Molecular Dynamics of Membrane Proteins
Build, equilibrate, and analyze a real lipid bilayer system with CHARMM-GUI Membrane Builder.
About this course
A hands-on follow-on to Introduction to Molecular Dynamics focused entirely on membrane protein systems - a genuinely different setup and analysis problem from soluble proteins. You'll use CHARMM-GUI Membrane Builder to embed a protein in a lipid bilayer, run a membrane-appropriate staged equilibration with semi-isotropic pressure coupling, and compute the structural metrics unique to membranes: area per lipid, bilayer thickness, and deuterium order parameters, closing with an analysis of how the protein perturbs its local lipid environment.
Who it's for
Graduates of Introduction to Molecular Dynamics (or anyone who passes its qualifying exam) who want to extend their simulation skills to membrane proteins - a substantial fraction of all drug targets and a genuinely different system-building and analysis problem from soluble proteins.
Prerequisites
Requires Introduction to Molecular Dynamics with GROMACS and CHARMM-GUI - OR solid prior background and hands-on practical experience with MD simulation using GROMACS, proven by scoring at least 85% on the qualifying exam.
Either of the following qualifies you:
- Completed Introduction to Molecular Dynamics with GROMACS and CHARMM-GUI
- Or: solid prior background and hands-on experience with MD simulation using GROMACS, proven by scoring at least 85% on the qualifying exam
Learning outcomes
By the end of this course you will be able to build a membrane protein system with CHARMM-GUI Membrane Builder, run a correctly staged membrane equilibration with semi-isotropic pressure coupling, compute and validate area per lipid, bilayer thickness, and deuterium order parameters against experimental references, and assess local protein-lipid perturbation.
Weekly structure
Building a Membrane Protein System with CHARMM-GUI
Why membrane systems need a fundamentally different build process than soluble proteins, and using CHARMM-GUI's Membrane Builder to embed a protein in a lipid bilayer.
Membrane-Specific Equilibration
Why a lipid bilayer needs a fundamentally different, more staged equilibration protocol than a soluble protein, and how to verify it actually worked.
Production and Membrane-Specific Analysis
Running production dynamics on an equilibrated membrane system and computing the structural metrics unique to membrane simulations: area per lipid over production, bilayer thickness, and deuterium order parameters.
Protein-Lipid Interactions and Capstone
How the embedded protein influences the surrounding bilayer's local structure, and a capstone bringing together the full membrane simulation and analysis pipeline.
- Duration
- 4 weeks
- Commitment
- Approximately 5–7 hours per week, including one scheduled live laboratory session.
- Certificate
- Included
- Cost
- Free
Cohorts
No cohort has been scheduled yet.
No cohort is open for applications right now.