Modelling Protein-Micelle Systems in Implicit Water

Rodney E. Versace, Themis Lazaridis
2015 Biophysical Journal  
enhanced-dynamics HMMM membrane model. For each protein, we have performed a total of 30 independent simulations with different lipid compositions (1:1 PC:PS and 7:3 PC:PS), providing robust statistics to characterize the membrane-bound form of these proteins. The results suggest that, despite the overall structural similarity, TIM1 and TIM3 establish different interactions with the membrane upon binding. Moreover, simulations show that in addition to the PS-binding pocket found in TIM
more » ... other specific proteinmembrane ionic interactions can be formed in each case, suggesting a molecular basis for their different biological roles. In addition to MD simulations, the orientation of TIM1 and TIM3 in model PScontaining membranes has been characterized using X-ray scattering. The agreement between the X-ray experiments and the MD simulations provide a detailed description of the membrane-binding mechanism of TIM proteins.
doi:10.1016/j.bpj.2014.11.1378 fatcat:h3ckoirmcvaabpjwhgx4rlik6i