Protein Truncated viral proteins

The molecular mechanism of TAP inhibition by US6 is poorly defined mostly because of the lack of isolated viral protein. By use of photoactive peptides it was shown that US6, in contrast to ICP47, does not prevent peptide binding to TAP (Ahn et al. 1997 Hengel et al. 1997). The analysis of chimeras with E3/19K or CD8, as well as of a carboxy-terminal truncation, led to the conclusion that the luminal domain, US6(20-139), is still functional (Ahn et al. 1997). 

NS3 is a 631 amino acid protein, and its first 180 amino acids encode a serine protease of the chymotrypsin family (Figure 2.2A). It has a typical chymotrypsin-family fold consisting of two jS-barrels, with catalytic triad residues at the interface. His-57 and Asp-81 are contributed by the N-terminal jS-barrel and Ser-139 from the C-terminal jS-barrel. NS3 and closely related viral proteases are significantly smaller than other members of the chymotrypsin family, and many of the loops normally found between adjacent jS-strands in trypsin proteases are truncated in NS3 [31]. Probably... 

One might also question whether the truncation of the expansion at the second viral coefficient level and the neglect of the protein-protein interaction term in Equation 30 is valid (24). While the inclusion of three-body terms (and of the protein-protein term) should improve the comparison with experiment quantitatively, we suspect that the trends predicted for the protein partition coefficient as a function of molecular weight would be the same. 

The RNA genome is surrounded by P7 nucleocapsid proteins and by several viral enzymes—namely, reverse transcriptase, integrase, and protease. The truncated cone consists of P24 capsid protein subunits. The P17 matrix (another layer of protein) lies inside the envelope, which consists of a lipid bilayer and glycoproteins, such as gp41 and gpl20. 

The K2R ORF of SPV, a poxvirus that causes mild infections in pigs, encodes a 370 amino acid protein with -30% amino acid sequence identity to mammalian chemokine receptors. A truncated and probably non-functional copy of the K2R ORF, designated C3L, is found at the other end of the viral genome. 

Figure 1 Structural comparison of viral capsids and a heat shock protein assembly that are commonly used to build nanoscale materials. All structures are shown to scale except for Ml 3. The length of the TMV capsid has been truncated. The colors have been added to highlight the morphological units, and are not necessarily indicative of different protein sequences. All structural renderings were generated using UCSF Chimera.

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