ON THE ROLE OF MODELING IN STRUCTURAL BIOLOGY RESEARCH

The field of structural biology has enjoyed phenomenal growth and development over the past three decades. By 1970, only 11 protein structures had been solved. These initial structures were of proteins, like hemoglobin, that were easily purified in large amounts, and then conveniently crystallized. Since that time, advances in molecular biology and protein crystallization, along with improvements in computer hardware and software, have transformed this field from a small fraternity of scientists working on a few obscure problems, into a mainstream approach that impacts the work of virtually all biological scientists. The number of protein structures solved during this time has been increasing at an exponential rate, from 15-20 structures per year in the 1980's to approximately 100 per month in 1994. The Protein Data Bank is projected to contain over 30,000 structures by the year 2004.

The construction of a model representing the electron density of a protein has always been a critical exercise in any protein structure determination. Initially, this was done by tracing electron density contour maps onto thin sheets of Plexiglas that were then stacked up to give the initial impression of a three-dimensional model. This approach was later refined in the use of a "Richard's box", in which the protein model was constructed from appropriately scaled parts by fitting them into the electron density that was observed through the use of a half-silvered mirror that reflected the model into the density. Still later, a device invented by Byron Rubin made it possible to bend steel wire into a backbone model of a protein, using the phi psi angles of each alpha carbon atom.

The development in the late 1970's of FRODO, the first software package to generate three-dimensional computer models of proteins from electron density data, eliminated in large part the need for crystallographers to continue the laborious and painstaking job of physical model construction. In subsequent years, these software packages have been enhanced and refined. Combined with dramatically increased computer power, these molecular visualization programs can now generate an image, or a stereoscopic pair of images, that with a combination of shading, depth cueing and kinetic depth effects, produces an amazingly "real" three-dimensional model of a protein. Indeed, most of a student's or post-doc's time in a structural lab is now spent sitting at a Silicon Graphics workstation interacting with and analyzing computer-generated protein models. . Although these computer visualization programs were originally developed for UNIX-based computer workstations, desktop versions of this software now exists (e.g. RasMol, Protein Explorer, Swiss PDB Viewer), This public-domain software can be downloaded from the Internet and used free of charge. They are powerful programs that will run on both the PC or Mac platform.

Given the existence of molecular visualization software, why are physical models of proteins still needed? The preceding description of the development of structural biology and molecular visualization over the past 30 years pertains primarily to practicing structural biologists. However, as structural biology has become a mainstream approach in virtually all the biosciences, a much larger group of biochemists and molecular biologists are now experiencing the need to visualize and analyze these new structures. It is with this later group of biological scientists that physical models are of special value.

A common scenario today is that a biochemist/molecular biologist will clone the gene encoding their protein, over-express the protein in a heterologous system, purify the protein, and deliver the purified protein to a collaborating crystallographer. Sometimes the crystallographer is down the hall, but often they are in another building, on another campus, or even in a different country. Several months later, if all goes well, the structure is known. At that time, it is necessary for that structural information to be communicated back to the research group investigating that protein. This is usually accomplished by the biochemist/molecular biologist visiting the crystallographer, and while sitting together at the graphics workstation, the structure is revealed. Following that session, a variety of 2-D images of the structure are generated, and these 2-D images then serve as the primary means whereby this structural information is communicated to other members of the research group. It is in this scenario that we envision a role for an inexpensive, readily available, physical model of the newly acquired protein structure. This model would accurately portray not only the alpha carbon backbone of the protein, but also critical amino acid side chains as well as important bound substrates or inhibitors. The physical model requires neither a molecular graphics workstation nor personnel experienced in using such systems. The physical model also presents several advantages to the biochemist over the computer-generated model. First, the physical model is both tactile and interactive. It can be viewed from the top, bottom and side in quick succession, faster than even the most adept computer graphics user. In other words, it is the ideal portable graphical display. Second, unlike the computer-generated model, the physical model is always "on". It is "on" as it sits on the lab bench, where it can be used for impromptu discussions of new experiments. It is "on" at lab group meetings where it can be used to explain the interpretation of a recent experiment. And it is "on" in the P.I.'s office, where it constantly invites consideration from whatever new perspective it is viewed.

Parallel developments in rapid prototyping technology make accurate 3-D protein models possible. At the same time that structural biology was experiencing a period of rapid growth and development, a similar phenomenon was occurring in an engineering discipline known as Solid Freeform Fabrication. As in structural biology, new developments in both software and hardware combined to revolutionize this area of manufacturing. Computer-assisted design (CAD) software was developed to allow engineers to quickly and accurately design three dimensional objects in the computer environment. At the same time, rapid prototyping technologies were developed which used the output from the CAD software packages to drive equipment that rapidly constructed a physical model of the part. Today, five different prototyping technologies are widely used in the design and manufacture of everything from automobile engines to soda bottles and child-proof caps for prescription drug bottles.

Eric Martz has compiled an interesting History of Molecular Visualization on the RasMol Home Page.