Regularities in Mutational Variability in Selected Protein Families and the Markovian Model of Amino Acid Replacement

Three families of proteinase inhibitors and the trypsin family were the subjects of the analysis of amino acid replacements at aligned positions. This approach concerned some specific types of replacement and the mechanisms that can be involved in their control. The usefulness of the Markovian model for interpretation of mutational replacement within homologous proteins was examined. The same sequences were also analyzed with the use of the non-Markovian algorithm of genetic semihomology. This study leads to the conclusion that the Markovian model is not suitable for the interpretation of protein mutational variability since: (1) The information about the history of a variable unit is included in its genetic code. (2) This information plays an important role in the probability of further possible changes of the unit.