Tag Archive | protein structure

“Without 3D information it is very difficult to understand how the genome works”

Marc A. Marti-Renom is interested in three-dimensional structures. After eight years in the US dedicated to the world of proteins, the biophysicist returned to his native country, first Valencia and then Barcelona, to specialise in RNA and DNA folding. In 2006 he set up his own group, which today is divided between the CNAG, where there are ten people, and the CRG, where there are two. “We do the experimental part, the sample preparation, here in the CRG, and the sequencing and analysis happens in the CNAG”, he explains. For his research he requires a large sequencing and computing capacity, which he can get at the CNAG, the second-most important sequencing analysis centre in Europe. “We are fortunate to be in one of the best places in the world to do these studies,” he says proudly.

3, MARC MARTI RENOM_14_group

 

Proteins with clinical application

Proteins caught his attention while he was doing his PhD, and in 2004, when he was at the University of California (UCSF), he collaborated in the creation of the “Tropical Disease Initiative,” a drug-discovery initiative linking people from both academia and companies to try to reposition drugs in favour of neglected diseases such as malaria and tuberculosis. “The idea was to make it all open source so everything we found was published directly to the web and couldn’t be patented”, says Marti-Renom.

The Structural Genomics group was a major player in one of the first instances that genome sequencing was used at the clinical level. “There was a patient with tuberculosis and a high resistance to antibiotics. We sequenced samples from the patient and found out he was infected by two different strains, and one of them was mutated. When we made models of the protein structure resulting from this mutation we saw how it was affecting the function”, explains the scientist. According to Marti-Renom, in a few years not only will everyone have their genome sequenced, but it will happen several times. “When someone develops a disease like cancer we will sequence them again to see what has changed and why”, he predicts.

Beyond proteins: RNA and DNA

Proteins, the cell’s building blocks, are not the be-all and end-all of life. Since the 1960s we have known that RNA has essential functions other than converting the information in DNA into proteins. But of its three-dimensional structure very little is known, and in the end, the function occurs in 3D. For this reason the group is developing computational tools to incorporate experimental data and make structural predictions.

The most recent biological component to enter the ‘3D world’ was the genome. In this case, too, little is known about how it folds in space. The group of Marti-Renom, along with three other groups at the CRG (Miguel Beato, Guillaume Fillion and Thomas Graf) is carrying out the 4DGenome project, which has a budget of 12.2 million euros, in order to understand the structure of the genome and how it changes over time. “We know the genome sequence very well, thanks to molecular biology and the big genome projects. We also understand the chromosomal macrostructure, thanks to advances in microscopy; but we can’t see the middle ground, the step between the tangled skein and the well-defined chromosome”, says the head of the group. In 2006 they began using Chromosome Conformation Capture (3C) data to develop software that allows you to view the entire genome at high-resolution, a kind of ‘molecular microscope’. With this and other technologies, like Hi-C, and using computational algorithms they have been able to observe how different regions of the same chromosome tend to interact with each other. They have also seen that the 3D ‘photo’ of a moment when, for example, there is high gene expression may be very different to another where the expression is low. “Without this three-dimensional information it is much more difficult to characterise how the genome works”, concludes the researcher.

This article was published by Maruxa Martinez, Scientific Editor, at the El·lipse publication of the PRBB.

Amyloids: the good, the bad and the ugly

Amyloids – insoluble fibrous protein aggregates that share specific structural traits – are well known for their involvement in diseases such as Alzheimer’s, Parkinson’s, prions diseases and even diabetes 2 and some cancers. As evil as they seem, however, they also have a kinder side. Stavros Hamodrakas, head of the Biophysics and Bioinformatics laboratory at the Faculty of Biology, University of Athens (Greece), talked today at the PRBB about functional, non-pathogenic amyloids.

He actually was the first person to propose that the silk moth eggshell (or chorion) was a natural, protective amyloid. The chorion is a multi-layered structure that protects the egg from desiccation and infections and which provides thermal insulation.

Bombyx mori, the silk moth

Hamodrakas reviewed in this talk his research over the last 30 years on this field. Since those first days, many more examples of protective amyloids have been found, from bacteria to human – including the covers of the eggs of many species such as fish, mouse and humans.  Skipping through all the details, the conclusion was that tandem hexapeptide repeats present in the aminoacid sequence of the central domain of chorion proteins is what dictates the folding and self-assembly of those amyloid-like protein. One peculiarity he mentioned was the fact that all the proteins that form amyloids are very different amongst them at the sequence level. However, the structure – the focus of Hamodrakas’ research – has similarities.

The audience was very involved in the talk, and an interesting debate originated afterwards around the question: why are some amyloids functional, protective either, and others pathological? One of the potential answers is the fact that all protective amyloids are extracellular, so they don’t affect the functioning of the cell. And even thought they were synthesized within the cell, they were ‘protected’ within vesicles until they were secreted.

There’s still a lot to learn about protective amyloids, and the more we know about them, the better we can understand the pathological ones.

Report by Maruxa Martinez, Scientific Editor at the PRBB

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