Superoxide dismutase hydrogen bonding

Most proteins contain more than one polypeptide chain. The manner in which these chains associate determines quaternary structure. Binding involves the same types of noncovalent forces mentioned for tertiary structure van der Waals forces, hydrophobic and hydrophilic attractions, and hydrogen bonding. However, the interactions are now interchain rather than infrachain (tertiary structure determination). The quaternary structure of hemoglobin (four almost identical subunits) will be discussed in Chapter 4, that of superoxide dismutase (two identical subunits) will be discussed in Chapter 5, and that of nitrogenase (multiple dissimilar subunits) will be discussed in Chapter 6. 

The chelate effect in proteins is also important, since the three-dimensional (3-D) structure of the protein can impose particular coordination geometry on the metal ion. This determines the ligands available for coordination, their stereochemistry and the local environment, through local hydrophobicity/hydrophilicity, hydrogen bonding by nearby residues with bound and non-bound residues in the metal ion s coordination sphere, etc. A good example is illustrated by the Zn2+-binding site of Cu/Zn superoxide dismutase, which has an affinity for Zn2+, such that the non-metallated protein can extract Zn2+ from solution into the site and can displace Cu2+ from the Zn2+ site when the di-Cu2+ protein is treated with excess Zn2+. 

Fig. 20. An example of antiparallel /3 sheet, from Cu,Zn superoxide dismutase (residues 93-98,28-33, and 16-21). Arrows show the direction of the chain on each strand. Main chain bonds are shown solid and hydrogen bonds are dotted. In the pattern characteristic of antiparallel /8 sheet, pairs of closely spaced hydrogen bonds alternate with widely spaced ones. The direction of view is from the solvent, so drat side chains pointing up are predominantly hydrophilic and those pointing down are predominantly hydrophobic.

Figure 19.6.2. Docked conformation of n-methylfonnainide and superoxide dismutase. Solvent reacts at the interface of dimeric enzyme. Ligand binds into enzyme cavity by hydrogen bonding. [Adapted, by permission, from Durai Kalyani, Kanagaraj Jyothi, Chinnarasu Sivaprakasam, Vasanthi Nachiappan, Spectrochim. Acta, Part A Molec. Biomolec. Sped, in press, 2014.]...

Fig. 12. Schematic drawing of the catalytic mechanism of CujZojSuperoxide dismutase. The superoxide displaces the axial water molecule at the Cu II) and reduces the copper to Cu(I). Concomitantly the bond from Cu to His 61 is broken and Oj is released. The Cu-facing nitrogen of His 61 becomes protonated and a second becomes bound. An electron is transferred from Cu(I), coupled with a proton transfer from His 61. After additon of a second proton from an active-site water, the uncharged hydrogen peroxide is rctosed. (With permission from Ref.

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