Histone post-translational modifications promote a chromatin environment that controls transcription, DNA replication and repair, but surprisingly few phosphorylations have been documented. We report the discovery of histone H3 serine-57 phosphorylation (H3S57ph) and show that it is implicated in different DNA repair pathways from fungi to vertebrates. We identified CHK1 as a major human H3S57 kinase, and disrupting or constitutively mimicking H3S57ph had opposing effects on rate of recovery from replication stress, 53BP1 chromatin binding, and dependency on RAD52. In fission yeast, mutation of all H3 alleles to S57A abrogated DNA repair by both non-homologous end-joining and homologous recombination, while cells with phospho-mimicking S57D alleles were partly compromised for both repair pathways, presented aberrant Rad52 foci and were strongly sensitised to replication stress. Mechanistically, H3S57ph loosens DNA-histone contacts, increasing nucleosome mobility, and interacts with H3K56. Our results suggest that dynamic phosphorylation of H3S57 is required for DNA repair and recovery from replication stress, opening avenues for investigating the role of this modification in other DNA-related processes.

Bioinformatics Unit Institute Pasteur of Montevideo Montevideo Uruguay

BPMP CNRS INRA Montpellier SupAgro University of Montpellier Montpellier France

Department of Biological Sciences CENUR North Riverside University of the Republic Salto Uruguay

Department of Experimental Biology Faculty of Science Palacký University Olomouc Olomouc Czech Republic

Equipe labellisée Ligue contre le Cancer Paris France

IBGC CNRS University of Bordeaux Bordeaux France

IGDR CNRS University of Rennes Rennes France

IGMM CNRS INSERM University of Montpellier Montpellier France

Institut Jacques Monod CNRS University Paris Diderot Paris France

IRB Barcelona BIST Barcelona Spain

Laboratory of Genome Evolution Department of Biology and Biotechnology Charles Darwin University of Rome Sapienza Rome Italy

School of Chemistry Raymond and Beverly Sackler Faculty of Exact Sciences Tel Aviv University Tel Aviv Israel

Schulich Faculty of Chemistry Technion Israel Institute of Technology Haifa Israel

The Rockefeller University New York NY USA

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Zeman MK, Cimprich KA. Causes and consequences of replication stress. Nat. Cell Biol. 2014;16:2–9. PubMed PMC

Macheret M, Halazonetis TD. DNA replication stress as a hallmark of cancer. Annu. Rev. Pathol. 2015;10:425–448. PubMed

Burrell RA, et al. Replication stress links structural and numerical cancer chromosomal instability. Nature. 2013;494:492–496. PubMed PMC

Ceccaldi R, Rondinelli B, D’Andrea AD. Repair pathway choices and consequences at the double-strand break. Trends Cell Biol. 2016;26:52–64. PubMed PMC

Rossi MJ, DiDomenico SF, Patel M, Mazin AV. RAD52: paradigm of synthetic lethality and new developments. Front. Genet. 2021;12:780293. PubMed PMC

Scully R, Panday A, Elango R, Willis NA. DNA double-strand break repair-pathway choice in somatic mammalian cells. Nat. Rev. Mol. Cell Biol. 2019;20:698–714. PubMed PMC

Karanam K, Kafri R, Loewer A, Lahav G. Quantitative live cell imaging reveals a gradual shift between DNA repair mechanisms and a maximal use of HR in mid S phase. Mol. Cell. 2012;47:320–329. PubMed PMC

Hustedt N, Durocher D. The control of DNA repair by the cell cycle. Nat. Cell Biol. 2016;19:1–9. PubMed

Mladenov E, et al. Strong suppression of gene conversion with increasing DNA double-strand break load delimited by 53BP1 and RAD52. Nucleic Acids Res. 2020;48:1905–1924. PubMed PMC

Audoynaud C, Vagner S, Lambert S. Non-homologous end-joining at challenged replication forks: an RNA connection? Trends Genet. 2021;37:973–985. PubMed

Neelsen KJ, Lopes M. Replication fork reversal in eukaryotes: from dead end to dynamic response. Nat. Rev. Mol. Cell Biol. 2015;16:207–220. PubMed

Ray Chaudhuri A, et al. Replication fork stability confers chemoresistance in BRCA-deficient cells. Nature. 2016;535:382–387. PubMed PMC

