Beta bulge loops are commonly occurring motifs in
proteins and
polypeptides consisting of five to six
amino acid
Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha a ...
s. There are two types: type 1, which is a pentapeptide; and type 2, with six
amino acid
Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha a ...
s. They are regarded as a type of
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.
Types
β-bulges can be grouped according to their length of the disruptio ...
, and have the alternative name of type G1 beta bulge. Compared to other
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.
Types
β-bulges can be grouped according to their length of the disruptio ...
s, beta bulge loops give rise to chain reversal such that they often occur at the loop ends of
beta hairpin
The beta hairpin (sometimes also called beta-ribbon or beta-beta unit) 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 ...
s; hairpins of this sort can be described as 3:5 (for a type 1 β bulge loop) or 4:6 (for type 2). Two websites are available for finding and examining β bulge loops in proteins, Motivated Proteins
and PDBeMotif
Type I beta bulge loops have two characteristic inter-main-chain
hydrogen bonds. One is between the CO of residue i and the NH of residue i+3 (a β-turn); the other is between the CO of residue i+4 and the NH of residue i.
Type 2 beta bulge loops have two characteristic inter-main-chain hydrogen bonds. One is between the CO of residue i and the NH of residue i+4 (an α-turn); the other is between the CO of residue i+5 and the NH of residue i.
Beta bulge loops often have an
aspartate,
asparagine
Asparagine (symbol Asn or N) is an α-amino acid that is used in the biosynthesis of proteins. It contains an α-amino group (which is in the protonated −NH form under biological conditions), an α-carboxylic acid group (which is in the depro ...
,
serine or
threonine at residue i, together with a
nest (protein structural motif) 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 w ...
at residues i+2 to i+4 (type 1) or residues i+3 to i+5 (type 2), with the side chain oxygen binding to the main chain NH groups of the nest. Site-directed mutagenesis of asx residues within a protein's β bulge loops has been described, showing that the side chain of an asx residue at various alternative positions within a β bulge loop binds to the nest and thereby helps stabilize the loop.
References
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Protein structural motifs