Subunits in protein structures

Role of the Amino Acid Sequence in Protein Structure Secondary Structure in Protein.s Protein Folding and Tertiary Structure Subunit Interaction.s and Quaternary Structure... 

Fig. 9. Coiled-coil spirals. For the phage coat proteins and flagellin, subunits are shown enlarged next to the structures, as well as the cross sections of the coiled-coil sheets they form. The positions of the subunits in the structures are indicated in white. The core packing layers are also shown for the phage coat proteins in order to illustrate the use of knobs-into-holes and ridges-into-grooves layers.

Figure 6.1. The role of HMW subunits in gluten structure and functionality. Amino acid sequences derived from direct analysis of purified proteins and the isolation and sequencing of corresponding genes show that the proteins have highly conserved structures, with repetitive domains flanked by shorter nonrepetitive domains containing cysteine residues (SH) available for formation of interchain disulphide bonds. Molecular modelling indicates that the individual repetitive domains form a loose spiral structure (bottom right) while SPM shows that they interact by noncovalent forces to form fibrils (centre right). Includes figures from Parchment et al. (2001) and Humphries et al. (2000).

Although mushroom and Neurospora PPO s catalyze the same reactions, they are quite different in protein structure. Strothkamp et al. (1976) reported two different size subunits in mushroom PPO, H - 45,000 and L - 13,000 daltons. Robb (1979) reported there are at least two types of heavy subunits, termed and with slightly different molecular weights. 

Quaternary structure refers to the arrangement of chains (or subunits) in proteins. It is maintained by interactions between amino acids on the individual chains. 

A possible hierarchy of protein folding corresponding to the hierarchy in protein structure was suggested (Schulz, 1977). It can be summarized by the following scheme for folding in stages with an additional level for oligomeric proteins, the subunit assembly ... 

Protein molecules that have only one chain are called monomeric proteins. But a fairly large number of proteins have a quaternary structure, which consists of several identical polypeptide chains (subunits) that associate into a multimeric molecule in a specific way. These subunits can function either independently of each other or cooperatively so that the function of one subunit is dependent on the functional state of other subunits. Other protein molecules are assembled from several different subunits with different functions for example, RNA polymerase from E. coli contains five different polypeptide chains. 

The number of helical turns in these structures is larger than those found so far in two-sheet p helices. The pectate lyase p helix consists of seven complete turns and is 34 A long and 17-27 A in diameter (Figure 5.30) while the p-helix part of the bacteriophage P22 tailspike protein has 13 complete turns. Both these proteins have other stmctural elements in addition to the P-helix moiety. The complete tailspike protein contains three intertwined, identical subunits each with the three-sheet p helix and is about 200 A long and 60 A wide. Six of these trimers are attached to each phage at the base of the icosahedral capsid. 

Steinbacher, S., et al. Crystal structure of P22 tailspike protein interdigitated subunits in a thermostable trimer. Science 265 383-386, 1994. 

Deisenhofer, J., et al. Structure of the protein subunits in the photosynthetic reaction center of Rhodopseudomonas viridis at 3 A resolution. Nature 318 618-624, 1985. 

We have seen in the structure of this simple satellite virus that 60 subunits are sufficient to form a shell around an RNA molecule that codes for the subunit protein, but there is little room for additional genetic information. 

Figure 16.6 A T = 3 icosahedral virus structure contains 180 subunits in its protein shell. Each asymmetric unit (one such unit is shown in thick lines) contains three protein subunits A, B, and C. The icosahedral structure is viewed along a threefold axis, the same view as in Figure 16.5. One asymmetric unit is shown in dark colors.

Since all members of this family of RNA phages have homologous coat proteins, their subunits are expected to have the same three-dimensional structure. It remains to be seen if the MS2 fold is also present in any other unrelated viruses. The fold is so far unique for the MS2 subunit, but similar structures have been observed in other proteins such as the major histocompatibility antigen, HLA, which was discussed in Chapter 15. 

Many proteins consist of two or more interacting polypeptide chains of characteristic tertiary structure, each of which is commonly referred to as a subunit of the protein. Subunit organization constitutes another level in the hierarchy of protein structure, defined as the protein s quaternary (4°) structure (Figure 5.10). Questions of quaternary structure address the various kinds of subunits within a protein molecule, the number of each, and the ways in which they interact with one another. 

There are several important reasons for protein subunits to associate in oligomeric structures. 

Despite the unity in secondary structural patterns, little is known about the three-dimensional, or tertiary, structure of rRNAs. Even less is known about the quaternary interactions that occur when ribosomal proteins combine with rRNAs and when the ensuing ribonucleoprotein complexes, the small and large subunits, come together to form the complete ribosome. Furthermore, assignments of functional roles to rRNA molecules are still tentative and approximate. (We return to these topics in Chapter 33.)... 

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