Modeling of the transition temperature for the helical denaturation of alpha-keratin intermediate filaments

Simulations of the stability of the secondary and ternary structure of the alpha-keratin intermediate filament (IF) monomeric unit of wool are reported. Based on the assumed secondary structure three segments of the primary structure were selected: 1A, L12, and a part of 2B. Starting with an ideal alpha-helical conformation for each IF-segment, molecular dynamics simulations were carried out on the atomistic level at various temperatures in vacuum using the CFF91 force field. In either simulation the expected destabilization of the helical structure with increasing simulation temperature was observed. By use of different procedures of analysis, transition temperatures for the alpha-helical denaturation were determined that are significantly higher for the supposedly alpha-helical segments 1A and 2B than for the linker segment L12. The different stabilities of segments 1A and L12 were further verified through simulations in water environment that show the linker segment to be non-helical at room temperature. The lower transition temperature of segment L12 confirms the expectation that its amino acid sequence leads to increased conformational flexibility. The mobility of the water molecules surrounding the IF-segment is found to be significantly decreased by protein/water interactions.