Amino acid residues, hydrogen bonds

The protein environment thus exerts a powerful influence over the cluster reduction potentials. This observation applies to all classes of electron transferases—the factors that are critical determinants of cofactor reduction potentials are poorly understood at present but are thought to include the low dielectric constants of protein interiors ( 4 for proteins vs. —78 for H2O), electrostatic effects due to nearby charged amino-acid residues, hydrogen bonding, and geometric constraints imposed by the protein. 

The C=O group of one amino acid is hydrogen bonded to an N - H group four amino add residues farther along the chain. Thus, hydrogen bonding occurs between two amino acids in the same chain. Note, too, that the hydrogen bonds are parallel to the axis of the helix. 

Two major elements of secondary structure are the a helix and the P strand. In the P helix, the polypeptide chain twists into a tightly packed rod. Within the helix, the CO group of each amino acid is hydrogen bonded to the NH group of the amino acid four residues along the polypeptide chain. In the p strand, the polypeptide chain is nearly fully extended. 

The orientation of the protein with respect to the DNA strand is an important issue in the protein-DNA interaction. As evident from Figure 11.2, this orientation is specific for each protein-DNA complex. Clearly, water molecules that are strongly hydrogen-bonded to the charged or polar amino acid residues remain bonded to... 

Also important for stabilizing a protein s tertiary stmcture are the formation of disulfide bridges between cysteine residues, the formation of hydrogen bonds between nearby amino acid residues, and the presence of ionic attractions, called salt bridges, between positively and negatively charged sites on various amino acid side chains within the protein. 

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