Literature DB >> 31226513

Minimal coarse-grained models for molecular self-organisation in biology.

Anne E Hafner1, Johannes Krausser1, Anđela Šarić2.   

Abstract

The molecular machinery of life is largely created via self-organisation of individual molecules into functional assemblies. Minimal coarse-grained models, in which a whole macromolecule is represented by a small number of particles, can be of great value in identifying the main driving forces behind self-organisation in cell biology. Such models can incorporate data from both molecular and continuum scales, and their results can be directly compared to experiments. Here we review the state of the art of models for studying the formation and biological function of macromolecular assemblies in living organisms. We outline the key ingredients of each model and their main findings. We illustrate the contribution of this class of simulations to identifying the physical mechanisms behind life and diseases, and discuss their future developments.
Copyright © 2019 Elsevier Ltd. All rights reserved.

Year:  2019        PMID: 31226513     DOI: 10.1016/j.sbi.2019.05.018

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  12 in total

1.  Modeling Fibrillogenesis of Collagen-Mimetic Molecules.

Authors:  Anne E Hafner; Noemi G Gyori; Ciaran A Bench; Luke K Davis; Anđela Šarić
Journal:  Biophys J       Date:  2020-09-23       Impact factor: 4.033

Review 2.  Challenges in protein docking.

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

3.  Bond Type and Discretization of Nonmuscle Myosin II Are Critical for Simulated Contractile Dynamics.

Authors:  Daniel B Cortes; Max Gordon; Francois Nédélec; Amy S Maddox
Journal:  Biophys J       Date:  2020-04-21       Impact factor: 4.033

4.  Liquid network connectivity regulates the stability and composition of biomolecular condensates with many components.

Authors:  Jorge R Espinosa; Jerelle A Joseph; Ignacio Sanchez-Burgos; Adiran Garaizar; Daan Frenkel; Rosana Collepardo-Guevara
Journal:  Proc Natl Acad Sci U S A       Date:  2020-06-01       Impact factor: 11.205

5.  Integrating transposable elements in the 3D genome.

Authors:  Alexandros Bousios; Hans-Wilhelm Nützmann; Dorothy Buck; Davide Michieletto
Journal:  Mob DNA       Date:  2020-02-04

6.  Physical modeling of multivalent interactions in the nuclear pore complex.

Authors:  Luke K Davis; Anđela Šarić; Bart W Hoogenboom; Anton Zilman
Journal:  Biophys J       Date:  2021-02-20       Impact factor: 4.033

7.  Thermodynamics and kinetics of phase separation of protein-RNA mixtures by a minimal model.

Authors:  Jerelle A Joseph; Jorge R Espinosa; Ignacio Sanchez-Burgos; Adiran Garaizar; Daan Frenkel; Rosana Collepardo-Guevara
Journal:  Biophys J       Date:  2021-02-09       Impact factor: 4.033

8.  Moltemplate: A Tool for Coarse-Grained Modeling of Complex Biological Matter and Soft Condensed Matter Physics.

Authors:  Andrew I Jewett; David Stelter; Jason Lambert; Shyam M Saladi; Otello M Roscioni; Matteo Ricci; Ludovic Autin; Martina Maritan; Saeed M Bashusqeh; Tom Keyes; Remus T Dame; Joan-Emma Shea; Grant J Jensen; David S Goodsell
Journal:  J Mol Biol       Date:  2021-02-02       Impact factor: 6.151

9.  Building an extensible cell wall.

Authors:  Daniel J Cosgrove
Journal:  Plant Physiol       Date:  2022-06-27       Impact factor: 8.005

Review 10.  "Dividing and Conquering" and "Caching" in Molecular Modeling.

Authors:  Xiaoyong Cao; Pu Tian
Journal:  Int J Mol Sci       Date:  2021-05-10       Impact factor: 5.923

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.