Tutorials

This tutorial provides a guide on how to construct a curved coarse-grained membrane system using the cmem builder. Depending on the research requirements, different Martini models can be selected, and a membrane system with curvature can be built based on PPM reference surfaces. ## 1. Main Options The web server provides three main entry points: - **PDB Options** - **Non-PDB** - **CG Page** This section will mainly explain PDB Options; Non-PDB and CG Page will be covered at the end.

### **PDB Options** This mode requires a PDB file that contains membrane curvature information. You can obtain such files in two ways: - **Download from OPM (Orientations of Proteins in Membranes)** The OPM database provides pre-oriented membrane protein structures, and a subset of them (~150 entries) include **precomputed curvature** information. These entries have been integrated into **CMEM**, so users only need to enter a **PDB ID** (e.g., `1xq8`) to proceed. - **Generate a PDB file with membrane curvature using PPM 3.0** Alternatively, you can **upload a PDB file** generated by **PPM 3.0**, . As illustrated using the example protein **1xq8** in **Figure 1A**, the web server will automatically extract Bezier control points from the uploaded or selected structure to generate a reference curvature profile (**Figure 1B**). You may **manually adjust the control points** if needed, to better reflect your desired membrane shape or to fine-tune alignment. ### 2. Select Martini Models The available Martini models are shown in **Figure 1A**. Please **choose the appropriate version** based on your research needs (e.g., Martini 2.2, Martini 3.0). Click the **"Martinize"** button to proceed with coarse-graining the uploaded or selected protein structure. This step uses the `martinize2` tool under the hood. If any errors occur, please refer to the error messages shown on the interface and **check your input PDB file**. ## 3. Selecting Lipid Composition In this step, you can choose the lipid composition of the **outer layer** and **inner layer** of the membrane: 1. Select the **Category**, then choose the specific **Lipid**. 2. Enter the proportion for each lipid. 3. Click **Add Lipid Layer** to confirm the addition. 4. If a lipid is added incorrectly, click **Delete** to remove it. Refer to **Figure 2A** for guidance.

## 4. Adjusting Membrane Parameters & Model Construction Before constructing the membrane system, the following parameters can be adjusted to optimize membrane density and structure. Please refer to the relevant publications for detailed explanations. In most cases, users only need to adjust the **simulation box size**, as shown in **Figure 2B**. ## 5. Selecting the Final Output

Finally, users can choose between two output formats, as shown in **Figure 3**: - **Membrane-Only System** - **Protein/Membrane System** With this, the construction process for the curved Martini coarse-grained membrane system is complete! ------ ### **Non-PDB Option** If you only want to construct a **Membrane-Only System**, no PDB file is required. Users can define a custom Bezier curve by specifying control points to generate the desired membrane shape. ------ ### **CG Option** Users can upload a `cg.pdb` file directly and define a custom Bezier curve to build the desired membrane shape. The uploaded CG structure will be inserted at the membrane center based on its **geometric center**. Users can further adjust the **Z-translation** to fine-tune the relative position between the protein and the membrane. ----- **References:** [1] Monticelli, L.; Kandasamy, S. K.; Periole, X.; Larson, R. G.; Tieleman, D. P.; Marrink, S.-J. The MARTINI Coarse-Grained Force Field: Extension to Proteins. *J. Chem. Theory Comput.* **2008**, *4* (5), 819–834. https://doi.org/10.1021/ct700324x. [2] Periole, X.; Cavalli, M.; Marrink, S.-J.; Ceruso, M. A. Combining an Elastic Network With a Coarse-Grained Molecular Force Field: Structure, Dynamics, and Intermolecular Recognition. *J. Chem. Theory Comput.* **2009**, *5* (9), 2531–2543. https://doi.org/10.1021/ct9002114. [3] Souza, P. C. T.; Alessandri, R.; Barnoud, J.; Thallmair, S.; Faustino, I.; Grünewald, F.; Patmanidis, I.; Abdizadeh, H.; Bruininks, B. M. H.; Wassenaar, T. A.; Kroon, P. C.; Melcr, J.; Nieto, V.; Corradi, V.; Khan, H. M.; Domański, J.; Javanainen, M.; Martinez-Seara, H.; Reuter, N.; Best, R. B.; Vattulainen, I.; Monticelli, L.; Periole, X.; Tieleman, D. P.; de Vries, A. H.; Marrink, S. J. Martini 3: A General Purpose Force Field for Coarse-Grained Molecular Dynamics. *Nat. Methods* **2021**, *18* (4), 382–388. https://doi.org/10.1038/s41592-021-01098-3. [4] Lomize, M. A.; Pogozheva, I. D.; Joo, H.; Mosberg, H. I.; Lomize, A. L. OPM Database and PPM Web Server: Resources for Positioning of Proteins in Membranes. *Nucleic Acids Res.* **2011**, *40* (D1), D370–D376. https://doi.org/10.1093/nar/gkr703. [5] Lomize, A. L.; Todd, S. C.; Pogozheva, I. D. Spatial Arrangement of Proteins in Planar and Curved Membranes by PPM 3.0. *Protein Sci.* **2022**, *31* (1), 209–220. https://doi.org/10.1002/pro.4219. [6] Kroon, P.; Grunewald, F.; Barnoud, J.; van Tilburg, M.; Souza, P.; Wassenaar, T.; Marrink, S. Martinize2 and Vermouth: Unified Framework for Topology Generation. **2024**. https://doi.org/10.7554/elife.90627.2. [7] Marrink, S. J.; Corradi, V.; Souza, P. C. T.; Ingólfsson, H. I.; Tieleman, D. P.; Sansom, M. S. P. Computational Modeling of Realistic Cell Membranes. *Chem. Rev.* **2019**, *119* (9), 6184–6226. https://doi.org/10.1021/acs.chemrev.8b00460.