ProteinStructures - Computational Molecular Biology Protein...

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Computational Molecular Biology Protein Structure: Introduction and Prediction
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My T. Thai mythai@cise.ufl.edu 2 Protein Folding One of the most important problem in molecular biology Given the one-dimensional amino-acid sequence that specifies the protein, what is the protein’s fold in three dimensions?
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My T. Thai mythai@cise.ufl.edu 3 Overview Understand protein structures Primary, secondary, tertiary Why study protein folding: Structure can reveal functional information which we cannot find from the sequence Misfolding proteins can cause diseases: mad cow disease Use in drug designs
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My T. Thai mythai@cise.ufl.edu 4 Overview of Protein Structure Proteins make up about 50% of the mass of the average human Play a vital role in keeping our bodies functioning properly Biopolymers made up of amino acids The order of the amino acids in a protein and the properties of their side chains determine the three dimensional structure and function of the protein
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My T. Thai mythai@cise.ufl.edu 5 Building blocks of proteins Consist of: An amino group (-NH2) Carboxyl group (-COOH) Hydrogen (-H) A side chain group (-R) attached to the central α- carbon There are 20 amino acids Primary protein structure is a sequence of a chain of amino acids C R R C α H N O OH H H Amino group Carboxyl group Side chain Amino Acid
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My T. Thai mythai@cise.ufl.edu 6 Side chains (Amino Acids) 20 amino acids have side chains that vary in structure, size, hydrogen bonding ability, and charge. R gives the amino acid its identity R can be simple as hydrogen (glycine) or more complex such as an aromatic ring (tryptophan)
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7 Chemical Structure of Amino Acids
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My T. Thai mythai@cise.ufl.edu 8 How Amino Acids Become Proteins Peptide bonds
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My T. Thai mythai@cise.ufl.edu 9 Polypeptide More than fifty amino acids in a chain are called a polypeptide . A protein is usually composed of 50 to 400+ amino acids. We call the units of a protein amino acid residues . carbonyl carbonyl carbon carbon amide amide nitrogen nitrogen
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My T. Thai mythai@cise.ufl.edu 10 Side chain properties Carbon does not make hydrogen bonds with water easily – hydrophobic. These ‘water fearing’ side chains tend to sequester themselves in the interior of the protein O and N are generally more likely than C to h-bond to water – hydrophilic Ten to turn outward to the exterior of the protein
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My T. Thai mythai@cise.ufl.edu 11
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My T. Thai mythai@cise.ufl.edu 12 Primary Structure Primary structure: Linear String of Amino Acids Backbone Backbone Side-chain Side-chain ... ALA PHE LEU ILE LEU ARG . .. Each amino acid within a protein is referred to as residues Each different protein has a unique sequence of amino acid residues, this  is its  primary structure  
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My T. Thai mythai@cise.ufl.edu 13 Secondary Structure Refers to the spatial arrangement of contiguous amino acid residues Regularly repeating local structures stabilized by hydrogen bonds
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This note was uploaded on 05/20/2011 for the course CAP 5515 taught by Professor Ungor during the Spring '08 term at University of Florida.

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ProteinStructures - Computational Molecular Biology Protein...

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