The protonation/oxidation state of proteins and other biomolecules can be related to their structure and function, and it can affect properties like stability, ligand binding, catalysis, absorption spectrum, among others. This happens because pH and/or the redox potential affect the charge distribution on the biomolecules due to changes in the predominant protonation/oxidation state of the relevant groups. Also, ligands can change their protonation/oxidation state upon protein binding process or during an enzymatic reaction. Therefore, theoretical methods that can correctly describe the protonation/reduction state at constant pH and/or at constant redox potential are very important.<br/><br/>On this presentation, we show the implementation on AMBER of an extension to constant redox potential of codes already implemented: constant pH Molecular Dynamics (CpHMD) and Replica Exchange Molecular Dynamics along the pH-dimension (pH-REMD). Due to the similarity between the Henderson-Hasselbalch equation (applied to acid-base reactions) and the Nernst equation (applied to electrochemistry, reduction reactions), the mathematical derivations used for CpHMD and pH-REMD can be extended to the redox potential. By making use of CUDA implementation, we obtain a high-performance code that can be used on simulations of large systems. REMD is an important technique that enhances the statistical ensemble of a simulation while takes advantage of parallelism. The REMD implementation along both the pH and redox potential dimensions (pH,E-REMD) is important because several experimental measures are done both at constant pH and at constant redox potential.<br/><br/>We also show how our results are in agreement with theoretical/experimental expectations, and how computational benchmarks show the high-performance of calculations using GPU in comparison with serial or MPI calculations for large systems.

High-performance molecular dynamics at constant pH and constant redox potential using AMBER

253rd National Meeting (2017)

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.