Polypeptides secondary structure

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. 

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... 

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.

Homologous proteins have similar three-dimensional structures. They contain a core region, a scaffold of secondary structure elements, where the folds of the polypeptide chains are very similar. Loop regions that connect the building blocks of the scaffolds can vary considerably both in length and in structure. From a database of known immunoglobulin structures it has, nevertheless, been possible to predict successfully the conformation of hyper-variable loop regions of antibodies of known amino acid sequence. 

FIGURE 5.8 Two structural motifs that arrange the primary structure of proteins into a higher level of organization predominate in proteins the a-helix and the /3-pleated strand. Atomic representations of these secondary structures are shown here, along with the symbols used by structural chemists to represent them the flat, helical ribbon for the a-helix and the flat, wide arrow for /3-structures. Both of these structures owe their stability to the formation of hydrogen bonds between N—H and 0=C functions along the polypeptide backbone (see Chapter 6). 

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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