Docking: Binding of Complementary Surfaces

Interactive model, with minimal support

Overview and Learning Objectives

This model allows students to explore a ligand-protein binding, showing a successful docking. By varying the model, students can discover the two most important factors in molecular recognition: attractive interactions between sites and shape complementarities. For example, if either one of the charges (or both) are removed, docking may not happen, or happen much more slowly (due to the weak van der Waals interactions between the complementary shapes, they may still have some chance to get together). If the shape compatibility is broken, for instance, if the ligand is made much larger than the cavity can accommodate, docking will never happen.

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Assessment

Imagine that an unwanted bacteria invades a cell. A certain molecule in the cell is capable of grabbing the bacteria and holding it so a bacteria-destroying macrophage can destroy it. Describe the properties and the forces of the "bacteria-capturing" molecule that enable it to attach and hold the invader.

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Central Concepts

Key Concept:

The binding of a protein with another is largely dictated by the topological and electrostatic complementarity of the two involved molecular surfaces and their response to water (hydrophobicity/hydrophilicity).

Additional Related Concepts

Biology

• Membrane

Molecular Biology

• Active site
• Complementarity
• Enzyme
• Molecular machine
• Protein
• Protein structure
• Recognition
• Self-assembly

Physics/Chemistry

• Charge
• Hydrophobicity
• Velocity

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Textbook References

• Biology: Concepts and Connections (Pearson) 5th Edition - Chapter 24: The Immune System
• Biology: Exploring Life - Chapter 5: The Molecules of Life
• BSCS Blue (8th Edition) - Chapter 23 - Immune System
• Cell Biology (Pollard and Earnshaw) Saunders 2002 - Chapter Four: Macromolecular AAssembly

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Activity Credits

Created by CC Project: CCATOMS using Molecular Workbench

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Requirements

• Java 1.5+ - Java 1.5+ is available for Windows, Linux, and Mac OS X 10.4 and greater. If you are using Mac OS X 10.3, you can download MW Version 1.3 and explore within it instead.

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