Constant-pH molecular dynamics with ionic strength effects: protonation-conformation coupling in decalysine.
A new implementation of the stochastic titration method for constant-pH molecular dynamics is presented, which introduces ionic strength effects in the simulations. In addition, the new implementation uses a faster molecular dynamics algorithm and an improved treatment of protonation events and of their effect on force field parameters. This new methodology is applied to a decalysine peptide, yielding very good quantitative agreement with experiments, both in terms of titration and helix-coil transition. The results show a significant dependence on ionic strength, illustrating the importance of including this parameter in constant-pH molecular dynamics simulations. Overall, the method seems to properly capture the protonation-conformation coupling and its dependence on ionic strength.
Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, EAN, Apartado 127, 2781-901 Oeiras, Portugal.
Miguel
M
Machuqueiro
António M
AM
Baptista
D000465:Algorithms; D003198:Computer Simulation; D006863:Hydrogen-Ion Concentration; D008958:Models, Molecular; D009994:Osmolar Concentration; D010455:Peptides / Q000737:chemistry*; D017433:Protein Structure, Secondary; D011522:Protons; D013997:Time Factors; D017186:Titrimetry
D010455:Peptides; D011522:Protons