scholarly journals ProBLM Web Server: Protein and Membrane Placement and Orientation Package

2014 ◽  
Vol 2014 ◽  
pp. 1-7 ◽  
Author(s):  
Taylor Kimmett ◽  
Nicholas Smith ◽  
Shawn Witham ◽  
Marharyta Petukh ◽  
Subhra Sarkar ◽  
...  
Keyword(s):  
Membrane Protein ◽  
Lipid Bilayer ◽  
Lipid Membrane ◽  
3D Structure ◽  
Web Server ◽  
Bilayer Lipid Membrane ◽  
Lipid Bilayer Membranes ◽  
Heavy Atoms ◽  
Membrane Complex ◽  
Position And Orientation

The 3D structures of membrane proteins are typically determined without the presence of a lipid bilayer. For the purpose of studying the role of membranes on the wild type characteristics of the corresponding protein, determining the position and orientation of transmembrane proteins within a membrane environment is highly desirable. Here we report a geometry-based approach to automatically insert a membrane protein with a known 3D structure into pregenerated lipid bilayer membranes with various dimensions and lipid compositions or into a pseudomembrane. The pseudomembrane is built using the Protein Nano-Object Integrator which generates a parallelepiped of user-specified dimensions made up of pseudoatoms. The pseudomembrane allows for modeling the desolvation effects while avoiding plausible errors associated with wrongly assigned protein-lipid contacts. The method is implemented into a web server, the ProBLM server, which is freely available to the biophysical community. The web server allows the user to upload a protein coordinate file and any missing residues or heavy atoms are regenerated. ProBLM then creates a combined protein-membrane complex from the given membrane protein and bilayer lipid membrane or pseudomembrane. The user is given an option to manually refine the model by manipulating the position and orientation of the protein with respect to the membrane.

scholarly journals Efficient Lipid Bilayer Formation by Dipping Lipid-Loaded Microperforated Sheet in Aqueous Solution

Micromachines ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 53
Author(s):  
Nobuo Misawa ◽  
Satoshi Fujii ◽  
Koki Kamiya ◽  
Toshihisa Osaki ◽  
Shoji Takeuchi
Keyword(s):  
Aqueous Solution ◽  
Membrane Protein ◽  
Organic Solvent ◽  
Lipid Membrane ◽  
Coating Layer ◽  
Bilayer Lipid Membrane ◽  
Contact Method ◽  
Electrical Measurements ◽  
Droplet Interface Bilayer ◽  
Perforated Sheet

This paper describes a method for a bilayer lipid membrane (BLM) formation using a perforated sheet along with an open chamber. Microscopic observation of the formed membrane showed a typical droplet interface bilayer. We proved that the formed membrane was a BLM based on electrical measurements of the membrane protein α-hemolysin, which produces nanopores in BLMs. Unlike the conventional approach for BLM formation based on the droplet contact method, this method provides aqueous surfaces with no organic solvent coating layer. Hence, this method is suitable for producing BLMs that facilitate the direct addition of chemicals into the aqueous phase.

A tethered bilayer lipid membrane that mimics microbial membranes

2018 ◽  
Vol 20 (18) ◽  
pp. 12958-12969 ◽  
Author(s):  
Jakob Andersson ◽  
Melanie A. Fuller ◽  
Kathleen Wood ◽  
Stephen A. Holt ◽  
Ingo Köper
Keyword(s):  
Outer Membrane ◽  
Lipid Bilayer ◽  
Lipid Membrane ◽  
Bilayer Lipid Membrane ◽  
Gram Negative Bacteria ◽  
Gram Negative ◽  
Bilayer Lipid ◽  
Self Assembled

This work presents a self-assembled lipid bilayer architecture mimicking the outer membrane of Gram negative bacteria.

scholarly journals Discrete Conductance Fluctuations in Lipid Bilayer Protein Membranes

1969 ◽  
Vol 53 (6) ◽  
pp. 741-757 ◽  
Author(s):  
R. C. Bean ◽  
W. C. Shepherd ◽  
H. Chan ◽  
Joellen Eichner
Keyword(s):  
Lipid Bilayer ◽  
Lipid Membranes ◽  
Lipid Membrane ◽  
Membrane Lipids ◽  
Initial Reaction ◽  
Lipid Bilayer Membranes ◽  
Conductance Fluctuations ◽  
Excitable Membranes ◽  
Conductance States ◽  
High Conductance

Discrete fluctuations in conductance of lipid bilayer membranes may be observed during the initial stages of membrane interaction with EIM ("excitability inducing material"), during destruction of the EIM conductance by proteolysis, and during the potential-dependent transitions between low and high conductance states in the "excitable" membranes. The discrete conductance steps observed during the initial reaction of EIM with the lipid membranes are remarkably uniform, even in membranes of widely varying lipid composition. They range only from 2 to 6 x 10-10 ohm-1 and average 4 x 10-10 ohm-1. Steps found during destruction of the EIM conductance by proteolysis are somewhat smaller. The transition between high conductance and low conductance states may involve steps as small as 0.5 x 10-10 ohm-1. These phenomena are consistent with the formation of a stable protein bridge across the lipid membrane to provide a polar channel for the transport of cations. T6he uniform conductance fluctuations observed during the formation of these macromolecular channels may indicate that the ions in a conductive channel, in its open state, are largely protected from the influence of the polar groups of the membrane lipids. Potential-dependent changes in conductance may be due to configurational or positional changes in the protein channel. Differences in lipid-lipid and lipid-macromolecule interactions may account for the variations in switching kinetics in various membrane systems.

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