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Molecular dynamics in collagen and model peptides

Courtier Murias, D.; (2010) Molecular dynamics in collagen and model peptides. Doctoral thesis , UCL (University College London).

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About a quarter of the total mass of proteins in vertebrates is collagen, so, improved knowledge of this protein is desirable and it should provide a new insight into biological interactions in human bodies. Two of the three main residues constituting collagen are proline and its derivative, hydroxyproline, which are responsible for some of the properties of collagen. Using solid-state NMR we studied the influence of water and temperature on motional changes in collagen. The results showed that increasing water content leads to significant increase of frequencies of protein motions with correlation times of the order of μs. It was found that pyrrolidine rings of L-prolines are not static in the solid state and cyclic carbon atoms librate about their mean position. Similarly, proline and hydroxyproline cyclic carbons in collagen were found to show librational dynamics. Detailed solution NMR analysis of proline peptides have been carried out. Using a two-site equilibrium model, geometries and populations of both conformers of prolines were established using the analysis of 3 J-couplings. The results of these studies were used for the verification of the performance of MD and QM calculations in the solution state. The effect of solvent on the pyrrolidine ring conformation and cis/trans rotamerisation along the amide bond preceding Pro was investigated by temperature dependent NMR followed by detailed transition state (TS) searches using QM methods. The coalescence temperature measurements were undertaken in order to determine the free energy of activation for the cis/trans-rotamerisation, which showed significant solvent dependence. The QM calculations revealed the energetic characteristics of the TS, which were in satisfactory agreement with NMR, as well as the corresponding TS geometries. For our pilot studies of a combined NMR/MD/QM approach for structure and dynamics elucidations in the solution state we chose two open chain tetrapeptides. We used an NMR/MD analysis in order to identify the most plausible structures. These conformations were used for further geometry optimisations using QM methods. In summary, a multidisciplinary approach has been developed, where experimental (NMR) and computational techniques (MD and QM) have been applied in a complementary manner in order to achieve a better understanding of proline containing peptides and collagen.

Type: Thesis (Doctoral)
Title: Molecular dynamics in collagen and model peptides
Language: English
Additional information: Authorisation for digitisation not received
UCL classification: UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Maths and Physical Sciences > Dept of Chemistry
URI: https://discovery.ucl.ac.uk/id/eprint/19199
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