BISC 330L Biochemistry Spring 2015 USC Lecture 6 Monday Jan 26 2015 More Chapter 2 material 2 3 Secondary Structure helix strands sheets Turns loops Rotation about single bonds in a polypeptide Horton R H Moran L A Ochs R Rawn J D and Scrimgeour K G 1996 Principles of Biochemistry 2nd ed Copyright Prentice Hall 1996 allows unique folding of proteins into many different 3 D structures locally globally and higher order Levels of Protein Structure Primary Structure Amino acid sequence of polypeptide chain Sequence of amino acid residues joined by peptide bonds Secondary Structure Regular chain folding held by noncovalent H bonding between peptide groups e g helix sheet Tertiary Structure 3 dimensional folding held by side chain interactions between polypeptide chain secondary structures Quaternary Structure Multi subunit complex formed by interactions between tertiary structures of two or more polypeptide chains The Helix Rod like in structure Inner backbone with R groups extending outward C O and N H bonding Right handed most common H bonding pattern i C O H N i 4 Alpha a helix H bonding scheme 1 C O H N 5 2 C O H N 6 3 C O H N 7 4 C O H N 8 5 C O H N 9 etc H bonds in alpha helix structure 1 2 3 6 4 5 7 9 8 1 C O H N 5 2 C O H N 6 3 C O H N 7 4 C O H N 8 5 C O H N 9 The helix structural features Right handed helix 3 6 residues turn 1 5 residues rise 5 4 turn pitch H bond between every 4th aa between the oxygen of the carboxyl group and the hydrogen of the amino group R groups project out from helix generally towards the N terminal end of the helix H bonds orange are parallel to axis of the helix alpha helix seen in crystal structure alpha helix in Ramachandran plot alpha helix in proteins The strands and sheets Strand strand sheets Fully extended Distance between adjacent a a is 3 5A Parallel and anti parallel sheets unique H bonding properties Antiparallel sheet C N N C Adjacent chains run in opposite directions H bonding between N H group and the C O group of each amino acid H bonded to the C O group and the N H group of a partner on the adjacent chain Antiparallel arrangement can arise by hairpin folding of a single strand Parallel sheet C C N N Adjacent chains run in same direction H bonding between N H group and the C O group of one amino acid on the adjacent strand C O group and the N H group on the a a two residues farther along the chain Mixed sheet C C N N N C Beta strand in Ramachandran plot Twisted sheet C Fatty acid binding protein Primary Secondary Structures Can predict secondary structures by analyzing primary structure of a given protein http www topsan org api deki files 6387 secondary structure seq overlay bmp turn Hairpin turn C O group of residue i is H bonded to the N H group of residue i 3 Stabilizes the turn Loops or loops Part of antibody molecule Loops lie on the surface of proteins Participate in interactions between proteins helical coiled coil proteins Two right handed helices intertwined Can be 1000 or more in length The Heptad Repeat The Leucine zipper 3 5 residues per turn instead of 3 6 Allows the pattern of side chain interactions to repeat every 7 amino acids Two helices can interact Knob into holes Collagen Rod shaped 3000 long and 15 in diameter Three helical polypeptide chains Gly every 3rd residue No H bonds Stabilized by steric repulsion of pyrrolidine rings the single helix Shape cmplementarity van der Waals h bonds interactions the triple helix The Superhelical Cable Important for Gly to be at every 3rd position More bulky groups on the outside End of Lecture 6