1
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Watson M, Sabirova D, Hardy MC, Pan Y, Carpentier DCJ, Yates H, Wright CJ, Chan WH, Destan E, Stott K. A DNA condensation code for linker histones. Proc Natl Acad Sci U S A 2024; 121:e2409167121. [PMID: 39116133 DOI: 10.1073/pnas.2409167121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 06/27/2024] [Indexed: 08/10/2024] Open
Abstract
Linker histones play an essential role in chromatin packaging by facilitating compaction of the 11-nm fiber of nucleosomal "beads on a string." The result is a heterogeneous condensed state with local properties that range from dynamic, irregular, and liquid-like to stable and regular structures (the 30-nm fiber), which in turn impact chromatin-dependent activities at a fundamental level. The properties of the condensed state depend on the type of linker histone, particularly on the highly disordered C-terminal tail, which is the most variable region of the protein, both between species, and within the various subtypes and cell-type specific variants of a given organism. We have developed an in vitro model system comprising linker histone tail and linker DNA, which although very minimal, displays surprisingly complex behavior, and is sufficient to model the known states of linker histone-condensed chromatin: disordered "fuzzy" complexes ("open" chromatin), dense liquid-like assemblies (dynamic condensates), and higher-order structures (organized 30-nm fibers). A crucial advantage of such a simple model is that it allows the study of the various condensed states by NMR, circular dichroism, and scattering methods. Moreover, it allows capture of the thermodynamics underpinning the transitions between states through calorimetry. We have leveraged this to rationalize the distinct condensing properties of linker histone subtypes and variants across species that are encoded by the amino acid content of their C-terminal tails. Three properties emerge as key to defining the condensed state: charge density, lysine/arginine ratio, and proline-free regions, and we evaluate each separately using a strategic mutagenesis approach.
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Affiliation(s)
- Matthew Watson
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Dilyara Sabirova
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Megan C Hardy
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Yuming Pan
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - David C J Carpentier
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Henry Yates
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Charlotte J Wright
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - W H Chan
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Ebru Destan
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Katherine Stott
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
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2
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Skowicki M, Tarvirdipour S, Kraus M, Schoenenberger CA, Palivan CG. Nanoassemblies designed for efficient nuclear targeting. Adv Drug Deliv Rev 2024; 211:115354. [PMID: 38857762 DOI: 10.1016/j.addr.2024.115354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/23/2024] [Accepted: 06/04/2024] [Indexed: 06/12/2024]
Abstract
One of the key aspects of coping efficiently with complex pathological conditions is delivering the desired therapeutic compounds with precision in both space and time. Therefore, the focus on nuclear-targeted delivery systems has emerged as a promising strategy with high potential, particularly in gene therapy and cancer treatment. Here, we explore the design of supramolecular nanoassemblies as vehicles to deliver specific compounds to the nucleus, with the special focus on polymer and peptide-based carriers that expose nuclear localization signals. Such nanoassemblies aim at maximizing the concentration of genetic and therapeutic agents within the nucleus, thereby optimizing treatment outcomes while minimizing off-target effects. A complex scenario of conditions, including cellular uptake, endosomal escape, and nuclear translocation, requires fine tuning of the nanocarriers' properties. First, we introduce the principles of nuclear import and the role of nuclear pore complexes that reveal strategies for targeting nanosystems to the nucleus. Then, we provide an overview of cargoes that rely on nuclear localization for optimal activity as their integrity and accumulation are crucial parameters to consider when designing a suitable delivery system. Considering that they are in their early stages of research, we present various cargo-loaded peptide- and polymer nanoassemblies that promote nuclear targeting, emphasizing their potential to enhance therapeutic response. Finally, we briefly discuss further advancements for more precise and effective nuclear delivery.
