Polypeptides chain dynamics probed by fluorescence

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Proteins are chains made of units called amino acids. Proteins are of interest to scientists because they conduct a number of key processes that enable the body to function. They achieve these tasks thanks to the tight and compact structure they fold into. A lot of research is done trying to characterize the structure of proteins and many protein structures are now known. Furthermore, since the human genome has been deciphered, the composition of all human proteins is known. In other words, the starting point (protein composition) and the end-point (protein structure) are known, but very little is actually known on how a protein chain goes from start to finish. This proposal aims at mapping out the folding process of proteins by using fluorescently labeled polypeptides. Polypeptides are long chains made of amino acids which are used as protein mimics. In solution, polypeptides undergo internal motions which can be probed by fluorescence. In particular, fluorescence experiments can provide information on how far a single amino acid labeled with a fluorophore moves within the volume defined by the chain in solution. The fluorescently labeled polypeptides take advantage of the internal watch inherently built with any fluorophore. As a matter of fact, a fluorophore is excited for a well-defined period of time which is determined by its lifetime. The lifetime of any fluorophore can be adjusted by addition of an external quencher. Since a fluorescence experiment reports solely on those fluorophores that are excited, and since experimental means are available to control the time fluorophores remain excited for, the volume probed by a labeled amino acid will be monitored as a function of time. This study will probe the mobility of amino acids in solution and provide information on how far an amino acid can move within the volume of the polypeptide coil as a function of time. These experiments are expected to provide useful experimental data that can be used to model how a protein chain folds in solution.