Revealing the 3D structure of proteins
10/14/13

At the present time, it is still difficult and costly to obtain a representation of the three-dimensional structure of proteins. But such a representation contains important indications about their function. That is why scientists have been trying to develop computer-based methods of making predictions about the properties of certain proteins that are faster than current methods. 
Julien Becker, Francis Maes and Louis Wehenkel are using their automatic predictive tool to predict the formation of disulfide bridges (connections that form between the sulfur atoms of two amino acids called cysteines) that are present within a certain protein. Their work has led to the creation of a predictive tool known as x3CysBridges, which allows them to calculate the probability that the cysteines of a single protein will form disulfide bridges. The international scientific community has already begun to use this predictive tool.

protein strucutreProteins are very large molecules that serve a variety of functions within a cell or an organism; proteins are essential to all life forms. They are made up of one or more chains of amino acids, which in virtue of their sequences and their interactions give to each protein a particular three-dimensional structure, which is closely related to the function of the protein.

From a simple sequence of amino acids to its final three-dimensional structure, the macromolecule which a protein is passes through four levels of structuring known as primary, secondary, tertiary, and quaternary. At the end of these stages the protein begins to fold up into a stable three-dimensional structure that will allow it to fulfil its proper function. At that point the protein may assume in one or the other of two general types of structure: a helix or a sheet.

When proteins have a similar sequence of amino acids, they tend to have similar three-dimensional structures. But it sometimes happens that two proteins that have identical sequences have a three-dimensional structure (and thus a function) that is different with regard to the solvent or the environment in which they are found. In fact, proteins interact with other elements in their environments, and these influence the final shape of their structure.

Bridges that stabilize proteins

In a general way, different types of interactions between different amino acids, and between these amino acids and their environment, permit stabilization of the structure of proteins. Among these interactions, we find covalent bonds, and disulfide bridges in particular. These connections form through oxidation, and they are formed between atoms of sulphur contained in two amino acids that are called cysteines. “We find disulfide bridges especially at the level of extracellular proteins, which are excreted, or at the level of membranes because that allows them to be stabilized, said Julien Becker, a doctoral candidate working under the supervision of Prof Louis Wehenkel in the Systems and Modeling research unit that is part of GIGA. “Inside the cell, the environment is fairly stable and there is not so much of a need to further stabilize proteins.” For example, disulfide bridges are found in the proteins of snake or scorpion venom, in antibodiesproduced by the immune system, in insulin - the hormone that regulates the concentration of sugar in the blood – and in many other proteins.

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