# Linking specific macromolecular motions to enzyme rate acceleration in the TIM barrelsuperfamily of proteins

> **NIH NIH F32** · UNIVERSITY OF CALIFORNIA BERKELEY · 2020 · $16,862

## Abstract

Project Summary
Enzymes have evolved complex structures that sequester catalytic sites and achieve rates 1026 times faster than
non-catalyzed reactions. Extensive studies of active sites and de novo design efforts have been unable to
replicate or fully explain this rate acceleration, implicating that the greater protein structure has a critical role in
catalysis. Research over the last few decades has highlighted the importance of local and global motions in
enzyme activity, but much remains to be known about the link between distal motions and rate accelerations.
The TIM barrel scaffold is the focus of this investigation due to its ubiquity, an estimated 10% of all proteins
contain a TIM barrel domain, and because it catalyzes a diverse range of chemical reactions. The objective of
this proposal is to provide insight into the specific protein motions that are relevant to catalysis and enzymatic
rate enhancement, and that could be relevant to a wide selection of enzymes. The TIM barrel-containing enzyme
enolase from Saccharomyces cerevisiae was chosen as a model system for this Research Strategy due to its
well-characterized chemistry and importance in human diseases, such as Alzheimer’s disease and ischemia.
This proposal has two aims: 1) map the flexibility of native enolase across a temperature gradient using
hydrogen-deuterium exchange coupled with mass spectrometry (HDX-MS), and 2) correlate changes in catalytic
efficiency with local motions through the development and study of mutants. In order to investigate the role of
local and global motions and what information these flexibilities can impart, motions will be measured and studied
as functions of temperature over a 10s - 4h time scale. This temperature-dependent information will be correlated
with analogous kinetic data and assessed for potential catalytically-relevant networks and emergent trends.
This study is a fundamental investigation into the role of protein motions in catalytic rates, but could have
dramatic effects on our understanding of structure-function relationships and catalysis. In turn, these finding will
inform and improve de novo enzyme design and bioengineering approaches. Furthermore, a greater
understanding of the role of protein motions in enolase could inspire new inhibitor targets or suggest novel
methods of modulating enolase activity to address its role in human diseases.
This Research Strategy will facilitate the applicant’s transition from synthetic inorganic chemistry into an
academic career studying metalloenzymes. The training plan will develop the applicant’s scientific skills in protein
biochemistry, bioinformatics, and mechanistic enzymology, and facilitate the applicant’s career path through
conferences, workshops, and mentorship. This proposal will be carried out with Professor Judith Klinman at the
California Institute for Quantitative Biosciences (QB3) at the University of California, Berkeley. QB3 was
established in 2000, as a collaborative, multidi...

## Key facts

- **NIH application ID:** 10241236
- **Project number:** 5F32GM130031-02
- **Recipient organization:** UNIVERSITY OF CALIFORNIA BERKELEY
- **Principal Investigator:** Emily Jordan Thompson
- **Activity code:** F32 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $16,862
- **Award type:** 5
- **Project period:** 2019-07-01 → 2020-09-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10241236

## Citation

> US National Institutes of Health, RePORTER application 10241236, Linking specific macromolecular motions to enzyme rate acceleration in the TIM barrelsuperfamily of proteins (5F32GM130031-02). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10241236. Licensed CC0.

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