Computational studies of protein helix kinks

Wilman, H; Henry Wilman

Oxford Thesis Collection

Thesis

Computational studies of protein helix kinks

Abstract:: Kinks are functionally important structural features found in the alpha-helices of many proteins, particularly membrane proteins. Structurally, they are points at which a helix abruptly changes direction. Previous kink definition and identification methods often disagree with one another.

Here I describe three novel methods to characterise kinks, which improve on existing approaches. First, Kink Finder, a computational method that consistently locates kinks and estimates the error in the kink angle. Second the B statistic, a statistically robust method for identifying kinks. Third, Alpha Helices Assessed by Humans, a crowdsourcing approach that provided a gold-standard data set on which to train and compare existing kink identification methods.

In this thesis, I show that kinks are a feature of long -helices in both soluble and membrane proteins, rather than just transmembrane -helices. Characteristics of kinks in the two types of proteins are similar, with Proline being the dominant feature in both types of protein. In soluble proteins, kinked helices also have a clear structural preference in that they typically point into the solvent.

I also explored the conservation of kinks in homologous proteins. I found examples of conserved and non-conserved kinks in both the helix pairs and the helix families. Helix pairs with non-conserved kinks generally have less similar sequences than helix pairs with conserved kinks. I identified helix families that show highly conserved kinks, and families that contain non-conserved kinks, suggesting that some kinks may be flexible points in protein structures.

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APA Style

Wilman, H., & Wilman, H. (2014). Computational studies of protein helix kinks [PhD thesis]. Oxford University, UK.

MLA Style

Wilman, H, and Henry Wilman. Computational Studies of Protein Helix Kinks. 2014. Oxford University, UK, PhD thesis.

Chicago Style

Wilman, H, and Henry Wilman. 2014. “Computational Studies of Protein Helix Kinks.” PhD thesis, Oxford University, UK.
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