When modeling conformational changes in proteins, one of the most common challenges is finding plausible transition pathways between different conformations. It’s especially valuable when you have experimentally resolved structures representing both the start and goal conformations, but no information on how the transition occurs in between. If you’re working with such data, you may have wondered: how much of the protein really needs to move?
The Protein Path Finder app in SAMSON offers a visual and interactive way to explore protein conformational transitions. One particularly useful feature is the ability to define active atoms that guide the movement of the rest of the protein structure. This focused approach can lead to more efficient and biologically meaningful path searches.
What Are Active ARAP Atoms?
The app makes use of the ARAP method to define how a protein moves during conformational transitions. In this method, you choose a small subset of atoms as active—these will be manipulated to generate movement—while the rest move in a way that preserves structural rigidity as much as possible.
This simplifies computations and allows finer control over the path search. Carefully selecting these atoms can result in faster searches and more interpretable conformational changes.
How to Select Active Atoms
In the tutorial example, the active atoms are alpha-carbon atoms from two residues: GLY 12 and ARG 123. These residues are often located in functionally important domains undergoing motion. Here’s how to select them:
- Use the Document view in SAMSON.
- Locate the group labeled
CA in GLY 12 and CA in ARG 123. - Double-click the group to select these atoms.
- In the Protein Path Finder app, click Add to register them as active ARAP atoms.
Once selected, these atoms will control the motion of the protein during the path search. You’ll immediately see visual feedback: active atoms appear in green, and a visualization of the sampling box is shown.
This makes it easy to review your selection and make changes before proceeding. You can also use SAMSON’s Node Specification Language to make complex selections, for example:
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1 |
("CA" in "GLY 12") or ("CA" in "ARG 123") |
This flexibility lets you tailor your search setup to the specific biological system you’re studying.
Why It Matters
Not every atom in a protein needs to be sampled directly to produce meaningful results. By defining just a few key atoms as active, you can:
- Reduce computational cost
- Guide the movement in a biologically relevant manner
- Simplify interpretation of the transition pathways
If your interest is in domain movements, hinge motions, or gate-type conformational changes, active atom selection is a practical strategy you can use today with SAMSON.
To learn more about the full process of setting up conformational path searches, see the complete tutorial at this link.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.