Part II_E_Proteins - Part II Proteins Three dimensional...

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Part II: Proteins Three dimensional structure 1
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2 proteins (polypeptides) – polymers of amino acids – peptide bond proteins function as 3-dimensional structures (dynamic) 3-D structure informed by linear sequence of amino acids - thermodynamic hypothesis ( Anfinsen’s postulate ) and the Levinthal paradox ultimate 3-D structure dependent on chemical properties of the protein chemical properties of proteins determined by the combined properties of individual amino acids (informed by chemical environment) 4 levels of protein structure: (primary) – linear sequence of amino acids (covalent attachment of main chain atoms) (secondary) – main chain, or peptide backbone conformation described by φ , ψ angles without regard to side chains (not dependent on side chains, but side chains may have stabilizing or destabilizing effects) (tertiary) – overall 3-D structure (fold) of individual polypeptides (side-chain interactions, longer distances) (domains) (quaternary) – inter-polypeptide interactions (multisubunit)
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3 10 20 30 40 50 60 70 80 MALKSLVLLS LLVLVLLLVR VQPSLGKETA AAKFERQHMD SSTSAASSSN YCNQMMKSRN LTKDRCKPVN TFVHESLADV 90 100 110 120 130 140 150 QAVCSQKNVA CKNGQTNCYQ SYSTMSITDC RETGSSKYPN CAYKTTQANK HIIVACEGNP YVPVHFDASV ribonuclease A (RNase 1) conformation – spatial arrangement of atoms - depends on the rotation of a bond or bonds conformation can change without breaking of covalent bonds (breaking and re-forming bonds involved in changing configuration ) biological function depends on protein’s native conformation under physiological conditions – conformation adopted by polypeptide (protein) – single and stable conformation
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4 dynamic (NMR solution structures)
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5
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6 Many molecular interactions of proteins depend on the “shape” of the surface area Dependent on the amino acid side chain identities
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4 levels of protein structure 7
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encoded genetically sequences written from N-terminus to C-terminus (biological synthesis) 8
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9 Secondary structure Secondary structure in proteins and polypeptides is determined by the bond rotations around the C α -N α -amino and the C α -C α -carboxyl bonds that result in regular, repeating conformation Secondary structure describes local conformation along the polypeptide chain of the main chain atoms . Secondary structure does NOT describe the conformation of the side chains Secondary structure forms through stabilizing hydrogen bonding interactions between the α - carboxyl and α -amino groups of the peptide bonds
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10 peptide bond peptide group : carbonyl carbon, and amide nitrogen, and their 4 substituents 6 atoms form the amide plane most stable in planar conformation because π - bonding overlap maximized polar unrestricted rotation about C-N ( peptide ) bond prevented rotation still possible around N-C α 2 and C α 1 -CO Linus Pauling and Robert Corey (late 1930s)
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