![]() This is because proline cannot form a regular alpha-helix due to steric hindranceĪrising from its cyclic side chain which also blocks the main chain N atom and chemically prevents it forming a hydrogen bond. Proline residues induce distortions of around 20 degrees in the direction of the helix axis.The packing of buried helices against other secondary structure elements in the core of the protein.These distortions arise from several factors including: The majority of alpha-helices in globular proteins are curved or distorted somewhat compared with the standard Pauling-Corey model. All the amino acids have negative phi and psi angles, typical values being -60 degrees and -50 degrees, respectively.Side chains point outward from helix axis and are generally oriented towards its amino-terminal end. The peptide planes are roughly parallel with the helix axis and the dipoles within the helix are aligned, ie all C=O groups point in the same direction and all N-H groups point the other way.This gives a very regular, stable arrangement. Every mainchain C=O and N-H group is hydrogen-bonded to a peptide bond 4 residues away (ie O(i) to N(i+4)).The separation of residues along the helix axis is 5.4/3.6 or 1.5 Angstroms, ie the alpha-helix has a rise per residue of 1.5 Angstroms. Alpha-helices have 3.6 amino acid residues per turn, ie a helix 36 amino acids long would form 10 turns. The structure repeats itself every 5.4 Angstroms along the helix axis, ie we say that the alpha-helix has a pitch of 5.4 Angstroms.For each hand the thumbs indicate the direction of translation and the fingers indicate the direction of rotation. An easy way to remember this is to hold both your hands in front of you with your thumbs pointing up and your fingers curled towards you. The figure below shows how a right-handed helix differs from a left-handed one. The most simple and elegant arrangement is a right-handed spiral conformation known as the 'alpha-helix'. Pauling and Corey twisted models of polypeptides around to find ways of getting theīackbone into regular conformations which would agree with alpha-keratin fibre diffraction data. In rare cases omega = 0 degrees for a cis peptide bond which, as stated above, usually involves proline.ĭevelopment of a Model for Alpha-Helix Structure. The planarity of the peptide bond restricts omega to 180 degrees in very nearly all of the main chain peptide bonds. The figure below shows the three main chain torsion angles of a polypeptide. However, the actual conformation of the GGAG peptide, if found as part of the primary structure of a protein, could adopt a whole range of other conformers with potentially different dihedral angles for each bond in the main chain.Peptide Torsion Angles and Secondary Structure Peptide Torsion Angles and Secondary Structure Back to Index The dihedral angles along the backbone would be, to a first approximation, around + 180° depending on whether the rotation is clockwise or counterclockwise from the syn conformer. The atoms in the main chain of the peptide, N, C a, C (the carbonyl C) are arranged in the familiar zig-zag fashion, characteristic of the lowest energy conformer. Notice the similarities in these two structures. \): Extended conformations of dodecanoic acids and a tetrapeptide
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