Minimal coarse-grained models for molecular self-organisation in biology
Tài liệu tham khảo
Robinson, 2007, The molecular sociology of the cell, Nature, 450, 973, 10.1038/nature06523
Bassereau, 2018, The 2018 biomembrane curvature and remodeling roadmap, J Phys D: Appl Phys, 51, 343001, 10.1088/1361-6463/aacb98
Dobson, 2019, The Amyloid Phenomenon and Its Significance in Biology and Medicine, Cold Spring Harbor Perspect Biol, a033878
Schiller, 2018, Mesoscopic modelling and simulation of soft matter, Soft Matter, 14, 9, 10.1039/C7SM01711A
Pak, 2018, Advances in coarse-grained modeling of macromolecular complexes, Curr Opin Struct Biol, 52, 119, 10.1016/j.sbi.2018.11.005
Marrink, 2019, Computational modeling of realistic cell membranes, Chem Rev, 119, 6184, 10.1021/acs.chemrev.8b00460
Perlmutter, 2013, Viral genome structures are optimal for capsid assembly, eLife, 2, 1, 10.7554/eLife.00632
Šarić, 2014, Crucial role of nonspecific interactions in amyloid nucleation, Proc Natl Acad Sci, 111, 17869, 10.1073/pnas.1410159111
Fusco, 2016, Soft matter perspective on protein crystal assembly, Colloids Surf B: Biointerfaces, 137, 22, 10.1016/j.colsurfb.2015.07.023
Paraschiv, 2019, Dynamic clustering regulates activity of mechanosensitive membrane channels, bioRxiv, 553248
Dear, 2018, Statistical mechanics of globular oligomer formation by protein molecules, J Phys Chem B, 122, 11721, 10.1021/acs.jpcb.8b07805
Davis, 2019, Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics, bioRxiv, 571687
Pannuzzo, 2018, The role of scaffold reshaping and disassembly in dynamin driven membrane fission, eLife, 7, 1, 10.7554/eLife.39441
Harker-Kirschneck, 2019, Transitions in filament geometry drive ESCRT-III-mediated membrane remodelling and fission, bioRxiv, 559898
Wedlich-Söldner, 2018, Self-organization: the fundament of cell biology, Philos Trans Roy Soc B: Biol Sci, 373, 20170103, 10.1098/rstb.2017.0103
Šarić, 2016, Physical determinants of the self-replication of protein fibrils, Nat Phys, 12, 874, 10.1038/nphys3828
Hemmat, 2018, Microtubule dynamics: moving toward a multi-scale approach, Curr Opin Cell Biol, 50, 8, 10.1016/j.ceb.2017.12.013
VanBuren, 2005, Mechanochemical model of microtubule structure and self-assembly kinetics, Biophys J, 89, 2911, 10.1529/biophysj.105.060913
Margolin, 2011, The mechanisms of microtubule catastrophe and rescue: implications from analysis of a dimer-scale computational model, Mol Biol Cell, 23, 642, 10.1091/mbc.e11-08-0688
Coombes, 2013, Evolving tip structures can explain age-dependent microtubule catastrophe, Curr Biol, 23, 1342, 10.1016/j.cub.2013.05.059
Zakharov, 2015, Molecular and mechanical causes of microtubule catastrophe and aging, Biophys J, 109, 2574, 10.1016/j.bpj.2015.10.048
Piedra, 2016, GDP-to-GTP exchange on the microtubule end can contribute to the frequency of catastrophe, Mol Biol Cell, 27, 3515, 10.1091/mbc.e16-03-0199
Castle, 2017, Mechanisms of kinetic stabilization by the drugs paclitaxel and vinblastine, Mol Biol Cell, 28, 1238, 10.1091/mbc.e16-08-0567
Castle, 2013, Brownian dynamics of subunit addition-loss kinetics and thermodynamics in linear polymer self-assembly, Biophys J, 105, 2528, 10.1016/j.bpj.2013.10.009
Lan, 2009, Condensation of FtsZ filaments can drive bacterial cell division, Proc Natl Acad Sci, 106, 121, 10.1073/pnas.0807963106
Ghosh, 2008, Origin of contractile force during cell division of bacteria, Phys Rev Lett, 101, 178101, 10.1103/PhysRevLett.101.178101
