BioSysBio:abstracts/2007/Sanne Abeln: Difference between revisions
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=== Fragments === | === Fragments === | ||
The fragment library generated for this study, contains fragment of length 10,15,20 and 30, with a maximum allowed gaplength of 2,3,4,6 respectively. All fragments are based on pairwise comparisons between structural domain as defined by SCOP | The fragment library generated for this study, contains fragment-pairs of length 10,15,20 and 30, with a maximum allowed gaplength of 2,3,4,6 respectively. All fragments are based on pairwise comparisons between structural domain as defined by SCOP . The pairs are scored for similarity purely on structural grounds using the coordinates of the c-alpha atoms only. | ||
All possible pairwise fragments between two domains are first screened and aligned using a method similar to the prefilter used by MAMMOTH <cite>Ortiz-2002</cite>. Each fragment pair with an alignment score above a threshold is then superimposed to create an RMSD score for the fragment pair. | All possible pairwise fragments between two domains of the given lengths are first screened and aligned using a method similar to the prefilter used by MAMMOTH <cite>Ortiz-2002</cite>. Each fragment pair with an alignment score above a threshold is then superimposed to create an RMSD score for the fragment pair. | ||
=== Age estimates === | === Age estimates === | ||
Revision as of 06:47, 28 September 2006
Linking evolution of protein structures through fragments
Author(s): Sanne Abeln, Charlotte M. Deane
Affiliations: University of Oxford
Contact:email: abeln@stats.ox.ac.uk
Keywords: 'protein structure' 'evolution' 'fragments' 'completed genomes'
Summary
Here we use a strucutural fragment library to investigate evolutionary links between protein folds. We show that 'older' folds have relatively more such links than 'younger' folds.
Motivation
At present there is no universal understanding how proteins can change topology during evolution, and how such pathways can be determined in a systematic way. The ability to create links between fold topologies would have important consequences for structural classification, structure prediction and homology modelling. It has been proven difficult however to show the evolutionary relevance of previously established geometric measures to create such links between topologies. Here we use our a previously determined age measure for protein folds or superfamilies to investigate the effect of evolution [1].
Results
Images/Tables
Add your images or tables here
Materials/Methods
Fragments
The fragment library generated for this study, contains fragment-pairs of length 10,15,20 and 30, with a maximum allowed gaplength of 2,3,4,6 respectively. All fragments are based on pairwise comparisons between structural domain as defined by SCOP . The pairs are scored for similarity purely on structural grounds using the coordinates of the c-alpha atoms only.
All possible pairwise fragments between two domains of the given lengths are first screened and aligned using a method similar to the prefilter used by MAMMOTH [2]. Each fragment pair with an alignment score above a threshold is then superimposed to create an RMSD score for the fragment pair.
Age estimates
Age estimates for protein folds or superfamilies are generated using fold recongnition of structural domains on a set of completed genomes. The occurrence patterns of such predictions, are analysed with a parsimony algorithm to estimate an age for a superfamily or fold, for more details see [1].
The age of a fold or superfamily is based on a score between [0.0,1.0] with 0.0 indicating a last common recent ancestor at the leafs (youngest), and 1.0 indicating present at the root of the species tree (oldest). Here an 'old' fold is defined as a fold with an age of 1.0, and a 'young' fold with an age < 0.5
Conclusion
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References
- Winstanley HF, Abeln S, and Deane CM. How old is your fold?. Bioinformatics. 2005 Jun;21 Suppl 1:i449-58. DOI:10.1093/bioinformatics/bti1008 |
- Ortiz AR, Strauss CE, and Olmea O. MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison. Protein Sci. 2002 Nov;11(11):2606-21. DOI:10.1110/ps.0215902 |
