Capsid polypeptide chains

A nucleic acid can never code for a single protein molecule that is big enough to enclose and protect it. Therefore, the protein shell of viruses is built up from many copies of one or a few polypeptide chains. The simplest viruses have just one type of capsid polypeptide chain, which forms either a rod-shaped or a roughly spherical shell around the nucleic acid. The simplest such viruses whose three-dimensional structures are known are plant and insect viruses the rod-shaped tobacco mosaic virus, the spherical satellite tobacco necrosis virus, tomato bushy stunt virus, southern bean mosaic vims. 

The protein capsid of picomaviruses contains four polypeptide chains... 

The asymmetric unit contains one copy each of the subunits VPl, VP2, VP3, and VP4. VP4 is buried inside the shell and does not reach the surface. The arrangement of VPl, VP2, and VP3 on the surface of the capsid is shown in Figure 16.12a. These three different polypeptide chains build up the virus shell in a way that is analogous to that of the three different conformations A, C, and B of the same polypeptide chain in tomato bushy stunt virus. The viral coat assembles from 12 compact aggregates, or pen tamers, which contain five of each of the coat proteins. The contours of the outward-facing surfaces of the subunits give to each pentamer the shape of a molecular mountain the VPl subunits, which correspond to the A subunits in T = 3 plant viruses, cluster at the peak of the mountain VP2 and VP3 alternate around the foot and VP4 provides the foundation. The amino termini of the five VP3 subunits of the pentamer intertwine around the fivefold axis in the interior of the virion to form a p stmcture that stabilizes the pentamer and in addition interacts with VP4. 

Another general role of post-translational cleavage of polypeptide chains in viral systems is the specific processing of structural proteins leading to the assembly of the virus (44,45). In this respect, the semliki-Forest virus may be considered as an interesting model to find out how proteins which have different cellular locations reach their final sites within the cell. A single messenger RNA directs the synthesis of the viral capsid protein and of two membrane proteins. 

Fig. 2. The YPMa trimer shown with trimeric structures of virus capsid proteins and members of the TNF superfamily highlights the diversity of trimerization of jelly roll folds. Only C atoms of the polypeptide chains are shown. Virus trimers were extracted from the Viper database of virus structures (http //viperdb.scripps.edu/) [64], SPMV = Satellite pan-icum mosaic virus STMV = satellite tobacco mosaic virus. Figures 1 and 2 were created using Swiss-PdbViewer [65],... 

Integral membrane proteins are more hydrophobic than an average protein, especially when a significant part of the polypeptide chain interacts with the lipid bilayer. The hydrophobicity and molecular weight of a number of integral membrane proteins, poliovirus capsid proteins, and hydrophilic proteins are summarized in Table 1. The percentage of the hydrophobic amino acids, leucine. 

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