Membrane Proteins, Coarse-Grain & Lipid Systems — Hands-on

Learn how to prepare and simulate membrane protein systems using both atomistic and coarse-grained approaches. This module covers bilayer building, lipid composition choices, protein insertion/orientation, CG mapping and system setup so that you can generate robust membrane and lipid systems for MD, free-energy and design workflows.

Membrane Proteins, Coarse-Grain & Lipid Systems

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Session Index

Session 1 — Membrane Protein Basics & Topology Session 2 — Bilayer Building, Lipid Mixes & Insertion Session 3 — Coarse-Grain Mapping & CG System Setup Session 4 — Mini Capstone: Atomistic↔CG Membrane System

Session 1

Fee: Rs 8800

Membrane Protein Basics & Topology

Membrane protein classes and architecture overview

single pass and multi pass helices beta barrels and channels peripheral vs integral proteins

Topology prediction and orientation in the membrane

transmembrane segment detection ideas inside outside and tilt considerations aligning structures to membrane normal

Preparing membrane protein structures for embedding

fixing loops and missing residues removing unwanted partners and detergents checking hydrophobic and polar exposure

Session 2

Fee: Rs 11800

Bilayer Building, Lipid Mixes & Insertion

Choosing bilayer composition and dimensions

simple vs mixed lipid systems headgroup and tail saturation effects asymmetric vs symmetric leaflets ideas

Bilayer building and quality checks before insertion

area per lipid and thickness checks packing issues and voids equilibration of pure lipid patches

Protein insertion and overlap removal concepts

punching lipids around the protein preserving tilt and orientation initial restrained equilibration of embedded system

Session 3

Fee: Rs 14800

Coarse-Grain Mapping & CG System Setup

Coarse-grain modeling principles for membranes

mapping atoms to beads concepts trade off between speed and detail when to choose CG vs atomistic

Protein and lipid mapping to CG force fields

standard mapping schemes overview tuning elastic networks for proteins ensuring proper lipid phase behaviour

Setting up and equilibrating CG membrane systems

box size and timestep choices CG specific thermostat and barostat settings converting CG outputs into analysis ready trajectories

Session 4

Fee: Rs 18800

Mini Capstone: Atomistic↔CG Membrane System

Select a membrane protein and define bilayer and CG strategy

Theory + Practical

Build atomistic and CG versions of the same system and equilibrate briefly

compare thickness, area per lipid and tilt qualitative comparison of dynamics prepare configurations for longer production runs

Deliverables: membrane system build files and comparison report

topology and coordinates for both resolutions summary tables for bilayer properties documented workflow for future membrane projects

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Membrane Proteins, Coarse-Grain & Lipid Systems Training | Bilayers, CG Mapping & Membrane MD

Membrane Proteins, Coarse-Grain & Lipid Systems — Hands-on