Activity Number
156
Editable
Overview and Learning Objectives
Central Concepts
Textbook References
Extensions and Connections
Activity Credits
Requirements

Protein Substrate Docking (3-interlinked pages of related demonstration models)

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, using real molecular thermodynamics, shows a docking process, in which one particle is "captured" by another. The user can manipulate the charge and participate in what is a central problem in enzyme catalysis and antigen-antibody interactions.

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Central Concepts

Key Concept:

The shapes of molecular surfaces and electrostatic potential distributions are believed to be the major factors that govern docking.

Additional Related Concepts

Molecular Biology

  • Active site
  • Antibody-antigen
  • Complementarity
  • Enzyme
  • Protein Function

Physics/Chemistry

  • Catalysis
  • Catalyst

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Textbook References

  • Biology (Miller and Levine) Prentice Hall 5th Edition - Unit 2: Chapter 7 - Nucleic Acids and Protein Synthesis
  • Cell Biology (Pollard and Earnshaw) Saunders 2002 - Chapter 18: Protein Synthesis and Folding in the Cytoplasm

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Extensions and Connections

Additional Protein Activities of Interest in the Database

The Structure of Proteins: Insulin (for high school)(#236)

The Structure of Proteins: Insulin (for college)(#228)

Forces for Folding: Charge

Effect of Charges on Folding: A Strongly Polar Conformation (#213) Effect of Charges on Folding: An Alternately-Charged Conformation (#209) Electrostatic Self-Assembly (#157) How a Protein Gets Its Shape: The Role of Charge (#76) Intermolecular interactions of proteins in water (#211)

Coding for Folds

How a Protein Gets Its Shape: The Role of DNA as Code (#161) Protein Shaping: (Module 4-5 days) From DNA to Proteins (#159)

Particular Proteins

Melittin Protein (#87) Sickle Cell Anemia Fragment (#162)

General teaching proteins

Protein folding starting from a random coil: a long polypeptide (#207) Amino Acids and Water: 20 Alanine Model (#160) Protein Polymer with 20 Glutamic Acids (#21) Protein Polymer with 48 Amino Acids (#22)

The Effect of Structures and Subforces on Protein (#132)

Functions

Docking: Binding of Complementary Surfaces (#154) Recognition and Self-Assembly

Tool to see a set of proteins: Molecular Viewer (#185)

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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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NSF Logo
These materials are based upon work supported
by the National Science Foundation under grant numbers
9980620, ESI-0242701, EIA-0219345, DUE-0402553, and 0628181.

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.