Evolution ancestral proteins

Several structurally different types of HNLs occur in nature, which likely originated hy convergent evolution from different ancestral proteins. The enzyme from almond (PaHNL) was first crystallized in 1994 and the structure was solved by multiple wavelength anomalous dispersion of a mercury derivative. The first 3D structure analysis of PaHNL was performed in 2001. ° (7 )-PaHNL from almond uses FAD as cofactor and is related to oxidoreductases it exhibits HNL activity only in the oxidized form of FAD." ... 

With tree analysis it is possible to infer sequences of ancestral proteins and probable evolutionary pathways to their modern descendants.1 The advent of site-directed mutagenesis makes possible the recreation of evolutionary intermediates based on these predictions. One may then compare the properties of reconstructed intermediates with one another and with proteins from contemporary creatures. These comparisons provide a way of testing theories about the mechanism of molecular evolution. For example, this approach has provided a new criterion for distinguishing between neutral and nonneutral events.2 This chapter describes the use of site-directed mutagenesis to recreate ancestral lysozymes and presents methods of evaluating their properties. 

Undoubtedly there are often questions about the mechanism of protein evolution that can be addressed by making ancestral proteins and testing their properties, especially the origin of new functions. Lysozyme provides an example for that type of investigation because on two occasions in mammalian evolution it has been recruited for functioning in the harsh conditions of the stomach fluid.41-42 The sequences of the common ancestor have been inferred by tree analysis, and at least four of the new selection pressures faced by this enzyme are known. Irwin et a/.43 have reviewed this subject and the speculations regarding the possibility that double or triple mutations were required to achieve new functions. 

Restriction enzymes constitute one of the largest families of related enzymes known so far and therefore exemplify how natural evolution has generated many different specificities from one (or a few) ancestral protein(s). A detailed comparison of the... 

A small number of ancestral proteins encoded by ancestral genes may have given rise to a multiplicity of active peptides in concert with the evolution of complementary receptor molecules. Our current knowledge of insect neuropeptides is consistent with and actually supports these views. 

Finally, the stereochemical divergence between the 3-carboxymuconate cyclo-isomerase (the last entry in Table XI) and the two corresponding muconate cycloisomerases catalyzing syn-eliminations (the last two entries in Table X) is intriguing. Whether this difference has a basis in mechanism or in convergent evolution from different ancestral proteins (or both) is unclear (310, 334). Additional mechanism studies on these enzymes would be most welcome. 

Many clues as to how to engineer better enzymes came from drawing parallel comparisons with nature and studying how nature has created authentic enzymes. By studying the evolution of bona fide proteins, it has been learned that they are hi ly adaptable, incessantly changing molecules. They can sometimes acclimatize to different environments and can even adopt unique functions, at least over evolutionary time scales. It is now known that the natural processes of mutation, recombination and se lection resulted in the creation of enzymes with varied functions through the evolution of a common ancestral protein of the same general structure (16),... 

Why did nature use an Fe-S cluster to catalyze this reaction, when an enzyme such as fumarase can catalyze the same type of chemistry in the absence of any metals or other cofactors One speculation would be that since aconitase must catalyze both hydrations and dehydrations, and bind substrate in two orientations, Fe in the comer of a cubane cluster may provide the proper coordination geometry and electronics to do all of these reactions. Another possibility is that the cluster interconversion is utilized in vivo to regulate enzyme activity, and thus, help control cellular levels of citrate. A third, but less likely, explanation is that during evolution an ancestral Fe-S protein, whose primary function was electron transfer, gained the ability to catalyze the aconitase reaction through random mutation. 

The mammalian serine proteases appear to represent a classic case of divergent evolution. All were presumably derived from a common ancestral serine protease.23 Proteins derived from a common ancestor are said to be homologous. Some nonmammalian serine proteases are 20 to 50% identical in sequence with their mammalian counterparts. The crystal structure of the elastase-like protease from Streptomyces griseus has two-thirds of the residues in a conformation similar to those in the mammalian enzymes, despite having only 186 amino acids in its sequence, compared with 245 in a-chymotrypsin. The bacterial enzymes and the pancreatic ones have probably evolved from a common precursor. 

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