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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

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

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Author(s):
Bortot, Leandro Oliveira [1] ; Bashardanesh, Zahedeh [2] ; van der Spoel, David [2]
Total Authors: 3
Affiliation:
[1] Univ Sao Paulo, Sch Pharmaceut Sci Ribeirao Preto, Phys Biol Lab, Ave Cafe S-N, BR-14040903 Ribeirao Preto, SP - Brazil
[2] Uppsala Univ, Dept Cell & Mol Biol, Sci Life Lab, Box 596, SE-75124 Uppsala - Sweden
Total Affiliations: 2
Document type: Journal article
Source: JOURNAL OF CHEMICAL INFORMATION AND MODELING; v. 60, n. 1, p. 322-331, JAN 2020.
Web of Science Citations: 0
Abstract

Biomolecular crowding affects the biophysical and biochemical behavior of macromolecules compared with 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. With increases in computational power, modeling and simulation of large-scale all-atom explicit-solvent models of the prokaryote cytoplasm have now become possible. In this work, we built an atomistic model of the cytoplasm of Escherichia coli composed of 1.5 million atoms and submitted it to a total of 3 mu s of molecular dynamics simulations. The model consisted of eight different proteins representing about 50% of the cytoplasmic proteins and one type of t-RNA molecule. Properties of biomolecules under crowding conditions were compared with those from simulations of the individual compounds under dilute conditions. The simulation model was 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. (AU)

FAPESP's process: 13/00927-7 - Molecular dynamics simulations for the identification of bioactive molecules: inhibitors of the interaction between the dengue virus envelope glycoprotein and cellular C-type lectins
Grantee:Leandro Oliveira Bortot
Support Opportunities: Scholarships in Brazil - Doctorate (Direct)
FAPESP's process: 16/04958-2 - Molecular mechanisms underlying the recognition of the Dengue Virus envelope glycoprotein by the cellular lectin DC-SIGN and potential inhibitors of such interaction
Grantee:Leandro Oliveira Bortot
Support Opportunities: Scholarships abroad - Research Internship - Doctorate (Direct)