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Lecture 4

Lecture 4 protein structural patterns.docx

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University of Toronto St. George
Stavroula Andreopoulos

Lecture 4 Structural Pattern of Proteins - proteins are unbranched polymers of amino acids linked head to tail through the formation of covalent peptide bonds (amide linkage) - proteins are read from carboxyl group to amino group - peptide bond formation – release of water - peptide backbone – repeated sequence of -N-C -C - α o - N represents the amide nitrogen; C reprαsents alpha carbon atom of an amino acid in the chain; C oepresents the final carbonyl carbon of the amino acid in the chain linked to the N of the next amino acid - carbonyl oxygen and amide hydrogen in trans conformation is energetically favoured due to less steric hindrance between nonbonded atoms in adjacent amino acids - chiral center of α-carbon atom created an asymmetric polypeptide chain (except in glycine) - only L-amino acids are found in proteins - peptide linkage is portrayed by a single bond between the carbonyl carbon and the aminde nitrogen - in principle, rotation may occur about any covalent bond – all three bonds re single bonds (N-C α Cα-C o Co-N peptide bonds) - another resonance is possible where rotation is prevented about the C -N bond doe to the formation of a double bond - real nature of the peptide bond is midway between the two resonance structures – partial double bond character - peptide bond resonance restricts free rotation around the peptide bond and the peptide backbone has only two degrees of freedom per amino acid group: rotation around the N-C α bond, angle of rotation Φ (phi); and rotation around the C -C boαd, oesignated angle of rotation Ψ (psi) - the six atoms that compose the peptide bond group are coplanar – forms the amide plane of the polypeptide backbone - the Co-N bond length is 0.133 nm, shorter than the normal C-N bond lengths (C -N bond isα 0.145 nm) but longer than typical C=N bonds (0.125 nm) Peptide Bonds - planar peptide bond – two degrees of freedom per residue for the peptide chain – rotation parameters phi (Φ) and psi (Ψ) - Ramachandran plot – sterically possible values of psi, phi angles Amide Plane - each C αs the joining point for two planes defined by peptide bonds - for bond angles phi and psi, a value of 0° corresponds to an orientation with the amide plane bisecting the H-C -Rαangle and a cis formation of the main chain around the rotating bond - entire path of a peptide backbone in a protein is known is both angles are all specified - some values of phi and psi are not allowed due to steric interference - phi values of Φ=180° and psi values of Ψ=0° have forbidden overlap of N-H hydrogens - psi values of Ψ=180° and phi values of Φ=0° have unfavourable overlap between carbonyl oxygens Secondary Structure of Proteins - hydrogen bonds that make up secondary structures involve amide proton of one peptide group and carbonyl oxygen of another – cooperative formation of structures - when hydrogen bonds form there are two general structures – α-helix and β-pleated sheet - in the α-helix each peptide carbonyl is hydrogen bonded to the peptide amide group four residues up the chain - the number of residues in an α-helix varies
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