# Biological dynamics for protein properties and functions

> **NIH NIH R35** · OHIO STATE UNIVERSITY · 2022 · $467,244

## Abstract

Project Summary/Abstract
Protein dynamics is essential for its biological function. With integration of molecular biology, state-of-the-art
femtosecond spectroscopy and computation simulations, the biological processes now can be studied from the
intial ultrafast dynamics to subsequent longtime motions on the most fundamental level and thus the molecular
mechanisms can be revealed. We have recently investigated the dynamics and mechanisms of several
biological photomachines such as photoenzymes and photoreceptors in nature. We mapped out the complete
repair photocycles of UV-damaged thymine dimer in DNA by photoenzyme photolayses in real time, including
ten steps of ultrafast elementary reactions, and reveled a unified electron-transfer molecular mechanism for
photolyase superfamily. In another direction, we also made significant advances on the understanding of
water-protein interactions and dynamics and elucidated the fundamental coupled motions between hydration
water and protein sidechains on the picosecond time scales, providing direct envidence that hydration water
controls sidechain fluctuations. The understanding of biological water is significant to a variety of biological
activities such as protein recognition and enzymatic catalysis. In this new, synergistic effort, we take challenges
to explore more new complex systems in three major areas: (1) investigating two photoenzymes of an intricate
(6-4)-photoproduct photolyase and a newly discoivered fatty-acid photodecarboxylase to map out the entire
enzymatic reactions and reveal complete catalytic photocycles. Both photoenzyems are significnat in nature to
repair UV-damaged DNA and produce hydrocarbon biofuels; (2) examining three photoreceptors of UV-light
UVR8, blue-light cryptochromes (DmCry and AtCry) and several red-light phytochromes to reveal the primary
dynamics for initial signaling and subsequent conformational changes. The entire dynamic processes may
occur from ultrafast femtoseconds to longtime milliseconds; (3) exploring further water-protein interactions
and dynamics of complex biological systems for better understanding the role of water in protein structure,
stability, dynamics and functions. We will systematically investigate the cavity-water dynamics in a giant
chaperonin protein (GroEL) for understanding trapped water in function of substrate protein folding. We will
add new powerful methods of the femtosecond x-ray free electron lasers (XFEL) technique and the high-level
quantum mechanics/molecualr mechanics (QM/MM) calcualtions in these studies. We will develop new
conceptes and make important discoveries. These frontiers we are pursuing will provide new knowledge for
further biomedical applications.

## Key facts

- **NIH application ID:** 10330205
- **Project number:** 1R35GM144047-01
- **Recipient organization:** OHIO STATE UNIVERSITY
- **Principal Investigator:** DONGPING ZHONG
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $467,244
- **Award type:** 1
- **Project period:** 2022-02-01 → 2026-11-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10330205

## Citation

> US National Institutes of Health, RePORTER application 10330205, Biological dynamics for protein properties and functions (1R35GM144047-01). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10330205. Licensed CC0.

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