# Specificity and Selectivity in Protein-Ion Binding

> **NIH NIH R01** · UNIVERSITY OF TEXAS AT AUSTIN · 2020 · $326,747

## Abstract

SUMMARY
Over 30% of all proteins bind metal ions, including transition metals, for structural and
functional purposes. Even though there are rich experimental structural and
thermodynamic information on protein-ion complexes, our understanding of the physical
basis for the specificity and selectivity in protein-ion recognition remains lacking. There is
a great need for accurate physical models and efficient simulation software to enable
computational study of protein-ion systems. We propose to develop a next generation
classical force field AMOEBA+, based on the existing AMOEBA potential, to
systematically model permanent electrostatics, repulsion, dispersion, charge
penetration, polarization, charge transfer, and ligand field effect after quantum
mechanical energy decomposition and experimental data. The new potential and high-
performance molecular simulation software (Tinker for CPU & GPU systems) will allow
us to comprehend the structural, physical and thermodynamic driving forces underlying
protein-ion recognition using molecular dynamics simulations. Given the fundamental
importance of protein interaction with transition metals including Zn, Cu, Ni, Co, Fe, and
Mn, this research will have a broad impact on advancing our scientific knowledge about
ions in biomolecular structure and function, and lead to new computational tools to
accelerate the design of new diagnostic and therapeutic molecules targeting protein-ion
interactions.

## Key facts

- **NIH application ID:** 9972498
- **Project number:** 2R01GM114237-05
- **Recipient organization:** UNIVERSITY OF TEXAS AT AUSTIN
- **Principal Investigator:** JAY PONDER
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $326,747
- **Award type:** 2
- **Project period:** 2015-05-01 → 2024-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9972498

## Citation

> US National Institutes of Health, RePORTER application 9972498, Specificity and Selectivity in Protein-Ion Binding (2R01GM114237-05). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/9972498. Licensed CC0.

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