Given that the length of the LPS molecule can vary, and it differs from phospholipids, it is important to ascertain if this impacts upon the orientation of Omps. The outer leaflet contains lipopolysaccharide (LPS) and the inner leaflet contains a mixture of zwitterionic and anionic phospholipids. For Omps, however the analyses is somewhat complicated by the biochemistry of the outer membrane the two leaflets differ in their lipid composition. (3) The study covers all known structures of membrane protein and is updated as more structures become available. in which coarse-grained simulations of membrane proteins embedded in symmetric phospholipid bilayers are performed, and the results are deposited in an online database. The most comprehensive study is perhaps that of Stansfeld et al. Molecular dynamics simulations at fine-grain and coarse-grain levels of resolution have been employed to study the orientations of many membrane proteins. To understand these interactions and how they are stabilized, it is important to characterize the orientation and dynamics of Omps in their native membrane environment, as well as the impact they have on the local membrane. For example, it is known that the translocation of vitamin B12 across the outer membrane is facilitated by binding to BtuB and then the subsequent formation of a translocon complex with OmpF. However, as with lipid-Omp interactions, Omp-protein interactions are also often specific and have functional consequences that may impact the life-cycle of the bacterium. In addition to their interaction with lipids, Omps also interact with each other as well as with peripheral membrane-binding proteins, which is perhaps not surprising given the crowded nature of the outer membrane. For example, experimental studies have shown that OmpF has a specific LPS-binding region on its outer surface. More recently it has become evident that the interactions of Omps with lipids within their local membrane environment can be of a specific nature these interactions are therefore likely to have functional consequences.
(1) The structure–function relationships of a number of Omps have been the focus of experimental and simulation studies over the last 20 years or so, and consequently many details have emerged some of these are reviewed in ref (2). coli, the sizes of Omps range from barrels composed of eight β strands to 22 strands for a monomer. coli, have β barrel architectures (see ). Currently the structures of >70 Omps from Gram-negative bacteria have been determined all of these, with the exception of Wza from E.
Given the range of functions they perform, it is not surprising that Omps have a wide range of sizes and oligomeric states. The outer membrane proteins (Omps) of Gram-negative bacteria perform a wide range of functions including signaling, host cell adhesion, catalysis of crucial reactions, and transport (active and passive) of solutes/nutrients into and out of the cell. Overall we present analyses from over 200 μs of simulation for each protein.
We show that each protein has a unique pattern of interaction with the surrounding membrane, which is influenced by the composition of the protein, the level of LPS in the outer leaflet, and the differing mobilities of the lipids in the two leaflets of the membrane. coli outer membrane OmpA, OmpX, BtuB, FhuA, OmpF, and EstA in a range of membrane environments, which are representative of the in vivo conditions for different strains of E. Here we report coarse-grained molecular dynamics simulations of six proteins from the E. coli, the outer membrane contains a wide range of proteins with a β barrel architecture, that vary in size from the smallest having eight strands to larger barrels composed of 22 strands. The outer membrane of Gram-negative bacteria has a highly complex asymmetrical architecture, containing a mixture of phospholipids in the inner leaflet and almost exclusively lipopolysaccharide (LPS) molecules in the outer leaflet.