Use of the "Cubic Snake" as a Molecular Model Chalm Gilon The Hebrew University of Jerusalem, Jerusalem 91904, Israel During preparation for a course in bioorganic chemistry, l found I nerded a proper model for demonstrating the eftert of changes in torsional angles on macromoleculaiconformation. I discovered that the "cubic snake" fulfills the requirements. The snake is a well-known children's game that consists of alternating colored prisms interconnected through their centers. The connection between units enables some free rotation hetween them, thus making it possible for the player to construct all kinds of formations that differ from each other by different ensembles of torsional angles. It is known that polymer conformation depends on torsional angles betweenmonomers.'The resemblance between the snake and a polymer makes the snake an attractive, cheap, and fun-to-play-with macromolecular model. I t can
be used for demonstrating conformational changes, especially serondary and tertiary structures of p r o t e k " J - ~few examples of the use of the snake for demonstratinn of polv. peptides conformations are shown in Figures 1-5. Acloser look a t the snake has shown that in certain conformations steric repulsions exist between the ith and i+2 units. This repulsion makes certain conformations more favorable than others and makes the snake more reliable as a molecular model. It is ~ossible.of course. to use the snake as a molecular model f;r othrr.molecules: The readers are inviced to try. The author is indehted to S.E'uechtwan~er - for taking- the photographs.
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Flory, P. J., "Statistical Mechanics of Chain Molecules," Interscience Publishers. New York, 1969, p. 248. * Schulz, G.H., and Shirmer. R. H.. "Principles of Protein Structure." Springer-Verlag. New York. 1978, p. 66. Lehninger. A. L., "Principles of Biochemistry," Worth, New York 1982, p. 147.
Figure 1. The cubic snake in a fully extended conformation;all torsional angles between units are 180'.
FipJre 4 The Cubic S M Y ~ in an Ml.cal cootmlion diltersnt p tch and helox radius can oe constructed
Figure 2. (left)The cubicsnake in a globular conformation. F w r e 3. (rghl) The cdbic snake in a giobuw cmtormaton shown9 two a o m ns, eg . the enzymes Ihermalyrin. whymotryps n. and elaslase I.
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Journal of Chemical Education
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Figvre 5. T n s c ~ oc snake n a c)c.nc conformat on staoil'zedby an anlipars Id 3-likecantormatton with two turns