Fischer-Friedrich, 2011, Modeling FtsZ ring formation in the bacterial cellâanisotropic aggregation via mutual interactions of polymer rods, Phys Biol, 8, 026007, 10.1088/1478-3975/8/2/026007
Nedelec, 2007, Collective Langevin dynamics of flexible cytoskeletal fibers, N J Phys, 9, 10.1088/1367-2630/9/11/427
Vavylonis, 2008, Assembly mechanism of the contractile ring for cytokinesis by fission yeast, Science (New York, N.Y.), 319, 97, 10.1126/science.1151086
Kim, 2009, Computational analysis of viscoelastic properties of crosslinked actin networks, PLoS Comput Biol, 5, e1000439, 10.1371/journal.pcbi.1000439
Gordon, 2012, Hierarchical self-organization of cytoskeletal active networks, Phys Biol, 9, 026005, 10.1088/1478-3975/9/2/026005
Popov, 2016, MEDYAN: mechanochemical simulations of contraction and polarity alignment in actomyosin networks, PLOS Comput Biol, 12, e1004877, 10.1371/journal.pcbi.1004877
Freedman, 2017, A versatile framework for simulating the dynamic mechanical structure of cytoskeletal networks, Biophys J, 113, 448, 10.1016/j.bpj.2017.06.003
Belmonte, 2017, A theory that predicts behaviors of disordered cytoskeletal networks, Mol Syst Biol, 13, 941, 10.15252/msb.20177796
Freedman, 2018, Nonequilibrium phase diagrams for actomyosin networks, Soft Matter, 14, 7740, 10.1039/C8SM00741A
Stam, 2017, Filament rigidity and connectivity tune the deformation modes of active biopolymer networks, Proc Natl Acad Sci, 114, E10037, 10.1073/pnas.1708625114
Roostalu, 2018, Determinants of polar versus nematic organization in networks of dynamic microtubules and mitotic motors, Cell, 175, 796, 10.1016/j.cell.2018.09.029
Blackwell, 2017, Physical determinants of bipolar mitotic spindle assembly and stability in fission yeast, Sci Adv, 3, e1601603, 10.1126/sciadv.1601603
Bun, 2018, A disassembly-driven mechanism explains F-actin-mediated chromosome transport in starfish oocytes, eLife, 7, 1, 10.7554/eLife.31469
Descovich, 2018, Cross-linkers both drive and brake cytoskeletal remodeling and furrowing in cytokinesis, Mol Biol Cell, 29, 622, 10.1091/mbc.E17-06-0392
Mund, 2018, Systematic nanoscale analysis of endocytosis links efficient vesicle formation to patterned actin nucleation, Cell, 174, 884, 10.1016/j.cell.2018.06.032
Wu, 2011, Coarse-grained models for protein aggregation, Curr Opin Struct Biol, 21, 209, 10.1016/j.sbi.2011.02.002
Ilie, 2019
Šarić, 2016, Kinetics of spontaneous filament nucleation via oligomers: Insights from theory and simulation, J Chem Phys, 145, 211926, 10.1063/1.4965040
Vácha, 2011, Relation between molecular shape and the morphology of self-assembling aggregates: a simulation study, Biophys J, 101, 1432, 10.1016/j.bpj.2011.07.046
Cohen, 2018, Distinct thermodynamic signatures of oligomer generation in the aggregation of the amyloid-β peptide, Nat Chem, 10, 523, 10.1038/s41557-018-0023-x
Michaels, 2018, Reaction rate theory for supramolecular kinetics: application to protein aggregation, Mol Phys, 116, 3055, 10.1080/00268976.2018.1474280
Meisl, 2017, Scaling behaviour and rate-determining steps in filamentous self-assembly, Chem Sci, 8, 7087, 10.1039/C7SC01965C
Michaels, 2018, Chemical kinetics for bridging molecular mechanisms and macroscopic measurements of amyloid fibril formation, Annu Rev Phys Chem, 69, 273, 10.1146/annurev-physchem-050317-021322
Ilie, 2016, A coarse grained protein model with internal degrees of freedom. Application to α -synuclein aggregation, J Chem Phys, 144, 085103, 10.1063/1.4942115
