Molecular Model Lending Library

Lending Library for
Physical Molecular Models
for Western Massachusetts, USA
A resource at MolviZ.Org
Website created February, 2005. Updated May 2005, February 2007.

The physical models described below are available for short-term loans to teachers in Western Massachusetts. The borrower is responsible for pick-up and return. (We do not have staff time to ship these models.) A security deposit of $50 will be required, which will be refunded in full when the models are returned in good condition. Pickup/return can be scheduled for any day of the week including weekends. Contact Eric Martz at emartz@microbio.umass.edu.

Except where otherwise noted, all models were manufactured by 3DMolecularDesigns.Com at the Milwaukee School of Engineering, where these or other models may be obtained. Some of the photos on this page, and the quoted passages of text, are courtesy 3DMolecularDesigns.Com.

The Molecule to rotate and zoom ... links below display the molecule in FirstGlance in Jmol, which requires no installation and works in Safari on Mac OS X as well as all popular browsers on Windows.

Single Amino Acid

Alpha Helix & Amino Acids made from a Darling Model Kit (darlingmodels.com). Already assembled as shown are an 8-amino acid alpha helix, a single amino acid, two peptide bonds (planar) emphasizing the phi and psi angle rotations about the intervening alpha carbon, and seven amino acid side-chains. These used most of the 335-piece kit ($41), but borrowers are free to reassemble the pieces to make beta strands, DNA bases, etc.

Click on these images for larger views!
3D computer tutorial: Alpha Helix & Protein Secondary Structure.
Molecule to rotate and zoom on computers: Alpha Helix.


Planar Peptide Bonds and Phi/Psi Angles		Sidechains (Ile, Phe, Tyr, Ala, Ala, Cys, Lys, Arg) (Ran out of white hydrogens)

Amino Acid Starter Kit. Students explore the shape and chemical properties of the 20 amino acid sidechains with engaging foam models. The sidechains feature dual coloring schemes - color on one side indicates chemical properties and on the other side students color-code atoms. Since understanding protein structure begins with this unique combination of shape and chemical properties of the amino acid sidechains, students will gain a bacis knowledge of the laws that determine protein folding. The 3-Group Amino Acid Starter Kitc includes 3 4-foot Mini-Toobers, 3 sets of 20 magnetic amino acid sidechains and 3 extra cysteines for the folding activity.
3D computer tutorial: Amino Acids, Peptides, Secondary Structure.

Anthrax protective antigen heptamer. This is a small (about 2 inches across) and somewhat brittle model. See toxins, in the Atlas of Macromolecules. Molecule to rotate and zoom on computers: Anthrax toxin heptamer.

Antibody bound to lysozyme antigen. Large (16 x 6 in) backbone model of the Fab fragment of a mouse IgG1k antibody bound to hen egg white lysozyme. The epitope (on lysozyme) and paratope (on the Fab) have spacefilled atoms, enabling one to feel the shape complementarity of the binding. The catalytic cleft of the lysozyme is not occluded by Fab binding, and a tetrasaccharide substrate model is available. Some hydrogen bonds, and all disulfide bonds, are shown. Glu35 and Asp52, the key catalytic residues of lysozyme, are spacefilled (Vocadlo et al., Nature 412:835, Aug 23 2001)

See Antibody in BioMolecular Explorer 3D, targeted to the high-school level and above.

This model is made of nylon and is moderately resiliant. Molecule to rotate and zoom on computers: Antibody (Fab):Lysozyme or Lysozyme:substrate analog.

DNA Construction Kit. (Two kits are available.) Let your students discover the structure of DNA -- just as Watson and Crick did. The DNA Discovery Kit combines powerful magnets with accurate, 3D nucleotides which makes the kit self-instructive. As your students correctly join the nucleotides, they will "feel" hydrogen bonding. Teacher-developed and field-tested, the classroom kit contains 12 base pairs (six of each nucleotide).

Double helices can also be modeled with toobers.

Excellent interactive computer graphics are available at DNA: Genetic Inheritance at BioMolecular Explorer 3D, a site targeted to the high-school level and above.
Molecules to rotate and zoom on computers:

DNA double helix. This DNA double helix is embedded in a glass block, which is not ideal for teaching since the shape cannot be felt. However it makes a nice supplement to the on-line interactive computer graphics linked below. It comes with an illuminated stand which makes it glow attractively. Double helices can also be modeled with toobers.

Excellent interactive computer graphics are available at DNA: Genetic Inheritance at BioMolecular Explorer 3D, a site targeted to the high-school level and above.

This DNA model is a "laser crystal" made by sculptor Bathsheba Grossman.

Enzyme: see lysozyme. Molecule to rotate and zoom on computers: Lysozyme:substrate analog.

Green fluorescent protein.

"This structure is composed of an 11-stranded beta-barrel which surrounds the fluorophore located in the center. Notice how the structure resembles a lantern -- perfect for explaining the structure-function nature of many proteins."

This model is about 6 inches tall and comes in a protective transparent plastic case (not in the photo). It is made of nylon and is moderately resiliant.

Molecule to rotate and zoom on computers: Green Fluorescent Protein.

Lysozyme: See Antibody:Lysozyme complex. Molecule to rotate and zoom on computers: Lysozyme:substrate analog.

Major histocompatibility class I. This model is about 6 inches tall and comes in a protective transparent plastic case (not in the photo). It is made of nylon and is moderately resiliant. Molecule to rotate and zoom on computers: MHC I:virus peptide.
An interactive tutorial with computer visualization of MHC classes I and II is available at MolviZ.Org (requires free Chime).

Nucleosome. This is a small (about 2 inches across) and somewhat brittle model. Molecule to rotate and zoom on computers: Nucleosome.

Ribosome. Although this model is not in the lending library, it may be available on special request. This is a small (about 3 inches across) and somewhat brittle model.

Rossman fold (the I domain of CD11a). This is a wire backbone trace model, about 10 inches across, made by Tim Herman using a wire-bending machine specialized for making protein backbone models. Dubbed "Byron's Bender", models made with this machine were of great importance to protein structure specialists in the 1970's before computers were readily available for molecular visualization.

Because this model vibrates easily, it helps to emphasize that proteins are not rigid static structures, a point also made in these molecular dynamics simulations of peptides (which require that MDL Chime be installed in your browser). Be sure to click on MDL in the right animation and select Display, Spacefill, van der Waals.

See Byron's Bender at the History of Visualization of Biological Macromolecules.

Toobers are flexible foam plastic rods about one meter long that can be bent to any shape, due to an aluminum wire down their centers. They are great for illustrating a wide range of molecular structural topics in lectures, as well as for protein folding activities in class. Here is more about toobers in science education.

Transfer RNA. "This spacefilled model of tRNA (the adapter molecule that delivers activated amino acids to the ribosome) will prompt students to ask many questions about protein synthesis. Both the 3' end where the amino acids are charged, and the anticodon that base-pairs with mRNA are clearly color-coded in this mini model."

This is a small (about 2 inches across) and somewhat brittle model.

Molecule to rotate and zoom on computers: tRNA.

Water with NaCl, EtOH, Ethane. Two "cups" are available. These water molecules have magnets that simulate hydrogen bonding. Included in each cup are one pair of NaCl ions, and a 2-carbon compound that can model either ethanol or ethane. The latter illustrates the hydrophobic effect since the ethane model lacks magnets.

"Your students can make ice, dissolve salt, evaporate water, explore transpiration, create ethanol and much much more."

Here is a simulation of water molecules condensing into a hydrogen-bonded micro-droplet (requires free Chime).