Chapter 63-D Structure of ProteinsChymotrypsin, a globular proteinGlycineProteins are large molecules.Each protein has a unique structure.Overview of protein structureEFor a protein numerous conformations are possible (without breaking a bond, by just rotation about single bonds)EHowever, a conformation existing under a given condition is the most stable thermodynamically having the lowest Gibbs free energyEProteins in any of their functional folded conformations are called native proteinPeptide bond1 32Electric dipoleThe peptide bond is rigid and planarv 6 atoms lie in a single planev Oxygen atom of the carbonyl group & the H of amide nitrogen are in trans v Bond between C and N has double bond character and is unable to rotatev Rotation is permitted between N – Cαand Cα– Cv Polypeptide backbone: series of rigid planes with consecutive planes sharing a common point of rotation at CαCOC = N 1.27 AoC N 1.47 AoCOCα – C bond(psi)Bond angles resulting from rotations at CαN – Cαbond(phi) Ø In the fully extended conformation φ = ψ = 180oØ ψ can have nay values between -180o to 180oØ But many values are prohibited by steric interference1. 2 peptide bonds are in the same plane2. φ = ψ = 0o3. This conformation is not allowed in proteins due to stericoverlap between α-carbonyl oxygen and α-amino hydrogen atomCRamachandran Plot for L-AlaNo steric overlap &Allowed conformationPermissibleIf little flexibility is allowed in the bond angleLevels 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 subunitsProtein Secondary StructureØ Refers to the local conformation of some part of polypeptideØ Prominent secondary structures that are stable and occur in proteins are 1) α helix2) β conformationα helixImaginaryaxis1. φ = -60o2. ψ = -45o to-50o3. Each helical turn includes 3.6 aa4. α helix found in all proteins is right handedShows the hydrogen bondsα helix Looking down the longitudinal axisAtoms in the center of the α helix are in very close contactα helix1. Form more readily2. Helical structure is very stable3. Because of internal hydrogen bonds 4. Between H attached to N of peptide linkage & the electronegative carbonyl O of the 4thaa on the N-terminal side of the peptide bond5. 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 α helix1. AA sequence affects helix stability2. For example, polypeptide with long block of Gluresidues will not form an α 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 αhelix5. Gly occurs infrequently as it is very flexible & takes coiled structure different from α helixElectric dipole of a peptide bond is transmitted through the hydrogen bonds along an α 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 helixThe β 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 β sheet)Hydrogen bonds cross-linksbetween adjacent chainsParallel β sheetMost common structures of β turns (connecting elements)1. Connects ends of 2 adjacent segments of an anti-parallel β sheet2. 180oturn involving 4 amino acids3. Gly and Pro occur in β turns CONHMore common(Gly at 3rdposition)Ramachandran plots for variety of structuresAlthough theoretically possible, not observed in proteinsRelative probability that a given amino acid will occur in the 3 common types of secondary structureProteins are classified into 2 major groups:Globular proteins• Polypeptide folded into globular shape• Contain more than 1 type of secondary structure• Soluble in waterExample: most enzymesFibrous proteins• Polypeptide chain arranged in sheets or strands• Contain single type of secondary structure• Insoluble in waterRelationship between protein structure and biological functionStructure of hairHigher order structures(right-handed α helix)A hair is an array of many α-keratin filamentsStructure of collagenUnique secondary structure distinct from αhelixRepeating tripeptidesequence Gly-X-Pro or Gly-X-HyProAdapts a left-handed helical structure with 3 residues per turnα chain3 separate αchains are supertwistedCollagenCollagen with a distinct tertiary and quaternary structureGly3 stranded collagen superhelix• Collagen is 35% Gly11% Ala21% pro and hyPro• Gelatin is derived from collagenStructure of silk• Silk or spider web made up of the protein fibroinLayers of Antiparallelβ sheetSmall R groups allow close packingGlobular protein structures are compact and variedHuman serum albumin585 residuesActual size of the proteinTertiary structure of sperm whale myoglobin8 α helixSome bends which are β turnsTertiary structure of sperm whale myoglobinHydophobicresidues(buried)Tertiary structure of sperm whale myoglobinThe heme group3-D structure of some small proteinsDisulfide bondsα helixβ sheetPolypeptides (with more than few 100 aas) fold into 2 or more stable globular units called domainsSupersecondary structures (or motifs or folds)Stable arrangements of several elements of secondary structure and the connections between themStable folding patterns in proteinsStable folding patterns in proteinsConstruction of large motifs from smaller onesThe quaternary structure of deoxyhemoglobinα subunitsβ subunitsProtein denaturation(loss of 3-D structure sufficient to cause loss of function)Renaturation of unfolded, denatured ribonucleaseA simulated folding pathwayThe thermodynamics of protein folding depicted as a free-energy funnelChaperonins in protein foldingE. Coli chaperoneE. Coli
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