How do proteins act as molecular clocks?
A molecular clock hypothesis was proposed by Zuckerkandl and Pauling in 1965.
It states that changes in proteins and DNA accumulate at approximately constant rates over geological time. So the number of mutations in DNA and therefore the number of substitutions in proteins , is approximately the same per generation.
This molecular data can be used for the prediction of time.
The longer two species have been evolving separately, the more amino acid differences accumulated in their proteins. Amino acid changes reflect in the genes.
The basic mutation rate is probably similar for all genes, but natural filters filter out those mutations that impair a protein function. These functional constraints affect the rate at which amino acids are substituted in a given protein.