“Beta bulge loop”的意思、由来-开放百科全书

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.^[7] 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.^[8]

References

1. ^{{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}}
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}}
3. ^{{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}}
4. ^{{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}}
5. ^{{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}}
6. ^{{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}}
7. ^{{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}}
8. ^{{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}}