In this proposal, a unique computational strategy is proposed for the first time to study proton translocation in two experimentally well-characterized biomolecular systems, the ion channel protein gramicidin A and the enzyme carbonic anhydrase. This research is made possible by a new technique developed in the investigator's group called """"""""Centroid Molecular Dynamics"""""""", allowing the quantum dynamical properties of complex systems to be studied computationally in an accurate and efficient manner. Such a methodology is essential for treating light particles such as protons, because of their high degree of quantization and possible quantum tunneling behavior. The problem of modeling the microscopic biomolecular interactions which influence proton translocation will also be dealt with in detail.
| Mayes, Heather B; Lee, Sangyun; White, Andrew D et al. (2018) Multiscale Kinetic Modeling Reveals an Ensemble of Cl-/H+ Exchange Pathways in ClC-ec1 Antiporter. J Am Chem Soc 140:1793-1804 |
| Madsen, Jesper J; Sinitskiy, Anton V; Li, Jianing et al. (2017) Highly Coarse-Grained Representations of Transmembrane Proteins. J Chem Theory Comput 13:935-944 |
| Sun, Rui; Sode, Olaseni; Dama, James F et al. (2017) Simulating Protein Mediated Hydrolysis of ATP and Other Nucleoside Triphosphates by Combining QM/MM Molecular Dynamics with Advances in Metadynamics. J Chem Theory Comput 13:2332-2341 |
| Liang, Ruibin; Swanson, Jessica M J; Wikström, Mårten et al. (2017) Understanding the essential proton-pumping kinetic gates and decoupling mutations in cytochrome c oxidase. Proc Natl Acad Sci U S A 114:5924-5929 |
| Arntsen, Christopher; Chen, Chen; Voth, Gregory A (2017) Reactive molecular dynamics models from ab initio molecular dynamics data using relative entropy minimization. Chem Phys Lett 683:573-578 |
| Parker, Joanne L; Li, Chenghan; Brinth, Allete et al. (2017) Proton movement and coupling in the POT family of peptide transporters. Proc Natl Acad Sci U S A 114:13182-13187 |
| Liang, Ruibin; Swanson, Jessica M J; Peng, Yuxing et al. (2016) Multiscale simulations reveal key features of the proton-pumping mechanism in cytochrome c oxidase. Proc Natl Acad Sci U S A 113:7420-5 |
| Taraphder, Srabani; Maupin, C Mark; Swanson, Jessica M J et al. (2016) Coupling Protein Dynamics with Proton Transport in Human Carbonic Anhydrase II. J Phys Chem B 120:8389-404 |
| Liang, Ruibin; Swanson, Jessica M J; Madsen, Jesper J et al. (2016) Acid activation mechanism of the influenza A M2 proton channel. Proc Natl Acad Sci U S A 113:E6955-E6964 |
| Lee, Sangyun; Liang, Ruibin; Voth, Gregory A et al. (2016) Computationally Efficient Multiscale Reactive Molecular Dynamics to Describe Amino Acid Deprotonation in Proteins. J Chem Theory Comput 12:879-91 |
Showing the most recent 10 out of 57 publications