Nickoloff JA, Sharma N, Taylor L, Allen SJ, Hromas R. The safe path at the fork: ensuring replication-associated DNA double-strand breaks are repaired by homologous recombination. Front. Genet. 2021;12:748033. PubMed PMC

Tsukuda T, Fleming AB, Nickoloff JA, Osley MA. Chromatin remodelling at a DNA double-strand break site in Saccharomyces cerevisiae. Nature. 2005;438:379–383. PubMed PMC

Li X, Tyler JK. Nucleosome disassembly during human non-homologous end joining followed by concerted HIRA- and CAF-1-dependent reassembly. Elife. 2016;5:e15129. PubMed PMC

Lashgari A, Kougnassoukou Tchara P-E, Lambert J-P, Côté J. New insights into the DNA repair pathway choice with NuA4/TIP60. DNA Repair. 2022;113:103315. PubMed

Huang T-H, et al. The histone chaperones ASF1 and CAF-1 promote MMS22L-TONSL-mediated Rad51 loading onto ssDNA during homologous recombination in human cells. Mol. Cell. 2018;69:879–892.e5. PubMed PMC

Millán-Zambrano, G., Burton, A., Bannister, A. J. & Schneider, R. Histone post-translational modifications - cause and consequence of genome function. Nat. Rev. Genet.10.1038/s41576-022-00468-7 (2022). PubMed

Fradet-Turcotte A, et al. 53BP1 is a reader of the DNA-damage-induced H2A Lys 15 ubiquitin mark. Nature. 2013;499:50–54. PubMed PMC

Botuyan MV, et al. Structural basis for the methylation state-specific recognition of histone H4-K20 by 53BP1 and Crb2 in DNA repair. Cell. 2006;127:1361–1373. PubMed PMC

Becker JR, et al. BARD1 reads H2A lysine 15 ubiquitination to direct homologous recombination. Nature. 2021;596:433–437. PubMed

Xu F, Zhang K, Grunstein M. Acetylation in histone H3 globular domain regulates gene expression in yeast. Cell. 2005;121:375–385. PubMed

Masumoto H, Hawke D, Kobayashi R, Verreault A. A role for cell-cycle-regulated histone H3 lysine 56 acetylation in the DNA damage response. Nature. 2005;436:294–298. PubMed

Han J, et al. Rtt109 acetylates histone H3 lysine 56 and functions in DNA replication. Science. 2007;315:653–655. PubMed

Driscoll R, Hudson A, Jackson SP. Yeast Rtt109 promotes genome stability by acetylating histone H3 on lysine 56. Science. 2007;315:649–652. PubMed PMC

Xhemalce B, et al. Regulation of histone H3 lysine 56 acetylation in Schizosaccharomyces pombe. J. Biol. Chem. 2007;282:15040–15047. PubMed

Vermeulen M, et al. Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers. Cell. 2010;142:967–980. PubMed

Zielinska DF, Gnad F, Jedrusik-Bode M, Wiśniewski JR, Mann M. Caenorhabditis elegans has a phosphoproteome atypical for metazoans that is enriched in developmental and sex determination proteins. J. Proteome Res. 2009;8:4039–4049. PubMed

Aslam A, Logie C. Histone H3 serine 57 and lysine 56 interplay in transcription elongation and recovery from S-phase stress. PLoS One. 2010;5:e10851. PubMed PMC

Fisher D, Krasinska L, Coudreuse D, Novák B. Phosphorylation network dynamics in the control of cell cycle transitions. J. Cell. Sci. 2012;125:4703–4711. PubMed

Saldivar JC, Cortez D, Cimprich KA. The essential kinase ATR: ensuring faithful duplication of a challenging genome. Nat. Rev. Mol. Cell Biol. 2017;18:622–636. PubMed PMC

Blow JJ. Control of chromosomal DNA replication in the early Xenopus embryo. EMBO J. 2001;20:3293–3297. PubMed PMC

Jbara M, Guttmann-Raviv N, Maity SK, Ayoub N, Brik A. Total chemical synthesis of methylated analogues of histone 3 revealed KDM4D as a potential regulator of H3K79me3. Bioorg. Med. Chem. 2017;25:4966–4970. PubMed

Drogaris P, et al. Histone deacetylase inhibitors globally enhance h3/h4 tail acetylation without affecting h3 lysine 56 acetylation. Sci. Rep. 2012;2:220. PubMed PMC

