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Like real proteins, these vector proteins show more structural divergence in regions of irregular structure (moves corresponding to loops) than in regions of regular structure (strokes corresponding to secondary structure).
Functional conservation acts as a strong restraint limiting sequence and, even more, structural divergence [57].
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Certainly there can be more measures to describe structural divergence between duplicated genes, and new biological insights can be generated based on novel measures for structural divergence.
For duplicated genes, structural divergence seems more complicated than nucleotide substitutions.
Structural divergence is much more prevalent in duplicated genes, leading to the generation of functionally distinct paralogs [ 56].
Although sequence divergence leads to structural divergence [21], protein structures retain clear similarity even past the point where sequence similarity becomes hard to detect [22], [23].
Thus, to ensure more accurate analyses, we did not use the correlation between structural divergence and Ks to investigate how structural divergence changes over time.
Structural divergence between duplicated genes were previously suggested to occur more or less randomly, i.e. correlated with evolutionary time [ 36].
Therefore, protein 3D structure comparison becomes an important tool to analyze structural divergence and in turn functional divergence.
Whenever indel substitutions do not imply drastic changes affecting protein function, structural divergence may be a source of variation able to promote advantageous changes more efficiently than nucleotide replacements.
The 3-D superimposition of protein structures obtained by using structure comparison tools is very useful in quantifying structural dissimilarity and in analyzing structural divergence.
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