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UCLA CHEM 153A - The 3-D Structure of Proteins

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PowerPoint PresentationSlide 2Slide 3Slide 4Slide 5Slide 6Slide 7Slide 8Slide 9Slide 10Slide 11Slide 12Slide 13Slide 14Slide 15Slide 16Slide 17Slide 18Slide 19Slide 20Slide 21Slide 22Slide 23Slide 24Slide 25Slide 26Slide 27Slide 28Slide 29Slide 30Slide 31Slide 32Slide 33Slide 34Slide 35Slide 36Slide 37Slide 38Slide 39Slide 40Slide 41Slide 42Slide 43Slide 44Slide 45Slide 46Slide 47Slide 48Slide 49Slide 50Slide 51Slide 52Slide 53Slide 54Slide 55Slide 56Slide 57Slide 58Chapter 6 The 3-D Structure of ProteinsAn unfolded protein will be coveredby a solvation layer. By burying thehydrophobic residues in its interior,a protein minimizes this highly orderedshell of water, for a net increase inentropy. Proteins also seek to maximizethe hydrogen bonds in their interior.What makes a protein fold into a specific three dimensional structure?The peptide bond has some characteristicsof a double bond. It does NOT rotate freely.A single C-N bond = 1.47 ÅA double C=N bond = 1.27 ÅA peptide C N bond = 1.32 ÅThe bond also has an electric dipole.After the peptide bond, the N-C bond canrotate through the angle and theC-C bond can rotate through the angle The extended conformation,  =180 and =180C, C, O, N, H and C+1 are forced to be coplanar because the partial double bond of the peptide bond prohibits rotation.The polypeptide backbone is made up of aseries of peptide planes, rotating only at Cs.Most  combinations are prohibited bysteric collision. Here   and thecarbonyl oxygen contacts an amino hydrogen.Very favorable configurationReasonable favorable configurationUnfavorable configurationRamachandran Plot for L-amino acidsSecondary Structure: amino acid segments which adopt particularly stable  angles that are repeatedly observed in the three-dimensional structures of proteinsAntiparallel-sheetRight handed-helixParallel -sheet310 -helixSecondary structure refers to the localconformation of part of a protein.Common, stable patterns include-helix-sheet-turnExperimental values from Pyruvate Kinasestructural dataA right handed helix,if grasped with fingersfollowing polypeptidefrom N-terminus to C-terminus, propagatesin the direction of theRIGHT thumb.The helix -=-60o= -45o to -50o5.4 Å (3.6 residues)per helical turnR-groups face awayfrom central axis and point towardsC-terminusThe helix makes optimal use of internal h-bonds. The hydrogen of the peptidyl N at residue n binds to the carbonyl O at n+3nn+3R-groups spiraling out from central axisThe helix is a closely packed conformationAmino acids at positions n and n+3 are near each otherin space.Here an Asp100 – Arg103ionic interaction stabilizes a helix.An all Glu helix would notform due to repulsion of chargedneighboring R-group carboxyls at pH 7-Helices have distinct facesAmino acid #4Amino acid #8Amino acid #12Amino endCarboxyl endAsp(100) side chainArg (103) side chainInteractions between R groups of aas 3 residues apart in  helix•AA sequence affects helix stability1. Bulk shape of Cys, Ser, Thr can destabilize the helix if they are close together in a chain2. Proline introduces destabilizing kink in  helix3. Gly occurs infrequently as it is very flexible & takes coiled structure different from  helixThe dipolar nature of the peptidebond and the alignment of thepeptide bonds by the hydrogenbonding pattern of the helixresults in a net partial positivedipole at the Amino terminus and a net partial negative dipoleat the carboxyl terminus.Charged amino acids at thetermini will stabilize the helixif they are negative at the aminoor positive at the carboxyl end.The backbone strands alternate direction inan antiparallel -sheetCCCNNO HHOCCCNNHOHOhe backbone strands are unidirectional ina Parallel-SheetCCCNNO HHOCCCNNO HHO-turns are stabilized by an h-bond to glycinecis-Pro often occurs in -turnsDihedral angles define secondary structureRelative probabilities that a given aminoacid will be within a given 2o structureThree Broad Categories of StructuresWater Soluble GlobularFibrousMembrane ProteinsFibrous Proteins: Usually are very elongated and consist of single type of secondary structure. Functionally have a structural role (provide support, shape or protection).Hair is made up of twisted  KeratinThe twisted -keratin is a coiled coilCollagen forms a unique 3 residue per turnleft handed helix. Three form a coiled coil.Collagen supercoilsare crosslinked bythe unusual amino aciddehydrohydroxylysin-onorleucine. Overaccumulation of crosslinksas people age makes theircollagen increasinglyrigid and brittle.CollagenConnective tissue (tendons, cartilage, organic matrix of bone, cornea)Consists of three polypeptide chains that each form left-handed helices (not -helices!)Humans have 16 distinct versions of collagenthat differ in their primary sequence.Example sequence~33% Glycine~15-30% Proline and Hyp (4-hydroxyproline)Hydroxyl is added after collagen is formedin process requiring vitamin-C (Ascorbic acid). The disease Scurvy is caused by vitamin-C deficiency The hydroxyl group may strengthen the collagenfibers by enabling inter-strand hydrogen bonding.Left handed helix Twisted into a right handed coiled coilSilk is made up of -sheets with the sidechains being eitheralanine (purple) orglycine (yellow).This allows tight packing of each layered sheet, asshown in this side view. The conformation does not allow stretching, butis very flexible.Membrane Proteins: Proteins that are embedded into orloosely associated with the membrane.Function as receptors, transporters, enzymes, ion channels.Water (aqueous)Water (aqueous)Non-PolarHuman serum albumin would be too longif it were all orbut with both  helix and coiled regions takes a compact globular form.The Tertiary structure of myoglobinHydrophobic(blue) residuesare hidden in the core.Heme- a cofactor for O2 transportProtein crystals diffract, providing informationon the location of atoms within a protein.Even small proteins have diverse structuresThe Secondary structural content variesSome protein chains have multiple domainsTroponin C has 2 Ca binding domainsSupersecondary structures (or motifs or folds)Stable arrangements of several elements of secondary structure and the connections between themStable folding patterns in proteinsConstruction of large motifs from smaller onesQuaternary


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UCLA CHEM 153A - The 3-D Structure of Proteins

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