![]() The R group substituent attached to the alpha C can also rotate around the alpha C and the beta C of the side chain. The rotation angles for the two planes are called phi (f) and psi (y) are analogous to the torsion angles in the acyl chains of fatty acid. The two planes can twist around the alpha carbon. The alpha C serves as the corner attachment point of two different planes, each which can rotate independently of the other plane. This greatly simplifies the number of conformations which a protein can adopt since these 6 atoms can be considered to reside and move in a plane. These resonance structures lead to a planar arrangement of the peptide carbonyl C and amide N and the two other atoms connected to each, since the hybridization of the C and N has sp 2 character, with 120° bond angles. This can be accounted for by delocalizing the nonbonding electron pair of the N to the carbonyl C forming a double bond, with the pi bonded electrons of the carbonyl C-O bond moving to the O. X-ray analysis shows that the the C-N bond has double bond character. ![]() The peptide bonds connect the carbonyl C of the i th amino acid to the alpha amine N of the i th+1 amino acid. For proteins, we must consider the covalent links which attach the amino acids together, as well as the rotations possible in 20 different amino acids. With fatty acid chains, we dealt only with torsion or dihedral angles around the methylene carbons. Just as saturated fatty acid chains have preferred conformations (all ttt), peptide chains also have preferred conformations. Then we will discuss the thermodynamics and intermolecular forces which stabilize the folded (or native) shape and the unfolded (or denatured state) of proteins, in a fashion similar to how we discussed micelle and bilayer stability. The next chapter section will discuss the actual processes of folding and of unfolding (denaturation), both in vitro and in vivo. ![]() This chapter section will investigate the possible conformations available to proteins, just as we studied the conformations of free fatty acids and acyl chains in lipid aggregates. In contrast to micelles and bilayers, which are composed of aggregates of single and double chain amphiphiles, proteins are covalent polymers of 20 different amino acids, which fold, to a first approximation, in a thermodynamically spontaneous process into a single unique conformation, theoretically at a global energy minimum. ![]()
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