Protein! s polypeptide chains

Figure 1.1 The amino acid sequence of a protein s polypeptide chain is called Its primary structure. Different regions of the sequence form local regular secondary structures, such as alpha (a) helices or beta (P) strands. The tertiary structure is formed by packing such structural elements into one or several compact globular units called domains. The final protein may contain several polypeptide chains arranged in a quaternary structure. By formation of such tertiary and quaternary structure amino acids far apart In the sequence are brought close together in three dimensions to form a functional region, an active site.

What can be accomplished by protein turnover One benefit is the removal of proteins that have sustained spontaneous hydrolytic damage or oxidative damage. Another benefit is that protein turnover makes possible the control of enzyme levels by means of genetic regulation. In a condition where an increase in the acbvity of a parbcular enzyme is needed, the rale of transcripbon of the mRNA coding for the enzyme can be increased. This increase results in an increase in translation, that is, the synthesis of the protein s polypeptide chain. In a condition... 

The amino acid sequence of a protein s polypeptide chain is called its primary or one- dimensional (ID) structure. It can be considered as a word over the 20-letter letter amino acid alphabet. 

The primary structure of a protein refers to the specific identify and ordering of amino acids in a protein s polypeptide chain. The primary stmcture is sometimes called the protein s amino acid sequence. 

His early work on the proteins mainly involved the isolation, characterization, and identification of individual members. Then he turned to the question of their structure, and from a study of the racemization of synthetic diketopiperazines, came to the conclusion that the structure of the giant molecules of proteins could be explained (in terms of Emil Fischer s polypeptide chains) by the classical theories of valency, without the neces-... 

Fig. 5. Protein folding. The unfolded polypeptide chain coUapses and assembles to form simple stmctural motifs such as -sheets and a-hehces by nucleation-condensation mechanisms involving the formation of hydrogen bonds and van der Waal s interactions. Small proteins (eg, chymotrypsin inhibitor 2) attain their final (tertiary) stmcture in this way. Larger proteins and multiple protein assembhes aggregate by recognition and docking of multiple domains (eg, -barrels, a-helix bundles), often displaying positive cooperativity. Many noncovalent interactions, including hydrogen bonding, van der Waal s and electrostatic interactions, and the hydrophobic effect are exploited to create the final, compact protein assembly. Further stmctural...

The differences in the amino acid chemistry of the hide coUagen and the hair keratin are the basis of the lime-sulfide unhairing system. Hair contains the amino acid cystine. This sulfur-containing amino acid cross-links the polypeptide chains of mature hair proteins. In modem production of bovine leathers the quantity of sulfide, as Na2S or NaSH, is normally 2—4% based on the weight of the hides. The lime is essentially an unhmited supply of alkah buffered to pH 12—12.5. The sulfide breaks the polypeptide S—S cross-links by reduction. Unhairing without sulfide may take several days or weeks. The keratin can be easily hydrolyzed once there is a breakdown in the hair fiber stmcture and the hair can be removed mechanically. The coUagen hydrolysis is not affected by the presence of the sulfides (1—4,7). 

Figure 1.2 shows one way of dividing a polypeptide chain, the biochemist s way. There is, however, a different way to divide the main chain into repeating units that is preferable when we want to describe the structural properties of proteins. For this purpose it is more useful to divide the polypeptide chain into peptide units that go from one Ca atom to the next Ca atom (see Figure 1.5). Each C atom, except the first and the last, thus belongs to two such units. The reason for dividing the chain in this way is that all the atoms in such a unit are fixed in a plane with the bond lengths and bond angles very nearly the same in all units in all proteins. Note that the peptide units of the main chain do not involve the different side chains (Figure 1.5). We will use both of these alternative descriptions of polypeptide chains—the biochemical and the structural—and discuss proteins in terms of the sequence of different amino acids and the sequence of planar peptide units.

Figure 13.4 Schematic diagram (a) and topology diagram (b) of the polypeptide chain of cH-ras p21. The central p sheet of this a/p structure comprises six p strands, five of which are parallel a helices are green, p strands are blue, and the adenine, ribose, and phosphate parts of the GTP analog are blue, green, and ted, respectively. The loop regions that are involved in the activity of this protein are red and labeled Gl-GS. The Gl, G3, and G4 loops have the consensus sequences G-X-X-X-X-G-K-S/T, D-X-X-E, and N-K-X-D, respectively. (Adapted from E.R Pai et al., Nature 341 209-214, 1989.)...

