Biochemistry and Biotechnology
Wiley InterScience Backfile Collection 1832-2000
A systematic survey of seven parallel α/β barrel protein domains, based on exhaustive structural comparisons, reveals that a sizable proportion of the αβ loops in these proteins - 20 out of a total of 49 - belong to either one of two loop types previously described by Thornton and co-workers. Six loops are of the αβ1 type, with one residue between the α-helix and β-strand, and 13 are of the αβ3 type, with three residues between the helix and the strand. Protein fragments embedding the identified loops, and termed αβ connections since they contain parts of the flanking helix and strand, have been analyzed in detail revealing that each type of connection has a distinct set of conserved structural features. The orientation of the β-strand relative to the helix and loop portions is different owing to a very localized difference in backbone conformation. In αβ1 connections, the chain enters the β-strand via a residue adopting an extended conformation, while in αβ3 it does so via a residue in a near α-helical conformation. Other conserved structural features include distinct patterns of side chain orientation relative to the β-sheet surface and of main chain H-bonds in the loop and the β-strand moieties. Significant differences also occur in packing interactions of conserved hydrophobic residues situated in the last turn of the helix. Yet the α-helix surface of both types of connections adopts similar orientations relative to the barrel sheet surface. Our results suggest furthermore that conserved hydrophobic residues along the sequence of the connections, may be correlated more with specific patterns of interactions made with neighboring helices and sheet strands than with helix/strand packing within the connection itself. A number of intriguing observations are also made on the distribution of the identified αβ1 and αβ3 loops within the α/β-barrel motifs. They often occur adjacent to each other; αβ3 loops invariably involve even numbered β-strands, while αβ1 loops involve preferentially odd β-strands; all the analyzed proteins contain at least one αβ3 loop in the first half of the eightfold α/β barrel. Possible origins of all these observations, and their relevance to the stability and folding of parallel α/β barrel. Possible origins of all these observations, and their relevance to the stability and folding of parallel α/β barrel motifs are discussed.
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