Beta-barrel protein

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

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

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. 

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... 

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

Kutik S, Stojanovski D, Becker L, Becker T, Meinecke M, Kruger V, Prinz C, Meisinger C, Guiard B, Wagner R, Pfanner N, Wiedemann N. Dissecting membrane insertion of mitochondrial beta-barrel proteins. Cell 2008 132 1011-1024. 

J. Skolnick and A. Kolinski, J. Mol. Biol., 212, 787 (1990). Dynamic Monte Carlo Simulations of Globular Protein Folding/Unfolding Pathways. I. Six-Member, Greek Key Beta-Barrel Proteins. 

The SDEL algorithm has also been applied to more complicated systems, such as the wild type human Cu, Zn superoxide dismutase (SOD) dimer. SOD is a 153-residue, homodimeric, anti-oxidant enzyme that dismutates superoxide ion to hydrogen peroxide and oxygen [87]. It is an eight-strand, flattened, beta-barrel protein with one copper and one zinc ion per monomer [88]. There are over 100... 

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-... 

Simulations of the Folding Pathway of Triose Phosphate Isomerase-type Alpha/Beta Barrel Proteins. 

Confinement and Crowding on the Thermodynamics and Kinetics of Folding of a Minimalist Beta-barrel Protein. 

Another class of facial amphiphilic protein domains are the amphiphilic beta sheets. Like alpha helices, amphiphilic beta sheets can be a snbstmcture of larger proteins, as in beta-barrel proteins, or these beta sheets can be the entire peptide, as is the case with the smaller antibiotic facial amphiphilic beta sheets. If the sequence of beta-sheet peptides alternates between hydrophobic and hydrophilic residues, one face of the beta sheet is hydrophilic and the other is hydrophobic. An example of such a facial amphiphilic beta-sheet peptide strand is the synthetic antibiotic described by Prasad Kari and coworkers. This 18-sequence peptide has alternating hydrophobic and hydrophilic amino acids and it has been shown that it folds into a facial amphiphilic beta sheet in the presence of a bilayer (Figure 4). 

A nice example of pore formation by beta-barrel proteins is the Perfringolysin O (PFO) pore-forming protein. PFO is part of the family of cholesterol-dependent cytolysins (CDCs), a class of pore-forming toxins which form pores as large as 30nm in diameter by oligomerization of 40-50... 

Heuck AP, Hotze EM, Tweten RK, Johnson AE. Mechanism of membrane insertion of a multimeric beta-barrel protein perfringolysin O creates a pore using ordered and coupled conformational changes. Mol Cell. 2000 6(5) 1233-1242. 

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. 

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... 

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... 

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. 

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. 

Tamm, L.K., Hong, H. and Liang, B. (2004) Folding and assembly of beta-barrel membrane proteins. Biochim. Biophys. Acta. 1666, 250-263. 

Jacoboni, I., Martelli, P. L., Fariselli, P., De Pinto, V. Casadio, R. (2001). Prediction of the transmembrane regions of beta-barrel membrane proteins with a neural network-based predictor. Protein Sci 10(4), 779-87. 

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]. 

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