Membrane barrels are taller, fatter, inside-out soluble barrels

Abstract

Up-and-down β-barrel topology exists in both the membrane and soluble environment. However, β-barrels are virtually the only topology that exist in the outer membrane. By comparing features of these structurally similar proteins, we can determine what features are particular to the environment rather than the fold. Here we compare structures of membrane β-barrels to soluble β-barrels and evaluate their relative size, shape, amino acid composition, hydrophobicity, and periodicity. We find that membrane β-barrels are generally larger than soluble β-barrels in with more strands per barrel and more amino acids per strand, making them wider and taller. We also find that membrane β-barrels are inside-out soluble β-barrels. The inward region of membrane β-barrels have similar hydrophobicity to the outward region of soluble β-barrels, and the outward region of membrane β-barrels has similar hydrophobicity to the inward region of the soluble β-barrels. Moreover, even though both types of β-barrel have been assumed to have strands with amino acids that alternate in direction and hydrophobicity, we find that the membrane β-barrels have more regular alternation than soluble β-barrels. These features give insight into how membrane barrels maintain their fold and function in the membrane.

Protein Design: From the Aspect of Water Solubility and Stability

“…The rationale aligned well with a recent analysis on native proteins suggesting that membrane barrels are taller, fatter and inside-out soluble barrels. 569 However, experimental success was not achieved until additional destabilization with β-hairpins on the trans side and reduced β-sheets propensity were incorporated to slow down undesired nucleation and allowed proper folding of the structure. Compared to the soluble variants, transmembrane designs had a smaller population of glycine kinks and preglycine hydrogen bonds which were disfavored due to the lipid environments and lack of water molecules to stabilize exposed carbonyls.…”

General Features of Transmembrane Beta Barrels From a Large Database

“…One of the difficulties of generalizing about the family of outer membrane β-barrels is the small number of solved crystal structures for proteins with low sequence similarity (6, 46, 47) With 1,894,206 sequences, our high-accuracy IsItABarrelDB database contributes a large set of sequences for analyzing TMBBs. The IsItABarrel algorithm can also be used to identify more TMBBs within genomes sequenced in the future.…”

“…Such constraint induces an imperfect hydrophobicity alternation pattern on residues of each strand. (Dhar et al, 2021; Slusky & Dunbrack, 2013) Also, there are significant differences in amino acid abundance at different depths across the membrane, with more hydrophobic residues in the central region of the membrane. (Wimley, 2002) Attempts have been made to computationally identify TMBBs using amino acid composition (Gromiha & Suwa, 2006; Liu et al, 2003; Zhai & Saier, 2002), using specific knowledge about TMBBs and their environment (Freeman & Wimley, 2010; Hayat et al, 2016; Wimley, 2002) and by identification of sequence motifs (Berven et al, 2004; Gromiha, 2005).…”

Outer membrane β-barrel structure prediction through the lens of AlphaFold2

“…Different OMBB families are composed of different numbers of β-strands [22,48]. The diameter of the barrel depends on the numbers of βstrands, but also on the shear number, which is, simply put, a measure of the parallel displacement of the strands relative to each other [23][24][25].…”