An Inexpensive Molecular Model Meredith Brlckley and R. A. Silva California State University, Northridge, CA 91330 Any true understandina of the physical and chemical prnp&ties of proteins nlusi include a k;iowledge of the m1,lecular archirecture 18t these remarkable molecules. Fortunately, detailed structural informati~mabout mans polypeptidm has become available through the trrhniques of X-ray crvstalloeranhv. " . "However. it is freauentlv dif'tirult for students to grasp or retain certain key features of polypeptide structure. One of these is the essential nlanaritv of atoms around the peptide bond. Another is the arrangement of the ventide chain into a helix. narticularlv an a helix. A third feature is the twisting and folding inhkrent in the pleatedsheet structure (10 sheet). The use of molecular models can often be used to advantage to help students obtain a better understanding of these aspects of protein structure. Unfortunately, all the models of which we are aware suffer from one or more disadvantages. Space-filling models are generally the most useful but they are relatively expensive. In addition, a space-filling model of a protein, or even a portion of one, is often seen as a confusing mass of atoms rather than an orderly array of amino acids. On the other hand, the use of devices such as cards' to
'
Davis. A. Keith, Edoc. Chern.. 71 (1976). 2Dickerson. R. E.. and &is. I.. "The Structure and Action of Proteins," ~arper& ROW, New fork, 1969.
represent the atoms about the peptide bond can effectively convey the planarity of the peptide bond and the spiral of an a helix. However, in these models, nonbonded interactions, hydrogen bonds, and the close-packed nature of t h e n helix or the pleated sheet structure are not very obvious. We have devised an inexpensive molecular model that we hope will help students to ohtain a better understanding of protein structure, though the same principles can be used to construct models of other large molecules as well. Our model, like one described earlier1 is fabricated around a central unit which includes the carbon and nitrogen atoms composing the amide group. The unit which is made to the same scale (1.65 cm = 0.10 nm) as a commercially available, inexpensive set of space-filling models is cut from 114-in. Lucite with 118in. holes drilled on the edges as shown on the scale drawing (Fig. 1).Wooden dowels (118-in. diameter) are glued in the holes with white glue and the appropriate expanded polystyrene space-filling atoms are attached to the dowels. A photographof the completed peptide unit including both n carbon atoms is shown in Figure 2. The a carbon atoms are fitted with vinyl receptors to accept the wooden dowels so that the attached atoms are free to rotate in order to accommodate any desired conformation. The completed polypeptide backbone is then seen as an alternating sequence of Lucite units and a carbon atoms.2 Any desired amino acid can he represented in the polypeptide chain simply by attaching the
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Figure 1. Lucite core ldimensions in nm).
Figure 3. Comparison of models of I I helix: left, this model: right, commercial model.
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Figure 4. Pleated sheet ( t i structurel.
F~gure2 Assembled Luctte core
corresponding amino acid residue to an a carhon atom. Colored tape may be attached to the Lucite as shown on the photograph to identify the nitrogen and carhon atoms. The a Helix
The polypeptide chain can he easily coiled into an a helix and either left flexible or pinned or glued in place. A wooden dowel attached to a suitable wooden base serves as a useful axis about which to wind the helix. In the photograph (Fig. 3) a glass rod has been used to increase visibility. White glue may be applied at those places where hydrogen honds are possible between different parts of the helix to increase the rigiditv of the model. The helix can be more firmly attached to-thecentral axis with colorless fishing line. The model clearly reinforces the idea of planarity in the peptide bond and the helix i j visible as a spiral arrangement of planar i.ucite units. Hvdrocen bonds and nonhonded interktions are easily reco&zahle. Amino acid residues may he attached to the periphery of the helix as desired. The pitch of the helix can be measured as well as distances between various parts of the helix. The distances on the model are accurate tdahout 0.01 nm. As is obvious from the photograph the transparency of the Lucite units provides a distinct visual advantage The Pleated Sheet
Twisting the Lucite units about the a carbon atoms generates the pleated sheet structure. Two or three such twisted 1078
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chains can then be -clued or pinned together on a hoard to provide areasonable representation of one layer of the pleated sheet structure (Fig. 4). If desired, other layers may be stacked one on another. Glycine or alanine units can he seen to fit reasonably well between layers. Larger residues are not as easily accommodated. In the model, the pleated sheet description is easily recognizable. Other Models
We have also devised a Lucite core to represent a orphyrin ring that can be easily incorporated into a model of heme-containing proteins. Other units such as purines and pyrimidines can he constructed for models of RNA or DNA. Fabrlcatlon Details
All necessary dimensions for hondlengths and angles were obtained from Dickerson and Geis.= Expanded polystyrene space-filling units and vinyl connectors were purchased from Science Related Materials, Inc., P.O. Box 1422, Janesville, WI, 53545. Lucite was obtained from a local plastics supply store. The total cost of our completed helix with 20 peptide honds was about $16. For ease of fabrication, an alternate Lucite core with dimensions of a parallelogram (35 X 40 mm; long axis 65 mm) may be used. This will provide a model with nonhonded distances accurate to about 0.02 nm. Acknowledgment
One of us (MB) is indebted to the Los Virgenes School District for a sahattical leave during which time this project was completed.
