# Molecular Simulations of the Cell

> **NIH NIH R35** · UNIVERSITY OF IOWA · 2021 · $475,713

## Abstract

Project Summary
Experimental data from such fields as structural biology, proteomics, and genomics are providing enormous
amounts of information about the intracellular world of bacteria. What is currently missing is a combined
structural model of the bacterial cell that integrates these disparate sources of data in such a way that allows
key biological processes to be simulated as they might occur in vivo. The goal of the proposed project,
therefore, is to continue development of computational methods intended in the long-term to allow structural
models of entire bacterial cells to be constructed and simulated. The laboratory has previously reported a
structural model of the cytoplasm of the gram-negative bacterium Escherichia coli. Current and future work
will seek to extend that work and focus on developing high-resolution models of the chromosome of E. coli
and its nucleoid-associated proteins: current chromosome models are at levels of resolution too coarse to
allow molecular-level interpretations of behavior. The resulting models will be used to explicitly simulate
proteins searching for their genomic binding sites and to model aspects of short-time chromosomal dynamics
that have recently become amenable to experimental study. In both cases it is anticipated that the ability to
directly interpret the observed behavior in terms of the underlying chromosomal structure will provide
important mechanistic insights unattainable by any other method. In addition to chromosomal work, efforts
will continue to construct quantitatively-predictive models of the effects of crowded intracellular conditions
on protein folding behavior. Accompanying these application-oriented studies will be method-development
work focused on developing simple but realistic descriptions of interactions between all types of biomolecule
that are found in the cell and on implementing methods to rapidly compute these and other interactions (e.g.
hydrodynamics) on the cellular scale. Progress in each of these general project areas will be assessed by
making repeated quantitative comparisons with experimental data that are already available in the literature
for the exact same biomolecular systems. As well as potentially providing quantitative insights into a number
of aspects of protein and chromosomal behavior in vivo, the proposed work will deliver to the community
computer simulation code and accompanying potential functions suitable for modeling a wide range of
biomolecular systems. The simulation code, the high-resolution models of the chromosome, and all other data
accrued during pursuit of the proposed work, will be made freely available in downloadable form.
The proposed work is relevant to public health because its long-term goal is the construction of a complete
structural model of an important bacterial pathogen – Escherichia coli – and because it seeks to understand,
through the use of molecular simulations, how the biological processes that underpin life operate in ...

## Key facts

- **NIH application ID:** 10220989
- **Project number:** 5R35GM122466-05
- **Recipient organization:** UNIVERSITY OF IOWA
- **Principal Investigator:** ADRIAN Hamilton ELCOCK
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $475,713
- **Award type:** 5
- **Project period:** 2017-08-01 → 2023-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10220989

## Citation

> US National Institutes of Health, RePORTER application 10220989, Molecular Simulations of the Cell (5R35GM122466-05). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10220989. Licensed CC0.

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