Polypeptides mechanical stretching

Mechanical Stretching of ot-Helical Polypeptides 8.1 Poly-L-Lysine... 

Serpins consist of a conserved core of three P-sheets and eight or nine a-helices that act collectively in the inhibitory mechanism. As with the Kazal- and Kunitz-type inhibitors, the mechanism involves a surface exposed loop that is termed the reactive center loop (RCL). The RCL presents a short stretch of polypeptide sequence bearing the Pl-Pl scissile bond. Like other serine protease inhibitor families, the PI residue dominates the thermodynamics that govern the interaction between protease and inhibitor. Exposure of the PI residue to solvent is typically brokered by 15 amino acids N-terminal to the PI residue and 5 residues on the C-terminal prime side of the scissile bond. Evidence for dramatic conformational change in the inhibitory mechanism was first provided by the crystal structure of the cleaved form of ai-antitrypsin (37). In this structure and unlike the native form, the reactive center loop was not solvent exposed but occurred as an additional P-strand within the core of the structure. 

The structure of lactose permease has been determined (Figure 13.11). As expected from the sequence analysis, this structure consists of two halves, each of which comprises six membrane-spanning a helices. Someot these helices are somewhat irregular. The two halves are well separated and are joined by a single stretch of polypeptide. In this structure, the sugar lies in a pocket in tlie center of the protein and is accessible from a path leads from the interior of the cell. On the basis of these structures and a wide range of other experiments, a mechanism for symporter action has been... 

Under ideal, thermodynamically reversible conditions, this mechanical work is equal to the Gibbs free energy change (AG) for the process. The numbers obtained here cannot be compared directly with the values obtained for molecules in solution using bulk thermodynamic methods (Chapter 5) because they include the additional elastic work involved in stretching the unfolded polypeptide as the tethered ends are pulled further apart than they would normally be for an unfolded protein free in solution. 

Implicit in the kinetic mechanism proposed here is the idea that a helix (probably an a-helix) is the main protein secondary structure and that all the other secondary structures arise from the breaking and destabilization of the a-helices. This new kinetic mechanism may explain the high helidty of short polypeptides that are part of jS-strands, as well as the presence of a-helical intermediates in the folding of predominantly j8-sheet proteins. The hierarchical nature of protein structure is also a natural consequence of the mechanism since that main secondary structure is present from the beginning and the tertiary structure results from the breaks and, either the packing of the helical stretches that arise in that early process, or the packing of the jS-sheets that form later when the first process happens to lead to unfavourable side chain interactions. 

The hydrophobic stretch of 72 residues in the oleosin is the longest one foimd in all prokaryotic and eukaryotic proteins. The mechanism by which it has evolved is intriguing. A postulation can be made partly based on the length of 72 residues being roughly 4 times that of a transmembrane polypeptide and on the occurrence of several relatively hydrophilic residues at the center of the stretch. Initially, a short hydrophilic polypeptide joining two transmembrane hydrophobic polypeptides, of possibly an ER membrane protein, became hydrophobic through DNA sequence mutation. A continuous hydrophobic stretch resulted, which consisted of about half of the final 72 residues. This primitive hydrophobic stretch could stabilize an oil body,... 

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