The role of histone tails in nucleosome stability: An electrostatic perspective

Computational and Structural Biotechnology Journal - Tập 18 - Trang 2799-2809 - 2020
Artemi Bendandi1,2, Alessandro S. Patelli3, Alberto Diaspro1,2, Walter Rocchia4
1DIFILAB, Department of Physics, University of Genoa, Via Dodecaneso 33, 16149 Genoa, Italy
2CHT Erzelli, Nanoscopy, Istituto Italiano di Tecnologia, Via Enrico Melen 83, 16152 Genoa, Italy
3LCVMM, Institute of Mathematics, Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland
4Concept Lab, Istituto Italiano di Tecnologia, Via Enrico Melen 83, 16152 Genoa, Italy

Tài liệu tham khảo

Biswas, 2011, Role of histone tails in structural stability of the nucleosome, PLoS Comput Biol, 7, 10.1371/journal.pcbi.1002279 McGinty, 2014, Nucleosome structure and function, Chem Rev, 115, 2255, 10.1021/cr500373h Shaytan, 2016, Coupling between histone conformations and DNA geometry in nucleosomes on a microsecond timescale: Atomistic insights into nucleosome functions, J Mol Biol, 428, 221, 10.1016/j.jmb.2015.12.004 Pasi, 2016, Structure and dynamics of DNA loops on nucleosomes studied with atomistic, microsecond-scale molecular dynamics, Nucleic Acids Res, 44, 5450, 10.1093/nar/gkw293 Becker, 2009, DNA nanomechanics: How proteins deform the double helix, J Chem Phys, 130, 10.1063/1.3082157 Szerlong, 2011, Biochem Cell Biol, 89, 24, 10.1139/O10-139 Brandani, 2018, DNA sliding in nucleosomes via twist defect propagation revealed by molecular simulations, Nucleic Acids Res, 46, 2788, 10.1093/nar/gky158 Freeman, 2014, DNA shape dominates sequence affinity in nucleosome formation, Phys Rev Lett, 113, 10.1103/PhysRevLett.113.168101 Rychkov, 2017, Partially assembled nucleosome structures at atomic detail, Biophys J, 112, 460, 10.1016/j.bpj.2016.10.041 Gansen, 2015, Opposing roles of h3- and h4-acetylation in the regulation of nucleosome structure–a FRET study, Nucleic Acids Res, 43, 1433, 10.1093/nar/gku1354 Kireeva, 2002, Nucleosome remodeling induced by RNA polymerase II, Molecular Cell, 9, 541, 10.1016/S1097-2765(02)00472-0 Li, 2004, Rapid spontaneous accessibility of nucleosomal DNA, Nature Struct Molecular Biol, 12, 46, 10.1038/nsmb869 Ozer, 2015, The chromatin fiber: multiscale problems and approaches, Current Opinion Struct Biol, 31, 124, 10.1016/j.sbi.2015.04.002 Gebala, 2019, Ion counting demonstrates a high electrostatic field generated by the nucleosome, eLife, 8, 10.7554/eLife.44993 Rocchia, 2001, Extending the applicability of the nonlinear poisson-boltzmann equation: multiple dielectric constants and multivalent ionsy, J Phys Chem B, 105, 6507, 10.1021/jp010454y Collepardo-Guevara, 2014, Chromatin fiber polymorphism triggered by variations of DNA linker lengths, Proc National Acad Sci, 111, 8061, 10.1073/pnas.1315872111 Gan, 2010, Chromatin ionic atmosphere analyzed by a mesoscale electrostatic approach, Biophys J, 99, 2587, 10.1016/j.bpj.2010.08.023 Izadi, 2016, Implicit solvent model for million-atom atomistic simulations: Insights into the organization of 30-nm chromatin fiber, J Chem Theory Comput, 12, 5946, 10.1021/acs.jctc.6b00712 Materese, 2009, Counterion atmosphere and hydration patterns near a nucleosome core particle, J Am Chem Soc, 131, 15005, 10.1021/ja905376q Baker, 2001, Electrostatics of nanosystems: application to microtubules and the ribosome, Proc National Acad Sci, 98, 10037, 10.1073/pnas.181342398 Beard, 2001, Modeling salt-mediated electrostatics of macromolecules: The discrete surface charge optimization algorithm and its application to the nucleosome, Biopolymers, 58, 106, 10.1002/1097-0282(200101)58:1<106::AID-BIP100>3.0.CO;2-# Kato, 2009, Characterization of the n-terminal tail domain of histone h3 in condensed nucleosome arrays by hydrogen exchange and NMR, J Am Chem Soc, 131, 15104, 10.1021/ja9070078 Saurabh, 2016, Atomistic simulation of stacked nucleosome core particles: Tail bridging, the h4 tail, and effect of hydrophobic forces, J Phys Chem B, 120, 3048, 10.1021/acs.jpcb.5b11863 Widom, 1997, Chromatin: The nucleosome unwrapped, Current Biol, 7, R653, 10.1016/S0960-9822(06)00327-7 Andresen, 2013, Solution scattering and FRET studies on nucleosomes reveal DNA unwrapping effects of h3 and h4 tail removal, PLoS ONE, 8, 10.1371/journal.pone.0078587 Bertin, 2004, Role of histone tails in the conformation and interactions of nucleosome core particlesy, Biochemistry, 43, 4773, 10.1021/bi036210g Winogradoff, 2015, The acetylation landscape of the h4 histone tail: Disentangling the interplay between the