PowerPoint PresentationSlide 2Overview of protein structureSlide 4Slide 5Figure 8-2 The cis-peptide group.Slide 7Figure 8-4. The torsional degrees of freedom in a peptide unit.Slide 9Slide 10Slide 11The Ramachandran diagram.Conformation angles in proteinsThe Ramachandran diagram of Gly residues in a polypeptide chainSlide 15Protein Secondary StructureSlide 17Slide 18Slide 19Slide 20Slide 21Slide 22Slide 23Stereo, space-filling representation of the 6-stranded antiparallel b pleated sheet in jack bean concanavalin A as determined by crystal X-ray analysisSlide 25Slide 26Slide 27Slide 28Slide 29Slide 30Slide 31Slide 32Slide 33Slide 34Slide 35Slide 36Slide 37Slide 38Slide 39Slide 40Slide 41Slide 42The NMR structure of a 64-residue polypeptide comprising the Src protein SH3 domainChapter 83-D Structures of ProteinsChymotrypsin, a globular proteinGlycineProteins are large molecules.Each protein has a unique structure.Read entire chapterOverview of protein structure1. Numerous conformations of a protein are possible (without breaking a bond, by just rotation about single bonds)2. However, a conformation existing under a given condition is the most stable thermodynamically, having the lowest Gibbs free energy3. Proteins in any of their functional folded conformations are called native proteinPeptide bondElectric dipoleFrom LehningerPrinciples of BiochemistryThe carbonyl oxygen has a partial negative charge and the amide nitrogen a partial positive charge, setting up a small electric dipole. Virtually all peptide bonds are planar and have this trans configuration.The peptide bond is rigid and planar 6 atoms lie in a single plane Oxygen atom of the carbonyl group & the H of amide nitrogen are in trans Bond between C and N has double bond character and is unable to rotate Rotation is permitted between N – C and C– C Polypeptide backbone: series of rigid planes with consecutive planes sharing a common point of rotation at COC = N 1.27 Ao C N 1.47 AoFigure 8-2 The cis-peptide group.Page 220A polypeptide chain in its fully extended conformation showing the planarity of each of its peptide groupsFigure 8-4. The torsional degrees of freedom in a peptide unit.Page 221N – C bond(phi) C– C bond(psi)•In the fully extended conformation 180o•can have any values between -180o to 180o• But many values are prohibited by steric interference.1 o , = 30o2. This conformation is not allowed in proteins due to steric overlap between the carbonyl oxygen and the amide hydrogen atom.CRamachandran Plot for poly- L-AlaNo steric overlap &Allowed conformationPermissible if a little flexibility is allowed in the bond anglePhi-Psi DemoThe Ramachandran diagram.Page 222Conformation angles in proteinsPage 222The Ramachandran diagram of Gly residues in a polypeptide chainPage 223Levels of structure in proteinsLinking of aaStable arrangement of aa give rise to structural patterns3-dimensional folding of polypeptidesArrangement in space of 2 or more polypeptide subunitsFrom LehningerPrinciples of BiochemistryProtein Secondary Structure Refers to the local conformation of some part of polypeptide Prominent secondary structures that are stable and occur in proteins are 1 helix conformationFrom LehningerPrinciples of Biochemistry helix .1 = -57o. = -47o 3. Each helical turn includes 3.6 AA.4 helix found in all proteins is right handed----- Shows the hydrogen bondsFrom LehningerPrinciples of BiochemistryOCHN helix Looking down the longitudinal axisFrom LehningerPrinciples of BiochemistryAtoms in the center of the helix are in very close contact helix1. Forms readily2. Helical structure is very stable due to internal hydrogen bonds3. Between H attached to N of peptide linkage & the electronegative carbonyl O of the 4th AA on the N-terminal side of the peptide bond4. Within the helix, every peptide bond participates in such H bonding (except the last 4 amino acids that are close to the end of the helix)Asp(100) side chainArg (103) side chainInteractions between R groups of aas 3 residues apart in a helix1. AA sequence affects helix stability2. For example, polypeptide with long block of Glu residues will not form an helix at pH 73. Bulk shape of Cys, Ser, Thr can destabilize the helix if they are close together in a chain4. Proline introduces destabilizing kink in helix5. Gly occurs infrequently as it is very flexible & takes coiled structure different from helixFrom LehningerPrinciples of BiochemistryElectric dipole of a peptide bond is transmitted through the hydrogen bonds along an helix resulting in an overall helix dipoleNegatively charged amino acids near the end of the amino terminal stabilize the positive charge of the helix electric dipolePositively charged amino acids near the end of the N-terminal destabilize the helixFrom LehningerPrinciples of BiochemistryThe conformation of the polypeptide chainsThe backbone of the polypeptide chain is extended into a zigzag structureZigzag structures arranges side by side to form a structure resembling a series of pleats (called sheet)Hydrogen bonds cross-linksbetween adjacent chainsA two-stranded antiparallel pleated sheet drawn to emphasize its pleated appearanceStereo, space-filling representation of the 6-stranded antiparallel pleated sheet in jack bean concanavalin A as determined by crystal X-ray analysis Page 228Contains 8-stranded mixed sheet that forms a saddle-shaped curved surface with a right handed twistTriose phosphate isomeraseForms an 8-stranded parallel sheet that forms a cylindrical structure known as a barrelThe connection between adjacent polypeptide strands in pleated sheetsCONHMore common(Gly at 3rd position)From LehningerPrinciples of BiochemistryThe Beta Turn (aka beta bend, tight turn) •Allows the peptide chain to reverse direction •Carbonyl C of one residue is H-bonded to the amide proton of a residue three residues away •Proline & glycine are prevalent in beta turnsRamachandran plots for variety of structuresAlthough theoretically possible, not observed in proteinsFrom LehningerPrinciples of BiochemistryRelative probability that a given amino acid will occur in the 3 common types of secondary structureFrom
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