From dynamics to structure and function of model biomolecular systems

The purpose of this thesis was to extend recent works on structure and dynamics of hydrogen bonded crystals to model biomolecular systems and biological processes. The tools that we have used are neutron scattering (NS) and density functional theory (DFT) and force field (FF) based simulation methods. The quantitative and parameterfree link (in the case of DFT methods) between structure and dynamics has been applied to strong hydrogen bonded crystals and bio-polymers such as collagen and DNA. In several SSHB crystals, DFT normal modes and molecular dynamics calculations revealed the mechanism of proton transfer as being driven by low frequency phonons. The natural extension of these methods was oriented to polymers. Due to the lack of long range order, obtaining structural information of amorphous bio-polymeric systems requires the determination of the amide bands, which are the vibrations of the peptide groups C(=O)-N-H. We have used the DFT and inelastic neutron scattering approach to determine the spectral profile of the amide-V band and therefore the packing of 2D molecular sheets in Kevlar and the signature of the tertiary structure in Collagen. Depending on the secondary structure, the trends of the amide-I band has been well reproduced for simple polypeptides chains like polyglycine and polyproline. Water surrounding the protein is a huge subject of research. Water molecules are linked together to form different amorphous hydration shells. DFT methods are seen to suffer from a poorly defined minimum in the PES, resulting in negative frequencies in a normal mode analysis. Using force fields methods overcomes this problem but introduces a parameterization of the total energy calculation. In DNA, the structure-dynamics-function that we have focused on is base-pair opening, which is related to various bio-physical processes like replication and transcription. We used force field methods and normal mode analysis to identify modes with base-pair opening character. The oriented DNA films for experiments were made using the wet spinning method and the equipment was successfully installed and modernized during the thesis at ILL