Molecular Surfaces:
2. Physical Molecular Models

Michael L. Connolly

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Physical models of molecules have been (and continue to be) made and used; even after the widespread use of computer graphics. These models are made of plastic, rubber, metal, wood, paper, dye, and paint. There are four basic categories:

  1. atom and bond models (most important for organic chemistry);
  2. regular polyhedral, lattice, and repeated pattern models for fields where symmetry is important (such as inorganic chemistry and crystallography);
  3. molecular and atomic orbital models (important in quantum chemistry); and
  4. folded chain models (important for linear polymers such as proteins).

Atom and bond models may be further classified along a spectrum between an emphasis on atom representation to an emphasis on bond representation. Space-filling models represent the atoms as spheres whose radii are proportional to the atom's van der Waals radius. The best known of this type of model is the Corey-Pauling-Koltun model. The original models of Corey and Pauling (1953) were made of hard wood (1 inch per angstrom) and plastic (0.5 inch per angstrom). The wood models were connected with steel rods and clamps, the plastic models with snap fasteners. In 1960 the NIH biophysics and biophysical chemistry study section requested its principal consultant, W.L. Koltun, to convene an ad hoc committee to design and develop new models to represent biological macromolecules. The new models were based on Corey-Pauling models. However, they were lighter and more accurate with respect to conformational angles because they were more rigid and had better connectors (designed by Koltun). They are called CPK models. Building a macromolecule with CPK models is a lengthy process. For example, Yankeelov and Coggins (1971) built a CPK model of myoglobin at the rate of 50 amino acid residues per week.

At the other extreme are skeletal models, where the bonds are represented by metal rods, and the atoms only as junctions of the rods. Brass wire rods made by Cambridge Repetition Engineers were used by Kendrew and colleagues (1960) in their work on myoglobin. The scale used was two centimeters per angstrom. Andre Dreiding (Fieser, 1963) has patented a stainless steel skeletal model. Rupley and Bruice (1968) and also Clarke (1977) have developed hybrids of skeletal and space-filling models. Barret (1979) has invented an even more varied system for nucleic acids.

Several books have been written on the subject of physical molecular models. The book by Wells (1970) shows how inorganic chemistry can be taught using five kinds of models: polyhedra, nets, sphere packings, tetrahedral structures and octahedral structures. Walton (1978) also discusses polyhedral models. Her book gives the best survey of all kinds of physical molecular models (including ones for atomic and molecular orbitals) and has a long table of commercial suppliers. The book of Bassow (1968) teaches organic chemistry and crystallography by having the student build models. The Journal of Chemical Education has published several papers on molecular models, including a history by Petersen (1970) and a list of suppliers by Gordon (1970).

Finally, let us discuss folded chain models. These models are based on an idealization or simplification of the polypeptide chain as a series of virtual bonds connecting the alpha carbons of a protein. The bend angles at each alpha carbon and the torsion angles along virtual bonds specify the protein fold. There are basically two examples of this class: Byron Rubin's wire-bender model, and Blackwell Molecular Models.

The wire-bender model is made of 3-mm-diameter steel rod bent to the pattern of an alpha-carbon chain of a protein. The bending is accomplished by means of a machine (Byron's Bender) and a list of torsion and bend angles. The machine is made up of a fixed clamp, a sliding clamp, a bending anvil, a torsion-angle dial, a bending-angle dial and a micrometer for segment length (Rubin, 1985). Unlike virtually all other systems, the scale is variable, i.e. the alpha carbon to alpha carbon length is not fixed. The machine is commercially available from Charles Supper Co. of Natwick, Massachusetts.

Blackwell Molecular Models (Fletterick and Matela, 1982; Fletterick, Shroer and Matela, 1985) are more complicated and provide more chemical information. They are made out of plastic in twenty different colors to code for amino acid type. The scale is one cm per angstrom. There is one object per amino acid and each object is made of two pieces of plastic attached by a plastic rod protruding from one of the pieces (replacing the machine screw described in the original Biopolymers article). There are two angle scales embossed on the plastic, one for torsion angles and one for bend angles. Glue is used to fix the torsion angle between amino acid objects and the bend angle at an alpha carbon (originally fixed by tightening the machine crew). Before the model is constructed, the protein alpha carbon coordinates must be adjusted so that the virtual bond length is 3.80 cm. This is done by a Fortran computer program that the developers distribute through the protein data bank at Brookhaven national laboratory. The program uses Lagrange multipliers and the Newton-Raphson method to adjust the coordinates. Angles for some molecules are given in Fletterick, Schroer and Matela (1985) along with rod lengths. The metal rods are cut to order with pliers and each end is inserted into a plastic connector. These support rods are added after the model is build, to fix some of the alpha-carbon-to-alpha-carbon distances and stabilize the finished model.

[ 1. Introduction ] [ *** 2. Physical Molecular Models *** ] [ 3. Electron Density Fitting ] [ 4. Molecular Graphics ] [ 5. Solvent-Accessible Surfaces ] [ 6. Molecular Surface Graphics ] [ 7. Molecular Volume and Protein Packing ] [ 8. Shapes of Small Molecules and Proteins ] [ 9. Structure-based Drug Design ] [ 10. Protein-Protein Interactions ] [ 11. Surface Biology, Chemistry and Physics ] [ 12. Bibliography ]

All material in ths article Copyright © 1996 by Michael L. Connolly



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