Alpha Helix
An alpha helix is a common secondary structure found in proteins, characterized by a right-handed coiled shape resembling a spiral staircase. It is stabilized by hydrogen bonds between the amino acid residues in the protein chain. The alpha helix plays a crucial role in determining the overall shape and function of proteins.
7 Key excerpts on "Alpha Helix"
eBook - ePub- David P. Clark(Author)
- 2009(Publication Date)
- Academic Cell(Publisher)
...7.06), a single polypeptide chain is coiled into a right-handed helix and the hydrogen bonds run vertically up and down, parallel to the helix axis. In fact, the hydrogen bonds in an α-helix are not quite parallel to the axis. They are slightly tilted relative to the helix axis because there are 3.6 amino acids per turn rather than a whole number. The pitch (repeat length) is 0.54 nm and the rise per residue is about 0.15 nm. Figure 7.06 The Alpha Helix A) The general shape of an α-helix. B) The carbon backbone of the polypeptide chain. C) The hydrogen bonds between peptide groups. Hydrogen bonding is responsible for the formation of alpha-helix and beta-sheet structures in proteins. The hydrogen bonds hold successive twists of the helix together and run from the C˭O group of one amino acid to the NH group of the fourth amino acid residue down the chain. The α-helix is very stable because all of the peptide groups (—CO—NH—) take part in two hydrogen bonds, one up and one down the helix axis. A right-handed helix is most stable for L - amino acids.(A stable helix cannot be formed with a mixture of D - and L - amino acids, although a stable left-handed helix could theoretically be formed from D - amino acids). The R-groups extend outwards from the tightly packed helical polypeptide backbone. Of the 20 amino acids, Ala, Glu, Leu and Met are good α-helix formers but Tyr, Ser, Gly and Pro are not. Proline is totally incompatible with the α-helix, due to its rigid ring structure. Furthermore, when proline resides are incorporated, no hydrogen atoms remain on the nitrogen atom that takes part in peptide bonding. Consequently, proline residues interrupt hydrogen-bonding patterns. In addition, two bulky residues or two residues with the same charge that lie next to each other in the polypeptide chain will not fit properly into an α-helix...
eBook - ePubHow Enzymes Work
From Structure to Function
- Haruo Suzuki(Author)
- 2019(Publication Date)
- Jenny Stanford Publishing(Publisher)
...6.9), and the polypeptide chain shows ordered structures when the ϕ and ψ angles are in the range of certain values along the certain length of polypeptide. The structure is named the secondary structure. Figure 6.10 shows typical structures, α helix, anti-parallel β pleated sheet structures, and β turn. Figure 6.10 Secondary structures. Dark ribbons show the main chain conformation of bovine pancreatic trypsin (pdb code: 2qcp). Left: α helix, residues from Y234 to S244. Center: Completely stretched main chains are positioned anti-parallel each other (anti-parallel β pleated sheet). The residues from Q135 to G140 and from K156 to P161. Right: β turn, a polypeptide changes the direction 180°. The central amide plane (dotted square) has two conformations, I and II. The conformation of II is that of I rotated 180°. In each case, the main chain O atom is hydrogen-bonded to the H atom of the N-H, thus stabilizing the structures. 6.4.2.1 α helix The α helix is usually a right-handed helix of polypeptide composed of L -amino acid residues. A left-handed α helix must be rarely observed with polypeptides with L -amino acid residues if any because of the steric hindrance. The main chain carbonyl oxygen atom is hydrogen-bonded with the main chain imino hydrogen atom. The hydrogen bond forms a loop between n amino acid residues. The number of atoms forming the hydrogen bond is 3 n + 4. For one round of α helix, 3.6 amino acid residues are included, thus 13 atoms forms one hydrogen bond. Therefore, α helix is also called 3.6 13 helix. As shown in Fig. 6.10, the side chains are on the outside of the helix. The amino acid residues, Glu, Met, Ala, and Leu, have a tendency to be in an α helical structure. Gly residue has the smallest side chain (H atom), so it is free to take ϕ and ψ angles of the residue. On the other hand, Pro residue is hard to be in an α helix due to its unique structure (Fig. 6.11). Figure 6.11 Proline cis-trans isomerization...
