Proteins (e.g., ferritin) make up a class of very large molecules whose three-dimensional structure allows them to play important roles in biological systems. To understand how ferritin (or any of the many molecules that you will encounter in this course and throughout your experience in the sciences) performs its job, we must be able to visualize the three-dimensional structure of the molecule, and understand the relationship between the structural features and the function of the molecule. Furthermore, we must be able to communicate this image of the three-dimensional structure to others who want to learn about the molecule's structure and function.
There are several strategies that we could use to visualize the ferritin protein's three-dimensional structure, and communicate this image to others. We could make three-dimensional models to depict the structure of ferritin, but these models would be inconvenient for distributing the information widely. The most common formats for distributing information today- in books and on computer screens- necessitate that the image be displayed in two dimensions. Of course, there are many difficulties involved in converting all of the important structural information about a molecule into an easily understandable two-dimensional representation. No two-dimensional representation can show a three-dimensional structure in its entirety. Hence, a variety of molecular representation formats have been developed; each of these representations is designed to show a particular aspect of a molecule's structure. Thus, to illustrate a specific point about a molecule's structure, the type of representation must be chosen carefully. To provide a comprehensive view of a molecule's structure, multiple representations are used. In this tutorial, the 2D-ChemDraw, stick, CPK, and ribbon representations are used to examine the three-dimensional structure of ferritin. These four types of representations are described in the blue box, below.
Graphical computer modeling has greatly improved our ability to represent three-dimensional structures. One of the goals of graphical computer modeling is to create the computer-generated image such that the image seems three-dimensional. By replicating the effect of light on three-dimensional objects, computers can give the impression of depth to simulate the three-dimensional aspect. The ability of interactive molecular viewing (e.g., using the Jmol program) has enhanced our understanding of molecular structure even more, especially in the biochemical area. By interactively rotating the molecules, a clear picture of the three-dimensional structure emerges. In addition, this increases our chemical intuition by looking at two-dimensional images and visualizing the three-dimensional structure in our brains.
This tutorial uses different types of structural representations (Figure 2, Table 1), such as 2D-ChemDraw, stick, CPK, and ribbon, to illustrate the structure of ferritin. PDB files are also available for viewing the molecules interactively. By using these various representations to study the structure of ferritin, you will become familiar with the different types of information given by each type of molecular representation, as well as the strengths and limitations of each representation.
|Description of Model
||Shows labeled atoms and bonds connecting atoms in a flat representation.
||Shows the bonds between atoms as three-dimensional "sticks", often color-coded to show atom type.
||Shows atoms as three-dimensional spheres whose radii are scaled to the atoms' van der Waals radii.
||Shows molecules with a "backbone" (e.g. polymers, proteins), depicting alpha helices as curled ribbons.
Well by Model
|Connectivities between atoms in small molecules; can also include lone pairs (i.e., Lewis-dot structures).
||Connectivities between atoms; some idea of the molecule's three-dimensional shape.
||Relative volumes of the molecule's components. Usually a good indicator of the molecule's three-dimensional shape and size.
||Shows the secondary structure (such as locations of any alpha helices) of a protein.
|Drawbacks of Model
||Difficult to interpret for larger molecules; does not give a good idea of the molecule's three-dimensional structure.
||Does not depict the volume of the molecule or its atoms, and gives a limited view of the molecule's three-dimensional shape.
||Difficult to view all atoms in the molecule, and to determine how atoms are connected to one another.
||Used for proteins and other polymers. Does not show individual atoms and other important structural features.
This figure shows an alpha-helix (from the "Hemoglobin and the Heme Group: Metal Complexes in the Blood" tutorial) in four different types of computer-generated molecular representations. The representations are, from left to right, 2D-ChemDraw, stick, CPK, and ribbon. Although all four representations depict the same molecule, they look very different and offer different information about the molecule's structure.
This table lists some of the important attributes of the four types of representations pictured in Figure 2 (above)
Note: In the 2D-ChemDraw, stick, and CPK representations, carbon atoms are shown in gray (black), nitrogen atoms are shown in blue, and oxygen atoms are shown in red. In this figure, hydrogen atoms (light blue) are shown in the 2D-ChemDraw representation but hydrogen atoms are not shown in the other representations.
By examining the four representations in Figure 2, you can see that each picture tells us something different about the structure of the molecule. For instance, if we wanted to know how the atoms in an alpha helix are connected to one another, we would use the ChemDraw or stick representation. To see the relative sizes of the atoms in an alpha helix, we would use the CPK representation. Descriptions of the four types of representations, their major strengths, and their drawbacks are given in Table 1, below.
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