Amino acids subunit structure

Proteins are the most abundant organic molecules in animals, playing important roles in all aspects of cell structure and function. Proteins are biopolymers of a-amino acids, so named because the amino group is bonded to the a carbon atom, next to the carbonyl group. The physical and chemical properties of a protein are determined by its constituent amino acids. The individual amino acid subunits are joined by amide linkages called peptide bonds. Figure 24-1 shows the general structure of an a-amino acid and a protein. 

Primary structure Sequence of amino acid subunits along a peptide or protein chain or a polynucleotide. 

A polymer is a long-chain molecule composed of a large number of repeated subunits called monomers. These subunits can be as simple as a CHj group, as is the case for polyethylene, or the subunit can be a much more complex collection of atoms. Even molecules as complex as proteins are polymers, long chains of different amino acid subunits. The definition of a polymer can therefore be applied to an extremely wide variety of molecular structures, so the bulk properties of different polymers are diverse. Some examples are shown in Figure 4.2. 

There are at least three different classes of crystallins. The a and (3 are heterogeneous assemblies of different subunits specified by different genes, whereas the gamma (y) crystallins are monomeric proteins with a polypeptide chain of around 170 amino acid residues. The structure of one such Y crystallin was determined in the laboratory of Tom Blundell in London to 1.9 A resolution. A picture of this molecule generated from a graphics display is shown in Figure 5.11. 

Each subunit of the homotetrameric PFK of Escherichia coli comprises 320 amino acids arranged in two domains, one large and one smaller, both of which have an rx/p structure reminiscent of the Rossman fold (Figure 6.25). 

Figure 8.3 The DNA-binding protein Cro from bacteriophage lambda contains 66 amino acid residues that fold into three a helices and three P strands, (a) A plot of the Ca positions of the first 62 residues of the polypeptide chain. The four C-terminal residues are not visible in the electron density map. (b) A schematic diagram of the subunit structure. a helices 2 and 3 that form the helix-turn-helix motif ate colored blue and red, respectively. The view is different from that in (a), [(a) Adapted from W.F. Anderson et al., Nature 290 754-758, 1981. (b) Adapted from D. Ohlendorf et al., /. Mol. Biol. 169 757-769, 1983.]...

Many biochemical and biophysical studies of CAP-DNA complexes in solution have demonstrated that CAP induces a sharp bend in DNA upon binding. This was confirmed when the group of Thomas Steitz at Yale University determined the crystal structure of cyclic AMP-DNA complex to 3 A resolution. The CAP molecule comprises two identical polypeptide chains of 209 amino acid residues (Figure 8.24). Each chain is folded into two domains that have separate functions (Figure 8.24b). The larger N-terminal domain binds the allosteric effector molecule, cyclic AMP, and provides all the subunit interactions that form the dimer. The C-terminal domain contains the helix-tum-helix motif that binds DNA. 

Five of the six loop regions (G1-G5 in Figure 13.4) that are present at the carboxy end of the p sheet in the Ras structure participate in the GTP binding site. Three of these loops, G1 (residues 10-17), G3 (57-60), and G4 (116-119), contain regions of amino acid sequence conserved among small GTP-binding proteins and the Ga subunits of trimerlc G proteins. 

Figure 16.17 The subunit structure of the bacteriophage MS2 coat protein is different from those of other sphericai viruses. The 129 amino acid polypeptide chain is folded into an up-and-down antiparallei P sheet of five strands, P3-P7, with a hairpin at the amino end and two C-terminai a helices. (Adapted from a diagram provided by L. Liijas.)...

They started from the sequence of a domain, Bl, from an IgG-binding protein called Protein G. This domain of 56 amino acid residues folds into a four-stranded p sheet and one a helix (Figure 17.16). Their aim was to convert this structure into an all a-helical structure similar to that of Rop (see Chapter 3). Each subunit of Rop is 63 amino acids long and folds into two a helices connected by a short loop. The last seven residues are unstructured and were not considered in the design procedure. Two subunits of Rop form a four-helix bundle (Figure 17.16). 

---