Ilie, 2017, The attachment of α-synuclein to a fiber: A coarse-grain approach, J Chem Phys, 146, 115102, 10.1063/1.4978297
Lu, 2018, Understanding the twisted structure of amyloid fibrils via molecular simulations, J Phys Chem B, 122, 11302, 10.1021/acs.jpcb.8b07255
Mohajerani, 2018, The role of the encapsulated cargo in microcompartment assembly, PLOS Comput Biol, 14, e1006351, 10.1371/journal.pcbi.1006351
Brackley, 2017, Ephemeral protein binding to dna shapes stable nuclear bodies and chromatin domains, Biophys J, 112, 1085, 10.1016/j.bpj.2017.01.025
Michieletto, 2019, Physical principles of retroviral integration in the human genome, Nat Commun, 10, 575, 10.1038/s41467-019-08333-8
Dignon, 2018, Relation between single-molecule properties and phase behavior of intrinsically disordered proteins, Proc Natl Acad Sci, 115, 9929, 10.1073/pnas.1804177115
Weichsel, 2016, The more the tubular: dynamic bundling of actin filaments for membrane tube formation, PLOS Comput Biol, 12, e1004982, 10.1371/journal.pcbi.1004982
Noguchi, 2016, Membrane tubule formation by banana-shaped proteins with or without transient network structure, Sci Rep, 6, 20935, 10.1038/srep20935
Giani, 2017, Early stages of clathrin aggregation at a membrane in coarse-grained simulations, J Chem Phys, 146, 155102, 10.1063/1.4979985
Brackley, 2013, Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization, Proceedings of the National Academy of Sciences, 110, E3605, 10.1073/pnas.1302950110
Tootle, 2005, Post-translational modifications influence transcription factor activity: A view from the ETS superfamily, BioEssays, 27, 285, 10.1002/bies.20198
Buckle, 2018, Polymer simulations of heteromorphic chromatin predict the 3D folding of complex genomic loci, Mol Cell, 72, 786, 10.1016/j.molcel.2018.09.016
Michieletto, 2018, Shaping epigenetic memory via genomic bookmarking, Nucl Acids Res, 46, 83, 10.1093/nar/gkx1200
Fudenberg, 2016, Formation of chromosomal domains by loop extrusion, Cell Rep., 15, 2038, 10.1016/j.celrep.2016.04.085
Hagan, 2014, Modeling Viral Capsid Assembly, 1, 10.1002/9781118755815.ch01
Hagan, 2016, Recent advances in coarse-grained modeling of virus assembly, Curr Opin Virol, 18, 36, 10.1016/j.coviro.2016.02.012
Lázaro, 2018, Self-assembly of convex particles on spherocylindrical surfaces, Soft Matter, 14, 5728, 10.1039/C8SM00129D
Zeng, 2018, Defects and chirality in the nanoparticle-directed assembly of spherocylindrical shells of virus coat proteins, ACS Nano, 12, 5323, 10.1021/acsnano.8b00069
Schubertová, 2017, Design of multivalent inhibitors for preventing cellular uptake, Sci Rep, 7, 11689, 10.1038/s41598-017-11735-7
Lázaro, 2018, Why enveloped viruses need cores-the contribution of a nucleocapsid core to viral budding, Biophys J, 114, 619, 10.1016/j.bpj.2017.11.3782
Daumke, 2014, BAR domain scaffolds in dynamin-mediated membrane fission, Cell, 156, 882, 10.1016/j.cell.2014.02.017
Cooke, 2005, Solvent-free model for self-assembling fluid bilayer membranes: stabilization of the fluid phase based on broad attractive tail potentials, J Chem Phys, 123, 224710, 10.1063/1.2135785
Yuan, 2010, One-particle-thick, solvent-free, coarse-grained model for biological and biomimetic fluid membranes, Phys Rev E, 82, 011905, 10.1103/PhysRevE.82.011905
Šarić, 2013, Self-assembly of nanoparticles adsorbed on fluid and elastic membranes, Soft Matter, 9, 6677, 10.1039/c3sm50188d
