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UA BIOC 460 - Protein Secondary Structure

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BIOC 460, Spring 2008LEC 5: Protein Secondary Structure 1Lecture 5Protein Secondary StructureReading: Berg, Tymoczko & Stryer, 6th ed., Chapter 2, pp. 37-45Problems in textbook: chapter 2, pp. 63-64, #1,5,9Directory of Jmol structures of proteins:http://www.biochem.arizona.edu/classes/bioc462/462a/jmol/routines/routines.htmlBasic Jmol structure of the α helix:http://www.biochem.arizona.edu/classes/bioc462/462a/jmol/alpha/alpha.htmlJmol routine showing lots of views of α helix & 2 other kinds of helices:http://www.biochem.arizona.edu/classes/bioc462/462a/jmol/helices/helices.htmlJmol structures of some α-helical proteinshttp://www.biochem.arizona.edu/classes/bioc462/462a/jmol/alpha_domain/alpha_domain.htmlJmol structures of β barrel and β clam proteinshttp://www.biochem.arizona.edu/classes/bioc462/462a/jmol/beta_domain/beta_domain.htmlKey Concepts• Proteins: secondary structure– major types of secondary structure found in manyproteins:• α helix• β conformation• β turns– surface loops: not really secondary structure becausenot regular, repetitive– Unusual secondary structures - examples:• collagen helix (found in collagen) (not covered in thiscourse)• other kinds of helices, e.g. pi helix and 310 helix(not covered in this course)• Secondary structures are stabilized by all kinds ofnoncovalent bonds, but especially by hydrogen bonds.Learning Objectives• Define secondary structure (of a protein).• List examples of categories of secondary structure thatoccur in proteins.• Describe the α-helix, including what groups serve ashydrogen bond donors and acceptors, chirality of most α-helices in proteins (right- or left-handedness), number ofresidues per turn, orientation of R groups relative to axis ofthe helix, the helix dipole (which end is δ+, which is δ–), andpacking density of atoms.• Describe β-conformation, including which groups serve ashydrogen bond donors and acceptors, and orientation of Rgroups in a β pleated sheet.• Explain parallel and antiparallel β conformation.Learning Objectives, continued• Identify the most important noncovalent interactionsstabilizing the α-helix and β-conformations.• Explain what a β-turn is, where β-turns are often found inproteins, and what types of amino acid residues are oftenfound in β-turns.• Be able to identify α-helices and β-strands (or sheetsconsisting of 2 or more β-strands) on a ribbon depiction ofa protein structure.Protein Secondary Structure• Local, regular/recognizable conformations observed forparts of the peptide backbone of a protein• Examples:– α helix– β conformation– β turns– collagen helix• Properties of peptide bond & hydrogen bonds --> 2° structures–peptide bonds• planarity• adjacent planes related in space by set of 2 dihedral angles for each amino acid residue)–hydrogen bonds• Strongest are linear.• Protein functional groups capable of H-bonding tend to do so to maximum possible extent.• protein backbone amide groups (amide C=O: ---- H–N)Review: 4 successive planar peptide groups bounded bythe α C’s of 5 successive amino acid residues•6 coplanar atoms of 1 peptide bond: Cα(n)–CO–NH–Cα(n+1) (from α C of one residue to a C of next residue)•Jmol structure (planar peptide group)•Secondary structures stabilized mainly by hydrogen bonds between backbone amide N–H groups and carbonyl O:’sBIOC 460, Spring 2008LEC 5: Protein Secondary Structure 2α helix• backbone coiled (spiral) conformation -- rod-like structure• Usually right-handed in proteins• R groups radiate outward from helical “cylinder”• Backbone -- regular, repeating rotation, residue by residue:Each residue has close to the same (Ψ,Φ) coordinates.Berg et al., Fig. 2-29α helix• Basic Jmol structure of the α helix• Jmol routine showing α helix & 2 other kinds of helices• Hydrogen bonding pattern for α helix: H bonds almost parallel tohelix axis, from carbonyl O: of residue n to H–N group of residue (n+4).• 3.6 residues per 360° turn of α helix.(N)(δ+)(C)(δ–)3.6residuesN IHO IIC––––•Whole a helix a dipole:•N-term end δ+•C-term end δ–Ramachandran Plot: plot of (Ψ,Φ) coordinates ofeach amino acid residue• Every amino acid residue has its own set of (Φ,Ψ) angles defining directionfrom which rest of chain comes “into” that residue’s Cα atom (rotation aroundN–Cα bond), and angle at which rest of chain goes “out” from that Cα atom(rotation around Cα–Ccarbonyl bond)• Ramachandran Plot: (Ψ vs. Φ) for a large number of non-glycine amino acid residues in a protein (pyruvate kinase)Nelson & Cox, Lehninger Principlesof Biochemistry, 4th ed., Fig. 4-9b• Blue-shaded areas are sterically allowed (no steric clashes for these combinations of angles for residues with side chains larger than Gly)Ramachandran Plot, (Ψ,Φ) angles for α helix• For regular, repeating local structures like α helix, each residue has ~ thesame (Φ,Ψ) angles. (β conformation has a different set of (Φ,Ψ) values.)Berg et al. Fig. 2-31Proteins with a lot of the polypeptide chain inα-helical conformation• Jmol structures of some α-helical proteinshttp://www.biochem.arizona.edu/classes/bioc462/462a/jmol/alpha_domain/alpha_domain.htmlMyoglobin (O2-binding protein especially rich in muscle cells)<–– space-filling atoms (all non-H atoms shown)Ribbon rendition ––>shows only the polypeptide backbonetracing in spaceNelson & Cox, Lehninger Principles ofBiochemistry, 4th ed., Fig. 4-16 Ferritin (an iron storage protein)Berg et al., Fig. 2-33Examples:Coiled coils of α helices in some proteins• 2 right-handed α helices coiled around each other in left-handeddirection• Supercoiled structure has great tensile strength (like a rope with twistedstrands)• Examples:– α-keratin (a fibrous protein -- elongated 3-dimensional structure, water-insoluble) -- mammalian hair, quills, claws, horns– Some globular proteins (compact 3-D structure) -- examples:• Some transcriptional regulator proteins (“leucine zipper” motif)• Myosin (muscle)Berg et al., Fig. 2-43BIOC 460, Spring 2008LEC 5: Protein Secondary Structure 3β conformation• Backbone nearly fully extended (not coiled)• All residues in β sheet have ~ the same (Ψ,Φ) angles• Distance between adjacent AA residues ~3.5 Å (furtherapart, more stretched out, than in α helix)• Side chains (R groups) point in


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UA BIOC 460 - Protein Secondary Structure

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