Protein Evolution Flashcards
What are the three main mechanisms that drive the creation of evolutionary diverse protein families?
- Gene duplication
- Divergence
- Gene combination
How does gene duplication contribute to protein evolution?
Between 93% and 97% of animal genomes sequenced to date are the result of duplications.
In addition to the generation of whole protein homologs, partial gene duplications resulting in domain duplication and elongation are also common features of protein evolution.
What are some common features of protein evolution resulting from partial gene duplications?
What are examples of domain duplication in protein evolution?
Examples of domain duplication include cutinase and bovine bile-salt activated cholesterol esterase. While cutinase is the smallest enzyme of the α/β hydrolases, with five strands in the main β-sheet, bovine bile-salt activated cholesterol esterase has 11 strands and loop structures up to 79 residues in length.
How does divergence contribute to protein evolution?
Divergence further modifies existing paralogs, which are genes related by duplication within a genome, leading to even more diverse protein families.
What are the two types of protein structural divergence?
- Changes to the protein’s surface or peripheral regions
- Modifications to the protein’s interior or core.
Which type of protein structural divergence is more biologically acceptable?
- Mutations in the protein surface
- Four times more biologically acceptable
What is domain shuffling, and how does it contribute to protein divergence?
A process of recombination or permutation that can cause radical divergence.
What is circular permutation in protein evolution?
Circular permutations (CPs) represent a specific form of recombination event characterized by the presence of the same protein sub-sequences in the same linear order but different positions of the N and C termini. CPs of a protein can be visualized as if its original termini were linked and new ones created elsewhere.
What are functional analogs in protein evolution?
Functional analogs are proteins that may have quite divergent structures and/or sequences while retaining similar function. Such analogs may arise as a result of convergent evolution or by means of divergent evolution from a single ancestor.
What is an example of convergently functional analogs?
L-aspartate aminotransferase and D-amino acid aminotransferase are examples of convergently evolved functional analogs. Despite having a strikingly similar function, the two proteins have completely different architectures; differing in size, amino acid sequence, and in the fold of the protein domains.
What is an example of structural analogs that arise by means of divergent evolution from a single ancestor?
Human IL-10 (hIL-10) and the Epstein-Barr virus (EBV) IL-10 homolog (vIL-10) are examples of structural analogs that arise by means of divergent evolution from a single ancestor. Although vIL-10 suppresses inflammatory responses like hIL-10, it cannot activate many other immunostimulatory functions performed by the cellular cytokine.
What are structural analogs in protein evolution?
What is gene combination, and how does it result in changes to proteins?
Gene combination results in even more dramatic changes to the resulting proteins, as dictated by evolutionary pressure and the physiological fitness requirements of the organism.
What is an example of structural analogs in protein evolution?
How can combinations affect protein structure and function?
What is phylogenetics?
Phylogenetics is the study of the evolutionary history of species, organisms, genes, or protein sequences through the construction and analysis of mathematical entities known as trees or phylogenies.
What is the process behind the construction of a tree in phylogenetics?
Why do we have to infer the evolutionary history that has led to present-day proteins?
What is the best estimate of the evolutionary history of a family of sequences made on?
What is modern phylogenetic analysis?
What is a phylogenetic tree?
What is Newick format?
What are the two methods for inferring evolutionary relatedness?
What is the difference between distance-based methods and character-based methods?
What are the most common character-based approaches for tree building?
What is bootstrapping in phylogenetics?
What are bootstrap values in phylogenetics?
