Computational studies of protein helix kinks
<p>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.&l...
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| Format: | Thesis |
| Language: | English |
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2014
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| _version_ | 1817932214404382720 |
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| author | Wilman, H Henry Wilman |
| author2 | Deane, C |
| author_facet | Deane, C Wilman, H Henry Wilman |
| author_sort | Wilman, H |
| collection | OXFORD |
| description | <p>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.</p> <p>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.</p> <p>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.</p> <p>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.</p> |
| first_indexed | 2024-03-06T19:42:26Z |
| format | Thesis |
| id | oxford-uuid:21225f0e-efed-49c6-af27-5d3fe78fa731 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-12-09T03:34:21Z |
| publishDate | 2014 |
| record_format | dspace |
| spelling | oxford-uuid:21225f0e-efed-49c6-af27-5d3fe78fa7312024-12-01T17:55:25ZComputational studies of protein helix kinksThesishttp://purl.org/coar/resource_type/c_db06uuid:21225f0e-efed-49c6-af27-5d3fe78fa731Technology and Applied SciencesBioinformatics (biochemistry)Bioinformatics (life sciences)Physical SciencesMathematical genetics and bioinformatics (statistics)Polymers Amino acid and peptide chemistryComputational chemistryLife SciencesProtein chemistryMembrane proteinsBioinformatics (technology)EnglishOxford University Research Archive - Valet2014Wilman, HHenry WilmanDeane, CShi, J<p>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.</p> <p>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.</p> <p>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.</p> <p>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.</p> |
| spellingShingle | Technology and Applied Sciences Bioinformatics (biochemistry) Bioinformatics (life sciences) Physical Sciences Mathematical genetics and bioinformatics (statistics) Polymers Amino acid and peptide chemistry Computational chemistry Life Sciences Protein chemistry Membrane proteins Bioinformatics (technology) Wilman, H Henry Wilman Computational studies of protein helix kinks |
| title | Computational studies of protein helix kinks |
| title_full | Computational studies of protein helix kinks |
| title_fullStr | Computational studies of protein helix kinks |
| title_full_unstemmed | Computational studies of protein helix kinks |
| title_short | Computational studies of protein helix kinks |
| title_sort | computational studies of protein helix kinks |
| topic | Technology and Applied Sciences Bioinformatics (biochemistry) Bioinformatics (life sciences) Physical Sciences Mathematical genetics and bioinformatics (statistics) Polymers Amino acid and peptide chemistry Computational chemistry Life Sciences Protein chemistry Membrane proteins Bioinformatics (technology) |
| work_keys_str_mv | AT wilmanh computationalstudiesofproteinhelixkinks AT henrywilman computationalstudiesofproteinhelixkinks |