09-19 - BIO 5099: Molecular Biology for Computer Scientists...

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BIO 5099: Molecular Biology for Computer Scientists (et al) Lecture 9: Protein structure, function and coding http://compbio.uchsc.edu/hunter/bio5099 Larry.Hunter@uchsc .edu Protein structure Proteins are polymers of amino acids linked by peptide bonds. Properties of proteins are determined by both the particular sequence of amino acids and by the conformation (fold) of the protein. Flexibility in the bonds around C : (phi) (psi) sidechain Protein folding For most proteins, each of the flexible angles has a single preferred value, and each of the thousands of atoms has a fixed position Dynamics (and even unordered regions) do play some role in protein function, but can be neglected for now Insulin: a very small example
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Protein Structure (1) Protein structure is described in four levels Primary structure: amino acid sequence Secondary structure: local (in sequence) ordering into ( )Helices: compressed, corkscrew structures ( )Strands: extended, nearly straight structures ( )Sheets: paired strands, reinforced by hydrogen bonds parallel (same direction) or antiparallel sheets Tertiary structure: global ordering (all angles/atoms) Quaternary structures: multiple, disconnected amino acid chains interacting to form a larger structure Protein structure cartoons Protein Structure Representations Different visualizations show various aspects of structure
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Protein Structure (2) Aspects of protein structure that are important for function and often discussed: Surface properties : Most interactions happen at the molecular surface. Determinants are charge and shape Active site : Often, just a few amino acids do the main (enzymatic) task of a protein. These are called the active site. The rest of the protein can provide specificity by ensuring that only certain molecules “see” the active site. (Hydrophobic)
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This note was uploaded on 09/20/2011 for the course CSC BIO 5099 taught by Professor Prof.larryhunter during the Fall '02 term at University of Colorado Denver.

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09-19 - BIO 5099: Molecular Biology for Computer Scientists...

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