Influence of amino acid properties for discriminating outer membrane proteins at better accuracy

2006 ◽  
Vol 1764 (9) ◽  
pp. 1493-1497 ◽  
Author(s):  
M. Michael Gromiha ◽  
Makiko Suwa
Keyword(s):  
Amino Acid ◽  
Membrane Proteins ◽  
Outer Membrane ◽  
Outer Membrane Proteins ◽  
Acid Properties ◽  
Amino Acid Properties

scholarly journals Structural and Functional Roles of the Surface-Exposed Loops of the β-Barrel Membrane Protein OmpA fromEscherichia coli

1999 ◽  
Vol 181 (12) ◽  
pp. 3688-3694 ◽  
Author(s):  
Ralf Koebnik
Keyword(s):  
Amino Acid ◽  
Membrane Proteins ◽  
Membrane Protein ◽  
Outer Membrane ◽  
High Efficiency ◽  
Outer Membrane Proteins ◽  
Protein Domain ◽  
Amino Acid Residues ◽  
Functional Roles ◽  
Ompa Protein

ABSTRACT The N-terminal domain of the OmpA protein from Escherichia coli, consisting of 170 amino acid residues, is embedded in the outer membrane, in the form of an antiparallel β-barrel whose eight transmembrane β-strands are connected by three short periplasmic turns and four relatively large surface-exposed hydrophilic loops. This protein domain serves as a paradigm for the study of membrane assembly of integral β-structured membrane proteins. In order to dissect the structural and functional roles of the surface-exposed loops, they were shortened separately and in all possible combinations. All 16 loop deletion mutants assembled into the outer membrane with high efficiency and adopted the wild-type membrane topology. This systematic approach proves the absence of topogenic signals (e.g., in the form of loop sizes or charge distributions) in these loops. The shortening of surface-exposed loops did not reduce the thermal stability of the protein. However, none of the mutant proteins, with the exception of the variant with the fourth loop shortened, served as a receptor for the OmpA-specific bacteriophage K3. Furthermore, all loops were necessary for the OmpA protein to function in the stabilization of mating aggregates during F conjugation. An OmpA deletion variant with all four loops shortened, consisting of only 135 amino acid residues, constitutes the smallest β-structured integral membrane protein known to date. These results represent a further step toward the development of artificial outer membrane proteins.

scholarly journals Short-Chain Fatty Acids Modulate Metabolic Pathways and Membrane Lipids in Prevotella bryantii B14

Proteomes ◽  
2020 ◽  
Vol 8 (4) ◽  
pp. 28
Author(s):  
Andrej Trautmann ◽  
Lena Schleicher ◽  
Simon Deusch ◽  
Jochem Gätgens ◽  
Julia Steuber ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Fatty Acids ◽  
Amino Acid ◽  
Membrane Proteins ◽  
Outer Membrane ◽  
Outer Membrane Proteins ◽  
Short Chain Fatty Acids ◽  
Isovaleric Acid ◽  
Short Chain ◽  
Prevotella Bryantii

Short-chain fatty acids (SCFAs) are bacterial products that are known to be used as energy sources in eukaryotic hosts, whereas their role in the metabolism of intestinal microbes is rarely explored. In the present study, acetic, propionic, butyric, isobutyric, valeric, and isovaleric acid, respectively, were added to a newly defined medium containing Prevotella bryantii B14 cells. After 8 h and 24 h, optical density, pH and SCFA concentrations were measured. Long-chain fatty acid (LCFA) profiles of the bacterial cells were analyzed via gas chromatography-time of flight-mass spectrometry (GC-ToF MS) and proteins were quantified using a mass spectrometry-based, label-free approach. Cultures supplemented with single SCFAs revealed different growth behavior. Structural features of the respective SCFAs were identified in the LCFA profiles, which suggests incorporation into the bacterial membranes. The proteomes of cultures supplemented with acetic and valeric acid differed by an increased abundance of outer membrane proteins. The proteome of the isovaleric acid supplementation showed an increase of proteins in the amino acid metabolism. Our findings indicate a possible interaction between SCFAs, the lipid membrane composition, the abundance of outer membrane proteins, and a modulation of branched chain amino acid biosynthesis by isovaleric acid.

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