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English

ID: <

50|dedup_wf_001::5fd93248873013c1013a4df4cdc19ba5

>

·

DOI: <

10.5061/dryad.ph510

>

Where these data come from
Data from: Force transduction and lipid binding in MscL: a continuum-molecular approach

Abstract

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. 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

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