Evolution from a Molecular Perspective: What Proteins Tell
Evolution from a Molecular Perspective: What Proteins Tell
All living organisms, from single-celled to multicellular, are highly complex entities. Questions about the origin of the first living organism, how the current and past species evolved from it, and the foundations upon which the differences between living beings are built have been important subjects of debate for many years. As the scientific community, we can provide satisfactory answers to many questions where our knowledge and understanding are extensive, as evidenced by the continuous work of thousands of scientists who contribute through their studies, patents, and published articles each year. On the other hand, there are situations where our knowledge is limited; one such case is the question of how the first living organism emerged and the physical principles underlying this formation, which remains a question awaiting illumination.
After the first living organism "somehow" emerged, the theory of evolution addresses the changes in this organism over time. While this topic is a constant subject of debate in everyday life, the existence of evolution is well beyond a point of discussion in the scientific community. Certainly, questions such as how this evolutionary process works, the adequacy of Darwin's view, and the principles underlying these changes are discussed; however, it is an undeniable fact that living beings originated and evolved from more primitive forms over time. Many examples can illustrate this change: variations in the color and mass of sparrows in North America according to regions, finches with different beak structures observed by Darwin in the Galapagos Islands, and differently colored snake species in the Americas are all examples of "macroevolution" [1-4]. On the other hand, the genetic changes underlying all these transformations and the consequences of these changes, first observed in proteins, also help us approach evolution from a "molecular" perspective.
The three-dimensional structure of the insulin receptor protein is a good example of how complex yet ordered structures proteins can have. Source: http://www.rcsb.org
The three-dimensional structure of the insulin receptor protein is a good example of how complex yet ordered structures proteins can have. Source: http://www.rcsb.org
Proteins are large molecules present in all living organisms (and, if viruses are considered, in them as well). They are formed by the addition of twenty different amino acids according to the genetic information in an organism and then folding into a specific three-dimensional structure in the living environment. In principle, proteins can be produced in infinite diversity, and this feature can easily be used to explain the thousands of different functions and structures observed in living organisms. Furthermore, since the amino acid sequence of proteins is directly controlled by genes, changes in a working gene manifest themselves in both the sequences and three-dimensional structures of the proteins it produces. Thanks to these features, proteins play a crucial role in measuring and examining genetic changes for us.
Let's briefly summarize the production of proteins inside living organisms. The genetic information contained in DNA (deoxyribonucleic acid) in every organism is transported to structures responsible for protein production via messenger RNA (mRNA). Here, with the help of transfer RNA (tRNA), the information on mRNA is read, and protein synthesis takes place. Both during the addition of amino acids and later, proteins fold from chain structures into their three-dimensional specialized structures; this folding is affected by both the amino acid sequence and the physical and chemical conditions within the cell. The proteins produced and correctly folded are ready to perform their functions within the organism. Proteins, found in various tasks in living organisms, include actin and myosin, which enable the movement of muscles, facilitating the displacement of multicellular organisms like us. Proteins like rhodopsin and photopsin found in the eye induce light perception, constituting the first step of our visual ability. Enzymes such as trypsin and pepsin speed up many chemical reactions in the organism.
As both an expression of genetic information and precursors of functionality within living organisms, proteins hold a fundamental and specific place. A protein without the correct amino acid sequence cannot fold into its three-dimensional structure and, even if it does, cannot perform any function. Small changes in body temperature can affect these fragile three-dimensional structures, and even if the protein has the correct sequence, it may fold into a different structure or completely melt. In either case, unexpected reactions will occur in the body. We can examine and classify the amino acid sequences of proteins, allowing us to make inferences about the genetic information of living beings and understand the changes that have led to differences between similar but different species by comparing the proteins of different species. Moreover, recent studies on glucocorticoid receptor proteins and their evolution serve as a suitable example of what proteins can tell us about evolution.
Glucocorticoid receptor proteins (GR) are receptors found in living organisms that bind to steroid hormones such as cortisol and aldosterone. After binding to these hormones, they regulate the development, metabolism, and immune response of the organism by allowing the functioning of specific genes. Similarly, mineralocorticoid receptors (MR) regulate ion balance in the body and the movements of the intestines and kidneys after aldosterone binding. The evolutionary history of both receptor protein groups can be traced back to approximately 450 million years ago, when corticoid receptors (CR) existed. In organisms with CR, gene duplication initially resulted in two CR genes, which later differentiated into GR and MR receptors through further modification of each copy. While MR proteins show significant functional similarity to CR proteins, GR proteins have evolved to respond exclusively to cortisol. Although questions such as how the evolutionary process worked and whether Darwin's view is sufficient are debated in the scientific world, it is now well-established that organisms have evolved from more primitive forms over time. The examples of change, such as variations in the color and mass of sparrows in North America according to regions, finches with different beak structures observed by Darwin in the Galapagos Islands, and differently colored snake species in the Americas, serve as examples of "macroevolution". However, these adaptations are just a few instances of the countless changes that have occurred throughout evolutionary history.
Among the hundreds of organisms containing MR and GR proteins, finding our way is very challenging. Therefore, let's focus on the ancestral CR and the first GR proteins that followed immediately after. The ancestral CR protein is the first receptor protein to emerge. With approximately 30 million years of evolution, the protein that served as an ancestor to shark GR proteins changes 25 amino acids to become GR1. GR1 in sharks binds to aldosterone, cortisol, and other hormones, but its binding affinity is weaker than that of the ancestral CR. Approximately 20 million years later, the GR protein in humans and fish evolves from the ancestral protein in sharks through a 36-amino acid change, becoming GR2, which now binds exclusively to cortisol. The commonality among these three proteins is that they
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