DOI: 10.5061/dryad.ph510
title: Data from: Force transduction and lipid binding in MscL: a continuum-molecular approach

description: The bacterial mechanosensitive channel MscL, a small protein mainly
 activated by membrane tension, is a central model system to study the
 transduction of mechanical stimuli into chemical signals. Mutagenic
 studies suggest that MscL gating strongly depends on both intra-protein
 and interfacial lipid-protein interactions. However, there is a gap
 between this detailed chemical information and current mechanical models
 of MscL gating. Here, we investigate the MscL bilayer-protein interface
 through molecular dynamics simulations, and take a combined
 continuum-molecular approach to connect chemistry and mechanics. We
 quantify the effect of membrane tension on the forces acting on the
 surface of the channel, and identify interactions that may be critical in
 the force transduction between the membrane and MscL. We find that the
 local stress distribution on the protein surface is largely asymmetric,
 particularly under tension, with the cytoplasmic side showing
 significantly larger and more localized forces, which pull the protein
 radially outward. The molecular interactions that mediate this behavior
 arise from hydrogen bonds between the electronegative oxygens in the lipid
 headgroup and a cluster of positively charged lysine residues on the
 amphipathic S1 domain and the C-terminal end of the second trans-membrane
 helix. We take advantage of this strong interaction (estimated to be 10–13
 kT per lipid) to actuate the channel (by applying forces on protein-bound
 lipids) and explore its sensitivity to the pulling magnitude and
 direction. We conclude by highlighting the simple motif that confers MscL
 with strong anchoring to the bilayer, and its presence in various integral
 membrane proteins including the human mechanosensitive channel K2P1 and
 bovine rhodopsin.
description: Membrane Protein
 EquilibrationThese are MD
 trajectories to accompany the paper: "Lipid Binding and Force
 Transduction in MscL: A Continuum-Molecular Approach" by Juan M.
 Vanegas and Marino Arroyo. PLoS ONE 2014. All trajectories were generated
 with GROMACS version 4.5.5 (www.gromacs.org). All trajectoories can be
 read and analyzed by the standard GROMACS utilities. Trajectories (.xtc)
 can also be visualized by common molecular graphics programs such as UCSF
 Chimera (http://www.cgl.ucsf.edu/chimera/) or VMD
 (http://www.ks.uiuc.edu/Research/vmd/). Topology files in text (.top) and
 binary (.tpr) form are included, as well as simulation parameters (.mdp).
 In some cases text files (.xvg) including coordinate information are also
 included. The file MscL_Equilibration.tar.gz contains the trajectory
 corresponding to the 500 ns equilibration period of the MscL Channel
 embedded in the POPE bilayer. The file Local_Stress_and_Traction.tar.gz
 contains the trajectories for the tensionless and tensioned simulations,
 as well as the files needed to visualize the traction on the surface of
 the protein. The stress tensor was calculated with a custom version of
 GROMACS (http://www.lacan.upc.edu/LocalStressFromMD) and the files can be
 visualized with the program ParaView. The file
 Arrhenius_Bell_unbinding.tar.gz contains the steered MD simulation
 trajectories used to estimate the strength of lipid binding to the MscL
 protein. The file Channel_Actuation.tar.gz contains the steered MD
 simulation trajectories used to actuate the MscL channel by pulling on
 protein-bound lipids. Finally, the file force_field_parameters.tar.gz
 contains the parameters used in all of the simulations. We used the
 G43A1-S3 lipid parameters in combination with the G54A7 protein
 parameters.Vanegas-MscL_Equilibration.tar.gzSteered Simulations to Estimate Lipid Binding InteractionThese are MD trajectories to accompany the paper: "Lipid Binding and Force Transduction in MscL: A Continuum-Molecular Approach" by Juan M. Vanegas and Marino Arroyo. PLoS ONE 2014. All trajectories were generated with GROMACS version 4.5.5 (www.gromacs.org). All trajectoories can be read and analyzed by the standard GROMACS utilities. Trajectories (.xtc) can also be visualized by common molecular graphics programs such as UCSF Chimera (http://www.cgl.ucsf.edu/chimera/) or VMD (http://www.ks.uiuc.edu/Research/vmd/). Topology files in text (.top) and binary (.tpr) form are included, as well as simulation parameters (.mdp). In some cases text files (.xvg) including coordinate information are also included. The file MscL_Equilibration.tar.gz contains the trajectory corresponding to the 500 ns equilibration period of the MscL Channel embedded in the POPE bilayer. The file Local_Stress_and_Traction.tar.gz contains the trajectories for the tensionless and tensioned simulations, as well as the files needed to visualize the traction on the surface of the protein. The stress tensor was calculated with a custom version of GROMACS (http://www.lacan.upc.edu/LocalStressFromMD) and the files can be visualized with the program ParaView. The file Arrhenius_Bell_unbinding.tar.gz contains the steered MD simulation trajectories used to estimate the strength of lipid binding to the MscL protein. The file Channel_Actuation.tar.gz contains the steered MD simulation trajectories used to actuate the MscL channel by pulling on protein-bound lipids. Finally, the file force_field_parameters.tar.gz contains the parameters used in all of the simulations. We used the G43A1-S3 lipid