Structural principles of α/β barrel proteins: The packing of the interior of the sheet

  title={Structural principles of $\alpha$/$\beta$ barrel proteins: The packing of the interior of the sheet},
  author={Arthur M. Lesk and C. I. Br{\"a}nd{\'e}n and Cyrus Chothia},
  journal={Proteins: Structure},
α/β barrel structures very similar to that first observed in triose phosphate isomerase are now known to occur in 14 enzymes. To understand the origin of this fold, we analyzed in three of these proteins the geometry of the eight‐stranded β‐sheets and the packing of the residues at the center of the barrel. The Packingin thisregion is seen in its simplest form in glycolate oxidase. It consists of 12 residues arranged in three layers. Each layer contains four side chains. The packing of RubisCO… 

On the evolution of alternate core packing in eightfold β/α‐barrels

It is demonstrated that simple genetic alterations may be responsible for switching the nature of side‐chain packing observed in β/α‐barrels and that convergent evolution to a stable fold need not be invoked to account for the emergence of 2 classes of β/β-barrel core.

Recurrent αβ loop structures in TIM barrel motifs show a distinct pattern of conserved structural features

The 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.

Identifying the structural boundaries of independent folding domains in the a subunit of tryptophan synthase, a β/α barrel protein

Results suggest that the residual structure in αTS requires the participation of hydrophobic residues in multiple β‐strands that span the entire sequence, suggesting the modular assembly of βαβ supersecondary structural elements.

Locating the stabilizing residues in (α/β)8 barrel proteins based on hydrophobicity, long‐range interactions, and sequence conservation

This work proposes a new consensus approach for locating stabilizing residues in TIM‐barrel domains based on long‐range interactions, hydrophobicity, and conservation of amino acid residues, and suggests that these residues are among the ones with less mobility in the considered proteins.

Analysis of interactive packing of secondary structural elements in α/β units in proteins

The β‐sheet unit (βu), defined as a pair of adjacent parallel or antiparallel hydrogen‐bonded β‐strands, packing with an α‐helix shows a better correlation between the interaxial distance and log (V/nda) for the residues in the packing interface.

The structure and evolution of a/β barrel proteins

  • Deirdre ReardonG. Farber
  • Biology
    FASEB journal : official publication of the Federation of American Societies for Experimental Biology
  • 1995
Arguments are made to support the divergence of all members of this family from a common ancestor and evidence is presented to suggest that convergent molecular evolution occurs when there is only one energetically reasonable pathway for a chemical reaction.

Packing constraints of hydrophobic side chains in (α/β)8 barrels

An analysis of possible tight packing of hydrophobic groups simultaneously at the both surfaces of β‐hyperboloid‐8 was conducted. This analysis shows that the disposition of amino acid side chains at



Structural principles of parallel beta-barrels in proteins.

Eight-stranded beta-sheets in nine protein structures containing "TIM (triose phosphate isomerase) barrels" are shown to be fitted satisfactorily by hyperboloids, the generating lines of which pass

Analysis and predication of structural motifs in the glycolytic enzymes.

General rules governing the topology and packing of alpha-helices against a beta-sheet provide a basis for the combinatorial prediction of the tertiary fold of glycolytic domains from their amino acid sequence and observed secondary structure.

Structure of glycolate oxidase from spinach.

  • Y. LindqvistC. Brändén
  • Chemistry, Physics
    Proceedings of the National Academy of Sciences of the United States of America
  • 1985
A high-resolution structure determination of glycolate oxidase from spinach is reported, and the subunit structure is essentially a structure of the eight-stranded alpha/beta-barrel type first described for triosephosphate isomerase.

Three-dimensional structure of the tryptophan synthase alpha 2 beta 2 multienzyme complex from Salmonella typhimurium.

The three-dimensional structure of the alpha 2 beta 2 complex of tryptophan synthase from Salmonella typhimurium has been determined by x-ray crystallography at 2.5 A resolution. The four polypeptide