PDB EDUCATION CORNER: Miriam Rossi, Vassar College
Miriam Rossi has been at Vassar since 1982 after she worked as a Research Associate at The Institute for Cancer Research of The Fox Chase Cancer Center in Philadelphia.
She received her Ph.D. at The Johns Hopkins University. Her work is concerned with the relationship between the structure and function of molecules, mainly those having biological activity. These include natural plant products that show anti-tumor activity as well as others that are active against some of the proteins in HIV. The technique she uses is single crystal X-ray crystallography, and she is co-author of a leading text in this area.
She has received grants from the National Science Foundation, the Petroleum Research Fund of the American Chemical Society, and the Camille and Henry Dreyfus Foundation.
Besides the U.S., she has taught courses in Australia, Italy, and most recently under the auspices of the Rotary Foundation, in Chile. Her work has appeared in the Journal of Medicinal Chemistry, Inorganic Chemistry, Organometallics, Archives of Biochemistry and Biophysics, and the Journal of Natural Products, among many others.
Her teaching interests include general chemistry, inorganic chemistry, and structural chemistry, and she particularly enjoys conducting research with undergraduates.
This interview about one of her courses will also appear in a Vassar College website that highlights courses that incorporate information technology in the teaching activities at http://computing.vassar.edu/news/faculty/facultyfocus/.
Q: What is your Structural Chemistry and Biochemistry course about? Tell us about its origin, goals and objectives.
A: Today, interdisciplinary research and areas of study are the norm in the sciences. The borderlines of research in chemistry, biology, physics, geology are vanishing, and increasingly molecular interactions and chemical transformations are found to be at the heart of biology, biochemical and biomedical phenomena as well as understanding the behavior of new materials, material sciences and geological sciences. For example, many diseases and their treatment are molecular in nature and medicinal chemistry and pharmaceutical companies have large components dedicated to drug design research that has structural information as its basis.
This course was developed to make students aware that the same fundamental principles that govern the molecular architecture for metals and small salt compounds also explain the structures of macromolecules and molecular assemblies, such as viruses. General texts in chemistry, biology, geology, biochemistry and solid-state physics are full of molecular structure representations obtained from the three-dimensional atomic coordinates determined by X-ray diffraction. Unfortunately, there is difficulty in interpreting these spatial arrangements, especially as the structures of increasingly larger molecules become available. This problem is not new. In 1925, Sir William Bragg wrote in the Preface to his book, Concerning the Nature of Things: "...There are some who think this difficulty is incurable, and that it is due to the want of some special capacity, which only a few possess. I am persuaded that this is not the case: we should have nearly as much difficulty in grasping events in two dimensions as in three were it not that we can so easily illustrate our two-dimensional thoughts by pencil and paper. If one can turn over a model in one's hand, an idea can be seized in a mere fraction of the time that is required to read about it, and a still smaller fraction of the time that is required to prepare the description." (Dover Phoenix Editions)
The goals of this course involve familiarizing students with basic concepts of molecular structure and geometry, chemical bonding and intermolecular interactions; to introduce students to X-ray crystallographic methods for determining molecular structure; how to read a crystal structure paper; to study the structures of molecules of chemical and biological interest; interpreting the complex images that accompany structural papers. The overall aim is to see how the molecular structure is one of the determinant features responsible for chemical and/or biological activity. It is an advanced level course open to chemistry and biochemistry majors or students declaring a chemistry or biochemistry correlate sequence (frequently called a "minor" subject area).
I am able to attain these goals by using different computer programs and databases that can be accessed in a computer classroom containing 15 desktop computers. An Academic Computing Consultant who is a science computation specialist maintains this computer classroom; his presence has ensured the successful outcome of this course.
Q: What were the technologies used and how did they change or enhance your course?
A: I use two main computer tools: the PDB, a large repository for the processing and distribution of 3-D biological macromolecular structure data, and the Cambridge Crystallographic Structural Database (CCSD, www.ccdc.cam.ac.uk), which is a database of bibliographic, chemical and crystallographic information for organic molecules and organo-metallic compounds. The CCSD is not freely available, but fortunately the college has a campus-wide license for it. The RCSB PDB is freely and widely available on the web.
The addition of these tools has made a huge difference in teaching this course. For example, the various visualization capabilities available in the two databases make the content easier to teach, since many structural features become self-evident when they are viewed. The ability to manipulate, rotate and edit structures allows instructors to convey these structural "rules" that are not easy to visualize or understand otherwise. While this is true for all three-dimensional structural data, it is essential for understanding macromolecular data; the PDB is an indispensable resource to achieve this objective.
Q: How have your students responded to your use of technology?
A: Students are very receptive to acquire information through interactive and visual experience. I hear students praise the software all the time; they like being able to see and manipulate molecules; it is intuitive, easy and fun. Frequently, in courses where the concepts of molecular shape and chemical properties derived from molecular shapes are introduced, for example, organic chemistry, students use model kits as a teaching aid. While this is a useful exercise, being able to rotate the structure on the screen and see how a molecule interacts with others is especially valuable. The use of these structural databases reinforces material that they learn about in their textbooks. It becomes clear that the connections between atoms to make molecules and how molecules are grouped together to make molecular assemblies all have similar foundations. Geometrical details can be calculated easily and displayed. These resources have made describing molecular features much easier, and since students can access the PDB online at anytime students can access information for problem sets at their convenience.
The use of interactive computer graphics software is especially indispensable when teaching macromolecular structure. The level of complexity in macromolecular structure is astounding. Proteins can have diverse shapes or motifs that make up their final 3-D structure. It is here that the PDB becomes such a useful teaching tool: it permits students to look at the complex protein or other large macromolecular assembly using options that permit a different perspective by zooming in to a particular site and rotating the structure. It becomes possible to view the same structural motif in many proteins, allowing for interesting discussion to take place in the classroom: the PDB reinforces material that they learn about in their textbooks (The text I use is Introduction to Protein Structure, 2nd Edition by Branden and Tooze, Garland Publishing). Geometrical details can be calculated easily and displayed. The Molecule of the Month feature is outstanding and almost forms the basis for the macromolecular part of this course; it features an in-depth look at a collection of well-studied molecules. It provides a well-written introduction to a molecule, its biological importance, how the structural features are utilized by the molecule to attain its function, and highlights the use of common structural motifs by related compounds. My students use this feature as a starting point in many of their in-depth analyses that are required for homework assignments. What I have found is that because the RCSB PDB is easy to use, students literally can spend hours manipulating these complex structures. And, every instructor knows that the more time a student spends on trying to understand course material, the more attracted they become to the subject.
Every year, I try to shape the course contents taking into account the particular interests of my students. They really enjoy being able to use these databases to find and visualize well-known structures they learn about in other contexts; for example, they can see how toxins such as cholera or anthrax toxins behave at an atomic level, as well as the common cold and influenza viruses. Some of the topics we discuss are how DNA modifies its shape as it interacts with a variety of proteins; the mathematical description of the morphology of virus particles, etc. Since students pick a topic for an end-of-the-year presentation, sometimes I get to see really interesting things happening in the classroom. I remember that a student who was an Art History major gave a presentation comparing the structural features that provide stability to molecules to those that are commonly used when building macroscopic structures such as bridges or buildings.
Q: What were the challenges you faced when teaching this course?
A: Even though these computer programs are very well built, and easy to use, there is always a learning curve that students must go through. Most of them are very quick learners, but with a few one has to be more patient and guide them through the first couple of sessions. For example, seeing complex protein structural patterns, such as the Greek key motif, need to be explained one-on-one. A good idea would be having an experienced student assistant helping students during lecture time.