Yilaine Hurtado

04/07/2022

Final Paper Draft

Evolution of molecular function: Proteins.

Abstract Section.

Proteins are the primary source of variation that makes organisms differ from each other. The structure of a protein defines its function, this means that the underlying genetic sequence of a protein controls what shape the protein will fold into, and that shape allows the protein to have a specific function. Organisms naturally create mutant proteins by slight changes to the genetic sequence proteins. There is a slight chance that these changes will cause mutant proteins to be more optimized or even to have new abilities. But most random mutations don’t enhance a protein; must changes break them. Minor changes to an underlying protein sequence can lead to significant and unpredictable protein structure and function changes. In this paper we are going to discuss how these minor changes in proteins sequence and structure, do to substitution mutations, are responsible for the evolution of species.

Introduction Section

Scientists have sequenced and compared the entire genome of both baker’s yeast and a worm. The gene used by the yeast, which is a very primitive organism, primarily does that deal with core biochemical functions that all organism most perform. Therefore, it was expected and proven true that the worm contains most of the same genes as the yeast. But the reverse is not true. Since the worn is a more modern creature than the yeast, the worn genes that deal with multicellularity are absent from the yeast. But more than that, these different genes are directly derived from the primitive genes that provide core cellular function. Newer genes are copiously created from more primitive forms to accommodate the requirements of more modern and more sophisticated organisms.

Some proteins are found in every living eukaryote on earth, and an example is the protein cytochrome C. This protein is in the mitochondria, the energy-generating machine of eukaryotes cells. But the gene that codes for these proteins has been buffered with sequence mutations over billions of years that it has existed.

Molecular evolution studies the mechanisms by which changes in gene sequence affect the function of a protein and, therefore, can change an organism's phenotype. Molecular evolution also examines the three-dimensional structures of proteins that form via molecular interactions. This is because protein structure also influences protein function, and changes in protein structure mediate the effects of mutations on function.

Body Section

Scientists compare protein structure through evolutionary time to discover how historical mutations generated new functions in proteins. However, protein structures are affected by conditions like temperature, salts, and pH effect. Therefore, stable protein crystals are prepared from pure and concentrated protein solutions and then studied by X-ray Crystallography.

In the article "Crystal Structure of an Ancient Protein: Evolution by Conformational Epistasis" by Eric A. Ortlund, scientists perform X-ray Crystallography on an ancestral protein from about 450 million years old. This protein is a precursor of vertebrate glucocorticoid receptors (GR) and mineralocorticoid receptors (MR). The glucocorticoid receptors (GR), to which cortisol binds, regulate genes that control metabolism and immune response in vertebrates, including humans. On the other hand, mineralocorticoid receptors (MR) regulate blood pressure in vertebrates. The study reveals historical substitution mutations, which exchange one base for another, repositioning crucial residues to create new receptor-ligand contact. These permissive substitution mutations have no immediate consequence, allowing the stabilization of the protein and allowing it to tolerate changes over time.

One important evolutionary topic that is well study is the question that why vertebrate ancestors appeared to live in shallow water environment, but modern species of vertebrates are abundant in variable niches. After numerous studies scientists assumed that the immense variety of phenotypes actual vertebrates have involved by the accumulation of advantageous mutations. Advantageous mutations are beneficial mutations that increases the fitness of an organism. However, proving this hypothesis by experimental test at molecular level is very difficult.

In the scientific paper called “Elucidation of phenotypic adaptations: Molecular analyses of dim-light vision proteins in vertebrates”, Yokoyama use the testable phenotype dim-light vision to explain this theory. In this study ancestral rhodopsin proteins were reconstructed to study specific amino acid changes and use this analysis to explain phenotypic differences in vertebrate dim-light vision. Rhodopsin is a G protein that allows the rods in vertebrates eyes to absorb photons and perceive light. Eleven ancestral rhodopsin’s proteins were reconstructed and show that those early ancestors observe light maximally at 501 nm. In the other hand rhodopsin’s proteins in actual vertebrates allow rods in the eyes to observe light at 480-525 nm. These highly environment-specific adaptations seem to have occurred largely by amino acid replacements at 12 sites, and most of those at the remaining 191 sites have undergone neutral evolution. (Page 3, Yokoyama).

Yokoyama and other scientist concluded that several significant amino acid changes occurred multiple times meaning that these sites are under positive selection, and that specific amino acid mutational trajectories lead to phenotypic rhodopsin diversity.

Crystal Structure of an Ancient Protein: Evolution by Conformational Epistasis. Eric A. Ortlund, et al. Science 317, 1544 (2007); DOI: 10.1126/science.1142819

Elucidation of phenotypic adaptations: Molecular analyses of dim-light vision proteins in vertebrates.

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