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Affiliation(s)
- Michal Skowicki
- Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 22, 4058 Basel, Switzerland; NCCR-Molecular Systems Engineering, BPR 1095, Mattenstrasse 24a, 4058 Basel, Switzerland
| | - Shabnam Tarvirdipour
- Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 22, 4058 Basel, Switzerland
| | - Manuel Kraus
- Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 22, 4058 Basel, Switzerland
| | - Cora-Ann Schoenenberger
- Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 22, 4058 Basel, Switzerland; NCCR-Molecular Systems Engineering, BPR 1095, Mattenstrasse 24a, 4058 Basel, Switzerland.
| | - Cornelia G Palivan
- Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 22, 4058 Basel, Switzerland; NCCR-Molecular Systems Engineering, BPR 1095, Mattenstrasse 24a, 4058 Basel, Switzerland.
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3
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Gien H, Morse M, McCauley MJ, Rouzina I, Gorelick RJ, Williams MC. Cationic Residues of the HIV-1 Nucleocapsid Protein Enable DNA Condensation to Maintain Viral Core Particle Stability during Reverse Transcription. Viruses 2024; 16:872. [PMID: 38932164 PMCID: PMC11209390 DOI: 10.3390/v16060872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 04/30/2024] [Accepted: 05/23/2024] [Indexed: 06/28/2024] Open
Abstract
The HIV-1 nucleocapsid protein (NC) is a multifunctional viral protein necessary for HIV-1 replication. Recent studies have demonstrated that reverse transcription (RT) completes in the intact viral capsid, and the timing of RT and uncoating are correlated. How the small viral core stably contains the ~10 kbp double stranded (ds) DNA product of RT, and the role of NC in this process, are not well understood. We showed previously that NC binds and saturates dsDNA in a non-specific electrostatic binding mode that triggers uniform DNA self-attraction, condensing dsDNA into a tight globule against extending forces up to 10 pN. In this study, we use optical tweezers and atomic force microscopy to characterize the role of NC's basic residues in dsDNA condensation. Basic residue mutations of NC lead to defective interaction with the dsDNA substrate, with the constant force plateau condensation observed with wild-type (WT) NC missing or diminished. These results suggest that NC's high positive charge is essential to its dsDNA condensing activity, and electrostatic interactions involving NC's basic residues are responsible in large part for the conformation, size, and stability of the dsDNA-protein complex inside the viral core. We observe DNA re-solubilization and charge reversal in the presence of excess NC, consistent with the electrostatic nature of NC-induced DNA condensation. Previous studies of HIV-1 replication in the presence of the same cationic residue mutations in NC showed significant defects in both single- and multiple-round viral infectivity. Although NC participates in many stages of viral replication, our results are consistent with the hypothesis that cationic residue mutations inhibit genomic DNA condensation, resulting in increased premature capsid uncoating and contributing to viral replication defects.
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Affiliation(s)
- Helena Gien
- Department of Physics, Northeastern University, Boston, MA 02115, USA; (H.G.); (M.M.); (M.J.M.)
| | - Michael Morse
- Department of Physics, Northeastern University, Boston, MA 02115, USA; (H.G.); (M.M.); (M.J.M.)
| | - Micah J. McCauley
- Department of Physics, Northeastern University, Boston, MA 02115, USA; (H.G.); (M.M.); (M.J.M.)
| | - Ioulia Rouzina
- Department of Chemistry and Biochemistry, Center for Retroviral Research and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA;
| | - Robert J. Gorelick
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA;
| | - Mark C. Williams
- Department of Physics, Northeastern University, Boston, MA 02115, USA; (H.G.); (M.M.); (M.J.M.)
