# Deciphering the relationship between structure, dynamics and function in helical bundle proteins

> **NIH NIH R35** · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · 2021 · $711,887

## Abstract

Project Summary/Abstract
 This proposal combines my two NIGMS grants. Our work on the M2 proton channel from influenza A
virus (GM56423) currently focuses on the mechanism of proton movement through the channel. M2 is also the
target of the amantadine class of influenza drugs, and most isolates of influenza A virus are now amantadine-
resistant. Crystallographic structures of M2 in various functional states will be solved at very high resolution
using the X-ray free electron laser to enable structure determination at room temperature. Parallel,
collaborative studies use single-molecule measurement and 2DIR to probe dynamics. Very high-resolution
structures of a series of small molecule inhibitors in complex with amantadine-resistant mutants of M2 are
being determined, to enable our collaborators to conduct structure-based drug design.
 De novo protein design (GM54616) provides a means to test and refine our understanding of protein
structure and function. We address questions of sequence-specific recognition in membranes. A variety of
methods exist for the design or selection of antibodies and other reagents that recognize the water-soluble
regions of proteins. However, companion methods for targeting Transmembrane (TM) regions are not
generally available. Therefore, we are developing methods for the computational design of peptides that target
TM helices in a sequence-specific manner, focusing on EGF receptors (collaboration with Natalia Jura) and
integrins (collaboration with A. Orr). To elucidate the mechanisms by which proton-coupled transporters
function, we have designed model proteins that use proton gradients to drive transport of transition metal ions
up a gradient. We are increasing the efficiency of these minimal models and also expanding our methods to
allow design of phosphate transporters and lipid flippases. We propose to continue work on the design of
model diiron proteins to determine how a protein tunes the properties of these cofactors to affect diverse O2-
dependent processes such as substrate oxidation and radical formation. We are designing water and
membrane-soluble versions of the protein; by varying the identity and geometry of ligands and the water-
accessibility of the center to determine how these parameters they define reactivity.
 We are studying the mechanisms by which bacterial histidine kinases transmit conformational
information through multi-domain TM proteins. HKs are widely used by bacteria to sense and respond to
diverse environmental cues such as nutrients or noxious substances. Crystal structures of various truncated
domains of HKs have been solved. However, there are no high-resolution structures for HK membrane-
spanning domains or full-length HKs, and their signaling mechanism is a matter of debate. By integrating
structural information from diverse experimental techniques and functional measurements of HKs we seek to
elucidate the mechanism of signaling in HKs.
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## Key facts

- **NIH application ID:** 10172923
- **Project number:** 5R35GM122603-05
- **Recipient organization:** UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
- **Principal Investigator:** WILLIAM DEGRADO
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $711,887
- **Award type:** 5
- **Project period:** 2017-05-01 → 2022-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10172923

## Citation

> US National Institutes of Health, RePORTER application 10172923, Deciphering the relationship between structure, dynamics and function in helical bundle proteins (5R35GM122603-05). Retrieved via AI Analytics 2026-05-27 from https://api.ai-analytics.org/grant/nih/10172923. Licensed CC0.

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