SPUR 2019: Determine the High-Resolution Structure of Octahedral Polyomavirus by Cryogenic Electron Microscopy

Background

Viruses are biological entities that encase a genome in a protective membranous covering or protein shell. The coverings or shells are found in a large diversity of shapes and sizes. Polyomaviruses are viruses that infect humans and many other animals. The capsids of polyomaviruses are made up of protein VP1. This protein has the unusual ability to form shells of different shapes. Different shapes are formed by treating the protein under different chemical conditions. One shape that can be formed is an octahedral shell. We will grow VP1 in bacteria, harvest the protein, form octahedral particles, and image particles by cryogenic electron microscopy (cryo-EM). Cryo-EM will include two-dimensional imaging followed by three-dimensional image reconstruction of the octahedral structure. Finally, we will model the atomic-resolution structure of the octahedral form and compare it to other known forms. This study should enable us to better understand how polyomavirus VP1 is able to form such divergent shells.

Student Role

The student will grow bacteria that have a gene inserted which allows them to make polyomavirus VP1. The student will harvest the protein and assemble octahedral particles. The student will be trained in use of a transmission electron microscope, which he or she will use to assess the quality and quantity of assembled octahedral particles. Once high-quality particles are obtained, the student will then assist in four important ways:

  1. Imaging the particles by cryo-EM (2D imaging)
  2. Reconstructing the 3D structure
  3. Modeling the atomic-resolution structure of the proteins
  4. Writing up the study for publication in a scientific journal.

Student Learning Outcomes & Benefits

  1. The student will participate in research into the "unknown", i.e. he or she will play a major role in learning something new.
  2. The student will learn new skills. For example, growing protein in bacteria, purifying proteins, use of a transmission electron microscope, and three-dimensional electron microscopy.
  3. As a major contributor to the study, the student will be a co-author on a paper in a scientific journal.

David Belnap
research Associate Professor

School of Biological Sciences
College of Science

Researching the unknown is a wonderful way to learn, but the path is full of ups and downs: ups when discoveries or progress is made, downs when equipment or experiments do not work as intended. One challenge for students is to know when to get help and when to keep trying. Weekly formal meetings provide a way to assess progress, make plans, or change directions. I will meet formally at least weekly with the student—but usually more often. I will advise the student throughout the project. I will train the student in use of the transmission electron microscope. We will work together to solve the three-dimensional structure from two-dimensional electron micrographs and to model the high-resolution structure. We will work together in writing the paper for publication.