Proteins evolutionary rates

Mclnerney, J.O. The causes of protein evolutionary rate variation. Trends Ecol. Evol. 2006, 21(5), 230-2. 

Yet despite these multifaceted functions of signal sequences, they are highly variable—between species, between related proteins, etc. Their sequence variability suggests remarkably few constraints on their evolutionary rate of change, whereas the apparent plethora of their functions... 

Features that are directly connected to protein structure have been shown to explain roughly 10% of the variation in evolutionary rate [7]. This result seems initially surprising, given that structure mediates all aspects of a protein s existence. In contrast, expression—the frequency and scale at which a protein is manufactured— may explain up to 40% of evolutionary rate variation [6]. Expression and evolutionary rate vary inversely, with highly expressed proteins tending to evolve at very slow rates. A protein s dispensability (effect on cell growth when absent) and the number of interactions in which it participates explain additional... 

Errors made during protein translation can result in misfolded proteins, which represent a burden to the cell. Mutations that make a protein more susceptible to error-induced misfolding will result in a loss of fitness. If the mutation occurs in a highly expressed protein, then translational errors (and misfolding events) will be more common, resulting in a larger fitness loss. Hence, protein expression will scale directly with selective constraint, and inversely with evolutionary rate [11]. 

An early study of the cytochrome c protein structure revealed that some portions of the surface seemed to be experiencing unusually high functional constraint [72]. These surface residues were determined to be sites of interaction with other proteins (interfaces). Subsequent studies have generally supported the notion that interfacial surfaces are more conserved than the remainder of the protein s solvent-exposed surface, and slightly less conserved than the protein s core [73]. Substitutions that do occur in the interface are heavily skewed toward more conservative changes [53], as defined by the Grantham classification scheme [74]. Exploiting the difference in evolutionary rate between interfacial and non-interfacial sections of a protein s surface has been proposed as a means by which to identify interfaces in newly characterized proteins this has proven to be difficult in practice [75]. 

The notion that evolutionary rate of an "average interface" is intermediate to those of buried and solvent-exposed portions of a protein seems very intuitive. Interfaces will likely spend at part of their lives in a buried state (when interacting) and another part in a solvent-exposed state (when not interacting). One might therefore expect the rate of evolution at an interface to scale inversely with the proportion of time that it is active indeed, this is precisely what has been found [76]. 

Evolutionary rate among residues belonging to transient interfaces is significantly higher than for those found in consfifufive (permanent) interfaces rafes for both are intermediate to those of buried and solvenf-exposed residues. Decreased evo-lufionary rate at constitutive interaction sites may also reflect specific structural constraints imposed by the protein s interaction partner [76]. This represents a case of coevolution between protein structures, an instance of a higher order sfructure-evolufion relationship. 

Graur, D. Amino acid composition and the evolutionary rates of protein-coding genes. J. Mol. Evol. 1985, 22(1), 53-62. 

Brown, C.J., et al. Evolutionary rate heterogeneity in proteins with long disordered regions. J. Mol. 

If prebiotic peptides and/or proteins were in fact initially formed in aqueous solution (the hypothesis of biogenesis in the primeval ocean ), the energy problems referred to above would have needed to be solved in order for peptide synthesis to occur. As discussed in Sect. 5.3, there is some initial experimental evidence indicating that the formation of peptide bonds in aqueous media is possible. An important criterion for the evolutionary development of biomolecules is their stability in the aqueous phase. The half-life of a peptide bond in pure water at room temperature is about seven years. The stability of the peptide bond towards cleavage by aggressive compounds was studied by Synge (1945). The following relative hydrolysis rates were determined experimentally, with the relative rate of hydrolysis for the dipeptide Gly-Gly set equal to unity ... 

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