Figure 16.S Schematic illustration of the way the 60 protein subunits are arranged around the shell of safellite tobacco necrosis virus. Each subunit is shown as an asymmetric A. The view is along one of the threefold axes, as in Figure 16.3a. (a) Three subunifs are positioned on one triangular tile of an Icosahedron, in a similar way to that shown in 16.4a. The red lines represent a different way to divide the surface of the icosahedron into 60 asymmetric units. This representation will be used in the following diagrams because it is easier to see the symmetry relations when there are more than 60 subunits in the shells, (b) All subunits are shown on the surface of the virus, seen in the same orientation as 16.4a. The shell has been subdivided into 60 asymmetric units by the red lines. When the corners are joined to the center of the virus, the particle is divided into 60 triangular wedges, each comprising an asymmetric unit of the virus. In satellite tobacco necrosis virus each such unit contains one polypeptide chain...

Picornaviruses construct their shells from 60 copies each of three different polypeptide chains. These 180 subunits are arranged within the shell in a manner very similar to the 180 identical subunits of bushy stunt virus. In some picornaviruses there are protrusions around the fivefold axes, which are surrounded by deep "canyons." In rhinoviruses, the canyons form the virus s attachment site for protein receptors on the surface of the host cells, and they are adjacent to cavities that bind antiviral drugs. 

The unique characteristic of each protein is the distinctive sequence of amino acid residues in its polypeptide chain(s). Indeed, it is the amino acid sequence of proteins that is encoded by the nucleotide sequence of DNA. This amino acid sequence, then, is a form of genetic information. By convention, the amino acid sequence is read from the N-terminal end of the polypeptide chain through to the C-terminal end. As an example, every molecule of ribonucle-... 

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. 

Later we return to an analysis of the 1° structure of proteins and the methodology used in determining the amino acid sequence of polypeptide chains, but let s first consider the extraordinary variety and functional diversity of these most interesting macromolecules. 

If the protein of interest is a heteromultimer (composed of more than one type of polypeptide chain), then the protein must be dissociated and its component polypeptide subunits must be separated from one another and sequenced individually. Subunit associations in multimeric proteins are typically maintained solely by noncovalent forces, and therefore most multimeric proteins can usually be dissociated by exposure to pEI extremes, 8 M urea, 6 M guanidinium hydrochloride, or high salt concentrations. (All of these treatments disrupt polar interactions such as hydrogen bonds both within the protein molecule and between the protein and the aqueous solvent.) Once dissociated, the individual polypeptides can be isolated from one another on the basis of differences in size and/or charge. Occasionally, heteromultimers are linked together by interchain S—S bridges. In such instances, these cross-links must be cleaved prior to dissociation and isolation of the individual chains. The methods described under step 2 are applicable for this purpose. 

Frequency of occurrence of each amino acid re.sidue in the polypeptide chain.s of 207 unrelated protein.s of known. sequence. 

FIGURE 6.13 Three different kinds of /3-bnlge strnctnres involving a pair of adjacent polypeptide chains. (Adapted from Richardson, J.. S ., 1981. Advances in Protein Chemisny 34 167-339.J... 

The secondary and tertiary structures of myoglobin and ribonuclease A illustrate the importance of packing in tertiary structures. Secondary structures pack closely to one another and also intercalate with (insert between) extended polypeptide chains. If the sum of the van der Waals volumes of a protein s constituent amino acids is divided by the volume occupied by the protein, packing densities of 0.72 to 0.77 are typically obtained. This means that, even with close packing, approximately 25% of the total volume of a protein is not occupied by protein atoms. Nearly all of this space is in the form of very small cavities. Cavities the size of water molecules or larger do occasionally occur, but they make up only a small fraction of the total protein volume. It is likely that such cavities provide flexibility for proteins and facilitate conformation changes and a wide range of protein dynamics (discussed later). 

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