Voet Chapter 8

Voet Chapter 8 - C hapter 8 Three Dimensional Structures o...

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Chapter 8 Three- Dimensional Structures of Proteins 1 • Secondary Structure A. The Peptide Group B. Helical Structures C. Beta Structures D. Nonrepetitive Structures 2 • Fibrous Proteins 0: Keratin-A Helix of Helices B. Cullagcn-A Triple Helical Cable 3 • Globu.lar Proteins Iuterpretation of Protein X-Ray and NMR Structures Tertiary Structure C. Structural Bioinfonnatics 4 • Protein Stability Electrostatic Forces Hydrogen Bonding Forces Hydrophobic Forces Disulfide Bonds E. Protein Denaturation F. Explaining the Stability of Themostable Proteins 5 • Quaternary Strut1ure Subunit Interactions Symmetry in Proteins C. Determination of Subunit Composition Appendix: Viewing Stereo Pictures The properties of a protein are largely determined by its three-dimensional structure. One might naively suppose that since proteins are all composed of the same 20 types of amino acid residues, they would be more or less alike in their properties. Indeed, denatured (unfolded) proteins have rather similar characteristics, a kind of homogeneolLs "averapL:" of their r,mdomly dangling side chains. How- ever, the three-dimensional structure of a native (physio- logically folded) protein is specified by its primary struc- t un:. so Lhat it has a unique set of characteristics. In Lhis chapter, we shall discuss the structural features of proteins, the forces that hold them together, and their hierarchical organization to form complex structures. This will form the hasis for understanding the structure-limc- tion relationships necessary to comprehend the biochemi- cal roles of proteins. Detailed consideration of the dynamic behavior or proteins and how they fold to their native structllfcs is deferred until Chapter 9. 1 • SECONDARY STRUCTURE A polymer's secondary structure (2 0 structure) is defined as the local conformation of its backbone. For proteins, this has come to mean the specification of regular polypep- tide hack bone folding patterns: helices, pleated sheets, and turns. However, before we begin our discussion of these hasic structural motifs, let us consider the geometrical properties of the peptide group because its understanding is prerequisite to that of any structure containing it. In the 1930s ancl 1940s, Linus Pauling and Rohert Corey determined the X-ray structures of several amino acids and dipeptides in an effort to elucidate the structural con- straints on the conformations of a polypeptide chain. These studies indicated that the peptide group has a ri~id, planar 219
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220 Ch(Jpll~r 8. nlree-Dimensional Stmclures of Proteins struclure (Fig. 8-1), which, Paulil1~ poimed out, is {/ conse- quence of res 011 once imeractiol1s thai give the peplide bond an -40% double-bond character: This explanation is supported by the observations that a peptide's C-N bond is 0.13 A shorter than its N -Cn sin- gle hond and that its C=O bond is O.()2 A. longer than that of aldehydes and ketones. The peptide bond's resonance energy has its maximum value, -85 kJ . mol-I, when the peptide group is planar because its 'IT-bonding overlap is maximized in this con formaLion. This overlap, and thus the
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Voet Chapter 8 - C hapter 8 Three Dimensional Structures o...

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