Pal S, et al. The commercial antibodies widely used to measure H3 K56 acetylation are non-specific in human and Drosophila cells. PLoS One. 2016;11:e0155409. PubMed PMC

Duncan EM, et al. Cathepsin L proteolytically processes histone H3 during mouse embryonic stem cell differentiation. Cell. 2008;135:284–294. PubMed PMC

Tvardovskiy A, et al. Top-down and middle-down protein analysis reveals that intact and clipped human histones differ in post-translational modification patterns. Mol. Cell Proteomics. 2015;14:3142–3153. PubMed PMC

Santos-Rosa H, et al. Histone H3 tail clipping regulates gene expression. Nat. Struct. Mol. Biol. 2009;16:17–22. PubMed PMC

Drogaris P, Wurtele H, Masumoto H, Verreault A, Thibault P. Comprehensive profiling of histone modifications using a label-free approach and its applications in determining structure-function relationships. Anal. Chem. 2008;80:6698–6707. PubMed

Ausio J, Dong F, van Holde KE. Use of selectively trypsinized nucleosome core particles to analyze the role of the histone ‘tails’ in the stabilization of the nucleosome. J. Mol. Biol. 1989;206:451–463. PubMed

Tropberger P, et al. Regulation of transcription through acetylation of H3K122 on the lateral surface of the histone octamer. Cell. 2013;152:859–872. PubMed

Sirbu BM, et al. Analysis of protein dynamics at active, stalled, and collapsed replication forks. Genes Dev. 2011;25:1320–1327. PubMed PMC

Jang SM, Azebi S, Soubigou G, Muchardt C. DYRK1A phoshorylates histone H3 to differentially regulate the binding of HP1 isoforms and antagonize HP1-mediated transcriptional repression. EMBO Rep. 2014;15:686–694. PubMed PMC

Himpel S, et al. Specificity determinants of substrate recognition by the protein kinase DYRK1A. J. Biol. Chem. 2000;275:2431–2438. PubMed

Zachos G, Rainey MD, Gillespie DAF. Chk1-deficient tumour cells are viable but exhibit multiple checkpoint and survival defects. EMBO J. 2003;22:713–723. PubMed PMC

Liu Q, et al. Chk1 is an essential kinase that is regulated by Atr and required for the G(2)/M DNA damage checkpoint. Genes Dev. 2000;14:1448–1459. PubMed PMC

Chambers VS, et al. High-throughput sequencing of DNA G-quadruplex structures in the human genome. Nat. Biotechnol. 2015;33:877–881. PubMed

Biffi G, Tannahill D, McCafferty J, Balasubramanian S. Quantitative visualization of DNA G-quadruplex structures in human cells. Nat. Chem. 2013;5:182–186. PubMed PMC

Rodriguez R, et al. Small-molecule-induced DNA damage identifies alternative DNA structures in human genes. Nat. Chem. Biol. 2012;8:301–310. PubMed PMC

Rogakou EP, Pilch DR, Orr AH, Ivanova VS, Bonner WM. DNA double-stranded breaks induce histone H2AX phosphorylation on serine 139. J. Biol. Chem. 1998;273:5858–5868. PubMed

Voigt P, et al. Asymmetrically modified nucleosomes. Cell. 2012;151:181–193. PubMed PMC

Groth A, et al. Regulation of replication fork progression through histone supply and demand. Science. 2007;318:1928–1931. PubMed

Xu Y, et al. 53BP1 and BRCA1 control pathway choice for stalled replication restart. Elife. 2017;6:e30523. PubMed PMC

Schmid JA, et al. Histone ubiquitination by the DNA damage response is required for efficient DNA replication in unperturbed S phase. Mol. Cell. 2018;71:897–910.e8. PubMed

Lundin C, et al. Methyl methanesulfonate (MMS) produces heat-labile DNA damage but no detectable in vivo DNA double-strand breaks. Nucleic Acids Res. 2005;33:3799–3811. PubMed PMC

Fenley AT, Anandakrishnan R, Kidane YH, Onufriev AV. Modulation of nucleosomal DNA accessibility via charge-altering post-translational modifications in histone core. Epigenetics Chromatin. 2018;11:11. PubMed PMC

