Md-simulation of α-keratin intermediate filaments

In recent years powerful computer systems have become readily accessible to simulate complex chemical problems. Based on the primary structure of the intermediate filament monomer unit of wool, small sequences are selected. Their molecular dynamic behaviour is simulated, in order to investigate the secondary and tertiary structure as well as their stability. The simulations are carried out for a helical segment and a linker segment, selecting the ideal α-helix as start conformation. In vacuum all simulations show an unstable α-helix due to shifts of the intrahelical hydrogen bonds. So a new helical structure with a larger helix diameter is formed. However in simulations with surrounding water the α-helix remains stable throughout the simulation time. Up to now it has not been possible to dectect any fundamental difference in the molecular dynamic behaviour of the helical and the linker segment.     

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

Simulations of the stability of the secondary and tertiary structure of the α-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 α-helical conformation for each IF-segment, molecular dynamics simulations were carried out on the atomistic level at various temperatures in vaccum 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 α-helical denaturation were determined that are significantly higher for the supposedly α-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.