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Title: Development of $$\mathrm{AMOEBA}$$ Polarizable Force Field for Rare-Earth La3+ Interaction with Bioinspired Ligands

Abstract

Rare-earth metals (REMs) are crucial for many important industries, such as power generation and storage, in addition to cancer treatment and medical imaging. One promising new REM refinement approach involves mimicking the highly selective and efficient binding of REMs observed in relatively recently discovered proteins. However, realizing any such bioinspired approach requires an understanding of the biological recognition mechanisms. In this report we developed a new classical polarizable force field based on the AMOEBA framework for modeling a lanthanum ion (La3+) interacting with water, acetate, and acetamide, which have been found to coordinate the ion in proteins. The parameters were derived by comparing to high-level ab initio quantum mechanical (QM) calculations that include relativistic effects. The AMOEBA model, with advanced atomic multipoles and electronic polarization, is successful in capturing both the QM distance-dependent La3+–ligand interaction energies and experimental hydration free energy. A new scheme for pairwise polarization damping (POLPAIR) was developed to describe the polarization energy in La3+ interactions with both charged and neutral ligands. Simulations of La3+ in water showed water coordination numbers and ion–water distances consistent with previous experimental and theoretical findings. Water residence time analysis revealed both fast and slow kinetics in water exchange around the ion.more » This new model will allow investigation of fully solvated lanthanum ion–protein systems using GPU-accelerated dynamics simulations to gain insights on binding selectivity, which may be applied to the design of synthetic analogues.« less

Authors:
ORCiD logo [1];  [1]; ORCiD logo [1]; ORCiD logo [2]; ORCiD logo [3]; ORCiD logo [1]
+ Show Author Affiliations
  1. University of Texas, Austin, TX (United States)
  2. Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States). Electronic, Optical, and Nano Materials Department,
  3. Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States). Center for Integrated Nanotechnologies
Publication Date:
Research Org.:
Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)
Sponsoring Org.:
USDOE National Nuclear Security Administration (NNSA); USDOE Office of Science (SC); USDOE Laboratory Directed Research and Development (LDRD) Program; National Institutes of Health (NIH); Welch Foundation
OSTI Identifier:
2311656
Report Number(s):
SAND-2023-13037J
Journal ID: ISSN 1520-6106
Grant/Contract Number:  
NA0003525; R01GM114237; F-2120
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Physical Chemistry. B
Additional Journal Information:
Journal Volume: 127; Journal Issue: 6; Journal ID: ISSN 1520-6106
Publisher:
American Chemical Society
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY

Citation Formats

Wait, Elizabeth E., Gourary, Justin, Liu, Chengwen, Spoerke, Erik David, Rempe, Susan B., and Ren, Pengyu. Development of $\mathrm{AMOEBA}$ Polarizable Force Field for Rare-Earth La3+ Interaction with Bioinspired Ligands. United States: N. p., 2023. Web. doi:10.1021/acs.jpcb.2c07237.
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Wait, Elizabeth E., Gourary, Justin, Liu, Chengwen, Spoerke, Erik David, Rempe, Susan B., & Ren, Pengyu. Development of $\mathrm{AMOEBA}$ Polarizable Force Field for Rare-Earth La3+ Interaction with Bioinspired Ligands. United States. https://doi.org/10.1021/acs.jpcb.2c07237
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Wait, Elizabeth E., Gourary, Justin, Liu, Chengwen, Spoerke, Erik David, Rempe, Susan B., and Ren, Pengyu. Fri . "Development of $\mathrm{AMOEBA}$ Polarizable Force Field for Rare-Earth La3+ Interaction with Bioinspired Ligands". United States. https://doi.org/10.1021/acs.jpcb.2c07237. https://www.osti.gov/servlets/purl/2311656.
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@article{osti_2311656,
title = {Development of $\mathrm{AMOEBA}$ Polarizable Force Field for Rare-Earth La3+ Interaction with Bioinspired Ligands},
author = {Wait, Elizabeth E. and Gourary, Justin and Liu, Chengwen and Spoerke, Erik David and Rempe, Susan B. and Ren, Pengyu},
abstractNote = {Rare-earth metals (REMs) are crucial for many important industries, such as power generation and storage, in addition to cancer treatment and medical imaging. One promising new REM refinement approach involves mimicking the highly selective and efficient binding of REMs observed in relatively recently discovered proteins. However, realizing any such bioinspired approach requires an understanding of the biological recognition mechanisms. In this report we developed a new classical polarizable force field based on the AMOEBA framework for modeling a lanthanum ion (La3+) interacting with water, acetate, and acetamide, which have been found to coordinate the ion in proteins. The parameters were derived by comparing to high-level ab initio quantum mechanical (QM) calculations that include relativistic effects. The AMOEBA model, with advanced atomic multipoles and electronic polarization, is successful in capturing both the QM distance-dependent La3+–ligand interaction energies and experimental hydration free energy. A new scheme for pairwise polarization damping (POLPAIR) was developed to describe the polarization energy in La3+ interactions with both charged and neutral ligands. Simulations of La3+ in water showed water coordination numbers and ion–water distances consistent with previous experimental and theoretical findings. Water residence time analysis revealed both fast and slow kinetics in water exchange around the ion. This new model will allow investigation of fully solvated lanthanum ion–protein systems using GPU-accelerated dynamics simulations to gain insights on binding selectivity, which may be applied to the design of synthetic analogues.},
doi = {10.1021/acs.jpcb.2c07237},
journal = {Journal of Physical Chemistry. B},
number = 6,
volume = 127,
place = {United States},
year = {Fri Feb 03 00:00:00 EST 2023},
month = {Fri Feb 03 00:00:00 EST 2023}
}
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