Pérez A, Luque FJ, Orozco M. Frontiers in molecular dynamics simulations of DNA. Acc. Chem. Res. 2012;45:196–205. PubMed

Wysocka J. Identifying novel proteins recognizing histone modifications using peptide pull-down assay. Methods. 2006;40:339–343. PubMed PMC

Lossaint G, et al. FANCD2 binds MCM proteins and controls replisome function upon activation of s phase checkpoint signaling. Mol. Cell. 2013;51:678–690. PubMed

Williams RS, et al. Mre11 dimers coordinate DNA end bridging and nuclease processing in double-strand-break repair. Cell. 2008;135:97–109. PubMed PMC

Zou L, Elledge SJ. Sensing DNA damage through ATRIP recognition of RPA-ssDNA complexes. Science. 2003;300:1542–1548. PubMed

Xu Y, et al. Histone H2A.Z controls a critical chromatin remodeling step required for DNA double-strand break repair. Mol. Cell. 2012;48:723–733. PubMed PMC

Contrepois K, et al. Histone variant H2A.J accumulates in senescent cells and promotes inflammatory gene expression. Nat. Commun. 2017;8:14995. PubMed PMC

Shimada K, et al. Ino80 chromatin remodeling complex promotes recovery of stalled replication forks. Curr. Biol. 2008;18:566–575. PubMed

Papamichos-Chronakis M, Peterson CL. The Ino80 chromatin-remodeling enzyme regulates replisome function and stability. Nat. Struct. Mol. Biol. 2008;15:338–345. PubMed

Mellacheruvu D, et al. The CRAPome: a contaminant repository for affinity purification-mass spectrometry data. Nat. Methods. 2013;10:730–736. PubMed PMC

Mirman Z, et al. 53BP1-RIF1-shieldin counteracts DSB resection through CST- and Polα-dependent fill-in. Nature. 2018;560:112–116. PubMed PMC

Noordermeer SM, et al. The shieldin complex mediates 53BP1-dependent DNA repair. Nature. 2018;560:117–121. PubMed PMC

Celic I, et al. The sirtuins hst3 and Hst4p preserve genome integrity by controlling histone h3 lysine 56 deacetylation. Curr. Biol. 2006;16:1280–1289. PubMed

Chen C-C, et al. Acetylated lysine 56 on histone H3 drives chromatin assembly after repair and signals for the completion of repair. Cell. 2008;134:231–243. PubMed PMC

Wurtele H, et al. Histone H3 lysine 56 acetylation and the response to DNA replication fork damage. Mol. Cell Biol. 2012;32:154–172. PubMed PMC

Hachinohe M, Hanaoka F, Masumoto H. Hst3 and Hst4 histone deacetylases regulate replicative lifespan by preventing genome instability in Saccharomyces cerevisiae. Genes Cells. 2011;16:467–477. PubMed

Muñoz-Galván S, Jimeno S, Rothstein R, Aguilera A. Histone H3K56 acetylation, Rad52, and non-DNA repair factors control double-strand break repair choice with the sister chromatid. PLoS Genet. 2013;9:e1003237. PubMed PMC

Che J, et al. Hyper-acetylation of histone H3K56 limits break-induced replication by inhibiting extensive repair synthesis. PLoS Genet. 2015;11:e1004990. PubMed PMC

Neumann H, et al. A method for genetically installing site-specific acetylation in recombinant histones defines the effects of H3 K56 acetylation. Mol. Cell. 2009;36:153–163. PubMed PMC

Garcia BA, et al. Organismal differences in post-translational modifications in histones H3 and H4. J. Biol. Chem. 2007;282:7641–7655. PubMed

Mateos-Gomez PA, et al. Mammalian polymerase θ promotes alternative NHEJ and suppresses recombination. Nature. 2015;518:254–257. PubMed PMC

Ceccaldi R, et al. Homologous-recombination-deficient tumours are dependent on Polθ-mediated repair. Nature. 2015;518:258–262. PubMed PMC

Acs K, et al. The AAA-ATPase VCP/p97 promotes 53BP1 recruitment by removing L3MBTL1 from DNA double-strand breaks. Nat. Struct. Mol. Biol. 2011;18:1345–1350. PubMed

Mallette FA, et al. RNF8- and RNF168-dependent degradation of KDM4A/JMJD2A triggers 53BP1 recruitment to DNA damage sites. EMBO J. 2012;31:1865–1878. PubMed PMC

