01- stoverview

01- stoverview - Structural Bioinformatics The Paradigm...

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Sequence Structure Function ⇒⇒ Structural Bioinformatics – The Paradigm Mutagenesis Transgenics “Gels and Cells” Confusion Comparative analyses Proteins Function through Structure! Sequence Structure Function The Analysis Paradigm G ly-G A la-A Va l-V I le-I Cys-C Leu-L Me t-M Hydrophobic Amino Acids Protein Structure Starts With the Amino Acids Asp - D Glu - E Ser - S Thr - T Asn - N Pro - P Gln - Q Polar and Negatively Charged (and Pro!)
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Aromatic Amino Acids Arg-R Lys-K H is-H Phe - F Tyr - Y Trp - W Positively Charged Amino Acids In Life L-Amino Acids Are Used The “CoRN” rule. Amino acids properties affect protein structure • The side chain defines the properties •Hydrophobic, Hydrophilic •Tiny, Small, Medium, Bulky •Polar, Non-Polar, Charged •Aromatic • These properties overlap • Some amino acids prefer to be in helices • Others prefer to be in sheets After Taylor, W.R., 1988, Prot. Eng. 2:77 A C D E F G H I K L M N P Q R S T V W Y Hydrophobic X X X X X X X X X X X X Hydrophobic+ X X X X X X Aliphatic X X X Aromatic X X X Small X X X X X X X X X Tiny X X X Polar X X X X X X X X X X X X Charged X X X X X Negative X X Positive X X X Hydroxyl X X X An amino acid can have many roles! Amino Acid Types
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Orders of Structure A Quick Look at Protein Structure and Folding Sequence Analysis Helix, Sheet, Turn, Coil 2D Structure Prediction Chou-Fasman etc Collections of Proteins X-ray crystallography and NMR Structure Formation From Mount • Hydrophobic Collapse • Hydropathy values • Accessible Surface • Hydrophobic residues inside • Hydrophilic residues outside • Hydrogen bonds are formed • Secondary Structure Formation • Helix, Sheet, Turn, Coil • Signal Peptides, Transmembrane • Stabilisation with
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01- stoverview - Structural Bioinformatics The Paradigm...

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