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4
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Oikeh E, Ziebarth J, Dinar MAM, Kirchhoff D, Aronova A, Dziubla TD, Wang Y, DeRouchey JE. DNA Packaging and Polycation Length Determine DNA Susceptibility to Free Radical Damage in Condensed DNA. J Phys Chem B 2024; 128:3329-3339. [PMID: 38557033 DOI: 10.1021/acs.jpcb.3c06116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
In nature, DNA exists primarily in a highly compacted form. The compaction of DNA in vivo is mediated by cationic proteins: histones in somatic nuclei and protamines in sperm chromatin. The extreme, nearly crystalline packaging of DNA by protamines in spermatozoa is thought to be essential for both efficient genetic delivery as well as DNA protection against damage by mutagens and oxidative species. The protective role of protamines is required in sperm, as they are sensitive to ROS damage due to the progressive loss of DNA repair mechanisms during maturation. The degree to which DNA packaging directly relates to DNA protection in the condensed state, however, is poorly understood. Here, we utilized different polycation condensing agents to achieve varying DNA packaging densities and quantify DNA damage by free radical oxidation within the condensates. Although we see that tighter DNA packaging generally leads to better protection, the length of the polycation also plays a significant role. Molecular dynamics simulations suggest that longer polyarginine chains offer increased protection by occupying more space on the DNA surface and forming more stable interactions. Taken together, our results suggest a complex interplay among polycation properties, DNA packaging density, and DNA protection against free radical damage within condensed states.
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Affiliation(s)
- Ehigbai Oikeh
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Jesse Ziebarth
- Department of Chemistry, University of Memphis, Memphis, Tennessee 38152, United States
| | - Md Abu Monsur Dinar
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Daniel Kirchhoff
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Anastasiia Aronova
- Chemical and Materials Engineering Department, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Thomas D Dziubla
- Chemical and Materials Engineering Department, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Yongmei Wang
- Department of Chemistry, University of Memphis, Memphis, Tennessee 38152, United States
| | - Jason E DeRouchey
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
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5
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Xie S, Yue C, Ye S, Li Z. Probing the hierarchical dynamics of DNA-sperm nuclear transition protein complexes through fuzzy interaction and mesoscale condensation. Phys Chem Chem Phys 2024; 26:10408-10418. [PMID: 38502252 DOI: 10.1039/d3cp05957j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Nuclear transition protein TNP1 is a crucial player mediating histone-protamine exchange in condensing spermatids. A unique combination of intrinsic disorder and multivalent properties turns TNP1 into an ideal agent for orchestrating the formation of versatile TNP-DNA assemblies. Despite its significance, the physicochemical property and the molecular mechanism followed by TNP1 for histone replacement and DNA condensation are still poorly understood. This study reports the first-time in vitro expression and purification of human TNP1 and investigates the hierarchical dynamics of TNP1-DNA interaction using a combination of computational simulations, biochemical assays, fluorescence imaging, and atomic force microscopy. We explored three crucial facets of TNP1-DNA interactions. Initially, we delve into the molecular binding process that entails fuzzy interactions between TNP1 and DNA at the atomistic scale. Subsequently, we analyze how TNP1 binding affects the electrostatic and mechanical characteristics of DNA and influences its morphology. Finally, we study the biomolecular condensation of TNP1-DNA when subjected to high concentrations. The findings of our study set the foundation for comprehending the potential involvement of TNP1 in histone replacement and DNA condensation in spermatogenesis.
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Affiliation(s)
- Shangqiang Xie
- School of Life Science, Tianjin University, 92 Weijin Road, Tianjin 300072, China.
| | - Congran Yue
- School of Life Science, Tianjin University, 92 Weijin Road, Tianjin 300072, China.
| | - Sheng Ye
- School of Life Science, Tianjin University, 92 Weijin Road, Tianjin 300072, China.
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin University, 92 Weijin Road, Tianjin 300072, China
| | - Zhenlu Li
- School of Life Science, Tianjin University, 92 Weijin Road, Tianjin 300072, China.
