lecture_8legge - Three Dimensional Protein Structures...

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1 Sd St t Proteins: 3D-Structure Chapter 6 (9 / 17/ 2009) Secondary Structure –The peptide group –Alpha helices and beta sheets –Nomenclature of protein secondary structure Tertiary Structure Three Dimensional Protein Structures Conformation: Spatial arrangement of atoms that depend on bonds and bond rotations. Proteins can change conformation, however, most proteins have a stable “native” conformation. The native protein is folded through weak interactions: a) Hydrophobic interactions b) Hydrogen-bonds c) Ionic interactions d) Van der Waals attractions There are four levels of protein structure 1. Primary structure 1 ° = Amino acid sequence, the linear order of AA’s. Remember from the N-terminus to the C-terminus Above all else this dictates the structure and function of the protein. 2. Secondary structure 2 ° = Local spatial alignment of amino acids without regard to side chains. Usually repeated structures Examples: α -helix, β -sheets, random coil, or β -turns 3. Tertiary Structure 3 ° = the 3-dimensional structure of an entire peptide. Great in detail but vague to generalize. Can reveal the detailed chemical mechanisms of an enzyme. 4. Quaternary Structure 4 ° two or more peptide chains associated with a protein. Spatial arrangements of subunits. Example of each level of protein structure Protein Structure Terminology
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2 The Amide bond In 1930s-1940s Linus Pauling and Robert Corey determined the structure of the peptide bond by X-ray. 40% double bond character. The amide bond or peptide bond C-N bond is 0.13Å shorter than C α -N bond.
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This note was uploaded on 02/22/2011 for the course BCHS 3304 taught by Professor Johnson during the Spring '08 term at University of Houston.

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lecture_8legge - Three Dimensional Protein Structures...

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