By Nicholas Sperelakis
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Extra info for Cell Physiology Source Book. A Molecular Approach
All of the methods used to predict protein structure are based on the physicochemical principle that the observed structure of a molecule is the one with the lowest free energy. If we can compute the energies for the possible conformations of a protein, we can pick out the structure of lowest energy, which is the structure that the protein is most likely to adopt. In order to perform this task, we must understand the types of energetic interactions within a polypeptide chain that must be optimized for the protein to fold correctly.
The filled circles are a-carbons; double dashed lines are drawn from C=O to NH (shorter dashed line) and from C=O to N (longer dashed line). (B) Two types of fl-sheets. The left side shows the antiparallel arrangement while the right side shows the parallel arrangement, as indicated by the arrows in both figures. (C) The arrangement of backbone atoms in a/3-bend showing how an i-to-i+3 hydrogen bond stabilizes the reverse turn structure. (D) Illustration of an extended a-helical chain showing how internal residues have both their NH and CO groups involved in hydrogen bonds.
At the end of this segment there is a hairpin turn followed by another a-helix involving 30-40 residues of the protein itself. Both the amino terminal end of the leader sequence and the carboxyl terminal end of the growing polypeptide chain lie on the same side of the membrane while the hairpin turn lies on the opposite side of the membrane. Because the leader sequence helix and the succeeding helical sequence are both independently stable, they interact minimally with one another so that the growing polypeptide chain can slide past the hydrophobic leader sequence in the membrane.
Cell Physiology Source Book. A Molecular Approach by Nicholas Sperelakis