den Otter, 2010, Self-assembly of three-legged patchy particles into polyhedral cages, J Phys: Condensed Matter, 22, 104103
Giani, 2016, Clathrin assembly regulated by adaptor proteins in coarse-grained models, Biophys J, 111, 222, 10.1016/j.bpj.2016.06.003
Schöneberg, 2017, Lipid-mediated PX-BAR domain recruitment couples local membrane constriction to endocytic vesicle fission, Nat Commun, 8, 15873, 10.1038/ncomms15873
Bonazzi, 2019, Membrane morphologies induced by arc-shaped scaffolds are determined by arc angle and coverage, Biophys J, 116, 1239, 10.1016/j.bpj.2019.02.017
Noguchi, 2017, Membrane structure formation induced by two types of banana-shaped proteins, Soft Matter, 13, 4099, 10.1039/C7SM00305F
Dignon, 2018, Sequence determinants of protein phase behavior from a coarse-grained model, PLOS Comput Biol, 14, e1005941, 10.1371/journal.pcbi.1005941
Das, 2018, Coarse-grained residue-based models of disordered protein condensates: utility and limitations of simple charge pattern parameters, Phys Chem Chem Phys, 20, 28558, 10.1039/C8CP05095C
Nguemaha, 2018, Liquid-liquid phase separation of patchy particles illuminates diverse effects of regulatory components on protein droplet formation, Sci Rep, 8, 6728, 10.1038/s41598-018-25132-1
Nuebler, 2018, Chromatin organization by an interplay of loop extrusion and compartmental segregation, Proc Natl Acad Sci, 115, E6697, 10.1073/pnas.1717730115
Coli D, Michieletto D, Marenduzzo D, Orlandini E, Magnetic Polymer Models for Epigenomic Organisation and Phase Separation, arXiv (1807.11101) (2018) 1-14.
Ghavami, 2018, Sol-gel transition in solutions of FG-Nups of the nuclear pore complex, Extreme Mech Lett, 22, 36, 10.1016/j.eml.2018.04.006
Schöneberg, 2013, ReaDDy - A software for particle-based reaction-diffusion dynamics in crowded cellular environments, PLoS ONE, 8, e74261, 10.1371/journal.pone.0074261
Biedermann, 2015, ReaDDyMM: Fast interacting particle reaction-diffusion simulations using graphical processing units, Biophys J, 108, 457, 10.1016/j.bpj.2014.12.025
Hoffmann, 2019, ReaDDy 2: Fast and flexible software framework for interacting-particle reaction dynamics, PLOS Comput Biol, 15, e1006830, 10.1371/journal.pcbi.1006830
van Zon, 2005, Simulating biochemical networks at the particle level and in time and space: green's function reaction dynamics, Phys Rev Lett, 94, 128103, 10.1103/PhysRevLett.94.128103
van Zon, 2005, Green's-function reaction dynamics: A particle-based approach for simulating biochemical networks in time and space, J Chem Phys, 123, 234910, 10.1063/1.2137716
Opplestrup, 2006, First-passage Monte Carlo algorithm: diffusion without all the hops, Phys Rev Lett, 97, 230602, 10.1103/PhysRevLett.97.230602
Donev, 2010, A first-passage kinetic Monte Carlo algorithm for complex diffusion-reaction systems, J Comput Phys, 229, 3214, 10.1016/j.jcp.2009.12.038
Vijaykumar, 2015, Combining molecular dynamics with mesoscopic Green's function reaction dynamics simulations, J Chem Phys, 143, 214102, 10.1063/1.4936254
Vijaykumar, 2017, Multiscale simulations of anisotropic particles combining molecular dynamics and Green's function reaction dynamics, J Chem Phys, 146, 114106, 10.1063/1.4977515
Sbailò, 2017, An efficient multi-scale Green's function reaction dynamics scheme, J Chem Phys, 147, 184106, 10.1063/1.5010190
Schermelleh, 2019, Super-resolution microscopy demystified, Nat Cell Biol, 21, 72, 10.1038/s41556-018-0251-8