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Literature DB >> 31299173

Whole-Cell Models and Simulations in Molecular Detail.

Abstract

Comprehensive data about the composition and structure of cellular components have enabled the construction of quantitative whole-cell models. While kinetic network-type models have been established, it is also becoming possible to build physical, molecular-level models of cellular environments. This review outlines challenges in constructing and simulating such models and discusses near- and long-term opportunities for developing physical whole-cell models that can connect molecular structure with biological function.

Entities: Chemical Disease Gene Species

Keywords: crowding; molecular dynamics simulation; network models; protein structure; systems biology

Mesh：

Year: 2019 PMID： 31299173 PMCID： PMC6783340 DOI： 10.1146/annurev-cellbio-100617-062542

Source DB: PubMed Journal: Annu Rev Cell Dev Biol ISSN： 1081-0706 Impact factor: 13.827

155 in total

Review 1. Development of novel statistical potentials for protein fold recognition.

Authors: N-V Buchete; J E Straub; D Thirumalai
Journal: Curr Opin Struct Biol Date: 2004-04 Impact factor: 6.809

2. A mechanical model of actin stress fiber formation and substrate elasticity sensing in adherent cells.

Authors: Sam Walcott; Sean X Sun
Journal: Proc Natl Acad Sci U S A Date: 2010-04-12 Impact factor: 11.205

Review 3. The macromolecular crowding effect--from in vitro into the cell.

Authors: David Gnutt; Simon Ebbinghaus
Journal: Biol Chem Date: 2016-01 Impact factor: 3.915

4. Simulating mesoscopic reaction-diffusion systems using the Gillespie algorithm.

Authors: David Bernstein
Journal: Phys Rev E Stat Nonlin Soft Matter Phys Date: 2005-04-08

Review 5. Structure, dynamics, assembly, and evolution of protein complexes.

Authors: Joseph A Marsh; Sarah A Teichmann
Journal: Annu Rev Biochem Date: 2014-12-08 Impact factor: 23.643

6. Coupling and Decoupling of Rotational and Translational Diffusion of Proteins under Crowding Conditions.

Authors: Matthias Roos; Maria Ott; Marius Hofmann; Susanne Link; Ernst Rössler; Jochen Balbach; Alexey Krushelnitsky; Kay Saalwächter
Journal: J Am Chem Soc Date: 2016-08-03 Impact factor: 15.419

7. Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm.

Authors: Sean R McGuffee; Adrian H Elcock
Journal: PLoS Comput Biol Date: 2010-03-05 Impact factor: 4.475

8. Crowding in Cellular Environments at an Atomistic Level from Computer Simulations.

Authors: Michael Feig; Isseki Yu; Po-Hung Wang; Grzegorz Nawrocki; Yuji Sugita
Journal: J Phys Chem B Date: 2017-07-12 Impact factor: 2.991

9. Liquid-Liquid Phase Separation of Patchy Particles Illuminates Diverse Effects of Regulatory Components on Protein Droplet Formation.

Authors: Valery Nguemaha; Huan-Xiang Zhou
Journal: Sci Rep Date: 2018-04-30 Impact factor: 4.379

Review 10. Molecular dynamics simulations of membrane proteins and their interactions: from nanoscale to mesoscale.

Authors: Matthieu Chavent; Anna L Duncan; Mark Sp Sansom
Journal: Curr Opin Struct Biol Date: 2016-06-21 Impact factor: 7.786

12 in total

Review 1. Challenges in protein docking.

Authors: Ilya A Vakser
Journal: Curr Opin Struct Biol Date: 2020-08-21 Impact factor: 6.809

2. Collective mechanical responses of cadherin-based adhesive junctions as predicted by simulations.

Authors: Brandon L Neel; Collin R Nisler; Sanket Walujkar; Raul Araya-Secchi; Marcos Sotomayor
Journal: Biophys J Date: 2022-02-10 Impact factor: 4.033

3. Building Structural Models of a Whole Mycoplasma Cell.

Authors: Martina Maritan; Ludovic Autin; Jonathan Karr; Markus W Covert; Arthur J Olson; David S Goodsell
Journal: J Mol Biol Date: 2021-11-10 Impact factor: 5.469

4. 'RNA modulation of transport properties and stability in phase-separated condensates.

Authors: Andrés R Tejedor; Adiran Garaizar; Jorge Ramírez; Jorge R Espinosa
Journal: Biophys J Date: 2021-11-09 Impact factor: 4.033

5. Bayesian metamodeling of complex biological systems across varying representations.

Authors: Barak Raveh; Liping Sun; Kate L White; Tanmoy Sanyal; Jeremy Tempkin; Dongqing Zheng; Kala Bharath; Jitin Singla; Chenxi Wang; Jihui Zhao; Angdi Li; Nicholas A Graham; Carl Kesselman; Raymond C Stevens; Andrej Sali
Journal: Proc Natl Acad Sci U S A Date: 2021-08-31 Impact factor: 11.205

6. When Is an In Silico Representation a Digital Twin? A Biopharmaceutical Industry Approach to the Digital Twin Concept.

Authors: Rui M C Portela; Christos Varsakelis; Anne Richelle; Nikolaos Giannelos; Julia Pence; Sandrine Dessoy; Moritz von Stosch
Journal: Adv Biochem Eng Biotechnol Date: 2021 Impact factor: 2.635

Review 7. Art and Science of the Cellular Mesoscale.

Authors: David S Goodsell; Arthur J Olson; Stefano Forli
Journal: Trends Biochem Sci Date: 2020-03-21 Impact factor: 13.807

8. Charge-driven condensation of RNA and proteins suggests broad role of phase separation in cytoplasmic environments.

Authors: Bercem Dutagaci; Grzegorz Nawrocki; Joyce Goodluck; Ali Akbar Ashkarran; Charles G Hoogstraten; Lisa J Lapidus; Michael Feig
Journal: Elife Date: 2021-01-26 Impact factor: 8.140

9. The analysis of living systems can generate both knowledge and illusions.

Authors: Antony M Jose
Journal: Elife Date: 2020-06-18 Impact factor: 8.140

10. Computer-Aided Whole-Cell Design: Taking a Holistic Approach by Integrating Synthetic With Systems Biology.

Authors: Lucia Marucci; Matteo Barberis; Jonathan Karr; Oliver Ray; Paul R Race; Miguel de Souza Andrade; Claire Grierson; Stefan Andreas Hoffmann; Sophie Landon; Elibio Rech; Joshua Rees-Garbutt; Richard Seabrook; William Shaw; Christopher Woods
Journal: Front Bioeng Biotechnol Date: 2020-08-07