Protein Classification and Structure Prediction Amino acid ...

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The Charged Amino Acids The Polar Amino Acids More Polar Amino Acids Planarity of the peptide bond And then there’s… Psi (ψ) – the angle of rotation about the Cα-C bond. Phi (φ) – the angle of rotation about the N-Cα bond. The planar bond angles and bond lengths are fixed. Krane & Raymer Primary & Secondary Structure • Primary structure = the linear sequence of amino acids comprising a protein: AGVGTVPMTAYGNDIQYYGQVT… • Secondary structure • Regular patterns of hydrogen bonding in proteins result in two patterns that emerge in nearly every protein structure known: the α-helix and the β-sheet • The location of direction of these periodic, repeating structures is known as the secondary structure of the protein The alpha helix φ ≈ ψ ≈ −60° Krane & Raymer 2
Properties of the alpha helix • φ ≈ ψ ≈ −60° • Hydrogen bonds between C=O of residue n, , and NH of residue n+4 • 3.6 residues/turn • 1.5 Å/residue rise • 100°/residue turn Properties of a-helices • 4 – 40+ residues in length • Often “dual-natured” • Half hydrophobic and half hydrophilic • Mostly when surface-exposed exposed • For many α-helices • Helix formers: Ala, Glu, Leu, Met • Helix breakers: Pro, Gly, Tyr, Ser Krane & Raymer Krane & Raymer The beta strand (& sheet) φ ≈ − 135° ψ ≈ +135° Properties of beta sheets • Formed of stretches of 5-105 residues in extended conformation • Pleated – each C α a bit above or below the previous • Parallel/aniparallel aniparallel, contiguous/non-contiguous Krane & Raymer Parallel and anti-parallel b-sheets Anti-parallel is slightly energetically favored Anti-parallel Parallel Turns and Loops • Secondary structure elements are connected by regions of turns and loops • Turns – short regions of non-α, , non-β conformation • Loops – larger stretches with no secondary structure. Often disordered. • “Random coil” • Sequences vary much more than secondary structure regions 3
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Protein Classification and Structure Prediction Amino acid ...

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