Abstract
Accurate potential energy functions are crucial for in-depth investigations of biological systems through molecular dynamics simulations. Classical additive force fields with fixed point charges has been proven to be insufficient for describing phenomenon such as ion binding to macromolecules. It is thus important to incorporate polarization effects in modeling of biological systems. In our previous work, we have developed a protocol for developing models of monovalent ions along with Ca2+, by bridging the gap between experimental measurements of bulk-phase properties and quantum mechanics (QM) calculation of gas phase clusters. With a focus on divalent cations and their interactions with amino acids, we have advanced the methodology of parametrization by utilizing a large number of configurations of model compound clusters from relevant condensed phase simulations. Cations currently being studied include (Fe2+), barium (Ba2+), zinc (Zn2+), and magnesium (Mg2+). Based on the classical Drude oscillator model, we have developed a Fe2+ model in fully solvated aqueous solution and in the protein environment. Despite challenges of describing accurately transitional metals through computational approaches, the developed model exhibits robust performance in predicting a wide range of properties that are critical to understanding the structure and function of cations in biological systems. These range from sophisticated coordination geometries to energetics such as water interaction energies and free energies of cation binding in liquids. The developed parameters will be enable discoveries in the area of metalloproteins and other relevant systems.
Published Version (
Free)
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
