Protein structure beta barrel

Normal mode analysis of the mechanical properties of a triosephosphate isomerase-barrel protein suggests that the region between the secondary structures plays an important role in the dynamics of the protein. The beta-barrel region at the core of the protein is found to be soft in contrast to the helical, strand and loop regions [62]. A detailed discussion of other properties of proteins is mechanically highly non-linear systems is given by Kharakoz [63]. 

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. 

Detailed protein structures have been reported for BPI and CETP. Given the aforementioned similarities within this gene family, these protein structures serve as a likely model for the protein structure of PLTP. CETP and BPI are elongated molecules, shaped like a boomerang. There are two domains with similar folds, and a central beta-sheet domain between these two domains. The molecules contain two lipid-binding sites, one in each domain near the interface of the barrels and the central beta-sheet. 

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

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... 

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. 

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. 

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. 

Srisailam S, Kumar TK, Rajalingam D, Kathir KM, Sheu HS, Jan FJ, Chao PC, Yu C (2003) Amyloid-like fibril formation in an all beta-barrel protein. Partially structured intermediate state(s) is a precursor fa-... 

Fairman JW, Noinaj N, Buchanan SK. The structural biology of beta-barrel membrane proteins a summary of recent reports. Curr Opin Struct Biol. 2011 21(4) 523-531. 

Figure 2.11 Beta sheets are usuaiiy represented simply by arrows in topology diagrams that show both the direction of each (3 strand and the way the strands are connected to each other along the polypeptide chain. Such topology diagrams are here compared with more elaborate schematic diagrams for different types of (3 sheets, (a) Four strands. Antiparallel (3 sheet in one domain of the enzyme aspartate transcarbamoylase. The structure of this enzyme has been determined to 2.8 A resolution in the laboratory of William Lipscomb, Harvard University, (b) Five strands. Parallel (3 sheet in the redox protein flavodoxin, the structure of which has been determined to 1.8 A resolution in the laboratory of Martha Ludwig, University of Michigan, (c) Eight strands. Antiparallel barrel in the electron carrier plastocyanln. This Is a closed barrel where the sheet is folded such that (3 strands 2 and 8 are adjacent. The structure has been determined to 1.6 A resolution in the laboratory of Hans Freeman in Sydney, Australia. (Adapted from J. Richardson.)...

Determining the Structure of Beta-Sheet Barrels in Proteins. 1. A Theoretical-Analysis. 

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