499B_lecture 4_09_proteins intro

499B_lecture 4_09_proteins intro - Protein Structures: Data...

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Protein Structures: Data Representation 1) 1) Primary Structure Primary Structure : character string. 2) 2) Secondary Structure Secondary Structure : 3) 3) Tertiary Structure Tertiary Structure : 4) 4) Quaternary Structure Quaternary Structure : Identifying sub-structures in a large protein based on sequence. 3-Dimensional Representation Protein Database Bank (PDB) This is a complicated file format structure that support numerous programs, and contains information regarding the primary structure (sequence), 3-D structures (x, y, z coordinates), size and linking of specific atoms in structures, etc.
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Secondary Structure Prediction: 1) Hydropathy Plot 2) Alpha Helix 3) Beta Sheet A Hydropathy plot identifies domains within a protein that are soluble (region of “charged” amino acids) or insoluble (region of “uncharged” amino acids). An alpha helix is a group of amino acids within a proteins that arrange themselves in a helical structure. A beta sheet is a group of amino acids within a protein that arrange themselves in a stable aligned (parallel) configuration.
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Secondary Structure Prediction: Hydropathy Plot Commonly used to identify alpha helices that span a membrane (i.e. anchor protein to cell wall). 1) Choose a “moving window” that travels along the protein sequence; a) calculates the overall “solubility” of the amino acids in the window. b) moves in amino acid c) repeat calculation d) continue this though the entire protein sequence. ELRLRYCAPAGFALLKCNDADYDGFKTNCSNVSVVHCTNLMNTTVTTGLLLNGSYSENRT Transmembrane domains are 20 amino acids, but any size window can be used. 1) Calculate average using amino acids- specific constants. 2) Move window 1 amino acid. 3) Calculate average.
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Solubility Constants A Alanine 1.8 R Arginine -4.5 N Asparagine -3.5 D Aspartic acid -3.5 C Cysteine 2.5 Z Glutamine -3.5 E Glutamic acid -3.5 G Glycine -0.4 H Histidine -3.2 I Isoleucine 4.5 L Leucine 3.8 K Lysine -3.9 M Methionine 1.9 F Phenylalanine 2.8 P Proline -1.6 S Serine -0.8 T Threonine -0.7 W Tryptophan -0.9 Y Tyrosine -1.3 V Valine 4.2 ELRLRYCAPAGFALLKCNDADYDGFKTNCSNVSVVHCTNLMNTTVTTGLLLNGSYSENRT X = (-3.5)+(3.8)+(-4.5)+(3.8)+(-4.5)+(-1.3)+(2.5)+(1.8)+(-1.6)+(1.8)+(-0.4)+(2.8)+(1.8)+(3.8)+(3.8)+(-3.9)+(2.5)+(-3.5)+(-3.5)+(1.8)
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This note was uploaded on 02/29/2012 for the course CNIT 458 taught by Professor Michaelkane during the Spring '11 term at Purdue University-West Lafayette.

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499B_lecture 4_09_proteins intro - Protein Structures: Data...

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