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Deciphering living organisms

Fifteen laboratories will analyze the structure of the proteins of genes

Brazilian researchers have already mastered the techniques of sequencing genes and FAPESP’s different genome projects have produced a great deal of information. Now, the analysis of the three dimensional structure of the proteins expressed by the genes is the next step in understanding the workings of living organisms and FAPESP has just launched the Structural Genome Project in partnership with the Ludwig Cancer Research Institute. The project provides for investment of US$ 3.5 million over four years. The money will be distributed over a network of 15 laboratories in the State of São Paulo to finance the purchase of supplies and equipment. The biochemist Rogério Meneghini, director of the Structural Molecular Biology Center of the National Synchrotron Light Laboratory, in Campinas, will be the project coordinator. “Biological work is increasingly done in synchrotron light laboratories. It is a worldwide tendency”, said Meneghini.

The Structural Genome Project envisions the study of protein which sequences have been generated by in a given genome project. “At first, we thought of using only genes expressed in the Human Cancer Genome Project as they are extremely relevant” says Meneghini, who is of one the fathers of project. “Now we are considering studying the genome structure of Xylella fastidiosa. Besides being interesting in itself, it will let us reach the crystallization stage faster than working with human proteins,” he adds. The Ludwig Institute will come in with the sequences produced in the Cancer Genome and already stored in its  gene database or those to be produced in the future. The idea is to choose 50 or 100 genes and carry out the so-called High Throughput Protein Structure Determination procedure: expression, in vitro synthesis, purification, crystallization, and resolution of the structure of the protein on a relatively large scale. This process, starting with the genome and ending with the structure, has been called the structural genome process.

Thorough analysis
In contrast to other genome projects, in which the first sequences began to appear in the first week, structural genome determination is more detailed. “If we manage to do ten relevant three-dimensional structures, we will be making a significant contribution to our knowledge of the structure of proteins”, says Meneghini. He explains that to obtain the structure is very  elaborated process, which demands to overcome bottlenecks in the way  that range from the expression to the resolution of the structure.

Knowledge of protein structure facilitates the understanding of their function in cells. Based on this, determining genome structure also make it possible to design molecules that inhibit the activity of the protein, when this is desired. Diseases, in particular those caused by viruses, bacteria, and protozoa, are related to the action of proteins. Hence the interest by laboratories and pharmaceutical companies in the knowledge of these protein  structures, which means that more specific drugs can be designed for treating these diseases. One of the components of the cocktail used by HIV carriers, for example, is a molecule whose design is based on the three-dimensional structure of a HIV protease. This molecule attaches to the protease, inhibiting it. This is what is known as drug design.

Workshop with specialists
Researchers interested in taking part in the project and scientists already working in this field in research centers in Brazil and abroad met in the Foundation’s auditorium on June 13, in a workshop to present the project. The scientists Roberto Poljak, of the Center for Advanced Research in Biotechnology of the University of Maryland, USA, Christina Redfield, of the  Center for Molecular Sciences  in Oxford, England, and William Studier, of the Biology Department of the Brookhaven National Laboratory, USA, who took part in the meeting, will be members of the committee monitoring the project. “We have come to learn about the Brazilian project, exchange information, make suggestions and assess the project”, said Poljak.

Christina Redfield heads a group of five researchers at one of the biggest NMR (Nuclear Magnetic Resonance) centers in the world. There, they focus on the dynamics of the structure being analyzed and the way it interacts with the molecules in its natural environment. “What I liked about the idea of this workshop was the diversity of the fields involved. Even though they work differently on the same problem, crystallographers and scientists involved with NMR end up competing. They do not collaborate. It seems to me that here the idea is to join forces to make progress in the work”, said Redfield.

The Argentine crystallographer Roberto Poljak began his project in the US with orphan genes, in other words, those with no known function. Out goal is to contribute ideas as to what the function of these genes might be”, he said.

The biologist, biophysicist, and biochemist William Studier uses protein cloning, purification, crystallization, and  protein expression in his routine research. “The Brookhaven National Laboratory is not yet working on a particular protein. First we are setting up the capacity to do so”, said Studier, whose pilot project, for studying yeast, began two years ago. “We have quite a big research community in this field. Besides this, yeast is eukaryotic and has many genes similar to those of humans”. By the end of this year, Studier’s laboratory will cease being funded by the US Department of Energy and will be included in National Institutes o  Health’s budget. Enthusiastic about what he has read of FAPESP’s genome projects in international scientific magazines, Studier believes it is important to share experiences so that Brazil can set up a good program. In his opinion, genome projects need coordinating so that groups spread out all over the world do not waste time duplicating activities. “The scientific community needs to communicate. It is not a question of stealing a march on others to be able to produce drugs. We leave that to the pharmaceutical industry. The important thing is to get basic information for the use of all”, he says.

The history of proteins
John Kenderw published the first work explaining the dimensional structure of a protein, myoglobin, at the end of the 40s. Later, in the 60s, the Australian Max Perutz, working in Britain, won the Nobel Prize for discovering the structure of hemoglobin. The technique used to discover the structure of the protein is crystallography. A pure solution of the protein is obtained and crystallization is attempted. Even today, crystallization is looked on as an art. Scientists joke that when you love the crystal it grows better. The difficulty lies in the need for a large number of protein molecules organized in a complex crystalline structure. Similarly, spectroscopy using nuclear magnetic resonance is another method of studying proteins that does not require crystallization. This method is advantageous in that it allows the study to be undertaken in solutions; nonetheless, it is still limited by the size of the proteins within its reach.