Alphavirus Structure. Part 2

The current molecular model for how the virus transfers its RNA into the cell is hypothesized to be by low pH mediated membrane fusion, after endocytosis of the virus attached to its receptor. E2 contains the receptor binding sequence while E1 is known to contain the properties necessary for membrane fusion. It is predicted that as the endosome is acidified, the virus membrane fuses with the endosome and releases the nucleocapsid into the cell cytoplasm. There are some reports which implicate ribosomes in the process of releasing RNA from its association with the capsid protein. The process by which E1 mediates membrane fusion can theoretically be supported by a crystal structure of E1* (PDB code: 1I9W) which displays the position and the conformation of the putative fusion domain and flexible regions within the protein. This structure was obtained by proteolytic cleavage from purified Semliki Forest Virus (SFV). A second structure was obtained by expression of the E1 ectodomain in E. coli. This crystal structure of E1 was subsequently fit into a cryoEM-reconstruction of SINV (PDB code: 1Z8Y). The crystal structure of the E1 protein has three primary domains I, II and III. Domain I is the NH proximal domain that contains the putative fusion loop. Domain II is the central domain and domain III is the most distal domain.
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One important caveat when interpreting structural data is that the data represents a native structure or structural intermediate of the entity in question. This condition would require that sound biochemical data confirm assumptions about the structural data without imposing other methods of confirmation to the analysis. A second condition would be that the fit of the higher resolution crystal structure not be distorted in the larger density landscape of the second much more diffuse cryoEM density. One such analysis put in question the number and location of the disulfide bonds in the native, infectious form of E1. In the crystal structure, there are a number of disulfide bonds identified; supporting the hypothesis that disulfide bonds play a role in protein assembly.

However some cystines identified as participating in disulfide bridges in the crystal structure were identified as free cystines using protein modification and mass spectrometry in the intact infectious virus. These conflicts are not unexpected because the protein crystal structure is dependent on how the protein is purified, the crystals are grown, and the structure is refined. It is the nature of the crystal analysis process that the structure is of a protein in its lowest energy conformation. This means that the crystal structure could be any one of the various intermediate conformations assumed when E1 is extracted by detergent (described above) or expressed without its membrane spanning domain in an environment other than the endoplasmic reticulum.