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A wonderful journey of superfamilies: Do you know how proteins in different species share mechanisms?
In the biological world, protein is a vital molecule that performs various functions of life. With the development of science and technology, researchers have gradually come to understand protein superfamilies, that is, a group of proteins with a common ancestor. It's a fascinating journey that reveals the mysteries of how protein machinery is shared and evolved between different species.
Definition of protein superfamily
Protein superfamilies are the largest groupings of proteins for which a common ancestry can be inferred. This is often based on structural alignment and mechanistic similarity and can be inferred even in the absence of sequence similarity. A superfamily usually contains several families of proteins, within which there is sequence similarity between them. This makes protein superfamilies an important tool for understanding the evolution of life.
"Members of the superfamily may be present in all kingdoms of life, suggesting that the common ancestor of the superfamily may have existed in the last common ancestor of all life (LUCA)."
Methods for identifying superfamilies
There are many ways to identify protein superfamilies, which can be divided into three categories: sequence similarity, structural similarity, and mechanistic similarity.
Sequence Similarity
Historically, the similarity of different amino acid sequences has been considered the most common method for inferring homology. Similar sequences are generally more likely to be the result of gene duplication and divergent evolution than of convergent evolution. However, using sequence similarity to infer homology has its limitations because during evolution, related proteins may show undetectable sequence similarities.
Structural similarity
Structure is often more evolutionarily conserved than sequence, so proteins with highly similar structures can still show homology even if their sequences are completely different. Some programs, such as DALI, use the three-dimensional structure of a protein to find proteins with similar folds.
Mechanical similarity
Enzymes within a superfamily often share similar catalytic mechanisms but may differ significantly in substrate specificity. Although some catalytic mechanisms may have evolved independently, thus forming different superfamilies, when different superfamilies display diverse catalytic mechanisms, this also demonstrates the complexity of biological systems.
"Members of the superfamily may have originated from duplication of the gene for a single protein."
Evolutionary significance and diversity
The identification of protein superfamilies represents the limit of our ability to identify common ancestors. These superfamilies are the largest evolutionary groupings based on evidence and therefore some of the oldest evolutionary events to study. Members of many superfamilies appear in different biological species, demonstrating evolutionary diversity.
Practical Examples
Different protein superfamilies each have their own specific structures and functions. For example, members of the α/β hydrolase superfamily have a typical α/β sheet covering a variety of catalytic activities, while the immunoglobulin superfamily structurally presents the characteristics of two layers of antiparallel β strands, which are involved in recognition and Adhesion process.
Protein superfamily resourcesThere are multiple biological databases that record information on protein superfamilies and protein folding, such as Pfam, PROSITE, and SUPERFAMILY. These resources facilitate researchers in exploring the evolutionary history of proteins and their similarities.
Advances in science and technology have enabled us to gain a deeper understanding of the structure and function of proteins, which has not only improved our understanding of how life works, but has also the potential to drive progress in areas such as medicine and drug development. But behind all this, there are still many unsolved mysteries. Can we gain insight into the mysteries of these superfamilies to understand the evolution of life?