eBook - ePub- Pieter Walstra(Author)
- 2002(Publication Date)
- CRC Press(Publisher)
...Contrariwise, the conformation mostly is highly ordered, and some higher levels of structural organization are distinguished, i.e., secondary, tertiary, and quaternary structures. 7.1.3 Secondary Structure This concerns fairly regular arrangements of adjacent amino acid residues. Several types exist, but the most common ones are α-helices and β -strands. In the right-handed α -helix, the peptide chain forms a helix (like a cork screw) with the side groups on the outside, where each turn takes 3.6 residues (18 residues making 5 turns); the translation of the helix is 0.15 nm per residue (i.e., a pitch of 0.54 nm per turn), compared to 0.36 nm per residue for a stretched chain (Figure 7.2). The helical conformation is stabilized by H-bonds, between the O of peptide bond i and the NH of peptide bond i +4. Moreover, enhanced van der Waals attraction is involved. The possibility for the latter to occur varies among amino acid residues, which means that not all of them readily partake in an α -helix. Ala, Glu, Phe, His, Ile, Leu, Met, Gln, Val, and Trp have strong tendencies to form helices, whereas Pro, owing to its cyclic structure, is a “helix breaker.” The formation of an á -helix is a clear example of a cooperative transition. Although each of the bonds involved is weak, at most a few times k B T, the collective bond energy of the whole structure may be sufficient to stabilize it. This is comparable to the formation of a molecular crystal from a solution, where bond energies often are 1 or 2 k B T per molecule. Doublets of these molecules would be very short-lived, but a crystal of sufficient size is stable, mainly because each molecule now is involved in a number of bonds, e.g., six. A prerequisite, both in a crystal and in a helix, is a very good fit of the bonds. This is the case in an β-helix, where the H-bonds are almost perfectly aligned. The cooperativity principle implies that an a-helix cannot be very short, as is indeed observed...
eBook - ePubProtein Physics
A Course of Lectures
- Alexei V. Finkelstein, Oleg Ptitsyn(Authors)
- 2016(Publication Date)
- Academic Press(Publisher)
...Therefore, it is no wonder that in proteins α-helices are numerous, and in fibrous proteins, they are extremely extended and incorporate hundreds of residues. Fig. 7.5 The right-handed α-helix. Hydrogen bonds in the main chain are shown as light-blue lines. (A) Atomic structure; R = side-chains. (B) Axial view of one turn of this α-helix. The arrow shows the turn of the helix (per residue) when it approaches the viewer (the closer to the viewer, the smaller the chain residue number). The circle depicts the cylindrical surface enveloping the C α atoms of the helix. Adapted from Schulz, G.E., Schirmer, R.H., 1979, 2013. Principles of Protein Structure. Springer, New York (Chapter 5). (C) Stereo drawing (see Appendix E) of an α-helix. In side chains, only С β atoms are shown. Left-handed α-helices are not (or hardly ever) observed in proteins. This is also true for 2 7 -helices that not only lie at the very edge of the allowed region but also have a large angle between their N–H and O C groups, that is energetically disadvantageous for hydrogen bonding. π-Helices are absent from proteins too. They also occur at the very edge of the allowed region and their turns are far too wide, which results in an energetically unfavorable axial “hole.” In contrast, 3 10 -helices (mainly right-handed; left-handed ones are good for glycines only) are present in proteins, although only as short (three to four residues) and distorted fragments: the 3 10 -helix is too tight and gives rise to steric strains; its conformation lies close to the edge of the allowed region. Pay attention to the feature clearly seen in Fig. 7.5A : the helical N-terminus is occupied by “free” H atoms of N–H groups uninvolved in intra-helical H-bonds, while the C-terminus is occupied by H-bond-free O atoms of C O groups...
