Introduction to Molecular Graphics Molecular Immunology (AIM 620) Assignments and Resources for class February 24 4:15-6:45 PM Luther Bonney 203 Gale Rhodes Chemistry Department University of Southern Maine   PLEASE NOTE: I DESIGN MY CLASSES FOR PREPARED STUDENTS. See assignments below.
Model of the D10 T cell receptor (TCR, blue and yellow ribbon), a 16-residue foreign peptide antigen (space filling model), and the I-A(k) self major histocompatibility complex (MHC) class II molecule (green and red ribbon). View produced with Swiss-PdbViewer from an x-ray crystallographic model of the complex at 3.2 angstroms. See Science, 286(5446), pages1913-1921 (1999 Dec 3).

Reading Assignments

Professor Ng will provide the following materials. Please read them BEFORE coming to class on February 10.

1. Crystallography Made Crystal Clear, 2nd edition, Gale Rhodes, Academic Press, 2000, Chapters 1, 2, 10, and 11. PLEASE NOTE: Some illustrations in this reading are color plates that do not make useable copies. You may see them by visiting the Chemistry Department office (161 Science Building, Portland), where a copy of the book is kept.
2. Reinherz EL, et al, The Crystal Structure of a T Cell Receptor in Complex with Peptide and MHC Class II., Science, vol 286 (#5446), pages1913-1921 (1999 Dec 3).
3. Molecular Modeling for Beginners -- A Tutorial Introduction to Deep View (formerly SwissPdb-Viewer).

Outline of Class

Brief Introduction to Protein Structure

Click HERE for structure basics.

Where Macromolecular Models Come From

Click HERE for slides in a new browser window.

1. X-Ray Crystallography
2. NMR Spectroscopy
3. Homology Modeling

Public Access to Models

1. Protein Data Bank
2. Other Repositories of Models
3. Tools For Viewing Models, featuring Swiss-PdbViewer.

Deep View Demonstration

(as many topics as time allows)

1. Viewing Models
2. Exploring an Unfamiliar Structure
3. Structure Analysis
4. Judging the Quality of Models
5. Comparison of Structures
6. Making Pictures for Publication

Resources

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Deep View (formerly SwissPdbViewer)

• All About Deep View
• Get and Install Deep View
• Set Your Web Browser to Use Deep View
• DON'T MISS THIS: Learn Deep View from a Tutorial for Beginners
• SEE MOLECULAR-STRUCTURE LIKE NEVER BEFORE: Learn to View Models in 3D.

Sources of Models

• Protein Data Bank ||| Repository of all public X-ray and NMR models
• SWISS-MODEL Repository ||| Automatically generated homology models
• HIC-UP ||| Models of small biomolecules (cofactors, prosthetic groups, substrates)

HELP: Protein Data Bank (X-ray and NMR Models)

• General Introduction to PDB
• Downloading Files from PDB
• SearchLite: Simple PDB Searches
• SearchFields: Advanced PDB Searches

HELP: Swiss-Model Repository (Theoretical Models)

• All About Swiss-Model
• 3DCrunch: Automated Generation of Homology Models
• Search the Swiss-Model Repository, a Database of Homology and Other Theoretical Models

HELP: Bioinformatics and Homology Modeling

• Bioinformatics for Beginners: Tutorial introduction to bioinformatics, including structure determination of the human retinal pigment-like protein peropsin.

Files Used in Deep View Demonstrations

• Cytochrome b5 ||| Good first crytstallographic model for beginners to explore with Deep View.
• Rusticyanin ||| Good first NMR model for beginners to explore with Deep View -- ensemble of 15 models.
• PDB File of TCR/MHC/Peptide Complex ||| Specially prepared Deep View file, color coded as in the figure above.
• PDB File 1D9K ||| Original PDB file of TCR/MHC/Peptide complex, containing all file header information. This file contains two full models.
• Comparison of Germline and Mature Antibodies ||| Specially Prepared Deep View Project files containing four Fab models: germline and mature antibodies with and without bound hapten.

More About Structure Determination

• ORDER the book Crystallography Made Crystal Clear: A Guide for Users of Macromolecular Models,by Gale Rhodes, Academic Press, 2000.
• CMCC Home: Resources for readers of Crystallography Made Crystal Clear, providing links to web sites that extend your knowledge of macromolecular structure. You don't need the book to make full use of this page.
• Judging the Quality of Macromolecular Models: Decipher the terminology in structure-determination papers with this illustrated, plain-language glossary of terms from crystallography, NMR, and homology modeling.

Other Goodies

• What's In a PDB File?
• ExPASy: The Expert Protein Analysis System
• Kevin Cowtan's Book of Fourier: Vivid demos show how x-ray diffraction reveals structure.

Images on this page prepared with SwissPdbViewer.

TO: Gale Rhodes's Home Page

TO: USM Chemistry Home Page

Copyright 2000 Gale Rhodes

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