Structures within Proteins
It is useful to focus attention on particular aspects of protein structures. The primary structure of a protein is its linear sequence of amino acids. The local spatial structure of small numbers of amino acids, inde-pendent of the orientations of their side groups, generates a secondary structure. The alpha helix, beta sheet, and beta turn are all secondary structures that have been found in proteins. Both the arrangement of the secondary structure elements and the spatial arrangement of all the atoms of the molecule are referred to as the tertiary structure. Quater-nary structure refers to the arrangement of subunits in proteins consist-ing of more than one polypeptide chain.
A domain of a protein is a structure unit intermediate in size between secondary and tertiary structures. It is a local group of amino acids that have many fewer interactions with other portions of the protein than they have among themselves (Fig. 6.10). Consequently, domains are independent folding units. Interestingly, not only are the amino acids of a domain near one another in the tertiary structure of a protein, but they usually comprise amino acids that lie near one another in the primary structure as well. Often, therefore, study of a protein’s structure can be done on a domain-by-domain basis. The existence of semi-inde-pendent domains should greatly facilitate the study of the folding of polypeptide chains and the prediction of folding pathways and struc-tures.
Particularly useful to the ultimate goal of prediction of protein structure has been the finding that many alterations in the structure of proteins produced by changing amino acids tend to be local. This has
Figure 6.11 Substitution of portions of theE.colitryptophan synthetaseαsubunit with corresponding regions from the Salmonella typhimurium syn-thetase subunit.
been found in exhaustive genetic studies of the lac and lambda phage repressors, in the thermodynamic properties of mutant proteins, and in the actual X-ray or NMR determined structures of a number of proteins. In the lac and lambda repressors, the majority of the amino acid changes that alter the ability to bind to DNA lie in the portion of the protein that makes contact with the DNA. Similar results can be inferred from alterations in the amino acid sequence of the tryptophan synthetase protein generated by fusing two related but nonidentical genes. Despite appreciable amino acid sequence differences in the two parental types, the fusions that contain various amounts of the N-terminal sequence from one of the proteins and the remainder of the sequence from the other protein retain enzymatic activity (Fig. 6.11). This means that the amino acid alterations generated by formation of these chimeric pro-teins do not need to be compensated by special amino acid changes at distant points in the protein.
The results obtained with repressors and tryptophan synthetase mean that a change of an amino acid often produces a change in the tertiary structure that is primarily confined to the immediate vicinity of the alteration. This, plus the finding that protein structures can be broken down into domains, means that many of the potential long-range interactions between amino acids can be neglected and interactions over relatively short distances of up to 10 Å play the major role in determining protein structure.
The proteins that bind to enhancer sequences in eukaryotic cells are a particularly dramatic example of domain structures in proteins. These proteins bind to the enhancer DNA sequence, often bind to small molecule growth regulators, and activate transcription. In the glucocor-ticoid receptor protein, any of these three domains may be inde-pendently inactivated without affecting the other two. Further, domains may be interchanged between enhancer proteins so that the DNA-bind-ing specificity of one such protein can be altered by replacement with the DNA-binding domain from another protein.
As we saw earlier in discussing mRNA splicing, DNA regions encod-ing different domains of a protein can be appreciably separated on the chromosome. This permits different domains of proteins to be shuffled so as to accelerate the rate of evolution by building new proteins from new assortments of preexisting protein domains. Domains rather than amino acids then become building blocks in protein evolution.
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