit Köhler’s favorite – along with virtual protein folding by visiting the model that deviates most from it. www.wissenschaft.de under menu item “The competition is about learning “Current Issue”. something, and it is best to learn from mistakes”, the doctoral candidate explains.

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