3D Protein Folding Simulation

Folding captionLive observation

Watch a connected amino-acid chain fold into a 3D structure.

ScenarioH—H

Fold fraction100%

Model contacts−28 kJ/mol

ShapeAttractive

3D Protein Folding LaboratoryPaused

ModeStudent

How does a protein chain fold?

Amino-acid sequence remains connected while the chain explores 3D shapes. Backbone hydrogen bonds and side-chain interactions can stabilize helices, sheets, and compact folds.

Primary: residue order.
Secondary: helix or sheet motifs.
Tertiary: distant regions pack together.

HydrophobicPolarPositiveNegative

Folding controls

Sound

Structure to explore

Temperature25°C

pH7.0

Hydrophobic attraction1.0×

Simulation speed1×

Contact guides Hydrophobic glow

Live folding measurements

Folded fraction86%

Contact guides formed0 / 0

Radius of gyration0.00 u

Free-energy score−7.5 model units

A coarse-grained demonstration, not a measured or predicted atomic structure.

3D camera and residue focus

Drag to rotate the chain in 3D; pinch or use zoom buttons.

Tap a residue to track its position and type.

Fold fraction history

Teacher demonstrations

Reveal quiz explanations

Guided visual lecture

Chapter 1 of 80%

Ready. The first ten seconds define protein folding with a changing 3D chain.

Language

Narrator

Playback speed1×

External recording: share this browser tab with tab audio enabled. No microphone is used. No built-in recorder is included.

1. What is protein folding?

Watch: A chain bends into a 3D shape.

Chapters

A simplified folding model

Thermodynamics: ΔG = ΔH − TΔS. A favorable negative free-energy change can favor a fold under specified conditions; real proteins have complex landscapes.

Classroom score: ΔG_model = scenario baseline − 2.5(h − 1) + 0.19(T − 25) + 0.55(pH − 7)². Here h is hydrophobic attraction, T is °C, and the score has arbitrary model units.

Model folded estimate: P(folded) = 1 / [1 + exp(ΔG_model / 2.2)]. The animation relaxes toward this estimate; it is not a measured probability for a named protein.

Radius of gyration: Rg = √[mean distance squared from chain center]. Smaller Rg means a more compact chain.

The 24-bead chain, contact guides, and preset shapes teach primary, secondary, and tertiary structure. They are not atomistic dynamics or an AI structure prediction. Denaturation here preserves the peptide backbone.

Learning objectives

Distinguish primary sequence, secondary motifs, and tertiary packing.
Identify alpha-helix and beta-sheet hydrogen-bond patterns.
Explain why hydrophobic side chains often pack inward.
Predict how heat or extreme pH can disrupt contacts.

Suggested investigations

Rotate a helix face-on and edge-on.
Trace the connected backbone through a beta sheet.
Heat the compact fold, then cool it and compare size.
Move pH toward an extreme and observe the contact count.

Questions for exploration

What remains unchanged when the chain unfolds?
Why might a hydrophobic interior stabilize a soluble fold?
Why does a simplified model not predict an exact real structure?

Teacher whiteboard

Use a finger, stylus, mouse, Android device, or smart board. Ten full-size pages keep their own drawings.

Pen color

Line width4

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Knowledge check

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