An alpha helix is a sequence of amino acids in a protein that are twisted into a coil.
The beta sheet, (β-sheet) is a common motif of the regular protein secondary structure. Beta sheets consist of beta strands (β-strands) connected laterally by at least two or three backbone hydrogen bonds, forming a generally twisted, pleated sheet. A β-strand is a stretch of polypeptide chain typically 3 to 10 amino acids long with backbone in an extended conformation. The supramolecular association of β-sheets has been implicated in the formation of the fibrils and protein aggregates observed in amyloidosis, Alzheimer's disease and other proteinopathies.
Threonine is an amino acid that is used in the biosynthesis of proteins. It contains an α-amino group, a carboxyl group, and a side chain containing a hydroxyl group, making it a polar, uncharged amino acid. It is essential in humans, meaning the body cannot synthesize it: it must be obtained from the diet. Threonine is synthesized from aspartate in bacteria such as E. coli. It is encoded by all the codons starting AC.
In cell biology, protein kinase A (PKA) is a family of serine-threonine kinase whose activity is dependent on cellular levels of cyclic AMP (cAMP). PKA is also known as cAMP-dependent protein kinase. PKA has several functions in the cell, including regulation of glycogen, sugar, and lipid metabolism. It should not be confused with 5'-AMP-activated protein kinase.
A catalytic triad is a set of three coordinated amino acids that can be found in the active site of some enzymes. Catalytic triads are most commonly found in hydrolase and transferase enzymes. An acid-base-nucleophile triad is a common motif for generating a nucleophilic residue for covalent catalysis. The residues form a charge-relay network to polarise and activate the nucleophile, which attacks the substrate, forming a covalent intermediate which is then hydrolysed to release the product and regenerate free enzyme. The nucleophile is most commonly a serine or cysteine amino acid, but occasionally threonine or even selenocysteine. The 3D structure of the enzyme brings together the triad residues in a precise orientation, even though they may be far apart in the sequence.
A turn is an element of secondary structure in proteins where the polypeptide chain reverses its overall direction.
A beta bulge can be described as a localized disruption of the regular hydrogen bonding of beta sheet by inserting extra residues into one or both hydrogen bonded β-strands.
A beta helix is a tandem protein repeat structure formed by the association of parallel beta sheet in a helical pattern with either two or three faces. The beta helix is a type of solenoid protein domain. The structure is stabilized by inter-strand hydrogen bonds, protein-protein interactions, and sometimes bound metal ions. Both left- and right-handed beta helices have been identified. These structures are distinct from jelly-roll folds, a different protein structure sometimes known as a "double-stranded beta helix".
The beta hairpin is a simple protein structural motif involving two beta strands that look like a hairpin. The motif consists of two strands that are adjacent in primary structure, oriented in an antiparallel direction, and linked by a short loop of two to five amino acids. Beta hairpins can occur in isolation or as part of a series of hydrogen bonded strands that collectively comprise a beta sheet.
BRAF is a human gene that encodes a protein called B-Raf. The gene is also referred to as proto-oncogene B-Raf and v-Raf murine sarcoma viral oncogene homolog B, while the protein is more formally known as serine/threonine-protein kinase B-Raf.
β turns are the most common form of turns—a type of non-regular secondary structure in proteins that cause a change in direction of the polypeptide chain. They are very common motifs in proteins and polypeptides. Each consists of four amino acid residues. They can be defined in two ways:
- By the possession of an intra-main-chain hydrogen bond between the CO of residue i and the NH of residue i+3;
- By having a distance of less than 7Å between the Cα atoms of residues i and i+3.
The Walker A and Walker B motifs are protein sequence motifs, known to have highly conserved three-dimensional structures. These were first reported in ATP-binding proteins by Walker and co-workers in 1982.
The Nest is a type of protein structural motif. It is a small recurring anion-binding feature of both proteins and peptides. Each consists of the main chain atoms of three consecutive amino acid residues. The main chain NH groups bind the anions while the side chain atoms are often not involved. Proline residues lack NH groups so are rare in nests. About one in 12 of amino acid residues in proteins, on average, belongs to a nest.
Schellman loops are commonly occurring structural features of proteins and polypeptides. Each has six amino acid residues with two specific inter-mainchain hydrogen bonds and a characteristic main chain dihedral angle conformation. The CO group of residue i is hydrogen-bonded to the NH of residue i+5, and the CO group of residue i+1 is hydrogen-bonded to the NH of residue i+4. Residues i+1, i+2, and i+3 have negative φ (phi) angle values and the phi value of residue i+4 is positive. Schellman loops incorporate a three amino acid residue RL nest, in which three mainchain NH groups form a concavity for hydrogen bonding to carbonyl oxygens. About 2.5% of amino acids in proteins belong to Schellman loops. Two websites are available for examining small motifs in proteins, Motivated Proteins: ; or PDBeMotif:.
The ST turn is a structural feature in proteins and polypeptides. Each consists of three amino acid residues in which residue i is a serine (S) or threonine (T) that forms a hydrogen bond from its sidechain oxygen group to the mainchain NH group of residue i + 2.
The Asx motif is a commonly occurring feature in proteins and polypeptides. It consists of four or five amino acid residues with either aspartate or asparagine as the first residue. It is defined by two internal hydrogen bonds. One is between the side chain oxygen of residue i and the main chain NH of residue i+2 or i+3; the other is between the main chain oxygen of residue i and the main chain NH of residue i+3 or i+4. Asx motifs occur commonly in proteins and polypeptides.
The ST motif is a commonly occurring feature in proteins and polypeptides. It consists of four or five amino acid residues with either serine or threonine as the first residue. It is defined by two internal hydrogen bonds. One is between the side chain oxygen of residue i and the main chain NH of residue i + 2 or i + 3; the other is between the main chain oxygen of residue i and the main chain NH of residue i + 3 or i + 4. Two websites are available for finding and examining ST motifs in proteins, Motivated Proteins: and PDBeMotif.
The term N cap describes an amino acid in a particular position within a protein or polypeptide. The N cap residue of an alpha helix is the first amino acid residue at the N terminus of the helix. More precisely, it is defined as the first residue (i) whose CO group is hydrogen-bonded to the NH group of residue i+4. Because of this it is sometimes also described as the residue prior to the helix.
Beta bulge loops are commonly occurring motifs in proteins and polypeptides consisting of five to six amino acids. There are two types: type 1, which is a pentapeptide; and type 2, with six amino acids. They are regarded as a type of beta bulge, and have the alternative name of type G1 beta bulge. Compared to other beta bulges, beta bulge loops give rise to chain reversal such that they often occur at the loop ends of beta hairpins; hairpins of this sort can be described as 3:5 or 4:6. Two websites are available for finding and examining β bulge loops in proteins, Motivated Proteins: and PDBeMotif:.
The ST staple is a common four- or five-amino acid residue motif in proteins and polypeptides with serine or threonine as the C-terminal residue. It is characterized by a single hydrogen bond between the hydroxyl group of the serine or threonine and the main chain carbonyl group of residue i. Motifs are of two types, depending whether the motif has 4 or 5 residues. Most ST staples occur in conjunction with an alpha helix, and are usually associated with a slight bend in the helix. Two websites are available for finding and examining ST staples in proteins: Motivated Proteins and PDBeMotif.