specific and cumulative effects, J Am Chem Soc, 137, 6245, 10.1021/jacs.5b00235 Zhou, 2012, Histone h4 k16q mutation, an acetylation mimic, causes structural disorder of its n-terminal basic patch in the nucleosome, J Mol Biol, 421, 30, 10.1016/j.jmb.2012.04.032 Gao, 2013, Histone h3 and h4 n-terminal tails in nucleosome arrays at cellular concentrations probed by magic angle spinning NMR spectroscopy, J Am Chem Soc, 135, 15278, 10.1021/ja407526s Mauney, 2018, Local DNA sequence controls asymmetry of DNA unwrapping from nucleosome core particles, Biophys J, 115, 773, 10.1016/j.bpj.2018.07.009 Norouzi, 2018, Dynamics of chromatin fibers: comparison of monte carlo simulations with force spectroscopy, Biophys J, 115, 1644, 10.1016/j.bpj.2018.06.032 Fan, 2013, An advanced coarse-grained nucleosome core particle model for computer simulations of nucleosome-nucleosome interactions under varying ionic conditions, PLoS ONE, 8 Becker, 2009, DNA nanomechanics in the nucleosome, Structure, 17, 579, 10.1016/j.str.2009.01.013 Shaytan, 2016, Trajectories of microsecond molecular dynamics simulations of nucleosomes and nucleosome core particles, Data Brief, 7, 1678, 10.1016/j.dib.2016.04.073 Davey, 2002, Solvent mediated interactions in the structure of the nucleosome core particle at 1.9Å resolution, J Mol Biol, 319, 1097, 10.1016/S0022-2836(02)00386-8 Decherchi, 2018, NanoShaper–VMD interface: computing and visualizing surfaces, pockets and channels in molecular systems, Bioinformatics, 35, 1241, 10.1093/bioinformatics/bty761 Dolinsky, 2004, PDB2pqr: an automated pipeline for the setup of poisson-boltzmann electrostatics calculations, Nucleic Acids Res, 32, W665, 10.1093/nar/gkh381 Decherchi, 2013, A general and robust ray-casting-based algorithm for triangulating surfaces at the nanoscale, PLoS ONE, 8, 10.1371/journal.pone.0059744 Cock, 2009, Biopython: freely available python tools for computational molecular biology and bioinformatics, Bioinformatics, 25, 1422, 10.1093/bioinformatics/btp163 Edayathumangalam, 2005, Nucleosomes in solution exist as a mixture of twist-defect states, J Mol Biol, 345, 103, 10.1016/j.jmb.2004.10.012 Tachiwana, 2010, Structural basis of instability of the nucleosome containing a testis-specific histone variant, human h3t, Proc National Acad Sci, 107, 10454, 10.1073/pnas.1003064107 Jin, 2010, Synergistic action of RNA polymerases in overcoming the nucleosomal barrier, Nature Struct Mol Biol, 17, 745, 10.1038/nsmb.1798 Iwasaki, 2013, Contribution of histone nterminal tails to the structure and stability of nucleosomes, FEBS Open Bio, 3, 363, 10.1016/j.fob.2013.08.007 Kono, 2018, Free energy profiles for unwrapping the outer superhelical turn of nucleosomal DNA, PLOS Comput Biol, 14, 10.1371/journal.pcbi.1006024 Brower-Toland, 2005, Specific contributions of histone tails and their acetylation to the mechanical stability of nucleosomes, J Mol Biol, 346, 135, 10.1016/j.jmb.2004.11.056 Tims, 2011, Dynamics of nucleosome invasion by DNA binding proteins, J Mol Biol, 411, 430, 10.1016/j.jmb.2011.05.044 Ferreira, 2007, Histone tails and the h3 n helix regulate nucleosome mobility and stability, Mol Cellular Biol, 27, 4037, 10.1128/MCB.02229-06 Kim, 2012, Mutagenesis of pairwise combinations of histone amino-terminal tails reveals functional redundancy in budding yeast, Proc National Acad Sci, 109, 5779, 10.1073/pnas.1203453109 Kameda, 2019, Histone tail dynamics in partially disassembled nucleosomes during chromatin remodeling, Front Mol Biosci, 6, 10.3389/fmolb.2019.00133 Kulaeva, 2012, Internucleosomal interactions mediated by histone tails allow distant communication in chromatin, J Biolog Chem, 287, 20248, 10.1074/jbc.M111.333104 Potoyan, 2012, Regulation of the h4 tail binding and folding landscapes via lys-16 acetylation, Proc Nat Acad Sci, 109, 17857, 10.1073/pnas.1201805109 Wang, 2000, Acetylation increases the a-helical content of the histone tails of the nucleosome, J Biolog Chem, 275, 35013, 10.1074/jbc.M004998200 Anderson, 2001, Effects of histone acetylation on the equilibrium accessibility of nucleosomal DNA target sites 1 1edited by r. ebright, J Mol Biol, 307, 977, 10.1006/jmbi.2001.4528 Polach, 2000, Effects of core histone tail domains on the equilibrium constants for dynamic dna site accessibility in nucleosomes, J Mol Biol, 298, 211, 10.1006/jmbi.2000.3644 Patelli AS, A sequence-dependent coarse-grain model of b-dna with explicit description of bases and phosphate groups parametrised from large scale molecular dynamics simulations, 261 (2019).