# Deciphering structure-function relationship in large protein complexes by modeling

> **NIH NIH R35** · IBM THOMAS J. WATSON RESEARCH CENTER · 2024 · $392,512

## Abstract

Project Summary
Most biological systems consist of many components (proteins, RNAs) that work together in a cooperative
manner to carry out specific functions, for example the ribosome for protein synthesis and the bacterial flagellar
motor for locomotion. One of the most important questions in biology is how “structure determines function”. As
the structural information for these complexes becomes available thanks to the recent development of high
resolution techniques such as Cryo-electron microscopy and tomography, the challenge is how this structural
information can be used to understand functions of these large complexes. The overall goal of this project is to
address this challenge by developing structure-based models to bridge the gap between structure and function
for large biological complexes. The structure-based mathematical models, which explicitly include interactions
of different components in the complex based on the complex structure, will be used to study/understand the
emergent dynamic properties of the complex and its input-output relationship in wildtype complex and different
mutants.
In the next funding period, we will focus on studying the structure, function, and dynamics of two large protein
complexes that are ubiquitous in the bacteria kingdom. The first functional complex we will study is the
bacterial MCP chemoreceptor cluster, which serve important cellular functions such as signal amplification and
enhancing adaptation. The fine structure of the MCP cluster is solved by cryo-EM studies, which show that the
core functional unit consists of 2 trimers of dimer (TOD) of the MCP receptors connected by two CheW
molecules and one CheA dimer and these basic units connect with each other through interactions between
CheW and CheA to form a regular two dimension lattice with six-fold symmetry. In this project, we plan to
develop a model of the chemorecptor cluster that include all pair-wise interactions among the key proteins
(MCP receptor, CheW, and CheA) based on the fine structure of the chemoreceptor clsuter, and use it to
investigate the molecular mechanism underlying signal amplification, the functional role of the coupling protein
CheW, and statistics of the stochastic switching dynamics of the MCP cluster in single cells. The second
functional complex we plan to study is the bacterial flagellar motor (BFM) complex, which drives the motility
and chemotaxis motion of bacteria. Recent cryo-EM studies of the BFM stator structure showed that the power
generating stator unit consists of a MotB dimer surrounded by a MotA pentamer ring, which suggested a new
mechanism for how proton-motive-force(PMF) is used to generate rotation of the rotor and how BFM switch
between clockwise (CW) and counter clockwise (CCW) rotations. In this project, we plan to develop a
structure-based model that describes the interactions between MotA and MotB in the stator unit and those
between MotA and FliG subunits of the rotor as well as the proton-a...

## Key facts

- **NIH application ID:** 10840685
- **Project number:** 2R35GM131734-06
- **Recipient organization:** IBM THOMAS J. WATSON RESEARCH CENTER
- **Principal Investigator:** Yuhai Tu
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $392,512
- **Award type:** 2
- **Project period:** 2019-09-01 → 2029-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10840685

## Citation

> US National Institutes of Health, RePORTER application 10840685, Deciphering structure-function relationship in large protein complexes by modeling (2R35GM131734-06). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10840685. Licensed CC0.

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