eBook - ePub- J. G. Salway(Author)
- 2011(Publication Date)
- Wiley-Blackwell(Publisher)
...an N terminus (H 3 N +) and a C terminus (COO −) (Fig. 6.4). The amino acid sequence defines the primary structure and determines how the protein folds into its three-dimensional shape. Figure 6.4 Primary structure of a protein. Polymerisation of amino acids to form a polypeptide chain. This is represented as a zig-zag with an arrow head at the C-terminus. Access a high quality version of this image at http://booksupport.wiley.com. 7 Secondary structure of proteins Secondary Structure Secondary structure largely depends on hydrogen bonding involving the peptide bonds, whereas tertiary structure (Chapter 8) depends on bonds involving the amino acid R-groups. β-Strands and β-Sheets The polypeptide chain is organised as β-strands. When several of these β-strands associate they form parallel or antiparallel β-sheets (Figs 7.1 and 7.2). Figure 7.1 Antiparallel β-sheet. The polypeptide chains organise in a zig-zag manner to form β-strands. The β-strands can associate by hydrogen bonding to form a β-sheet. When two strands run in opposite directions, they are described as “antiparallel”. Access a high quality version of this image at http://booksupport.wiley.com. Figure 7.2 Parallel β-sheet. The three β-strands associate by hydrogen bonding to form a β-pleated sheet. The strands run in the same direction and so are described as being “parallel”. Access a high quality version of this image at http://booksupport.wiley.com. α-Helices Polypeptide chains associate by hydrogen bonds to form a right-handed α-helix (Fig. 7.3 opposite). Figure 7.3 Right-handed α-helix. Access a high quality version of this image at http://booksupport.wiley.com. Abnormal Primary Structure Affects the Secondary Structure: Deletion of a Single Amino Acid Causes Cystic Fibrosis The primary structure refers to the amino acid sequence of the polypeptide chain. An error caused by a single incorrect amino acid amongst a chain of 1480 amino acids can seriously affect the function of the protein...
eBook - ePubPeptides
Synthesis, Structures, and Applications
- Bernd Gutte, Bernd Gutte(Authors)
- 1995(Publication Date)
- Academic Press(Publisher)
...These studies brought into question the prediction from the original host–guest studies (Wójcik et al., 1990) that short peptides (<20 residues) should not be able to form α helices in water. With the availability of several de novo designed peptide systems, including the alanine-based peptides as well as peptides designed with overlapping salt bridges similar to those found in troponin C (Lyu et al., 1989), there has been a renewed interest in measuring the intrinsic helix-forming tendencies, or helix propensities, of all of the amino acids, and also in analyzing the side-chain interactions that can help to stabilize α helices in aqueous solution. There are several uses of peptide helix studies. Peptide fragments from proteins often exhibit specific binding to receptors, and, if the fragment comes from a helical segment of the protein, then it is of interest to enhance helix formation by the isolated peptide. Factors that stabilize proteins often can be studied advantageously in peptide helices, where a given side-chain interaction can be isolated from other interactions present in the protein. Peptide helices in water typically have marginal stability, so that a small change in free energy resulting from making a specific side-chain interaction gives an easily measurable change in helix content. Currently there is wide interest in examining the factors that control helix propensities, and in relating the helix propensities found in peptide studies to results found by directed mutagenesis of proteins. Even the N-cap interactions found in studies of protein helices can be observed and analyzed in peptide helices...
eBook - ePubBiotensegrity
The Structural Basis of Life
- Graham Scarr(Author)
- 2019(Publication Date)
- Handspring Publishing Limited(Publisher)
...(A and C) Right-handed. (B) Left-handed. The molecular helix Biological helices are often thought of as continuous metal springs but of course they are nothing of the sort. They are formed from many modular parts connected together, just like tensegrity models. Molecular helices are tensegrity structures in their own right and thus spontaneously organize themselves into the most stable and energy-efficient arrangements (Figure 3.8). A great many helical molecules are made from globular proteins that contain even smaller helices such as g-actin and tubulin in the cytoskeleton (Figure 6.3). Similar helices can also wind around each other to form coiled coils that change their chirality (handedness) at each new structural level (Parry et al., 2008), such as filamentous spectrin (Figures 6.4 and 5.3), or further combine into more complex heterarchical structures with specialized functions, such as intermediate-filaments (keratin, vimentin) in the cytoskeleton (Moll et al., 2008; Qin et al., 2009), chromosomal DNA (Aranda-Anzaldo, 2016) and fibers of collagen in the ECM (Fratzl, 2008). Figure 6.3 Helical molecules in the cellular cytoskeleton. (Redrawn from Scarr 2010; © Elsevier) Complex heterarchies Collagens, of which there are 28 different types, consist of an even more complicated structural organization, and as the most widespread structural molecule in humans are one of the main distributors of tissue tension (Fratzl, 2008) (Figure 6.5). Figure 6.4 Schematic diagram of the spectrin heterarchy. (A) A spectrin filament basically consists of a series of tetramers made from α- and β-spectrin dimers (right-handed). (B) Each dimer is formed from a series of (left-handed) double- and triple-coiled coils of spectrin α-helices (right-handed) (C). (Reproduced with modifications from Scarr, 2010; © Elsevier) Figure 6.5 Schematic diagram of a collagen heterarchy within tendon...
