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Among the globular domains involved in peptide-mediated interactions, we found no correlation between sequence variability and energy contribution.
Finally, when mutational stress is controlled for, there is very little remaining correlation between sequence variability and dynamical flexibility.
We also used the more robust and conservative Spearman's non-parametric rank correlation test, in addition to the parametric test, to estimate correlations between sequence variability and folding stability.
Two trends for the mode of evolution of the three satDNA families were detected: 1) a positive correlation of sequence variability and copy number, and 2) a negative correlation between sequence variability and length of repeat.
Although our analyses yield similar negative correlations between sequence variability and folding stabilities for both RNA as well as DNA, we will be primarily discussing our results in the context of RNA.
The results presented here add a further aspect to the mode of evolution of the pDo500 satDNA in Dolichopoda - the evolutionary constraint brought upon the pDo500 repeats by the conserved HH ribozyme may explain the unexpected negative correlation between sequence variability and repeat length described by Bachmann et al. [ 34].
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The authors study possible correlations between protein sequence variability and a series of associated properties (polarity, electrostatic charge, secondary structure, molecular volume and amino acid composition) and find particular trends, which suggest that particular physico-chemical properties are associated with particular functional roles.
The existence of a continuous lineage from the Asian cluster, through the Indian Ocean cluster, and to the African cluster, reveal a remarkable correspondence between amino acid sequence variability and putative HLA class I-restricted recognition patterns.
Finally, we found no significant correlation between the levels of sequences variability and the levels of conservation of MFE signals, supporting the conjecture that positions with a conserved selection for strong/weak folding may be related directly to biophysical attributes of gene expression regulation and/or viral replication via folding.
In considering this idea, it is important to keep in mind that classification accuracy is determined both by within-sequence variability and by between-sequences differences.
To investigate the association between the sequence variability of our phages and the structure of the EAD and the CBD of the amidase, we constructed a structural model using as a template a related structure from a Listeria phage (PDB; 1XOV) previously solved with crystallography [ 22].
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