Li Q, et al. Acetylation of histone H3 lysine 56 regulates replication-coupled nucleosome assembly. Cell. 2008;134:244–255. PubMed PMC

Williams SK, Truong D, Tyler JK. Acetylation in the globular core of histone H3 on lysine-56 promotes chromatin disassembly during transcriptional activation. Proc. Natl Acad. Sci. USA. 2008;105:9000–9005. PubMed PMC

Skerra A, Plückthun A. Assembly of a functional immunoglobulin Fv fragment in Escherichia coli. Science. 1988;240:1038–1041. PubMed

Lamesch P, et al. hORFeome v3.1: A resource of human open reading frames representing over 10,000 human genes. Genomics. 2007;89:307–315. PubMed PMC

Sobecki M, et al. Cell-cycle regulation accounts for variability in Ki-67 expression levels. Cancer Res. 2017;77:2722–2734. PubMed

Sobecki M, et al. The cell proliferation antigen Ki-67 organises heterochromatin. Elife. 2016;5:e13722. PubMed PMC

Vera J, et al. Greatwall promotes cell transformation by hyperactivating AKT in human malignancies. Elife. 2015;4:e10115. PubMed PMC

Lossaint G, Besnard E, Fisher D, Piette J, Dulić V. Chk1 is dispensable for G2 arrest in response to sustained DNA damage when the ATM/p53/p21 pathway is functional. Oncogene. 2011;30:4261–4274. PubMed

Parisis N, et al. Initiation of DNA replication requires actin dynamics and formin activity. EMBO J. 2017;36:3212–3231. PubMed PMC

Forment JV, Jackson SP. A flow cytometry-based method to simplify the analysis and quantification of protein association to chromatin in mammalian cells. Nat. Protoc. 2015;10:1297–1307. PubMed PMC

Shechter D, Dormann HL, Allis CD, Hake SB. Extraction, purification and analysis of histones. Nat. Protoc. 2007;2:1445–1457. PubMed

Henikoff S, Henikoff JG, Sakai A, Loeb GB, Ahmad K. Genome-wide profiling of salt fractions maps physical properties of chromatin. Genome Res. 2009;19:460–469. PubMed PMC

Méndez J, Stillman B. Chromatin association of human origin recognition complex, cdc6, and minichromosome maintenance proteins during the cell cycle: assembly of prereplication complexes in late mitosis. Mol. Cell. Biol. 2000;20:8602–8612. PubMed PMC

Ruthenburg AJ, Li H, Patel DJ, Allis CD. Multivalent engagement of chromatin modifications by linked binding modules. Nat. Rev. Mol. Cell Biol. 2007;8:983–994. PubMed PMC

Girardot M, et al. PRMT5-mediated histone H4 arginine-3 symmetrical dimethylation marks chromatin at G + C-rich regions of the mouse genome. Nucleic Acids Res. 2014;42:235–248. PubMed PMC

Edmondson DG, Smith MM, Roth SY. Repression domain of the yeast global repressor Tup1 interacts directly with histones H3 and H4. Genes Dev. 1996;10:1247–1259. PubMed

Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10:R25. PubMed PMC

R: the R project for statistical computing. https://www.r-project.org/.

Flores O, Orozco M. nucleR: a package for non-parametric nucleosome positioning. Bioinformatics. 2011;27:2149–2150. PubMed

Moreno S, Klar A, Nurse P. Molecular genetic analysis of fission yeast Schizosaccharomyces pombe. Methods Enzymol. 1991;194:795–823. PubMed

Hayles J, Nurse P. Genetics of the fission yeast Schizosaccharomyces pombe. Annu. Rev. Genet. 1992;26:373–402. PubMed

Okazaki K, et al. High-frequency transformation method and library transducing vectors for cloning mammalian cDNAs by trans-complementation of Schizosaccharomyces pombe. Nucleic Acids Res. 1990;18:6485–6489. PubMed PMC

Parisis N, Metodieva G, Metodiev MV. Pseudopodial and β-arrestin-interacting proteomes from migrating breast cancer cells upon PAR2 activation. J. Proteomics. 2013;80:91–106. PubMed

Thingholm TE, Jensen ON, Larsen MR. Analytical strategies for phosphoproteomics. Proteomics. 2009;9:1451–1468. PubMed

