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Structural approaches to protein sequence analysis

Jones, David Tudor; (1993) Structural approaches to protein sequence analysis. Doctoral thesis (Ph.D), UCL (University College London). Green open access

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Various protein sequence analysis techniques are described, aimed at improving the prediction of protein structure by means of pattern matching. To investigate the possibility that improvements in amino acid comparison matrices could result in improvements in the sensitivity and accuracy of protein sequence alignments, a method for rapidly calculating amino acid mutation data matrices from large sequence data sets is presented. The method is then applied to the membrane-spanning segments of integral membrane proteins in order to investigate the nature of amino acid mutability in a lipid environment. Whilst purely sequence analytic techniques work well for cases where some residual sequence similarity remains between a newly characterized protein and a protein of known 3-D structure, in the harder cases, there is little or no sequence similarity with which to recognize proteins with similar folding patterns. In the light of these limitations, a new approach to protein fold recognition is described, which uses a statistically derived pairwise potential to evaluate the compatibility between a test sequence and a library of structural templates, derived from solved crystal structures. The method, which is called optimal sequence threading, proves to be highly successful, and is able to detect the common TIM barrel fold between a number of enzyme sequences, which has not been achieved by any previous sequence analysis technique. Finally, a new method for the prediction of the secondary structure and topology of membrane proteins is described. The method employs a set of statistical tables compiled from well-characterized membrane protein data, and a novel dynamic programming algorithm to recognize membrane topology models by expectation maximization. The statistical tables show definite biases towards certain amino acid species on the inside, middle and outside of a cellular membrane.

Type: Thesis (Doctoral)
Qualification: Ph.D
Title: Structural approaches to protein sequence analysis
Open access status: An open access version is available from UCL Discovery
Language: English
Additional information: Thesis digitised by ProQuest.
Keywords: Pure sciences; Biological sciences; Protein sequence analysis
URI: https://discovery.ucl.ac.uk/id/eprint/10097795
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