Polypeptide secondary

Although living organisms contain additional types of fibrous proteins, as well as polysaccharide-based structural motifs, we focused here on the three arrangements that are the most widely distributed. Two of these, the a-keratins and the /3-keratins incorporate polypeptide secondary structures that also commonly occur in globular proteins. Colla-... 

In describing protein structure it is usual to consider four levels of organization, termed primary, secondary, tertiary and quaternary structure. Primary structure refers to. the sequence of amino acids that makes up the chain of a particular protein (or synthetic polypeptide). Secondary structure is the ordered conformation that the chain (or usually parts of chains) can twist itself into. An example, a section of an a-helical chain is shown in Figure 9.9. More on this shortly. 

The aim of this review is to present these recent developments in the vibrational spectroscopy of peptides, polypeptides, and proteins. We will first discuss the necessary basic aspects of normal-mode calculations. We will then give results for those polypeptide secondary structures that have been studied to date, with an evaluation of the insights obtained from these analyses. Finally, we will comment on the preliminary studies being done on proteins and the prospects for the future. 

Keywords Aggregation, Biohybrid, Biomembrane, Block copolymer, Colloid, Glycopolymer, Polypeptide, Secondary structure, Self-assembly, Vesicle... 

In describing a polypeptide secondary structure, there are several terms to understand. 

Urry, D. W., Mitchell, L. W., and Ohnishi, T. (1974). Biochem. Biophys. Res. Comm. 59, 62. Solvent Dependence of Peptide Carbonyl Carbon Chemical Shifts and Polypeptide Secondary Structure The Repeat Tetrapeptide of Elastin. 

U.S.A. 71, 3265. Carbon-13 Magnetic Resonance Evaluation of Polypeptide Secondary Structure and Correlation with Proton Magnetic Resonance Studies. 

D.W. Urry and M.M. Long, Conformations of the Repeat Peptides of Elastin in Solution An Application of Proton and Carbon-13 Magnetic Resonance to the Determination of Polypeptide Secondary Structure. CRC Crit Rev. Biochemistry, 4,1-45,1976. 

K. M. Hawkins, S. S. S. Wang, D. M. Ford, D. F. Shantz, Poly-L-lysine templated silicas using polypeptide secondary structure to control oxide pore architectures,/. Am. Chem. Soc. 2004, 126, 9112-9119. 

Pleated sheet (Section 27.6B) A type of polypeptide secondary structure in which sections of polypeptide chains are aligned parallel or antiparaUel to one another. 

Hawkins, K.M., Wang, S.S.S., Eord, D.M. and Shantz, D.F. (2004) Poly-L-lysine templated silicas using polypeptide secondary strucmre to control oxide pore architecmres. Jourmil of the American Chemical Society, 126,9112-19. 

G. Wagner, A. Kumar, and K. Wuthrich, Systematic application of two-dimensional proton nuclear magnetic resonance techniques for studies of proteins. 2. Combined use of correlated spectroscopy and nuclear Overhauser spectroscopy for sequential assignments of backbone resonances and elucidation of polypeptide secondary structures, Eur. J. Biochem. 114, 375 (1981). 

Fourier transform infrared spectroscopy (FTIR) is a powerful tool used to monitor changes in protein and polypeptide secondary structure during processing. After exposure of a protein to infrared light, its secondary structure can be determined from the spectra obtained from the absorption of different wavelengths corresponding to specific vibration frequencies of the amide bonds (Jackson and Mantsch, 1995a). 

Section 27 19 Two secondary structures of proteins are particularly prominent The pleated sheet is stabilized by hydrogen bonds between N—H and C=0 groups of adjacent chains The a helix is stabilized by hydrogen bonds within a single polypeptide chain... 

The PSII complex contains two distinct plastoquiaones that act ia series. The first is the mentioned above the second, Qg, is reversibly associated with a 30—34 kDa polypeptide ia the PSII cote. This secondary quiaone acceptor polypeptide is the most rapidly tumed-over proteia ia thylakoid membranes (41,46). It serves as a two-electron gate and connects the single-electron transfer events of the reaction center with the pool of free... 

Fig. 2. Protein secondary stmcture (a) the right-handed a-helix, stabilized by intrasegmental hydrogen-bonding between the backbone CO of residue i and the NH of residue t + 4 along the polypeptide chain. Each turn of the helix requires 3.6 residues. Translation along the hehcal axis is 0.15 nm per residue, or 0.54 nm per turn and (b) the -pleated sheet where the polypeptide is in an extended conformation and backbone hydrogen-bonding occurs between residues on adjacent strands. Here, the backbone CO and NH atoms are in the plane of the page and the amino acid side chains extend from C ...

Through combined effects of noncovalent forces, proteins fold into secondary stmctures, and hence a tertiary stmcture that defines the native state or conformation of a protein. The native state is then that three-dimensional arrangement of the polypeptide chain and amino acid side chains that best facihtates the biological activity of a protein, at the same time providing stmctural stabiUty. Through protein engineering subde adjustments in the stmcture of the protein can be made that can dramatically alter its function or stabiUty. 

Some of these compounds could be considered as dietary additives, but various other terms, including pesticides, can also be used. They can have beneficial effects on the environment and this aspect will be discussed later. The ionophore monensin, which is an alicyclic polyether (Figure 1), is a secondary metabolite of Streptomyces and aids the prevention of coccidiosis in poultry. Monensin is used as a growth promoter in cattle and also to decrease methane production, but it is toxic to equine animals. " Its ability to act as an ionophore is dependent on its cyclic chelating effect on metal ions. ° The hormones bovine somatotropin (BST) and porcine somatotropin (PST), both of which are polypeptides, occur naturally in lactating cattle and pigs, respectively, but can also be produced synthetically using recombinant DNA methods and administered to such animals in order to increase milk yields and lean meat production. "... 

A Aszodi, WR Taylor. Secondary stiaicture formation m model polypeptide chains. Protein Eng 7 633-644, 1994. 

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.

Secondary structure occurs mainly as a helices and p strands. The formation of secondary structure in a local region of the polypeptide chain is to some extent determined by the primary structure. Certain amino acid sequences favor either a helices or p strands others favor formation of loop regions. Secondary structure elements usually arrange themselves in simple motifs, as described earlier. Motifs are formed by packing side chains from adjacent a helices or p strands close to each other. 

Domains are formed by different combinations of secondary structure elements and motifs. The a helices and p strands of the motifs are adjacent to each other in the three-dimensional structure and connected by loop regions. Sequentially adjacent motifs, or motifs that are formed from consecutive regions of the primary structure of a polypeptide chain, are usually close together in the three-dimensional structure (Figure 2.20). Thus to a first approximation a polypeptide chain can be considered as a sequential arrangement of these simple motifs. The number of such combinations found in proteins is limited, and some combinations seem to be structurally favored. Thus similar domain structures frequently occur in different proteins with different functions and with completely different amino acid sequences. 

Polypeptide chains are folded into one or several discrete units, domains, which are the fundamental functional and three-dimensional structural units. The cores of domains are built up from combinations of small motifs of secondary structure, such as a-loop-a, P-loop-p, or p-a-p motifs. Domains are classified into three main structural groups a structures, where the core is built up exclusively from a helices p structures, which comprise antiparallel p sheets and a/p structures, where combinations of p-a-P motifs form a predominantly parallel p sheet surrounded by a helices. 

Figure 6.2 The molten globule state is an important intermediate in the folding pathway when a polypeptide chain converts from an unfolded to a folded state. The molten globule has most of the secondary structure of the native state but it is less compact and the proper packing interactions in the interior of the protein have not been formed.

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