When comparing two proteins within a family, such as the yeast alpha2 protein and the Drosophila engrailed protein, what level of identity in their amino acid sequences is generally considered sufficient to indicate they share the same overall structure?
Explanation
This quantitative question addresses a key concept in bioinformatics and structural biology. Due to the degeneracy of the sequence-to-structure relationship, a sequence identity of over 25 percent is a widely used rule of thumb to infer that two proteins share the same three-dimensional fold and likely have a related function.
Other questions
What is the name for the covalent bond that links amino acids together in a protein chain, formed by a condensation reaction that eliminates a water molecule?
Which factor is considered the most important in governing the folding of a protein into its final conformation in an aqueous environment?
In a folded protein, where are the nonpolar (hydrophobic) side chains, such as those of phenylalanine and leucine, most likely to be found?
What does the process of denaturing a protein, for example by using certain solvents, typically involve?
What is the term for the specialized proteins that assist in the folding of other proteins by binding to partly folded chains and helping them progress along the most energetically favorable pathway?
An alpha helix is a common protein folding pattern. How many amino acids does it take for this helix to make one complete turn?
What type of bond is primarily responsible for stabilizing the alpha helix and beta sheet structures in proteins?
What is the term for the full, three-dimensional organization of a single polypeptide chain, including its alpha helices, beta sheets, and all other loops and folds?
A protein domain is defined as a structural unit that folds more or less independently. What is the typical size range for a single protein domain in terms of amino acids?
What is the term for a protein, such as hemoglobin, that is formed as a complex of more than one polypeptide chain?
According to sequence comparisons of protein families like serine proteases, which aspect of the protein is generally more highly conserved during evolution?
What type of covalent bond acts as an 'atomic staple' to reinforce the conformation of proteins that are destined for the extracellular environment, such as lysozyme?
Amyloid fibrils, associated with diseases like Parkinson's and Alzheimer's, are very stable aggregates built from a continuous stack of what type of secondary structure?
What is the defining characteristic of a prion disease that makes it 'infectious'?
What is the general term for a substance—whether an ion, small molecule, or macromolecule—that is bound by a protein?
The ability of a protein to bind selectively and with high affinity to a ligand depends on the formation of what?
What is the term for the region of an enzyme that binds to the substrate and contains the catalytic site?
For an enzyme-catalyzed reaction, what does the turnover number represent?
In enzyme kinetics, what does a low value of the Michaelis constant (Km) generally indicate?
What is the primary way that enzymes accelerate chemical reactions?
In the mechanism of the enzyme lysozyme, how does it catalyze the hydrolysis of a polysaccharide chain?
What type of regulation occurs when a product produced late in a reaction pathway inhibits an enzyme that acts earlier in the same pathway?
Allosteric enzymes are regulated by molecules that bind to a site distinct from the active site. What is this other site called?
What is a key feature of enzymes that undergo cooperative allosteric transitions, allowing them to have a steep, switchlike response to ligand concentration?
What general term describes the enzyme-catalyzed addition of a phosphate group from ATP to a protein?
What is the name of the enzyme class that catalyzes the addition of a phosphate group to a protein?
What family of proteins functions as molecular switches, being in an 'on' state when GTP is bound and an 'off' state after hydrolyzing GTP to GDP?
How do motor proteins, such as myosin and kinesin, achieve unidirectional movement along a cytoskeletal filament?
What is the primary function of large scaffold proteins, such as Dlg, in the cell?
What is the term for the dynamic, liquid-like cellular structures formed from multivalent proteins and RNAs held together by a network of weak, fluctuating interactions?
For a typical protein with a length of 300 amino acids, what is the estimated number of different possible polypeptide chains that a cell could theoretically make?
A coiled-coil structure, which provides a framework for many elongated proteins like alpha-keratin, is formed when two or more of which type of secondary structure wrap around each other?
The small protein ubiquitin can be covalently attached to a lysine side chain of a target protein. What is the major signal conveyed when a polyubiquitin chain linked through Lys48 is attached?
In the activation of the Src protein kinase, turning the kinase on requires at least two specific inputs. What are they?
What type of macromolecule is collagen, the most abundant fibrous protein in animal tissues?
What is the key principle behind using the 'evolutionary trace' method to identify a protein's ligand-binding sites?
Antibodies are Y-shaped molecules that recognize antigens with high specificity. Their antigen-binding sites are formed from what structural feature?
What is the general name for a large protein complex, composed of many individual protein subunits, that is highly coordinated to carry out a central process like DNA replication or protein synthesis?
Which property of intrinsically disordered protein regions allows them to be central to many regulatory mechanisms?
What structural protein, found in the extracellular matrix, is formed from a highly disordered polypeptide that is covalently cross-linked to produce a rubber-like elastic meshwork?
What is the name for the level of protein structure defined by the amino acid sequence?
An antibody binds to its primary antigen with an equilibrium constant, K, of 5 x 10 to the power of 9 M-1. When it binds to a related antigen, the interaction is weaker by 11.9 kJ/mole. What is the approximate equilibrium constant for its binding to the second, related antigen?
An actin filament is a long helical structure built from many molecules of the globular protein actin. This is an example of what type of protein assembly?
What is the reason that many protein molecules can self-assemble into complex structures like viral capsids in a test tube?
Retinal, the small molecule embedded in the protein rhodopsin that allows it to detect light, is derived from which vitamin?
What is the name for the small, non-protein, ring-shaped molecules containing an iron atom that bind to hemoglobin and enable it to carry oxygen?
What does a protein's quaternary structure refer to?
What is the term for a cellular structure that forms via liquid-liquid phase separation and serves to segregate and concentrate a subset of macromolecules?
What happens to the rate of an enzyme-catalyzed reaction as the substrate concentration increases, according to Michaelis-Menten kinetics?