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Fully Atomistic Modelling of Collagen Cross-linking

Collier, Thomas; (2016) Fully Atomistic Modelling of Collagen Cross-linking. Doctoral thesis (Ph.D), UCL (University College London). Green open access

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The extracellular matrix (ECM) undergoes progressive age-related stiffening and loss of proteolytic digestibility due to an increase in concentration of advanced glycation end products (AGEs). Detrimental collagen stiffening properties are believed to play a significant role in several age-related diseases such as osteoporosis and cardiovascular disease. Currently little is known of the potential location of covalently cross-linked AGEs formation within collagen molecules; neither are there reports on how the respective cross-link sites affect the physical and biochemical properties of collagen. Using fully atomistic molecular dynamics simulations (MD) we have identified preferential sites for exothermic formation of two lysine-arginine derived AGEs, glucosepane and DOGDIC. Identification of these favourable sites enables us to align collagen cross-linking with experimentally observed changes to the ECM. For example, formation of both AGEs were found to be energetically favourable within close proximity of the Matrix Metalloproteinase-1 (MMP1) binding site, which could potentially disrupt collagen degradation. With the aid of a number of dynamic analysis techniques we have provided an explanation for the site specificity of the two AGE cross-links. The mechanical properties of collagen were also investigated through the use of steered MD to determine the effect of the cross-links presence. Additionally the effect of the sequence on the collagen mechanical properties was also investigated, owing to the heterogeneous response of collagen to an applied load. A homology model for the Homo sapiens sequence was developed from the crystal structure of the Rattus norvegicus structure that was shown to produce stable simulations. Through the use of the homology model and implementation of a novel simulation technique we attempted to ascertain the orientations of the collagen molecules within a fibril, that is currently below the resolution limit of experimental techniques.

Type: Thesis (Doctoral)
Qualification: Ph.D
Title: Fully Atomistic Modelling of Collagen Cross-linking
Event: UCL (University College London)
Open access status: An open access version is available from UCL Discovery
Language: English
Additional information: Third party copyright material has been removed from ethesis.
Keywords: Collagen, glycation, Protein cross-linking, molecular dynamics, Advanced Glycation End Products, Glucosepane
UCL classification: UCL > Provost and Vice Provost Offices
UCL > Provost and Vice Provost Offices > UCL BEAMS
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Maths and Physical Sciences
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/1517916
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