Activity Number 154

	Overview and Learning Objectives
	Assessment
	Central Concepts
	Textbook References
	Activity Credits
	Requirements

Docking: Binding of Complementary Surfaces

Interactive model, with minimal support

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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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	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. return to top



	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. return to top



	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 return to top



	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 return to top



	Activity Credits Created by CC Project: CCATOMS using Molecular Workbench return to top



	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. return to top

These materials are based upon work supported by the
National Science Foundation under grant number DUE-0402553

Any opinions, findings, and conclusions
or recommendations expressed in this material are those of
the author(s) and do not necessarily reflect the views
of the National Science Foundation.

Docking: Binding of Complementary Surfaces

Overview and Learning Objectives

Assessment

Central Concepts

Additional Related Concepts

Textbook References

Activity Credits

Requirements