Structural Studies of Filamentous Biological Assemblies

Gerald Stubbs, Professor of Biological Sciences

We use fiber diffraction, protein crystallography and electron microsopy to look at disordered and partially ordered filamentous biological assemblies.

Most of our research interests fall into one of three areas:

Virus Pictures

Laboratory Publications

Trip to the APS, August 2001

Biological Sciences Home Page

Undergraduates in the Stubbs lab

RCN: FiberNet


SSRL Beamline 4-2

Prusiner Laboratory

Why study plant viruses?

Why use fiber diffraction?

Structural biology has generally concentrated on compact, ordered molecules and assemblies, simply because they are much more tractable, and can be studied, for example, by the highly successful and now almost routine methods of protein crystallography. But many biological polymers and assemblies are long, helical, filamentous structures. Examples include the filamentous viruses, cytoskeletal filaments, bacterial flagellae, chromatin, components of the extra-cellular matrix, and many simple polymers such as nucleic acids and polysaccharides. The components of these assemblies are difficult to crystallize, since their natural tendency is to form filaments. Even when they do crystallize, the molecular interactions in the crystals rarely correspond to the biologically significant interactions in the fibers. Fiber diffraction is the only practical method of structure determination at the molecular level for these assemblies.

The difference between fibers and crystals is that, in fibers, the molecules are parallel to each other (as they are in crystals), but they are randomly rotated about the long axis of the fiber. As a result, the data obtained from an x-ray fiber diffraction experiment are cylindrically averaged relative to the data that would be obtained from a hypothetical crystal of the same aggregate. Information is lost, but often not so much that the structure can not be determined. Much of the effort of this laboratory over the years has been directed toward obtaining structures from fibers comparable to those obtained from good crystals of similarly large assemblies.

Projects in this laboratory

We are working with a wide variety of filamentous plant viruses, and projects range from viruses new to this laboratory, where the focus is still on production and purification, to the venerable old tobacco mosaic virus (this project was 100 years old in 1998!). Most of the TMV work is now collaborative with other laboratories who are applying our structural results to such areas as biotechnology and crop protection. Among our other projects, the potexviruses and potyviruses are both important to agriculture and biotechnology; potato virus X has great potential in biotechnology, and the potyviruses (which some people have estimated to make up one third of all plant viruses) are responsible for half the viral crop damage in the world. Some of the viruses we are working with include:

We are happy to provide samples of our viruses to other laboratories. A few milligrams, particularly of TMV, can usually be provided on request; larger quantities may require special arrangements. Recipients are responsible for arranging any necessary permits etc.

Work in this laboratory is supported by National Science Foundation Grant MCB-0743931, National Institutes of Health Grant P01 AG010770, and by a Discovery Grant from Vanderbilt University. Any opinions, findings, and conclusions or recommendations expressed in this web site are those of the author and do not necessarily reflect the views of the National Science Foundation or the United States Department of Agriculture.

Students Andrew Wilson, Don Becker, and Zurabi Lominadze work on a helium tunnel during a trip to BioCAT in October 2006.

Fiber Diffraction Workshop, August 6 - 9, 2006, Fall Creek Falls State Park

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