Beta alpha barrel

R. Sterner, and M. Wilmanns, Structural evidence for evolution of the beta/alpha barrel scaffold by gene duplication and fusion, Science 2000, 289, 1546-1550. 

Lebioda L, Stec B, Brewer JM The structure of yeast enolase at 2.25-A resolution. An 8-fold beta + alpha-barrel with a novel beta beta alpha alpha (beta alpha)6 topology. J Biol Chem 1989 264 3685-3693. 

Bork, P. J., Gellerich, H., Groth, R., Hooft, A., and Martin, F., 1995, Divergent evolution of a beta/alpha barrel subclass detection of numerous phosphate-binding sites by motif search. Protein Sci 4 2689274. 

Raine, A. R., Scrutton, N. S., and Mathews, F. S., 1994, On the evolution of alternate core packing in eightfold beta/alpha- barrels, Protein Sci 3 1889-1892. 

Wilmanns, M., Hyde, C. C., Davies, D. R., Kirschener, K., and Jansonius, J. N., 1991, Structural conservation in parallel beta/alpha barrel enzymes diat catalyse diree sequential reactions in the pathway of tryptophan biosynthesis. Biochemistry 30 9161n9169. 

Table 2 shows the average diameter for each one of the studied families. We observe very close diameters between TIM Barrel and TIM beta/alpha-barrel and also between Lysozyme and Lysozyme-like families. This is explained by the fact that each pair of families contains almost the same proteins, in other worlds. Lysozyme topology in CATH is the equivalent of Lysozyme-like fold level in SCOP. 

Fig. 5. Average diameter of Rossman fold, left, and beta/alpha-barrel, right.

As defined earlier, the density measures the ratio between the number of available edges and the number of all possible edges. Results presented in Table 4 show that the two families TIM Barrel and TIM beta/ alpha-barrel have the minimum density. It has a consequence on their SSE-IN topology. When the density is low, the network is less connected and consequently, the diameter and the average distance are higher. Comp)aring these results to Tables 2 and 3 one can see the inversely proportional relation between density in one hand, and diameter and average distance on the other. 

Uhlin U, Eklund H. 1996. The ten-stranded beta/alpha barrel in ribonucleotide reductase protein Rl. 7Mo/Biol 262 358-369. 

Lee J, Michael AJ, Martynowski D, Goldsmith EJ, Phillips MA (2007) Phylogenetic diversity and the structural basis of substrate specificity in the beta/alpha-barrel fold basic amino acid decarboxylases. J Biol Chem 282 27115-27125... 

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

S. Hettwer, M. Wilmanns, and R. Sterner, Directed evolution of a (beta alpha) (8)-barrel enzyme to catalyze related reactions in two different metabolic pathways, Proc. Natl. Acad. Sci. 2000, 97(18), 9925-9930. 

R. Sterner, Stability, catalytic versatility and evolution of the (beta alpha) (8)-barrel fold, Current Opin. Biotechmol. 2001, 12, 376-381. 

Silverman, J. A., R. Balakrishnan and P. B. Harbury. From the Cover Reverse engineering the (beta/alpha)8 barrel fold. Proc Natl Acad Sci U S A (2001) 98(6) 3092-7. 

Schmidt DM, Mundorff EC, Dojka M, Bermudez E, Ness JE, Govindarajan S, Babbitt PC, Minshull J, Gerlt JA. Evolutionary potential of (beta/alpha)8-barrels functional promiscuity produced by single substitutions in the enolase superfamily. Biochemistry... 

THE STRUCTURE OF THE MONOMER IS AN EIGHT-FOLD ALPHA-BETA 6 BARREL WITH AN EXTENDED C-TERMINAL LOOP WHICH FACILITATES 6 AGGREGATION OF MONOMERS TO TETRAMERS. TETRAMERS ARE 6 POSITIONED ON THE 222 SYMMETRY SITE AT THE ORIGIN OF THE... 

Evolutionary Markers in the (Beta/Alpha)8-Barrel Fold. 

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

Figure 4.1 Alpha/beta domains are found in many proteins. They occur in different classes, two of which are shown here (a) a closed barrel exemplified by schematic and topological diagrams of the enzyme trlosephosphate isomerase and (b) an open twisted sheet with helices on both sides, as in the coenzymebinding domain of some dehydrogenases. Both classes are built up from p-a-p motifs that are linked such that the p strands are parallel. Rectangles represent a helices, and arrows represent p strands in the topological diagrams, [(a) Adapted from J. Richardson, (b) Adapted from B. Furugren.j...

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

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. 

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. 

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.

Figure 3. Model of (p a)s TIM barrel from triose phosphate isomerase. Numbered arrow and twisted ribbon structures are beta sheets and alpha helicies, respectively. (Adapted and reproduced from Ref. 66 with permission. Cop3night 1984 American Association for the Advancement of Science.)...

There is a wide variety of so-called globular proteins. Many of these have alpha and beta structures imbedded within the overall globular structure. Beta sheets are often twisted or wrapped into a barrel-like structure. They contain portions that are beta sheet structures... 

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

Molluscan hemocyanins. Two FUs from moUuscan hemocyanins were resolved, the oxy-form of O. dofleini He FU g (Figure 5b) and the deoxy-form of R. thomasiana He (Figure 5c ). Each FU consists of two domains. The N-terminal domain II carries the active site with a four alpha-helix bundle folding motif with two copper atoms. The C-terminal domain III replaces topologically the domain I in arthropod subunits and looks like a squeezed beta-barrel. Although the Rapana structure is not resolved as well as the Octopus FU, two different conformations can be deduced. In the oxy FU of Octopus hemocyanin, domain III covers the entrance to the active site completely while in the deoxy-form this domain is shifted a few degrees so that the channel to the active site becomes completely uncovered. 

It is a protein complex made up of five subunits, two of which are the same. The five subunits (two alpha, one beta, gamma, and delta) form a cylindrical or barrel shape which traverses the cell membrane as shown in Fig. 11.42. 

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