Evolutionary Rate Heterogeneity in Proteins with Long Disordered Regions
Note by Celeste: The content is good for what it tells us about evolutionary rate heterogeneity. But I hope that you also have a good feeling for how the INTRODUCTION was constructed.
- Testing whether disordered protein evolves more rapidly than ordered protein based on anecdotal reports: pairwise genetic distances compared between ordered and disordered regions of 26 protein families having at least one member with a structurally characterized region of disorder 30 residues or longer (pg 104)
Note by Celeste: ABOUT YOUR SECOND CHAPTER DRAFT
Homology means that two sequences or people or species share a common ancestor. So homology is a zero one thing, you either are homologous or you are not, hence you can not have "HIGH HOMOLOGY". Use similarity or identity or divergence when talking about the amount of difference between two sequences.
- Homologues found with BLASTP using entire protein sequence against nonredundant NCBI protein database
- Paralogues and orthologs used; identical sequences of same length reduced to one representative
- Alignments of homologues made with default settings of CLUSTALW and not corrected by hand
- Genetic distances calculated with Dayhoff PAM model using Protdist from PHYLIP (pg 105)
- Nineteen proteins with significantly faster rates of evolution in disordered regions, two with significantly slower in disordered region; no relationship between family size or method of detecting disorder (pg 106-108)
- Null hypothesis: residues in any aligned amino acid position are as likely to be in a region of disorder as a region of order and thus the pairwise genetic distances are equal (pg 108)
Note by Celeste: Yes, the region you have bolded here is the motivation for switching amino acid compositions for the matrices.
- Differences in rate of evolution may be related to amino acid composition differences: Aromatic amino acids in general have a lower substitution rate than charged, and disordered proteins have fewer aromatic amino acids and more charged amino acids than ordered proteins. Development of evolutionary models for disordered proteins will clarify importance of amino acid composition and physicochemical properties of disordered proteins to their evolutionary rate (pg 108)
Possible explanations for generally faster rates of evolution in disordered proteins:
- Disordered proteins serve no particular functions and have unconstrained evolution; however, absence of effects on a given activity and lack of a known function does not rule out another as yet unknown function for that region, and other rapidly evolving disordered regions do have known functions
- Not having a fixed structure is the function of disordered regions; many potential amino acid sequences can lead to unstructure and thus rapid rates of evolution
- May be due to positive selection for variability within regions of disorder or strong purifying selection in regions of order (pg 108)
Facts about Evolutionary Rate Heterogeneity in Proteins with Long Disordered RegionsRDF feed
| Date published | 1 June 2002 + |
| Has author | C. J. Brown +, S. Takayama +, A. M. Campen +, P. Vise +, T. W. Marshall +, C. J. Oldfield +, C. J. Williams +, A. K. Dunker +, P. E. Wright +, and H. J. Dyson + |
| Paper topic | Disordered proteins +, and Protein evolution + |
| PubMed ID | 12,165,847 + |
| Published in | Journal of Molecular Evolution + |
| Title | Evolutionary Rate Heterogeneity in Proteins with Long Disordered Regions + |