MolSlides.Org

Start or Spacebar for First Slide.
Copyright © 2005 by Karl Oberholser,
Messiah College, Grantham PA USA.
Permission is hereby granted to use this document, or portions thereof, for non-profit educational purposes, provided this copyright statement remains intact within this document, or any portions or derivatives. Other uses require explicit permission from the author(s).
Designed for window of 1024 x 768 pixels. Viewing Help & Troubleshooting.. (at bottom).
Spacebar/Enter for next slide, Backspace for previous. More keystrokes.. (at bottom)
1 Next Bottom 2 3 4 5 6 7 8 9 View Bpti_pipe in ProteinExplorer.Org Made with MolSlides.Org

BPTI Structure
Spacefill Display

Tertiary structure gives a distorted ellipsoidal shape.

Made with MolSlides.Org

2 Next Previous 1 3 4 5 6 7 8 9 View Bpti_pipe in ProteinExplorer.Org

Wireframe
Bound Water

A water soluble globular protein would be surrounded with a layer of water, and this view of BPTI shows a portion of the first layer of water. The molecular structure of this layer is highly organized. As you can observe, this order is due to the hydrogen bonding of water molecules to specific side chains and to other water molecules.

Made with MolSlides.Org

3 Next Previous 1 2 4 5 6 7 8 9 View Bpti_pipe in ProteinExplorer.Org

Backbone Trace
On the Wireframe

The tracing of the backbone shows how the backbone of the polypeptide is folded to give the ellipsoidal shape.

Made with MolSlides.Org

4 Next Previous 1 2 3 5 6 7 8 9 View Bpti_pipe in ProteinExplorer.Org

Backbone Only

XXXXXXXXXX XXXXXXXX XXXXXXXXXX XXXXXXXXX XXX XXXXXXXX XXXXXXXXXXX XXXXXX XXXXXX XXXXXX XXXXXXXXXX XXXXXXXXX XXXXXXXXXX

Made with MolSlides.Org

5 Next Previous 1 2 3 4 6 7 8 9 View Bpti_pipe in ProteinExplorer.Org

Secondary Structure
Alpha Helix

Secondary structural components are often an important part of the tertiary structure. BPTI contains the three most common secondary structural components that can be part of the tertiary structure, and in this display the alpha helices are highlighted.

Made with MolSlides.Org

6 Next Previous 1 2 3 4 5 7 8 9 View Bpti_pipe in ProteinExplorer.Org

Secondary Structure
Twisted Beta Sheet

The twisted beta sheet contains three strands with one being just a short segment.

Made with MolSlides.Org

7 Next Previous 1 2 3 4 5 6 8 9 View Bpti_pipe in ProteinExplorer.Org

Secondary Structure
Beta Turn

A beta turn occurs whenever the peptide chain makes a particularly sharp change in direction. The segments of the peptide that are colored grey are sometimes refered to as "random" segments but a better term would be ordered, nonrepetitive structure. These segments do not have a repetitve structure like the secondary structural components, but they do have an ordered structure which is not random.

Made with MolSlides.Org

8 Next Previous 1 2 3 4 5 6 7 9 View Bpti_pipe in ProteinExplorer.Org

Maintenance Force
Hydrogen Bonds

Hydrogen bonds are important forces maintaining both secondary and tertiary structures and are represented here as dashed lines. In the alpha helix they are formed between a carbonyl oxygen and a imino hydrogen which are four residues removed from each other. The hydrogen bonds in a twisted beta sheet are again formed between a carbonyl oxygen and a imino hydrogen of the backbone, but in this case they are in adjacent strands so that the two strands are held together by the hydrogen bonds.

Made with MolSlides.Org

9 LAST VIEW Previous Top 1 2 3 4 5 6 7 8 View Bpti_pipe in ProteinExplorer.Org

Maintenance Force
Disulfide Bond

Disulfide bond is a covalent bond between sulfur atoms in two different Cys. Among the forces that maintain the tertiary structure, it is the only one that is a covalent bond , and therefore it is the strongest and most permanent of the attractions. As illustrated in this model, disulfide bonds can play an important role in keeping the peptide strands in their native conformation, particularly the ordered, nonrepetitive segments.

Made with MolSlides.Org

Made with MolSlides.Org

Viewing Help for MolSlides:

Here are the recommended browsers.
Maximize your window, then View, Full Screen (F11).
For a small (800 x 600 pixel) window, reduce the text size (View, Text Size). Then Reload the MolSlides.
Keystroke controls (not all work in every browser, but the links above each slide Next, Previous, 1, 2, ... 9 always work.):

Next Slide: Spacebar, Enter, Down Arrow, Right Arrow, PgDn.
Previous Slide: Backspace, Up Arrow, Left Arrow, PgUp.
Slide Number: 1-9.
First Slide: Home, Esc.
Last Slide: End.

Download These MolSlides

Please respect the copyright statement, if any is present in these MolSlides.
Make a new folder (directory) to receive your MolSlides.
Save the MolSlides themselves with your browser's File, Save As.
Save each PDB file needed by this set of MolSlides (see list above under Troubleshooting). Click on the MDL frank at the lower right corner of each molecular view, and choose File, Save Molecule As.
Double-click on the MolSlides HTML file to view it, or drag and drop it onto or into the browser you wish to use.

Troubleshooting MolSlides:

This set of MolSlides requires the free MDL Chime plugin (to display the molecules) installed in a compatible browser.
If some (but not all) slides have blank rectangles without any molecules, some of the necessary PDB files may be missing from the folder (directory) supplying this MolSlides file. This set of MolSlides needs the following PDB files:
Bpti_pipe.pdb

36228 bytes in this MolSlides HTML document.