# Proton Conduction Pathways in Proton Channel Proteins

> **NIH NIH K99** · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · 2021 · $97,159

## Abstract

PROJECT ABSTRACT:
Proton channel proteins potentiate the flow of protons across cell membranes, and have evolved fine control
over proton selectivity and conductivity to efficiently achieve their function, while maintaining cellular integrity.
Through formation of dynamic proton conduction pathways which mimic the water wires observed in dilute acid
for proton diffusion, protons move rapidly and selectively along a hydrogen-bonding network composed of
confined water and ionizable sidechains scattered within the lumen of proton channel proteins. One way proton
channels mediate proton conductivity is through guide water wires, which are stable lumenal waters organized
by polar protein groups. Guide water wires are well-studied as they are observed in high-resolution crystal
structures, but whether they are mobile or static and how their dynamics affects proton conductivity remains
unclear. Another way to modulate proton selectivity and conductivity is through transient water wires, which are
thought to form and dissipate to allow for proton flux through well-packed apolar segments. While transient water
wires have been hypothesized in molecular dynamics (MD) simulations, they are fundamentally difficult to test
experimentally. Finally, proton channels also use proton shuttle mechanisms of protonation and deprotonation
through an ionizable sidechain, such as His, Glu, and Asp, to tune proton conductance, but it is unclear the
extent these sidechains mediate pore solvation, and whether the proton shuttle mechanism leads to a net transit
of water. This work will address these mechanisms by which proton channel proteins mediate proton flux: the
(1) seemingly stable hydrogen-bonding networks of guide water wires and protein polar groups, (2) transient
water wires, and (3) proton shuttles composed of ionizable sidechains.
Through our proposed study of a natural proton channel, the influenza A matrix protein 2 (M2), and de novo
designed proton channels, we will test the hypotheses that (1) guide and transient water wires within proton
channel proteins confer their selectivity and dictate their capacity to conduct protons, and (2) proton shuttles are
not only necessary in defining the conduction rates of these proton channels, but also play critical roles in
modulating proton and water permeability. In Aim 1, we will examine whether guide water wires are mobile or
static by multidimensional infrared spectroscopy on M2 proton channels and the disease-relative mutants. Our
measurements in the presence and absence of drugs will allow us to determine how the dynamics of these
networks affect proton conductance, and how they change with drug binding and resistance mutations, which is
critical to identifying new antiviral strategies. In Aim 2, we test the hypothesis of transient water wires through
the de novo design and characterization of novel proton channels with varying lengths of apolar regions. In the
R00 phase (Aim 3), we examine how ionizable sidechains...

## Key facts

- **NIH application ID:** 10244955
- **Project number:** 5K99GM138753-02
- **Recipient organization:** UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
- **Principal Investigator:** Huong Tran Kratochvil
- **Activity code:** K99 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $97,159
- **Award type:** 5
- **Project period:** 2020-09-01 → 2022-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10244955

## Citation

> US National Institutes of Health, RePORTER application 10244955, Proton Conduction Pathways in Proton Channel Proteins (5K99GM138753-02). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10244955. Licensed CC0.

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