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Cross-correlation of amino acid sequence data to explain fibril formation in a number of collagen subtypes

Pinali, Cristian 2008. Cross-correlation of amino acid sequence data to explain fibril formation in a number of collagen subtypes. PhD Thesis, Cardiff University.

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Abstract

Collagen is the most abundant protein in vertebrates. In particular, fibrillar collagens are found in bone, tendon, dermis, ligament, cartilage, cornea and blood vessel walls to mention but a few. Fibrillar collagens can be thought of as rigid linear structures and therefore are relatively simple to study from a theoretical point of view. In this thesis, a study on fibrillar collagen packing is presented. Since these collagens can be represented by a linear sequence of elements, it is possible to represent the hydrophobic or the electrostatic interactions between two collagen molecules by means of a cross correlation function. In fact, in this way we represent how many amino acids with a given property face each as a function of the displacement between the two sequences they belong to. Since cross correlation can be thought of as a scoring of the interactions between two adjacent molecules we will refer to it as the scoring method. In the first instance, the scoring method was applied to a linear amino acids sequence of type I collagen to probe the hydrophobic and attractive electrostatic interactions acting on it. Then, the method was applied systematically to type II, type III type XI collagens and to mixtures of type II and type III collagens. The appearances that these collagens would have in an electron microscope were calculated by a simulated staining method, and a comparison between real collagen fibrils and the models built in accordance to the findings of the scoring method was carried out. The scoring method allowed us to predict the correct stagger for collagen fibrils in parallel configuration. It also allowed us to predict and explain the correct axial stagger between type I collagen fibrils oriented in an antiparallel fashion. The scoring method was also used to explain oblique banding patterns found in reconstituted type II collagen fibrils. When applied to type II and type III collagen fibrils oriented in an antiparallel fashion, it shed light on a possible supercoiled structure. The validity of the scoring method was confirmed by its comparison with real collagen fibrils and, in principle, it could be extended to all proteins that can be represented as a simple linear sequence of amino acids.

Item Type: Thesis (PhD)
Status: Unpublished
Schools: Optometry and Vision Sciences
Subjects: R Medicine > RE Ophthalmology
ISBN: 9781303215445
Date of First Compliant Deposit: 30 March 2016
Last Modified: 19 Mar 2016 23:31
URI: http://orca-mwe.cf.ac.uk/id/eprint/54916

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