Making Soup: Preparing and Validating Models of the Bacterial Cytoplasm for Molecular Simulation.

07:00 EST 9th December 2019 | BioPortfolio

Summary of "Making Soup: Preparing and Validating Models of the Bacterial Cytoplasm for Molecular Simulation."

Biomolecular crowding affects the biophysical and biochemical behavior of macro- molecules when compared to the dilute environment in experiments on isolated proteins. Computational modeling and simulation are useful tools to study how crowding affects the structural dynamics and biological properties of macromolecules. As computational power increased, modeling and simulating large scale all-atom explicit solvent models of the prokaryote cytoplasm has now become possible. In this work, we build an atomistic model of the cytoplasm of Escherichia coli composed of 1.5 million atoms and submit it to a total of 3μs of molecular dynamics simulations. The model consists of 8 different proteins representing about 50% of the cytoplasmic proteins and one type of t-RNA molecule. Properties of biomolecules under crowding conditions are compared to those from simulations of the individual compounds under dilute conditions. The simulation model is found to be consistent with experimental data about the diffusion coefficient and stability of macromolecules under crowded conditions. In order to stimulate further work we provide a Python script and a set of files to enable other researchers to build their own E. coli cytoplasm models to address questions related to crowding.


Journal Details

This article was published in the following journal.

Name: Journal of chemical information and modeling
ISSN: 1549-960X


DeepDyve research library

PubMed Articles [20079 Associated PubMed Articles listed on BioPortfolio]

Establishment of a hybrid drying strategy for instant cream mushroom soup based on starch retrogradation behavior.

Starch retrogradation during freeze drying is a contributor to an undesirable decrease in the viscosity of soup prepared from instant soup with high starch content. Monitoring starch retrogradation du...

Challenges and Opportunities for Translation of Therapies to Improve Cognition in Down Syndrome.

While preclinical studies have reported improvement of behavioral deficits in the Ts65Dn mouse model of Down syndrome (DS), translation to human clinical trials to improve cognition in individuals wit...

The current state of animal models and genomic approaches towards identifying and validating molecular determinants of Mycobacterium tuberculosis infection and tuberculosis disease.

Animal models are important in understanding both the pathogenesis of and immunity to tuberculosis. Unfortunately, we are beginning to understand that no animal model perfectly recapitulates the human...

Bayesian Decision Models: A Primer.

To understand decision-making behavior in simple, controlled environments, Bayesian models are often useful. First, optimal behavior is always Bayesian. Second, even when behavior deviates from optima...

ChaRTr: An R toolbox for modeling choices and response times in decision-making tasks.

Decision-making is the process of choosing and performing actions in response to sensory cues to achieve behavioral goals. Many mathematical models have been developed to describe the choice behavior ...

Clinical Trials [5863 Associated Clinical Trials listed on BioPortfolio]

Effect of Peas in Soup on Blood Glucose Control

This study is part of a group of studies whose overall goal is to accurately define the physiochemical and structural effects of pea varieties and relate these to blood glucose attenuation...

Broccoli In Osteoarthritis

To determine whether dietary sulforaphane (SFN), naturally available from eating broccoli, improves pain in people with knee osteoarthritis (OA), the trial will compare broccoli soup (rich...

Impact of Inulin on Production of Phenolic Acids From Tomato Onion and Lovage Soup

This is an acute human bioavailability study in self-reported healthy participants aged 20-70 years old. The investigators hypothesize that combination of polyphenolics from a soup rich in...

Glycemic Index of Instant Noodle With and Without Soup: Does Serving Method Have an Effect?

Glycemic index is commonly used as a method to determine the effect of a food to blood glucose. Despite its carbohydrate and fat content, instant noodle is very popular in Asia, including ...

SMZL Molecular Prognostic Index

The study aims at developing and validating an integrated clinico-molecular model for an accurate survival prognostication in newly diagnosed SMZL.

Medical and Biotech [MESH] Definitions

Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.

Models connecting initiating events at the cellular and molecular level to population-wide impacts. Computational models may be at levels relating toxicology to adverse effects.

Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.

Statistical models in which the value of a parameter for a given value of a factor is assumed to be equal to a + bx, where a and b are constants. The models predict a linear regression.

Statistical models of the production, distribution, and consumption of goods and services, as well as of financial considerations. For the application of statistics to the testing and quantifying of economic theories MODELS, ECONOMETRIC is available.

Quick Search

DeepDyve research library

Relevant Topic

Biological Therapy
Biological therapy involves the use of living organisms, substances derived from living organisms, or laboratory-produced versions of such substances to treat disease. Some biological therapies for cancer use vaccines or bacteria to stimulate the body&rs...

Searches Linking to this Article