CHAPTER 4 (Figures)

CHAPTER 4 (Figures) - Lehninger Principles of Biochemistry...

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Unformatted text preview: Lehninger Principles of Biochemistry Fourth Edition Chapter 4: The Three-Dimensional Structure of Proteins Copyright 2004 by W. H. Freeman & Company David L. Nelson and Michael M. Cox 2 Protein Secondary Structure Secondary structure refers to local conformation of some part of the peptide. These structures include 1. -helix 2. -sheets and 3. -turns 4 Protein Secondary Structure i. The -helix This is the most common protein secondary structure. The simplest arrangement the polypeptide chain assumes with its rigid bonds a helical structure, which Pauling and Corey called the -helix ( Fig. 4-4 ). In this structure, the polypeptide backbone is tightly would around an imaginary axis drawn longitudinally through the middle of the helix, and the R groups of amino acid residues protrude outward from the helical backbone. Repeating unit is a single turn of the helix, which extend about 5.4 along the axis. The amino acid residues in an -helix have conformation with = -45 to 50 and = -60, and each helical turn include 3.6 amino acid residues . The helical twist of the -helix found in all proteins is right- handed . 6 Protein Secondary Structure Why does -helix form more rapidly than the other? Because -helix make the optimal use of the internal H-bonds. How? The structure is stabilized by H-bonds between H atom attached to the electronegative N atom of the linkage and the electronegative carbonyl oxygen atom of the fourth amino acid on the N-terminal side of the peptide bond ( Fig. 4- 4b ) Each successive turn of -helix is held to adjacent turns of three to four H- bonds . All the H-bonds combined give the entire helical structure considerable stability. Amino acid sequence vs -helix stability a). The electrostatic repulsion (or attraction) between successive amino residues with charged groups. Example ; Long chain of Glu residues will disrupt -helix structure at pH 7.0 because the vely charged carboxyl group of the adjacent glu residues repel each other and so strongly that they overcome the stabilizing influence of H-bonds on the -helix. b). The bulkiness of the adjacent R groups. Example ; The bulk and shape of Asn, Ser, Thr and Cys residues can destabilize an -helix if they are close together in the chain. 7 Protein Secondary Structure Amino acid sequence vs -helix stability (cont) c). The interactions between amino acid side chains spaced three (or four) residue apart. Example ; Positively charged amino acids are after found three residues away from negatively charged amino acids, permitting the formation of an ion-pair....
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This note was uploaded on 08/21/2008 for the course BIOCHEM 301 taught by Professor Vanes during the Spring '08 term at Rutgers.

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CHAPTER 4 (Figures) - Lehninger Principles of Biochemistry...

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