Lecture 1: Fundamentals of Protein StructurePowerPoint PresentationSlide 3Slide 4Slide 5Slide 6Slide 7Slide 8Slide 9Slide 10Slide 11Slide 12Slide 13Slide 14Amino Acids Are Joined By Peptide Bonds In PeptidesSlide 16Slide 17Slide 18Slide 19Slide 20Slide 21Slide 22Slide 23Slide 24Slide 25Slide 26Slide 27Slide 28Slide 29Slide 30Slide 31Lecture 1: Fundamentals of Protein StructureWood, brick, nails, glassMaterialsAmino acids, cofactors Temperature, earthquakes Environmental Factors Temperature, solubility How many people?Population Factors # partner proteins, # reactantsHow many doors and windows? PortalsPassages for substrates and reactantsSpanish, Victorian, Motifs/Styles Conserved domains or protein folds1950's blocky science building Julia MorganArchitectEvolutionTraditional ArchitectureMolecular ArchitectureFormfitsfunctionLevels of Protein StructurePrimary structure = order of amino acids in the protein chainAnatomy of an amino acidNon-polar amino acidsPolar, non-charged amino acidsNegatively-charged amino acidsPositively-charged amino acidsCharged and polar R-groups tend to map to protein surfacesNon-polar R-groups tend to be buried in the cores of proteinsMyoglobinBlue = non-polarR-groupRed = HemeSome R-groups can be ionizedThe Henderson-Hasselbalch equation allows calculation of the ratio of a weak acid and its conjugate base at any pHGeneral protein pK’ values Approximate pK'Group In a “Typical” Protein-carboxyl (free) 3 (C-terminal only)-carboxyl (Asp) 4-carboxyl (Glu) 4imidazole (His) 6sulfhydryl (Cys) 81˚-amino (free) 8 (N-terminal only)-amino (Lys) 10hydroxyl (Tyr) 102˚-amino (Pro)(free) 9 (N-terminal only)guanido (Arg) 12Some R-groups can modifiedAmino Acids Are Joined By Peptide Bonds In Peptides- -carboxyl of one amino acid is joined to -amino of a second amino acid (with removal of water)- only -carboxyl and -amino groups are used, not R-group carboxyl or amino groupsChemistry of peptide bond formationThe peptide bond is planarThis resonance restricts the number of conformations in proteins -- main chain rotations are restricted to  and Primary sequence reveals important clues about a proteinDnaG E. coli ...EPNRLLVVEGYMDVVAL...DnaG S. typ ...EPQRLLVVEGYMDVVAL...DnaG B. subt ...KQERAVLFEGFADVYTA...gp4 T3 ...GGKKIVVTEGEIDMLTV...gp4 T7 ...GGKKIVVTEGEIDALTV...: *:::* * : :small hydrophobiclarge hydrophobicpolarpositive chargenegative charge• Evolution conserves amino acids that are important to protein structure and function across species. Sequence comparison of multiple “homologs” of a particular protein reveals highly conserved regions that are important for function.• Clusters of conserved residues are called “motifs” -- motifs carry out a particular function or form a particular structure that is important for the conserved protein.motifSecondary structure = local folding of residues into regular patternsThe -helix• In the -helix, the carbonyl oxygen of residue “i” forms a hydrogen bond with the amide of residue “i+4”.• Although each hydrogen bond is relatively weak in isolation, the sum of the hydrogen bonds in a helix makes it quite stable.• The propensity of a peptide for forming an -helix also depends on its sequence.The -sheet • In a  -sheet, carbonyl oxygens and amides form hydrogen bonds.• These secondary structures can be either antiparallel (as shown) or parallel and need not be planar (as shown) but can be twisted.• The propensity of a peptide for forming -sheet also depends on its sequence. turns • -turns allow the protein backbone to make abrupt turns.• Again, the propensity of a peptide for forming -turns depends on its sequence.Which residues are common for -helix, -sheet, and -turn elements?Ramachandran plot -- shows  and  angles for secondary structuresTertiary structure = global folding of a protein chainTertiary structures are quite variedQuaternary structure = Higher-order assembly of proteinsExample of tertiary and quaternary structure - PriB homodimerQuickTime™ and aCinepak decompressorare needed to see this picture.Example is PriB replication protein solved at UW: Lopper, Holton, and Keck (2004) Structure 12, 1967-75.Example of tertiary and quaternary structure - Sir1/Orc1 heterodimerExample is Sir1/Orc1 complex solved at UW: Hou, Bernstein, Fox, and Keck (2005) Proc. Natl. Acad. Sci. 102, 8489-94.Examples of other quaternary structures Tetramer Hexamer Filament SSB DNA helicase Recombinase Allows coordinated Allows coordinated DNA binding Allows complete DNA binding and ATP hydrolysis coverage of an extended moleculeClasses of proteinsFunctional definition:Enzymes: Accelerate biochemical reactionsStructural: Form biological structuresTransport: Carry biochemically important substancesDefense: Protect the body from foreign invadersStructural definition:Globular: Complex folds, irregularly shaped tertiary structuresFibrous: Extended, simple folds -- generally structural proteinsCellular localization definition:Membrane: In direct physical contact with a membrane; generally water insoluble.Soluble: Water soluble; can be anywhere in the