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Title: Protein structure prediction : amino acid propensities and comparative modelling
Author: Deane, C.
Awarding Body: University of Cambridge
Current Institution: University of Cambridge
Date of Award: 2000
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The objectives are to look at the most serious problems post-alignment in comparative modelling and to develop new software to combat them. To that end I begin by examining the results of the comparative assessments of structure prediction (CASP) meetings and in particular the Blundell group participation in CASP3. I discuss the major problems and challenges for comparative modelling illustrating them with the five models I built for CASP3. The next part of the thesis concentrates on the amino acid propensities for regions of the Ramachandran plot. This work was originally carried out to examine the possibility of the use of a limited φ, ψ set for protein structure prediction and to examine in detail the reasons behind amino acid preferences for partially allowed regions of the Ramachandran plot. An understanding of this behaviour is useful for accurate modelling particularly in the variable regions of protein structure. I generated accurate distributions of the observed φ, ψ patterns for the twenty naturally occurring amino acids. The distributions define more clearly results and trends that have been seen in other studies. Using these distributions as a guide the different reasons for observing or not observing conformations of amino acids are discussed for several features already noted in the literature. Then features that have not been explained previously are explored and possible explanations for their occurrence given. The unusually high propensity of Asn and Asp in the αL region of the Ramachandran plot is explained in terms of carbonyl - carbonyl stacking. Helix termination residues and the cis conformation of Pro are also discussed.
Supervisor: Not available Sponsor: Not available
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available