Modelisation of protein circular dichroism : simple model and application ; Modélisation du dichroïsme circulaire des protéines : modèle simple et applications

Circular dichroism (CD) spectroscopy is one of the fundamental techniques in structural biology that allows us to investigate the secondary structure of proteins. Synchrotron radiation has considerably increased the usefulness of the method because it allows to work with a wider range of spectrum and much greater signal-to-noise ratios. The development of a theoretical model to establish a relationship between the structure of a protein and its CD spectra in an efficient manner proved to be a complex task. The calculation of the CD spectra of large molecules, such as protein, remains a challenge, due to the size and flexibility of the molecules. In this context, we have developed a “minimal” model to explain the CD spectroscopy of proteins, which associates each C-alpha position on the protein backbone with a classical Lorentz oscillator i.e. a mobile charge attaches to a corresponding atom by a quadratic potential. The coupling between charges is through the Coulomb potential and their displacements follow the direction of the respective local tangents to the Calpha space curve. This system is coupled to a planar electromagnetic wave describing the light source and the absorption phenomenon is modeled by frictional forces. We show that the model correctly reproduces the CD phenomenon of a helical polypeptide chain and in particular its sign depending on the orientation of the chain. At first, we have fitted a model to CD spectra of a polypeptide chain of 15 residues folded into alpha helix. The transferability of these parameters is then evaluated with myoglobin, a protein of 153 residues containing eight alpha helices. ; La spectroscopie de dichroïsme circulaire (CD) est une des techniques fondamentales en biologie structurale qui permet la détermination du contenu en structures secondaires d'une protéine. Le rayonnement synchrotron a considérablement augmenté l’utilité de la méthode, car il permet de travailler avec une gamme spectrale étendue et à meilleure intensité. Le développement de modèles permettant ...