Transcript Lecture 11
Protein Secondary Structure II Lecture 2/24/2003 Principles of Protein Structure Using the Internet • Useful online resource: http://www.cryst.bbk.ac.uk/PPS2/ • Web-based protein course Structural hierarchy in proteins The Polypeptide Chain Peptide Torsion Angles Torsion angles determine flexibility of backbone structure Rammachandran plot for L amino acids Indicates energetically favorable f/y backbone rotamers Steric hindrance limits backbone flexibility Side Chain Conformation Sidechain torsion rotamers • named chi1, chi2, chi3, etc. e.g. lysine chi1 angle is restricted • Due to steric hindrance between the gamma side chain atom(s) and the main chain • The different conformations referred to as gauche(+), trans and gauche(-) • gauche(+) most common Regular Secondary Structure Pauling and Corey Helix Sheet Helices A repeating spiral, right handed (clockwise twist) helix pitch = p Number of repeating units per turn = n d = p/n = Rise per repeating unit Fingers of a right - hand. Several types , 2.27 ribbon, 310 , helicies, or the most common is the helix. Examples of helices The Nm nomenclature for helices N = the number of repeating units per turn M = the number of atoms that complete the cyclic system that is enclosed by the hydrogen bond. The 2.27 Ribbon •Atom (1) -O- hydrogen bonds to the 7th atom in the chain with an N = 2.2 (2.2 residues per turn) 3.010 helix •Atom (1) -O- hydrogen bonds to the 10th residue in the chain with an N= 3. •Pitch = 6.0 Å occasionally observed but torsion angles are slightly forbidden. Seen as a single turn at the end of an helix. •Pi helix 4.416 4.4 residues per turn. Not seen!! The helix The most favorable F and Y angles with little steric hindrance. Forms repeated hydrogen bonds. N = 3.6 residues per turn P = 5.4 Å ( What is the d for an helix?) The C=O of the nth residue points towards the N-H of the (N+4)th residue. The N H O hydrogen bond is 2.8 Å and the atoms are 180o in plane. This is almost optimal with favorable Van der Waals interactions within the helix. alpha helix Properties of the helix • • • • • • 3.6 amino acids per turn Pitch of 5.4 Å O(i) to N(i+4) hydrogen bonding Helix dipole Negative f and y angles, Typically f = -60 º and y = -50 º Distortions of alpha-helices • The packing of buried helices against other secondary structure elements in the core of the protein. • Proline residues induce distortions of around 20 degrees in the direction of the helix axis. (causes two H-bonds in the helix to be broken) • Solvent. Exposed helices are often bent away from the solvent region. This is because the exposed C=O groups tend to point towards solvent to maximize their H-bonding capacity Top view along helix axis 310 helix • • • • Three residues per turn O(i) to N(i+3) hydrogen bonding Less stable & favorable sidechain packing Short & often found at the end of helices Proline helix Left handed helix 3.0 residues per turn pitch = 9.4 Å No hydrogen bonding in the backbone but helix still forms. Poly glycine also forms this type of helix Collagen: high in Gly-Pro residues has this type of helical structure Helical bundle Helical propensity Peptide helicity prediction • AGADIR http://www.embl-heidelberg.de/Services/serrano/agadir/agadir-start.html Agadir predicts the helical behaviour of monomeric peptides It only considers short range interactions Beta sheets •Hydrogen bonding between adjacent peptide chains. •Almost fully extended but have a buckle or a pleat. Much like a Ruffles potato chip Two types Parallel Antiparallel N N C C N C C N 7.0 Å between pleats on the sheet Widely found pleated sheets exhibit a right-handed twist, seen in many globular proteins. Antiparallel beta sheet Antiparallel beta sheet side view Parallel beta sheet Parallel, Antiparallel and Mixed BetaSheets beta (b) sheet • Extended zig-zag conformation • Axial distance 3.5 Å • 2 residues per repeat • 7 Å pitch