title: Exploring the conformational dynamics and membrane interactions of PorB from C. glutamicum: a multi-scale molecular dynamics simulation study.
abstract: Members of the gram-positive mycolata bacteria have unusual cell envelopes which help them to avoid the immune system and the effects of most antibiotics, whilst rendering them permeable to solutes of importance in industrial bioconversion. It is therefore of interest to understand the molecular mechanisms for this selective permeability. PorB is an unusual porin from the outer membrane (OM) of Corynebacterium glutamicum. It has been proposed as an atypical α-helical, symmetrical homo-pentameric architecture, with an unusual distribution of polar amino acids on its surface. The proposed structure is too short to traverse a typical phospholipid bilayer, in contrast with the β-barrel porins of Gram-negative bacteria. Nevertheless, it has been shown to form small anion-selective channels in membranes typical of Escherichia coli. To further understand its function, we have performed ~400 ns of all-atom and ~270 μs of coarse-grained simulations of PorB in a range of membrane mimetic and phospholipid milieus. Our results suggest that PorB can undergo spontaneous conformational rearrangements that allow it to adapt to its local lipid environment. We speculate that the increased flexibility of this α-helical porin in comparison with rigid β-barrels may be an adaptation for the heterogeneous mycolic OM, and explains its demonstrated ability to form measurable pores with phospholipid membranes.
authors.affiliation: Soft Matter and Molecular Biophysics Group, Department of Applied Physics University of Santiago de Compostela, Campus Vida, 15782, Santiago de Compostela, Spain. Angel.Pineiro@usc.es
authors.forename: Ángel
authors.initials: Á
authors.lastname: Piñeiro
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Bond
authors.forename: Syma
authors.initials: S
authors.lastname: Khalid
mesh_terms: D001425:Bacterial Outer Membrane Proteins / Q000737:chemistry* / Q000378:metabolism; D002462:Cell Membrane / Q000737:chemistry / Q000378:metabolism; D048230:Corynebacterium glutamicum / Q000378:metabolism*; D008051:Lipid Bilayers / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D010713:Phosphatidylcholines / Q000737:chemistry / Q000378:metabolism; D010743:Phospholipids / Q000737:chemistry / Q000378:metabolism; D018272:Porins / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D055503:Protein Multimerization; D020836:Protein Structure, Quaternary; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D021122:Protein Subunits / Q000737:chemistry / Q000378:metabolism
chemical_list: C508476:1,2-dilinolenoylphosphatidylcholine; D001425:Bacterial Outer Membrane Proteins; D008051:Lipid Bilayers; D010713:Phosphatidylcholines; D010743:Phospholipids; D018272:Porins; D021122:Protein Subunits; C028694:1-palmitoyl-2-oleoylphosphatidylcholine