Steger DJ, et al. DOT1L/KMT4 recruitment and H3K79 methylation are ubiquitously coupled with gene transcription in mammalian cells. Mol. Cell. Biol. 2008;28:2825–2839. PubMed PMC

Zhang Y, et al. Model-based analysis of ChIP-Seq (MACS) Genome Biol. 2008;9:R137. PubMed PMC

Shah N, et al. Tyrosine-1 of RNA polymerase II CTD controls global termination of gene transcription in mammals. Mol. Cell. 2018;69:48–61.e6. PubMed

Schindelin J, et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods. 2012;9:676–682. PubMed PMC

Perez-Burgos L, et al. Generation and characterization of methyl-lysine histone antibodies. Meth. Enzymol. 2004;376:234–254. PubMed

Sirbu BM, Couch FB, Cortez D. Monitoring the spatiotemporal dynamics of proteins at replication forks and in assembled chromatin using isolation of proteins on nascent DNA. Nat. Protoc. 2012;7:594–605. PubMed PMC

Davey CA, Sargent DF, Luger K, Maeder AW, Richmond TJ. Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution. J. Mol. Biol. 2002;319:1097–1113. PubMed

Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics. J. Mol. Graph. 1996;14:33–38. PubMed

UniProt Consortium, T. UniProt: the universal protein knowledgebase. Nucleic Acids Res. 2018;46:2699. PubMed PMC

Collepardo-Guevara R, et al. Chromatin unfolding by epigenetic modifications explained by dramatic impairment of internucleosome interactions: a multiscale computational study. J. Am. Chem. Soc. 2015;137:10205–10215. PubMed PMC

Dans PD, et al. Long-timescale dynamics of the Drew-Dickerson dodecamer. Nucleic Acids Res. 2016;44:4052–4066. PubMed PMC

Pérez A, Luque FJ, Orozco M. Dynamics of B-DNA on the microsecond time scale. J. Am. Chem. Soc. 2007;129:14739–14745. PubMed

Hornak V, et al. Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins. 2006;65:712–725. PubMed PMC

Homeyer N, Horn AHC, Lanig H, Sticht H. AMBER force-field parameters for phosphorylated amino acids in different protonation states: phosphoserine, phosphothreonine, phosphotyrosine, and phosphohistidine. J. Mol. Model. 2006;12:281–289. PubMed

Steinbrecher T, Latzer J, Case DA. Revised AMBER parameters for bioorganic phosphates. J. Chem. Theory Comput. 2012;8:4405–4412. PubMed PMC

Ivani I, et al. Parmbsc1: a refined force field for DNA simulations. Nat. Methods. 2016;13:55–58. PubMed PMC

Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 1983;79:926–935.

Smith DE, Dang LX. Computer simulations of NaCl association in polarizable water. J. Chem. Phys. 1994;100:3757–3766.

Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 1984;81:3684–3690.

Ryckaert J-P, Ciccotti G, Berendsen HJC. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 1977;23:327–341.

Hopkins CW, Le Grand S, Walker RC, Roitberg AE. Long-time-step molecular dynamics through hydrogen mass repartitioning. J. Chem. Theory Comput. 2015;11:1864–1874. PubMed

Darden T, York D, Pedersen L. Particle mesh Ewald: an N⋅log(N) method for Ewald sums in large systems. J. Chem. Phys. 1993;98:10089–10092.

Salomon-Ferrer R, Götz AW, Poole D, Le Grand S, Walker RC. Routine microsecond molecular dynamics simulations with AMBER on GPUs. 2. Explicit solvent particle mesh ewald. J. Chem. Theory Comput. 2013;9:3878–3888. PubMed

The amber molecular dynamics package. http://ambermd.org/.

Roe DR, Cheatham TE. PTRAJ and CPPTRAJ: software for processing and analysis of molecular dynamics trajectory data. J. Chem. Theory Comput. 2013;9:3084–3095. PubMed

Lavery R, Moakher M, Maddocks JH, Petkeviciute D, Zakrzewska K. Conformational analysis of nucleic acids revisited: curves+ Nucleic Acids Res. 2009;37:5917–5929. PubMed PMC

Vizcaíno JA, et al. 2016 update of the PRIDE database and its related tools. Nucleic Acids Res. 2016;44:D447–D456. PubMed PMC