beta bulge loop
Beta bulge loops are commonly occurring motifs in proteins and polypeptides consisting of five to six amino acids.{{cite journal|last=Milner-White|first=EJ|title= Beta bulges within loops as recurring features of protein structure |journal=Biochim Biophys Acta|year=1987|volume=911|pages=261–265|doi= 10.1016/0167-4838(87)90017-3|pmid=3801498|issue=2}}{{cite journal|last=Chan|first=EAW|author2=Hutchinson EG|title= Identification, classification and analysis of β-bulges in proteins |journal=Protein Science|year=1993|volume=2|pages=1574–1590|doi= 10.1002/pro.5560021004|pmid=8251933|pmc=2142268|issue=10}}{{cite journal|last=Blandl|first=T|author2=Cochran AG|title= Turn Stability in β-hairpin peptides. Investigation of peptides containing 3:5 type 1 G1 Bulge turns |journal=Protein Science|year=2003|volume=12|pages=237–247|doi= 10.1110/ps.0228603|issue=2|pmc=2312432|pmid=12538887}} 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 (for a type 1 β bulge loop) or 4:6 (for type 2).{{cite journal|last=Sibanda|first=BL|author2=Blundell TL|author3=Thornton JM|title= Conformation of β-hairpins in protein structures. A systematic classification with applications to modeling |journal=Journal of Molecular Biology|year=1989|volume=206|pages=759–777|doi= 10.1016/0022-2836(89)90583-4|pmid=2500530|issue=4}} Two websites are available for finding and examining β bulge loops in proteins, Motivated Proteins: [http://motif.gla.ac.uk/motif/index.html] {{cite journal|last=Leader|first=DP|author2=Milner-White EJ|title=Motivated Proteins: A web application for studying small three-dimensional protein motifs.|journal=BMC Bioinformatics|year=2009|volume=10|pages=60|doi=10.1186/1471-2105-10-60|pmid=19210785|pmc=2651126|issue=1 |doi-access=free }} and PDBeMotif: [http://www.ebi.ac.uk/pdbe-site/pdbemotif/].{{cite journal|last=Golovin|first=A|author2=Henrick K|title=MSDmotif: exploring protein sites and motifs.|journal=BMC Bioinformatics|year=2008|volume=9|pages=312|doi=10.1186/1471-2105-9-312|pmid=18637174|pmc=2491636|issue=1|doi-access=free}}
File:Type_1_beta_bulge_loop.pdf
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, serine or threonine at residue i, together with a nest (protein structural motif) 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.{{cite journal|last=Afzal|first=AM|author2=Al-Shubailly F|title=Bridging of anions by hydrogen bonds in nest motifs and its significance for Schellman motifs and other larger motifs within proteins|journal=Proteins|year=2014|volume=82|pages=3023–3031|doi= 10.1002/prot.24663|issue=11|pmid=25132631|s2cid=12131403 }} 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.{{cite journal|last=Lee|first=J|author2=Dubey VK|author3=Longo LM|author4=Blaber M|title=A logical OR redundancy within the Asx-Pro-Asx-Gly β-turn motif|journal=Journal of Molecular Biology|year=2008|volume=377|pages=1251–1264|doi= 10.1016/j.jmb.2008.01.055|issue=4|pmid=18308335}}