The experiments described here were undertaken to test the idea that low energy Ar+plasma etching could be employed as the basis of a method to order viral structural polypeptides according to their physical proximity to the virus surface. Since low energy (500 eV) Ar+ions do not penetrate deeply into virus surfaces. one expects that the outermost proteins will be damaged before internal ones when intact virions are irradiated. To test this expectation, we exposed adenovirus 2 to a 500-eV Ar+plasma and then employed sodium dodecyl sulfate-polyacrylamide gel electrophoresis to assess the extent of damage to the major structural polypeptides. Gel analyses showed that the proteins exposed on the virus surface (proteins II, III, and IV) were degraded rapidly during the first 10 s of irradiation while protein VII, the major core polypeptide, was almost completely protected. Proteins located between the capsid and the core, such as proteins IIIa and VI, were degraded at intermediate rates. Quantitative measurements demonstrated that the observed decay rate differences were not due simply to differences in protein target size; distance to the virion surface made an important contribution. The plasma etching technique, therefore, appears to have considerable potential for the structural analysis of viruses and other macromolecular assemblies where the proximity of individual proteins to the particle surface is unknown. © 1988.
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