Principles of Protein Structure - H. Schulz 1982

Protein Evolution
Phylogeny Based on Protein Structures
Proteins Suitable for Phylogenetic Studies

Each residue position in a chain is an independent character with 20 distinct states. To determine phylogenetic relationships, it is necessary to identify independent characters and then perform a quantitative comparison of the corresponding features. Therefore, when analyzing Protein Specialization to establish phylogenetic links, one must first determine which Features of protein structures can be considered independent characters. The most suitable candidates for this purpose appear to be the sequentially arranged amino acid residues in the Primary Cell/13.html">Protein Structure. When comparing any Proteins, these very residues provide the largest number of characters, i.e., the number of residue positions. In principle, each position can be occupied by any of the 20 standard Amino Acids, meaning each character has 20 potential differentiating states. Although these characters are clearly interdependent with respect to individual Mutations (the conservative substitution rule, Table 9.2), the data presented in Fig. 9.1 and numerous Amino Acid Sequence analyses [145] indicate that, to a first approximation, such characters can be treated as independent when considering A large number of mutations.

Cytochrome c satisfies most of the requirements of phylogenetic research. In principle, many Proteins can be used for such studies; however, mitochondrial cytochrome c (Fig. 7.8) has proven to be the most convenient in this regard, as first demonstrated by the works of Smith, Margoliash, and Fitch [502–506]. The criteria for such studies and The properties of cytochrome c that determined the choice of this specific protein are listed below in points (a) through (e).

a) Unambiguity of the Gene Lineage during evolution. The Construction of a Phylogenetic Tree is based on the assumption that the character in question is transmitted from ancestor to descendant and that no alternative pathways exist. The transfer of structural genes from a given species to unrelated species—mediated, for example, by viral vectors—renders protein comparison useless as a means of establishing phylogenetic relationships. To date, phenomena of intergenic gene transfer for structural genes have not been observed in eukaryotes. However, it is common in Bacteria [507, 508], which implies the impossibility of establishing a phylogenetic tree for prokaryotes based on structural protein comparisons.

b) Singularity of the gene encoding the protein. In the haploid genome of each eukaryotic Organism, there is only a single cytochrome c gene (baker's Yeast being the only known exception to this rule) [509]. The presence of multiple isofunctional homologous proteins within an organism would complicate the elucidation of relationships between genetically distant organisms, since it would be unclear which proteins should be compared. Isofunctional proteins are frequently encountered at different ontogenetic stages of an organism—such as the γ-, ε-, and ξ-chains of primate Hemoglobin, which are normally not expressed during postnatal life. For populations or species that utilize these types of chains in adult life [510], it would be impossible to establish correct relationships using a phylogenetic tree constructed from the α- and β-chains of adult hemoglobin [145]. Account should also be taken of Garstang's principle [511], according to which evolution frequently involves larval rather than adult forms; the evolutionary pathway of guanidine Kinases can only be traced by adhering to this principle [512]. It should be noted that Haeckel's biogenetic law (ontogeny recapitulates phylogeny) has not yet been confirmed at the protein level.

c) Identical role of the protein in all organisms being compared. According to available data, all mitochondrial c-type Cytochromes discovered to date perform the exact same biological function.

d) Ubiquity of the protein. Cytochrome c is found in all taxa for which Branches of the phylogenetic tree are considered.

e) Simplicity of amino acid sequence analysis. The ease of Protein Isolation and a chain length of approximately 110 amino acid residues—providing a sufficient number of characters while remaining relatively amenable to amino acid sequencing—are the factors that largely determined the choice of cytochrome c.