Zhang Z, Ryoo D, Balusek C, Acharya A, Rydmark MO, Linke D, Gumbart JC. Inward-facing glycine residues create sharp turns in β-barrel membrane proteins.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021;
1863:183662. [PMID:
34097860 DOI:
10.1016/j.bbamem.2021.183662]
[Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 04/15/2021] [Accepted: 05/17/2021] [Indexed: 11/29/2022]
Abstract
The transmembrane region of outer-membrane proteins (OMPs) of Gram-negative bacteria are almost exclusively β-barrels composed of between 8 and 26 β-strands. To explore the relationship between β-barrel size and shape, we modeled and simulated engineered variants of the Escherichia coli protein OmpX with 8, 10, 12, 14, and 16 β-strands. We found that while smaller barrels maintained a roughly circular shape, the 16-stranded variant developed a flattened cross section. This flat cross section impeded its ability to conduct ions, in agreement with previous experimental observations. Flattening was determined to arise from the presence of inward-facing glycines at sharp turns in the β-barrel. An analysis of all simulations revealed that glycines, on average, make significantly smaller angles with residues on neighboring strands than all other amino acids, including alanine, and create sharp turns in β-barrel cross sections. This observation was generalized to 119 unique structurally resolved OMPs. We also found that the fraction of glycines in β-barrels decreases as the strand number increases, suggesting an evolutionary role for the addition or removal of glycine in OMP sequences.
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