What is the very latest means using Gromacs for inserting a TM alpha helical dimer into a lipid bilayer?
Also, what are the latest techniques for measuring lipid bilayer surface area with an embedded protein?
And finally, are there any Gromacs tools to measure protein tilt (relative to the bilayer z-axis) and the dimer crossing angle?
I would like to keep this up to date and within the confines of Gromacs. I've been working on soluble enzymes and QM reaction pathways during the last two years, I'm a bit out of date.
Thanks
Anthony
Dear Anthony,
regarding the first question, please find a recent paper on the use of Achembed:
1-J Chem Theory Comput. 2015 Jun 9; 11(6): 2743–2754.
Published online 2015 May 14. doi: 10.1021/ct501111d
PMCID: PMC4467903
Alchembed: A Computational Method for Incorporating Multiple Proteins into Complex Lipid Geometries
Elizabeth Jefferys,† Zara A. Sands,‡ Jiye Shi,‡ Mark S. P. Sansom,† and Philip W. Fowler*†
A necessary step prior to starting any membrane protein computer simulation is the creation of a well-packed configuration of protein(s) and lipids. Here, we demonstrate a method, alchembed, that can simultaneously and rapidly embed multiple proteins into arrangements of lipids described using either atomistic or coarse-grained force fields. During a short simulation, the interactions between the protein(s) and lipids are gradually switched on using a soft-core van der Waals potential. We validate the method on a range of membrane proteins and determine the optimal soft-core parameters required to insert membrane proteins. Since all of the major biomolecular codes include soft-core van der Waals potentials, no additional code is required to apply this method. A tutorial is included in the Supporting Information.
Regarding the latest techniques for measuring lipid bilayer surface area with an embedded protein, please see attached recent publication:
Int J Mol Sci. 2013 Nov; 14(11): 21561–21597.
Published online 2013 Oct 31. doi: 10.3390/ijms141121561
PMCID: PMC3856022
Engineering Lipid Bilayer Membranes for Protein Studies
Muhammad Shuja Khan,1 Noura Sayed Dosoky,2 and John Dalton Williams1,*
Author information ► Article notes ► Copyright and License information ►
This article has been cited by other articles in PMC.
Go to:
Abstract
Lipid membranes regulate the flow of nutrients and communication signaling between cells and protect the sub-cellular structures. Recent attempts to fabricate artificial systems using nanostructures that mimic the physiological properties of natural lipid bilayer membranes (LBM) fused with transmembrane proteins have helped demonstrate the importance of temperature, pH, ionic strength, adsorption behavior, conformational reorientation and surface density in cellular membranes which all affect the incorporation of proteins on solid surfaces. Much of this work is performed on artificial templates made of polymer sponges or porous materials based on alumina, mica, and porous silicon (PSi) surfaces. For example, porous silicon materials have high biocompatibility, biodegradability, and photoluminescence, which allow them to be used both as a support structure for lipid bilayers or a template to measure the electrochemical functionality of living cells grown over the surface as in vivo. The variety of these media, coupled with the complex physiological conditions present in living systems, warrant a summary and prospectus detailing which artificial systems provide the most promise for different biological conditions. This study summarizes the use of electrochemical impedance spectroscopy (EIS) data on artificial biological membranes that are closely matched with previously published biological systems using both black lipid membrane and patch clamp techniques.
Regarding the last question, Gromacs tools to measure protein tilt (relative to the bilayer z-axis) and the dimer crossing angle, please see attached file.
Hoping this will be helpful and Happy New Year,
Rafik
Dear Anthony,
regarding the first question, please find a recent paper on the use of Achembed:
1-J Chem Theory Comput. 2015 Jun 9; 11(6): 2743–2754.
Published online 2015 May 14. doi: 10.1021/ct501111d
PMCID: PMC4467903
Alchembed: A Computational Method for Incorporating Multiple Proteins into Complex Lipid Geometries
Elizabeth Jefferys,† Zara A. Sands,‡ Jiye Shi,‡ Mark S. P. Sansom,† and Philip W. Fowler*†
A necessary step prior to starting any membrane protein computer simulation is the creation of a well-packed configuration of protein(s) and lipids. Here, we demonstrate a method, alchembed, that can simultaneously and rapidly embed multiple proteins into arrangements of lipids described using either atomistic or coarse-grained force fields. During a short simulation, the interactions between the protein(s) and lipids are gradually switched on using a soft-core van der Waals potential. We validate the method on a range of membrane proteins and determine the optimal soft-core parameters required to insert membrane proteins. Since all of the major biomolecular codes include soft-core van der Waals potentials, no additional code is required to apply this method. A tutorial is included in the Supporting Information.
Regarding the latest techniques for measuring lipid bilayer surface area with an embedded protein, please see attached recent publication:
Int J Mol Sci. 2013 Nov; 14(11): 21561–21597.
Published online 2013 Oct 31. doi: 10.3390/ijms141121561
PMCID: PMC3856022
Engineering Lipid Bilayer Membranes for Protein Studies
Muhammad Shuja Khan,1 Noura Sayed Dosoky,2 and John Dalton Williams1,*
Author information ► Article notes ► Copyright and License information ►
This article has been cited by other articles in PMC.
Go to:
Abstract
Lipid membranes regulate the flow of nutrients and communication signaling between cells and protect the sub-cellular structures. Recent attempts to fabricate artificial systems using nanostructures that mimic the physiological properties of natural lipid bilayer membranes (LBM) fused with transmembrane proteins have helped demonstrate the importance of temperature, pH, ionic strength, adsorption behavior, conformational reorientation and surface density in cellular membranes which all affect the incorporation of proteins on solid surfaces. Much of this work is performed on artificial templates made of polymer sponges or porous materials based on alumina, mica, and porous silicon (PSi) surfaces. For example, porous silicon materials have high biocompatibility, biodegradability, and photoluminescence, which allow them to be used both as a support structure for lipid bilayers or a template to measure the electrochemical functionality of living cells grown over the surface as in vivo. The variety of these media, coupled with the complex physiological conditions present in living systems, warrant a summary and prospectus detailing which artificial systems provide the most promise for different biological conditions. This study summarizes the use of electrochemical impedance spectroscopy (EIS) data on artificial biological membranes that are closely matched with previously published biological systems using both black lipid membrane and patch clamp techniques.
Regarding the last question, Gromacs tools to measure protein tilt (relative to the bilayer z-axis) and the dimer crossing angle, please see attached file.
Hoping this will be helpful and Happy New Year,
Rafik
Many thanks Rafik,
Happy new year to you too :) This should make for some reading.
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