Beta barrel

Alpha/beta barrels occur in many different enzymes... 

Alpha/beta barrels provide examples of evolution of new enzyme activities... 

A beta barrel is a three-dimensional protein fold motif in which beta strands connected by loops form a barrellike structure. For example, this fold motif is found in many proteins of the immunoglobulin family and of the chymotrypsin family of serine proteases. 

Amaro, R. Luthey-Schulten, Z., Molecular dynamics simulations of substrate channeling through an alpha-beta barrel protein, Chem. Phys. 2004, 307, 147-155... 

E. A. MacGregor, H. M. Jespersen, and B. Svensson, A circularly permuted alpha-amylase-type alpha/beta-barrel structure in glucan-synthesizing glucosyl-transferases, FEBS Lett., 378 (1996) 263-266. 

Afonin S, Durr UHN, Wadhwani P, Salgado J, Ulrich AS (2008) Solid state NMR structure analysis of the antimicrobial peptide gramicidin S in lipid membranes concentration-depen-dent re-alignment and self-assembly as a beta-barrel. Top Curr Chem 273 139-154... 

For an important recent development in this area ( Directed evolution of new catalytic activity using the alpha/beta-barrel scaffold ) see M. M. Altamirano, J. M. Blackburn, C. Aguayo, A. R. Fersht, Nature 403 (2000) 617-622. 

Buchanan, S. K. (1999). Beta-barrel proteins from bacterial outer membranes structure, function and refolding, Curr. Opin. Struct. Biol., 9, 455-461. 

Leader Beta barrel Central beta, alpha/beta... 

Fig. 8. Comparison of the subunit structures of a small subunit catalase (BLC) (A) and a large subunit catalase (HPII) (B). Segments including the N-terminal domain, the beta barrel core, the wrapping domain, the alpha helical domain, and the C-terminal domain (HPII) are indicated and are described in Section V,A.

Initially, it was suspected that the nitrophorins were insect hemoglobins. Indeed, they showed 45-48% homology with monomeric hemoglobins from insects, annelids, mollusks, nematodes, and even human 3 chains and leghemoglobin (44). However, in due time it became clear that these proteins were not globins at all, but rather, beta-barrel proteins called lipocalins (see Section III). As for the four nitrophorins, the sequences of NPl and NP4 are 90% identical, whereas those of NP2 and NP3 are 79% identical NPl and NP2, however, are only 38% identical. 

We have completed several structures each of NPl, NP2, and NP4 (31, 46 9, 110). These structures reveal the Rhodnius nitrophorins to have a fold dominated by an eight-stranded antiparallel beta-barrel, as shown in Fig. 15, and to rely on a remarkable ligand-induced conformational change for NO transport, described later. The structures confirm that the nitrophorins are completely unrelated to the globins, the only other heme-based gas transport proteins whose structures are known. Rather, their fold places them in the lipocalin family, for which several other examples are known (111-113). Our initial nitrophorin structure was of NPl and was determined using standard MIR and... 

Ishikawa D, Yamamoto H, Tamura Y, Moritoh K, Endo T (2004) Two novel proteins in the mitochondrial outer membrane mediate beta-barrel protein assembly. J Cell Biol 166 621-627... 

Nunnari J, Fox TD, Walter P (1993) A mitochondrial protease with two catalytic subunits of nonoverlapping specificities. Science 262 1997-2004 Osborne AR, Rapoport , van den Berg (2005) Protein translocation by the Sec61/SecY channel. Annu Rev Cell Dev Biol 21 529-550 Paschen SA, Neupert W, Rapaport D (2005) Biogenesis of beta-barrel membrane proteins of mitochondria. Trends Biochem Sci 30 575-582 Paschen SA et al. (2003) Evolutionary conservation of biogenesis of beta-barrel membrane proteins. Nature 426 862-866... 

Wimley WC (2003) The versatile beta-barrel membrane protein. Curr Opin Struct Biol 13 404-411... 

D. Reardon, and G. K. Farber, Protein motifs. 4. The structure and evolution of alpha/beta barrel proteins, FASEB J. 1995, 9, 497-503. 

The comparison of protein folds has proved to be difficult the three-dimensional structures are frequently complicated, and quite significant differences can exist between structures that are, on the basis of sequence similarity, clearly related in evolutionary terms. On the other hand structures may sometimes resemble each other very closely, but fail to display any sequence similarity the classic example of this is the parallel beta barrel structure which has now been found in more than twenty proteins with no amino-acid sequence homology [35], In these cases the interpretation of the meaning of a similarity can be less than straightforward it may indicate that the proteins are evolutionary related ( divergent evolution ), that they are unrelated but have evolved similar structures because they carry out similar functions ( convergent evolution ) or the common structure may simply be a particularly stable one that is adopted by a large number of proteins. In addition to three similarities between complete protein folds, there may also be partial similarities. 

Aggeli, A., Boden, N., Hunter, M., and Knowles, C., Self-assembling beta-barrel channelforming peptides for wound dressing and other pharmaceutical uses, 2002-GB3212 2003006494 (2003). 

Bishop, R.E. Structural biology of membrane-intrinsic beta-barrel enzymes sentinels of the bacterial outer membrane. Biochim Biophys Acta 1778 (2008) 1881-1896. 

Zubieta C, Krishna SS, Kapoor M et al (2007) Crystal structures of two novel dye-decolorizing peroxidases reveal a beta-barrel fold with a conserved heme-binding motif. Proteins 69 223-233... 

Tamm, L. K., Arora, A., and Kleinschmidt, J. H. (2001). Structure and assembly of beta-barrel membrane proteins./. Biol. Chem. 276, 32399-32402. 

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