2011_09_21_secondary_tertiary_structure_domains

2011_09_21_secondary_tertiary_structure_domains - Loops and...

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Loops and turns Helices and strands are connected by loops Loops are usually found at the surface of the protein and consist usually of polar residues Loops do not have periodic structures (i.e. non-repeating ! / " values) Insertions and deletions during evolution often occurs in loop regions Loops can form binding sites and enzyme active sites
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Hairpin loops (reverse turns) residue i i + 1 i + 2 i + 4 Often Gly Often Pro
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Relative frequencies of amino acids in secondary structures Can Secondary Structure be Predicted? -manually, one can look at propensities of amino acids to form a certain type of secondary structure -can look at patterns of residue conservation
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! "# $# %$ ! # - helix periodicity = 3.6 Residue i, i+3, i+4, i+7 lie on one face Prediction of Amphipathic Helices and Strands $ -strand periodicity = 2 Residues i, i+2, i+4, i+6 lie on one face T V E L K C Q V 1 st helix in Myoglobin Polar face Hydrophobic face 1 2 3 4 5 6 7 8 Second strand in CD8 Polar face Hydrophobic face 1 2 3 4 5 6 7 8
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Automated Prediction of Secondary Structure -Early prediction methods suffered from lack of data (1984) -with increases in both sequence and 3D structure information on proteins, and using of residue preferences, capping residues, multiple sequence alignments, and sophisticated computing techniques ! about 70-80% accuracy attainable Automated Predict Protein server takes as input your primary sequence of interest and returns the secondary structure prediction
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This note was uploaded on 10/21/2011 for the course BIOC 450 and 45 taught by Professor Various during the Fall '11 term at McGill.

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2011_09_21_secondary_tertiary_structure_domains - Loops and...

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