What is b bulge?

What is b bulge?

A b-bulge is that region between two consecutive b-type hydrogen bonds that includes two residues (called positions 1 and 2) on one b-strand opposite a single residue (position X) on the other b-strand (2).

What is beta sheet protein structure?

The beta sheet, (β-sheet) (also β-pleated 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.

What is a beta strand in proteins?

A beta strand is an element of secondary structure in which the protein chain is nearly linear. Adjacent beta strands can hydrogen bond to form a beta sheet (also referred to as a beta pleated sheet).

Are beta sheets quaternary structure?

Intermolecular interactions between the hydrogen-bonding edges of β-sheets constitute a fundamental form of biomolecular recognition (like DNA base pairing) and are involved protein quaternary structure, protein-protein interactions, and peptide and protein aggregation.

What is alpha helix capping?

Abstract. Helix-capping motifs are specific patterns of hydrogen bonding and hydrophobic interactions found at or near the ends of helices in both proteins and peptides. In an alpha-helix, the first four >N-H groups and last four >C=O. groups necessarily lack intrahelical hydrogen bonds.

What is beta pleated structure?

The Beta-pleated sheet is a series of anti-parallel chains of covalently-linked amino acids, with adjacent chains linked by hydrogen bonds. The regular folding of each amino acid chain leads to a regular pleated pattern across chains. Note that the R-groups are directed perpendicularly to the plane of the sheet.

Is a beta turn a secondary structure?

β turns (also β-bends, tight turns, reverse turns, Venkatachalam 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.

Is beta pleated sheet tertiary structure?

The α-helix and β-pleated sheet structures are found in many globular and fibrous proteins. The unique three-dimensional structure of a polypeptide is known as its tertiary structure. This structure is caused by chemical interactions between various amino acids and regions of the polypeptide.

What is an n cap?

The term N cap (N-cap, Ncap) 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.

Where do beta turns occur in proteins?

The Beta Turn Turns generally occur when the protein chain needs to change direction in order to connect two other elements of secondary structure. The most common is the beta turn, in which the change of direction is executed in the space of four residues.

What is a beta bulge?

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.

What is the function of a bulge in a protein?

The most basic function of bulges is to accommodate an extra residue added due to mutation etc., while maintaining the bonding pattern and thus the overall protein architecture. Other bulges are involved with protein binding sites.

What are the two types of beta bulge loops?

Two types occur commonly. One, the classic beta bulge, occurs within, or at the edge of, antiparallel beta-sheet; the first residue at the outwards bulge typically has the α R, rather than the normal β, conformation. The other type is the beta bulge loop (also named type G1 β-bulge), often occurs in association with an antiparallel sheet,…

What are ββ-bulges and how are they classified?

β-bulges can be grouped according to their length of the disruption, the number of residues inserted into each strand, whether the disrupted β-strands are parallel or antiparallel and by their dihedral angles (which controls the placement of their side chains). Two types occur commonly.