# Protein structure and dynamics in ultra-heterogeneous environments

> **NIH NIH R35** · UNIVERSITY OF TEXAS AT AUSTIN · 2020 · $205,169

## Abstract

SUMMARY
Crowding and heterogeneity: Biomolecular organization in vivo is driven by crowding and heterogeneity. To
date, protein structure, dynamics, and folding have been studied almost exclusively in simple buffer solutions,
yet it is has recently become evident that most “test tube” studies cannot be directly translated to cellular
environments. Nonspecific electrostatic interactions, excluded volume effects, and disrupted hydrogen-bond
networks dictate protein thermodynamics in these complex environments. While the prevailing view from these
is that excluded-volume effects favor the more compact native states, our group, along with others, found that
enthalpic contributions strengthen protein-water hydrogen bonds. These interactions can increase backbone
exposure and consequently destabilize folded states. Thus, there is an immediate need to quantify interactions
between biomolecules in accurate cell-like environments. The present studies are critical first step towards
understanding protein structure and dynamics in vivo. Our project aims to characterize the structure, dynamics,
and stability of proteins in crowded solutions that accurately mimic the cytoplasm. Specifically, we will quantify
the degree of molecular heterogeneity and establish the role of macromolecular crowding on protein-protein and
protein-water contacts.
Protein-protein interactions and ion channel gating mechanisms: Calmodulin (CaM) regulates biological
function by modulating the behavior of a wide range of proteins including many ion channels. CaM mutations or
mutations within CaM-regulated ion channels are responsible for neurological and cardiovascular diseases. CaM
can be considered a “Ca-sensing domain” for multiple ion channels, but the dynamic association between CaM
and ion channels make mechanistic studies challenging. The first complete structures of an ion channel with
CaM were solved earlier this year (2018). These underscore the fact that the gating mechanisms remain
incompletely understood. For example, eight states are required to model patch clamp measurements, but only
two structures (open/closed) are known. We propose to investigate gating mechanisms through a detailed
biophysical examination of dynamic CaM-channel interactions using a peptide that mimics the CaM binding
domain of the SK2 channel (KCa2.2). SK channels are important in a wide variety of physiological systems and
offer many advantages as a system for understanding Ca2+-CaM-mediated gating. If successful, our studies will
produce a stepwise mechanistic view of CaM-mediated channel activation.

## Key facts

- **NIH application ID:** 9984447
- **Project number:** 5R35GM133359-02
- **Recipient organization:** UNIVERSITY OF TEXAS AT AUSTIN
- **Principal Investigator:** Carlos Raul Baiz
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $205,169
- **Award type:** 5
- **Project period:** 2019-08-01 → 2024-05-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9984447

## Citation

> US National Institutes of Health, RePORTER application 9984447, Protein structure and dynamics in ultra-heterogeneous environments (5R35GM133359-02). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/9984447. Licensed CC0.

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