Lecture 7 & 8:PROTEIN ARCHITECTURE IV:Tertiary and Quaternary StructureMargaret DaughertyFall 2004BIOC 205right-handed α-helixleft-handed α-helixPoint your thumb up in thedirection of the α-helix(N-->C).Look where the “base” of thehelix spirals are. If theymatch the knuckles on yourright hand it is a right-handed helix.----------or-----------If the helix spirals up in acounterclockwise direction, itis a right-handed helix.How to tell a left- vs. right-handed a-helixTertiary Structure• Tertiary structuredescribes how thesecondary structureunits associatewithin a singlepolypeptide chain togive a three-dimensionalstructureflavodoxinBIOC 205formation of large number of intramolecular hydrogen bondsreduction in hydrophobic surface area from solventTertiary Structure: Basic Tenets - the “truths”1). All information for folding is contained in the primary sequence.2). Secondary structure formation is spontaneous - a consequence of theformation of hydrogen bonds.3). No protein is stable as a single layer - hence secondary structuralelements pack together in sheets.4). Connections between structural elements are short - minimization ofdegrees of freedom - keeps structures compact.Consequences1). Secondary structures are arranged in a few common patterns - i.e,resulting in protein “families”.2). Proteins fold to form the most stable structure. Stability arises from:BIOC 205All alpha(human growth hormone)Note that someparts of a proteinstructure are notregular (i.e., helical-like or sheet-like).These are oftenreferred to asdisordered orrandom coil regions.However a betternomenclature is“natively random”.All beta(retinol binding protein)Tertiary StructuresAlpha-beta barrel(triose isomerase)BIOC 205Tertiary StructuresGlobularproteins: compact structures;different folds fordifferent functionsMembraneProteins:found associatedwith variousmembrane systemsBIOC 205Fibrousproteins:Filamentous; playa majorstructural role incells & tissuesFibrous Proteins• Share properties that give strength &/or flexibilityto the structures in which they occur;• Fundamental unit is a simple repeating element ofsecondary structure;• Insoluble in water; large percentage of hydrophobicamino acids;• Usually the hydrophobic surfaces are hidden in theelaborate supramolecular complexes;• mechanically strong ; perform important structuralfunctions• Strength is enhanced by cross-links (disulfidebonds).BIOC 205BIOC 205Secondary Structures andProperties of Fibrous ProteinsStructure CharacteristicsExamples ofoccurrenceα-Helix, Cross-linkedby disulfide bondsTough, insolubleprotective structures ofvarying hardness andflexibilityα – Keratin of hair,feathers and nailsβ-Conformation Soft, flexible filaments Silk fibroinCollagen triple helix High tensile strength,without stretchCollagen of tendons,bone matrixFIBROUS PROTEINS: α-Keratin What: Part of the “intermediate filament proteins” which have majorstructural roles in nuclei, cytoplasm and cell surfacesWhere: Found in hair, fingernails, claws, horns, animal skinComposition: Long stretches of α-helices (> 300 residues)BIOC 205Coiled-Coils• Interactions are stabilized byhydrophobic interactions between the α-helices;• Heptad repeat (a-b-c-d-e-f-g)n where a &d are nonpolar & lie in the center of thecoiled coil;BIOC 205Evolved for strength; helicalnature confers flexibilityCoiled-coil is a “super twist”left-handed helixDistortion of helix to 3.5residues/turnHydrophobic faces interactingin a close interlocking patternα-keratin: Contact side chains (red balls) interlockFIBROUS PROTEINS: β-Keratin What: Part of the “fibroin proteins”Where: silk, bird feathersComposition: stacked anti-parallel β-sheets; strengthSequence: Alternating Gly-Ala/SerBIOC 205Ala/Ser facesinteract withone anotherGly faceinteracts withanother glyfaceCOLLAGENWhat: Greek for glue; defined as “thatconstituent of connective tissue whichyields gelatin on boiling”Where: Principal component ofmammalian tissue; constitutes ~25% ofa mammals protein content; more than30 varietiesComposition: Triple helixSequence: Gly-X-Y; X usually Pro, Yusually Pro/HyPro> 3000Å long; 15Å in diameterBIOC 205Collagen Primary Structure• Approx 1000 AA/chain• Repeats of Gly-X-Y where X is often Pro and Y isoften hydroxyproline or prolineComposition G ~ 35% A ~ 11% P/HP ~ 30%BIOC 205MODIFIED AMINO ACIDSpost-translational modifications add functionality to amino acidHyp: stabilizestropocollagen viaintrachain H-bondsHyl: stabilizes fibrilsvia its ability to cross-link; attachment ofCHO groupsBIOC 205Consequences of Collagen Primary StructureDistortion of backbonedue to high content ofglycines and prolinesCan’t form “normal”secondary structuresForms triple helixEvery third residuefaces insideInterior is compact;hence interior residueis glycineBIOC 205Consequences of Collagen Primary StructureFit occurs because Glystrand1 lies adjacent to Xstrand2 and Ystrand3Stabilization from hydrogen bonds Glystrand1 N-H to Xstrand2 C=O hydrogen bondHydroxyproline forms hydrogen bonds BIOC 205• Folding of 2˚ structural elements;• Side chain location varies withpolarity;– Non-polar are inside• (A, V, L, I, M & F);– Charged on the surface• (D, E, K, R, H);– Uncharged polar mostly surface,but interior as well• (S, T, N, Q, Y & W);– Nearly all H-bond donors have anH-bond acceptor;– Interior of a structure isTIGHTLY packed;•3˚ structures are frequently built ofdomains.GLOBULAR PROTEINBIOC 205Globular Proteins: 4 major classesI: antiparallel α-helixPacks in bundles; Left-handed twistUsually regular, uniform; Usually 4-helix bundles Globin proteinsII: Parallel or mixed β-sheet proteins parallel β-sheetshave hydrophobes on both sides of sheet ---> thesemust be core structuresIII. Antiparallel β-sheet structures antiparallel β-sheetshave hydrophobes on one side of sheet and polarresidues on the other side. These β-sheet structurescan be surface exposed.IV: Metal & Disulfide rich proteins Small, < 100 a.a.Structure dependent upon either the metal or disulfideCORES OF PROTEINS: α-HELICES AND β-SHEETSRibonuclease ACitrate synthaseBIOC 205GLOBULAR PROTEINS AND α-HELICES:return of the helical wheel!SURFACE HELIX: AMPHIPATHICBIOC 205GLOBULAR PROTEINS AND α-HELICES:return of the helical wheel!INTERIOR HELIX: HYDROPHOBICBIOC 205GLOBULAR PROTEINS AND α-HELICES:return of the helical wheel!SOLVENT-EXPOSED HELIX: POLAR/CHARGED BIOC 205β-sheets: an