Graphics Gallery

Gale Rhodes
Chemistry Department
University of Southern Maine

Revised 2006/08/02

Learn how to use Swiss-PdbViewer. Work through sections 1-4 of the Swiss-PdbViewer Tutorial.

Topic: Regulation of Gene Expression

Examples

Molecules commonly discussed in biochemistry texts

Lac Repressor

To study the structure of lac repressor bound to DNA, obtain the file 1EFA from the Protein Data Bank.

This file contains half of the functional dimer illustrated in most textbooks. The information needed to construct the full dimer should be in REMARK lines 350, but instead of appropriate transformation matrices, the file provides identity matrices, which will not change any of the coordinates. For a procedure for generating oligomers using such matrices, see CAP, below.

1. What structural motifs in the protein are involved in binding to DNA?
2. Does binding occur in the major of minor groove of DNA?
3. Find sequence-nonspecific interactions between the protein and the DNA backbone.
4. Find sequence-specific interactions between protein and DNA bases.
5. B-DNA is distorted by binding to this protein. Describe the effects of binding on the width of the major and minor grooves and on the curvature of the DNA.
6. Approximately what is the angle made by the two ends of the bound DNA? Can Deep View help you to measure this angle?

Catabolite Gene Activator Protein (CAP)

To study the structure of CAP bound to cyclic AMP (cAMP) and DNA, obtain the file 2CGP from the Protein Data Bank.

This file contains half of the functional dimer illustrated in most textbooks. The information needed to construct the full dimer is contained in REMARK lines 350. Here's how to generate the dimer:

1. Open file 2CGP.
2. Open the file again, giving two superimposed copies.
3. Click on the document icon of the Tool Bar to open the PDB file. Scroll down the file to lines number 350. You will find information about generating the full biological molecule, a dimer, from the monomer provided.
4. The numbers to the right of "BIOMT1 2", "BIOMT2 2", and "BIOMT3 2" (starting with -0.5, ending with with 48.6) constitute a transformation matrix, which moves a set of atomic coordinates to new positions.
5. Shrink the text window and move it down to the bottom of the screen. Scroll to display the transformation matrix.
6. Make the second 2CGP model active and Select: All.
7. Select Tools: Apply Transformation on Current Layer. A matrix table appears. Copy the leftmost 3 columns of numbers from the transformation matrix into the rotation table (first three rows of the matrix table). Copy the rightmost three numbers into the translation table (bottom three rows of the matrix table).
8. Click OK.

Display both layers, and you will see the full dimeric CAP model. Select Color: Layer to see the two components of the dimer. Select Color: Chain to see individual chains of both models.

You can save the combined model by selecting Save: Project.

1. Find the cAMP binding sites. What interactions hold the cAMP molecules in place?
2. What structural motifs in the protein are involved in binding to DNA?
3. Does binding occur in the major of minor groove of DNA?
4. Find sequence-nonspecific interactions between the protein and the DNA backbone.
5. Find sequence-specific interactions between protein and DNA bases.
6. B-DNA is distorted by binding to this protein. Describe the effects of binding on the width of the major and minor grooves and on the curvature of the DNA.
7. Approximately what is the angle made by the two ends of the bound DNA? Can Deep View help you to measure this angle?

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