Graphics Gallery

Gale Rhodes
Chemistry Department
University of Southern Maine

Revised 2006/08/02

Learn how to use Swiss-PdbViewer. Work through sections 1-6 of the Swiss-PdbViewer Tutorial.

Topic: Protein Function

Studies of some proteins commonly discussed in biochemistry texts.

All files are Swiss-PdbViewer compressed project files, requiring version 3.5 or later.

 

Examples

NOTE: Some files for this page and the other DeepView Exercise pages were corrupted and are being repaired -- file links will reappear (and become blue) soon.

1) Myoglobin

File: MbCompare: Deoxymyglobin (5MBN) and oxymyoglobin (1MBO) superimposed by Tools: Magic Fit acting on all CA atoms.

  1. The file opens with heme and its neighbors (to 4.5 angstroms) on display. Blink back and forth (control-tab) to see the differences between the deoxy- and oxy-forms in the heme region.
  2. Compute H-bonds in both layers. Find the hydrogen bond between O2 and the distal histidine (his-64).
  3. Compare the shapes of the heme in the two layers. Which heme is flatter?
  4. Display the full structure (Select: All, return) in each layer. Blink to compare overall structures.

TRUTH IN ADVERTISING STATEMENT

When you make this comparison of myoglobin with and without oxygen bound, it is tempting to imagine that you are observing the binding process itself, as if you were seeing myoglobin breathe. Remember that you are merely comparing two models; you are not seeing molecules move. In the conversion of deoxymyoglobin to oxymyoglobin, there must be intermediate states that are not detected by crystallographic analysis. Proof of this statement lies in the absence, in either model, of any pathway by which oxygen could get into or out of the molecule. So the molecule must exist in transient conformational states that create such a path. Remeber this whenever you compare models of a molecule in two or more different states.

2) Hemoglobin

File: HbCompare: Views of deoxyhemoglogin (3HHB) and oxyhemoglobin(1HHO).

  1. In the Layer Infos window, put check marks in the cyc column for the first two layers only (3HHBTet and 1HHOTet). Blink to compare the overall structures of the deoxy- and oxy- forms. These two models were superimposed by least-squares fitting (Tools: Fit Molecules (from selection)...), acting on the four heme groups only.
  2. Arrange the view so you can see into the cavity in the center of the tetramer. Blink to compare. Which model has the smaller cavity? How is this difference related to the effect of 2,3-DPG on oxygen binding?
  3. In the Layer Infos window, put check marks in the cyc column for the third and fourth layers only (3HHBSw and 1HHOSw). Blink to compare the two views. Your are looking at the "switch region", which might be described in your text. Layers were superimposed as in #1.
  4. Compute H-bonds in both layers and find hydrogen bonds that break or form as conformation changes.
  5. Go back to the first two layers and find this region in the ribbon model. Blink layers one and two again to see the "movement" (Why the quotes?) that occurs in this region upon oxygen binding.

File: HbBetaCompare: Views of the beta subunit of deoxyhemoglogin (3HHB) and oxyhemoglobin(1HHO).

  1. Blink to compare the structures of the deoxy- and oxy- forms of one beta subunit. These two models were superimposed by three-point superposition, acting on the hemes only. So the hemes appear to stand still while everything around them moves.
  2. Compute H-bonds in both layers. Find the hydrogen bond between O2 and the distal histidine (his-63).
  3. Compare the shapes of the heme in the two layers. Which heme is flatter?
  4. Blink the views and notice the "motion" (Why the quotes?) of the proximal histidine (his-92). How is this motion (no more quotes, but don't forget...) related to the cooperativity of O2 binding?
  5. Center and zoom in on his-146 and notice its interaction with asp-94. Blink to see how the interaction differs between the two models. How is this interaction related to the Bohr effect?

3) Muscle Proteins

For access to spectacular pictures, animations, and PDB files of muscle and other motility proteins, look at Lecture 16: Motility: Flagella, muscles, cilia, microtubules, in Anthony Crofts's excellent Biophysics 354, Biological Energy Conversion page at University of Chicago.

4) Antibodies

File: 1hzh. Model of a full IGG antibody molecule made by combining PDB files 2IG2, 1FC2, and a theoretical hinge region (Eduardo A. Padlan, Mol Immunol. 31, 169, 1994).

  1. Color the model by chain to distinguish the two heavy and light chains.
  2. Identify these elements of antibody structure: Fab, Fc, VH, VL.

All of the following antibody models are VH and VL regions only.

File: AbCompare. Views of antigen binding to germline and mature antibodies. This file contains four different models: germline antibody without hapten (GrmAb) and with hapten (GrmAbH), and mature antibody without hapten (MatAb) and with hapten (MatAbH).

To learn more about these structures, see Structural Insights into the Evolution of an Antibody Combining Site, G. J. Wedemayer, P. A. Patten, L. H. Wang, P. G., Schultz, R. C. Stevens (USM Chemistry, class of 1986), Science, 276, 1665 (1997). Article available from Gale Rhodes on request.

  1. In the Layer Infos window, put check marks in the cyc column for the first two layers only (GrmAb and GrmAbH). Blink to compare the models. GrmAbH is colored by RMS deviations of its residue positions from those in GrmAbH, with smallest differences in blue, largest differences in red. So blue residues are in almost the same position in the two models, while other colors indicate residues that move to accomodate the hapten. Try to retain a general impression of the amount of local movement needed to accomodate the hapten.
  2. After comparing the models in the hapten-binding region, display the full models and compare them. Try to retain a general impression of the amount of difference between them.
  3. In the Layer Infos window, put check marks in the cyc column for the third and fourth layers only (MatAb and MatAbH). Blink to compare the models. Coloring is the same as in the first two layers. Which antibody, the germline or the mature, appears to change its conformation more in the binding region as it accommodates the hapten?
  4. After comparing the models in the hapten-binding region, display the full models and compare them. Which antibody, the germline or the mature, appears to change its conformation more overall as it accommodates the hapten?
  5. In the Layer Infos window, put check marks in the cyc column for the fifth and sixth layers only (GrmAbH and MatAbH). This allows you to compare the germline and mature antibodies directly. Yellow residues are those that mutated as germline antibody evolved into mature antibody. These mutations are responsible for the fact that mature antibody has much higher affinity for hapten. How many of these mutations are in direct contact with hapten? How do you think they can affect hapten binding if they are distant from the hapten?

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