parameters in combination with the G54A7 protein parameters.Vanegas-Arrhenius_Bell_unbinding.tar.gzLocal Stress and TractionThese are MD trajectories to accompany the paper: "Lipid Binding and Force Transduction in MscL: A Continuum-Molecular Approach" by Juan M. Vanegas and Marino Arroyo. PLoS ONE 2014. All trajectories were generated with GROMACS version 4.5.5 (www.gromacs.org). All trajectoories can be read and analyzed by the standard GROMACS utilities. Trajectories (.xtc) can also be visualized by common molecular graphics programs such as UCSF Chimera (http://www.cgl.ucsf.edu/chimera/) or VMD (http://www.ks.uiuc.edu/Research/vmd/). Topology files in text (.top) and binary (.tpr) form are included, as well as simulation parameters (.mdp). In some cases text files (.xvg) including coordinate information are also included. The file MscL_Equilibration.tar.gz contains the trajectory corresponding to the 500 ns equilibration period of the MscL Channel embedded in the POPE bilayer. The file Local_Stress_and_Traction.tar.gz contains the trajectories for the tensionless and tensioned simulations, as well as the files needed to visualize the traction on the surface of the protein. The stress tensor was calculated with a custom version of GROMACS (http://www.lacan.upc.edu/LocalStressFromMD) and the files can be visualized with the program ParaView. The file Arrhenius_Bell_unbinding.tar.gz contains the steered MD simulation trajectories used to estimate the strength of lipid binding to the MscL protein. The file Channel_Actuation.tar.gz contains the steered MD simulation trajectories used to actuate the MscL channel by pulling on protein-bound lipids. Finally, the file force_field_parameters.tar.gz contains the parameters used in all of the simulations. We used the G43A1-S3 lipid parameters in combination with the G54A7 protein parameters.Vanegas-Local_Stress_and_Traction.tar.gzSteered Simulations to Actuate the ChannelThese are MD trajectories to accompany the paper: "Lipid Binding and Force Transduction in MscL: A Continuum-Molecular Approach" by Juan M. Vanegas and Marino Arroyo. PLoS ONE 2014. All trajectories were generated with GROMACS version 4.5.5 (www.gromacs.org). All trajectoories can be read and analyzed by the standard GROMACS utilities. Trajectories (.xtc) can also be visualized by common molecular graphics programs such as UCSF Chimera (http://www.cgl.ucsf.edu/chimera/) or VMD (http://www.ks.uiuc.edu/Research/vmd/). Topology files in text (.top) and binary (.tpr) form are included, as well as simulation parameters (.mdp). In some cases text files (.xvg) including coordinate information are also included. The file MscL_Equilibration.tar.gz contains the trajectory corresponding to the 500 ns equilibration period of the MscL Channel embedded in the POPE bilayer. The file Local_Stress_and_Traction.tar.gz contains the trajectories for the tensionless and tensioned simulations, as well as the files needed to visualize the traction on the surface of the protein. The stress tensor was calculated with a custom version of GROMACS (http://www.lacan.upc.edu/LocalStressFromMD) and the files can be visualized with the program ParaView. The file Arrhenius_Bell_unbinding.tar.gz contains the steered MD simulation trajectories used to estimate the strength of lipid binding to the MscL protein. The file Channel_Actuation.tar.gz contains the steered MD simulation trajectories used to actuate the MscL channel by pulling on protein-bound lipids. Finally, the file force_field_parameters.tar.gz contains the parameters used in all of the simulations. We used the G43A1-S3 lipid parameters in combination with the G54A7 protein parameters.Vanegas-Channel_Actuation.tar.gzForce Field ParametersThese are MD trajectories to accompany the paper: "Lipid Binding and Force Transduction in MscL: A Continuum-Molecular Approach" by Juan M. Vanegas and Marino Arroyo. PLoS ONE 2014. All trajectories were generated with GROMACS version 4.5.5 (www.gromacs.org). All trajectoories can be read and analyzed by the standard GROMACS utilities. Trajectories (.xtc) can also be visualized by common molecular graphics programs such as UCSF Chimera (http://www.cgl.ucsf.edu/chimera/) or VMD (http://www.ks.uiuc.edu/Research/vmd/). Topology files in text (.top) and binary (.tpr) form are included, as well as simulation parameters (.mdp). In some cases text files (.xvg) including coordinate information are also included. The file MscL_Equilibration.tar.gz contains the trajectory corresponding to the 500 ns equilibration period of the MscL Channel embedded in the POPE bilayer. The file Local_Stress_and_Traction.tar.gz contains the trajectories for the tensionless and tensioned simulations, as well as the files needed to visualize the traction on the surface of the protein. The stress tensor was calculated with a custom version of GROMACS (http://www.lacan.upc.edu/LocalStressFromMD) and the files can be visualized with the program ParaView. The file Arrhenius_Bell_unbinding.tar.gz contains the steered MD simulation trajectories used to estimate the strength of lipid binding to the MscL protein. The file Channel_Actuation.tar.gz contains the steered MD simulation trajectories used to actuate the MscL channel by pulling on protein-bound lipids. Finally, the file force_field_parameters.tar.gz contains the parameters used in all of the simulations. We used the G43A1-S3 lipid parameters in combination with the G54A7 protein parameters.Vanegas-force_field_parameters.tar.gz