Protein Structure C483 Spring 2013 1. Which statement is false about a globular protein that performs its biological function as a single independent polypeptide chain? A) Its tertiary structure is likely stabilized by the interactions of amino acid side chains in non-neighboring regions of the polypeptide chain. B) It could contain α-helices that are stabilized by hydrogen bonding. C) It likely has extensive quaternary structure to maintain its globular shape. D) Non-covalent forces are the primary source of stability for the secondary and tertiary structure. 2. The conformation of the backbone of a polypeptide is described completely by the angle(s) of rotation about which bond(s)? A) The peptide bond only. B) N-Cα only. C) N-Cα, Cα-C and C-N bonds. D) N-Cα and Cα-C bonds only. 3. Which structure indicates the proper hydrogen-bonding pattern between amino acids in an α-helix? (Dashed lines represent the hydrogen bonds.) 4. What would you expect about the formation of an α-helix for a segment of a protein chain that contains lysine approximately every fourth residue with all other residues being mostly hydrophobic? A) Helix formation would be favored at low pH. B) Helix formation would be favored at high pH. C) Helix formation would be favored at neutral pH. D) Helix formation would never occur regardless of pH. 5. Supersecondary structures that contain recognizable combinations of αhelices, β-strands and loops (e.g. the Greek Key) are called ________. A) domains B) folds C) homologous regions D) motifs 6. The principle forces holding subunits of an oligomeric protein to each other are ________. A) peptide bonds B) hydrophobic interactions C) covalent bonds D) disulfide bonds Protein Structure • Configuration and conformation • Native structure – Fibrous – Globular • Atomic level and cartoon level Structural Determination • Crystallography • NMR Structural Hierarchy C483 goals • Secondary structure dictated by – Peptide bond structure – Atomic level intermolecular interactions • Tertiary and quaternary structure – Importance to protein folding and activity – Familiar with vocabulary so that you can read a paper to learn the details Peptide Bond • Resonance – 6 planar atoms form a unit • Highly polar • Trans vs cis conformation Conformational Flexibility • If each peptide bond is relatively locked, backbone conformation can be defined by phi and psi • NOT cis/trans – Both stuctures to the right are trans Ramachandran Plots Alpha Helix • Right handed • Polarity • Phi = -57o and psi = -47o • n and n + 4 • Ala vs. Tyr • Gly and Pro • The average ahelix is 12 residues long. What is its length in nm? • How many amino acids/turn of an alpha helix? Amphipathic Helices Structural Implications Coiled-Coil Placement in Protein Beta-Sheets Real Beta Sheets • Technically, often tertiary structure • Generally bent/twisted • Alternating sidechains can lead to amphipathic sheets Loops and Turns • Nonrepeating • Change of direction • Turns have about 4 residues • Internal H-bonds • Gly, Pro Tertiary Structure • Longer range interactions of secondary features • Driven by hydrophobic effect • Disulfide bridges • Diversity Tertiary Structure • Too many shapes to memorize • But not an infinite number of possibilities • Take away the ability to read a paper – Discussions of motifs and why important – Discussion of domains and why important Motifs (Super Secondary Structure) • Recognizable combinations of helices, loops, and sheets • Match – Helix-loophelix – Helix bundle – Hairpin – b-sandwich Studying Motifs • Some Motifs are highly studied • Know the Lingo – Leucine zipper – Zinc finger • Often have recurring applications Domains • Discrete, independently folded unit (may maintain shape when cleaved on loop) • May have separate activities: “ATP binding domain” or “catalytic domain” • Similar activity = similar structure across many proteins • Binding pockets at interfaces How many domains? Common Domains Quaternary Structure • Multiple subunits: Oligomers • Homodimer, heterotrimer • Advantages – Economy – Stability – regulation a2 a3 a2b2 From your discussion paper… Answers 1. 2. 3. 4. 5. 6. C D B B D B