Secondary Structures, Protein Alpha-Helix

The secondary structure of a protein is determined by the spatial arrangement of the polypeptide chain. Evidence obtained mainly from X-ray diffraction patterns (Linus Pauling, 1951, and others) has shown that the chain is typically wound into a helix. The helical form is maintained by hydrogen bonds located at spaced intervals, as shown in Fig. 26.8. The entire structure is called the ALPHA-HELIX. Other secondary structures of proteins include pleated sheets and random coils. 

Secondary protein structure defines the arrangement of the amino acid sequence (or primary structure) into larger motifs. The two most common ways that the amino acid chains can fold to form the secondary structure are into a beta sheet or an alpha helix. These secondary structures are held in place by hydrogen bonding. 

Figure 11.4 The structural hierarchy in proteins, (a) A segment of primary structure (b) secondary structure illustrated as a segment of alpha helix (c) tertiary structure in which helices are interspersed with coils, and (d) quaternary structure. (Illustration, Irving Geis/Geis Archive Trust. Copyright Howard Hughes Medical Institute. Reproduced with permission.)...

JPRED [66,67] is a neural network-based program for predicting protein secondary structure sequence residues are assigned to one of three secondary-structure elements (alpha helix, beta sheet, or random coil). 

Figure 2.2 The a helix is one of the major elements of secondary structure in proteins. Main-chain N and O atoms ate hydrogen-bonded to each other within a helices, (a) Idealized diagram of the path of the main chain in an a helix. Alpha helices are frequently illustrated in this way. There are 3.6 residues per turn in an a helix, which corresponds to 5.4 A (1.5 A pet residue), (b) The same as (a) but with approximate positions for main-chain atoms and hydrogen bonds Included. The arrow denotes the direction from the N-terminus to the C-termlnus.

The essential distinction between the approaches used to formulate and evaluate proteins, compared with conventional low molecular weight drugs, lies in the need to maintain several levels of protein structure and the unique chemical and physical properties that these higher-order structures convey. Proteins are condensation polymers of amino acids, joined by peptide bonds. The levels of protein architecture are typically described in terms of the four orders of structure [23,24] depicted in Fig. 2. The primary structure refers to the sequence of amino acids and the location of any disulfide bonds. Secondary structure is derived from the steric relations of amino acid residues that are close to one another. The alpha-helix and beta-pleated sheet are examples of periodic secondary structure. Tertiary... 

Alpha helix one form of secondary structure in proteins in which the polypeptide chain forms a helix having 3.6 amino acid residues per turn. 

Secondary structure those protein structures that result from hydrogen bond formation between the amino and carbonyl groups of peptide bonds. The most important ones are the alpha helix and beta sheets. 

The alpha helix and beta sheets are two types of secondary structures exhibited by polypeptides and proteins. (Rae Dejur)... 

Secondary structure refers to regularities or repeating features in the conformation of the protein chain s backbone. Four major types of secondary structure in proteins are (1) the alpha (a) helix, formed from a single strand of amino acids (2) the beta (P) sheet, formed from two or more amino acid strands (from either the same chain or from different chains) (3) the beta (P) bend or reverse turn, in a single strand and (4) the collagen helix, composed of three strands of amino acids. 

The wavelengths of IR absorption bands are characteristic of specific types of chemical bonds. In the past infrared had little application in protein analysis due to instrumentation and interpretation limitations. The development of Fourier transform infrared spectroscopy (FUR) makes it possible to characterize proteins using IR techniques (Surewicz et al. 1993). Several IR absorption regions are important for protein analysis. The amide I groups in proteins have a vibration absorption frequency of 1630-1670 cm. Secondary structures of proteins such as alpha(a)-helix and beta(P)-sheet have amide absorptions of 1645-1660 cm-1 and 1665-1680 cm, respectively. Random coil has absorptions in the range of 1660-1670 cm These characterization criteria come from studies of model polypeptides with known secondary structures. Thus, FTIR is useful in conformational analysis of peptides and proteins (Arrondo et al. 1993). 

The structure of proteins determines their function and can be described on four levels, illustrated on page 447. The primary structure is the sequence of amino acids in the polypeptide chain. The secondary structure describes how various short portions of a chain are either wrapped into a coil called an alpha helix or folded into a thin pleated sheet. The tertiary structure is the way in which an entire polypeptide chain may either twist into a long fiber or bend into a globular clump. The quaternary structure describes how separate proteins may join to form one larger complex. Each level of structure is determined by the level before it, which means that ultimately it is the sequence of amino acids that creates the overall protein shape. Fhis final shape is maintained both by chemical bonds and by weaker molecular attractions between amino acid side groups. 

The primary stucture of a protein is simply the sequence of amino acids within that protein. These linked amino acids can either curl into an alpha helix or crisscross to form pleated sheets, which are examples of secondary protein structures. The protein chain of amino acids is typically quite long, such that it may have regions of alpha helices and regions of pleated sheets. The larger structure of the protein that includes all the various contours of the whole protein is the tertiary structure. In some instances, two or more tertiary structures will come together to form an even larger complex known as the quaternary structure. 

Fig. 7.10. Plot of the PCA coefficients for the two most important basis functions for a set of 78 polypeptide, protein and virus ROA spectra. Definitions of the structural types analysed are all alpha, > 60% a-helix with little other secondary structure mainly alpha, > 35% a-helix and a small amount of (3-sheet ( 5-15%) alpha beta, similar significant amounts of a-helix and (3-sheet mainly beta, > 35% 13-sheet and a small amount of a-helix ( — 5—15%) all beta, > 45% (3-sheet with little other secondary structure mainly disordered/irregular, little secondary structure all disordered/irregular, no secondary structure...

Secondary Structure of Proteins The secondary structure of a protein is how the polypeptide chain is twisted. There are two common types of secondary structure the alpha helix and the beta pleated sheet. 

Figure 3.3 The alpha helix is one of the most common secondary structure patterns. Pictured here are (a) the molecular structure of the alpha helix and (b) a protein consisting of several spiraling alpha helices.

Figure 3-2 Secondary Structures of Proteins, (A) Alpha Helix, (B) Antiparallel Sheet...

A few scanning dispersive VCD instruments are still in use for biological applications in the mid-IR region [46,47]. In 2009, a newly designed and optimized dispersive VCD instrument was reported [47]. A collection of spectra for peptides and proteins having different dominant secondary structures (alpha-helix, beta-sheet, and random coil) measured with this new instrument showed substantially improved signal-to-noise (S/N) ratios as compared with the earlier version. The instrument provides protein VCD spectra for the amide I region that are of comparable or better quality than those obtained with a standard commercial FTIR-VCD spectrometer [47]. 

In alpha-keratin, shown in Figure 5, the entire length of the protein has an a-helix structure. However, other proteins will have only sections that are a-helixes. Different sections of the same protein may have a pleated sheet secondary structure. These different sections of a protein can fold in different directions. These factors, combined with the inter-molecular forces acting between side chains give each protein a distinct three-dimensional shape. This shape is the tertiary structure of the protein. 

Fig. 1. Hierarchical protein structure Left Small part of the protein backbone. The peptide bond itself is marked by a shaded rectangle, R denotes one of the 20 amino acid side-chains. Middle Secondary structure in the form of an alpha-helix and beta-sheet. Only the backbone is shown and highlighted by a ribbon. The hydrogen bonds are indicated by dashed lines. Right Tertiary structure in the native state. The alpha-helices and beta-sheets are indicated by thick ribbons and arrows respectively...

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