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin University, 92 Weijin Road, Tianjin 300072, China
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6
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Franck CO, Bistrovic Popov A, Ahmed I, Hewitt RE, Franslau L, Tyagi P, Fruk L. A catch-and-release nano-based gene delivery system. NANOSCALE HORIZONS 2023; 8:1588-1594. [PMID: 37691551 DOI: 10.1039/d3nh00269a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
The design of nanomaterial-based nucleic acid formulations is one of the biggest endeavours in the search for clinically applicable gene delivery systems. Biopolymers represent a promising subclass of gene carriers due to their physicochemical properties, biodegradability and biocompatibility. By modifying melanin-like polydopamine nanoparticles with poly-L-arginine and poly-L-histidine blends, we obtained a novel catch-and-release gene delivery system for efficient trafficking of pDNA to human cells. A synergistic interplay of nanoparticle-bound poly-L-arginine and poly-L-histidine was observed and evaluated for pDNA binding affinity, cell viability, gene release and transfection. Although the functionalisation with poly-L-arginine was crucial for pDNA binding, the resulting nanocarriers failed to release pDNA intracellularly, resulting in limited protein expression. However, optimal pDNA release was achieved through the co-formulation with poly-L-histidine, essential for pDNA release. This effect enabled the design of gene delivery systems, which were comparable to Lipofectamine in terms of transfection efficacy and the catch-and-release surface modification strategy can be translated to other nanocarriers and surfaces.
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Affiliation(s)
- Christoph O Franck
- BioNano Engineering Lab, Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, UK.
| | - Andrea Bistrovic Popov
- BioNano Engineering Lab, Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, UK.
| | - Ishtiaq Ahmed
- BioNano Engineering Lab, Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, UK.
| | - Rachel E Hewitt
- Department of Veterinary Medicine, University of Cambridge, Madingley Rd, Cambridge CB3 0ES, UK
| | - Luise Franslau
- Institut für Physikalische Chemie, Georg-August-Universität Göttingen, Tammanstraße 6, Göttingen 37077, Germany
| | - Puneet Tyagi
- AstraZeneca, One MedImmune Way, Gaithersburg, MD 20878, USA
| | - Ljiljana Fruk
- BioNano Engineering Lab, Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, UK.
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7
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Jennings CE, Zoss CJ, Morrison EA. Arginine anchor points govern H3 tail dynamics. Front Mol Biosci 2023; 10:1150400. [PMID: 37261328 PMCID: PMC10228543 DOI: 10.3389/fmolb.2023.1150400] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 04/11/2023] [Indexed: 06/02/2023] Open
Abstract
Chromatin is dynamically reorganized spatially and temporally, and the post-translational modification of histones is a key component of this regulation. The basic subunit of chromatin is the nucleosome core particle, consisting of two copies each of the histones H2A, H2B, H3, and H4 around which ∼147 base pairs of DNA wrap. The intrinsically disordered histone termini, or tails, protrude from the core and are heavily post-translationally modified. Previous studies have shown that the histone tails exist in dynamic ensembles of DNA-bound states within the nucleosome. Histone tail interactions with DNA are involved in nucleosome conformation and chromatin organization. Charge-modulating histone post-translational modifications (PTMs) are poised to perturb the dynamic interactions between histone tails and DNA. Arginine side chains form favorable interactions with DNA and are sites of charge-modulating PTMs such as citrullination. Our current focus is on the H3 tail, the longest histone tail. Four arginine residues are relatively evenly spaced along the H3 tail sequence, suggesting multivalent interactions with DNA poised for regulation by PTMs. In this study, we use NMR nuclear spin relaxation experiments to investigate the contribution of arginine residues to H3 tail dynamics within the nucleosome core particle. By neutralizing arginine via mutation to glutamine, we begin to work towards a comprehensive understanding of the contribution of individual residues to H3 tail dynamics. We find that neutralization of arginine residues results in increased regional mobility of the H3 tails, with implications for understanding the direct effects of arginine citrullination. Altogether, these studies support a role for dynamics within the histone language and emphasize the importance of charge-modulating histone PTMs in regulating chromatin dynamics, starting at the level of the basic subunit of chromatin.
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Affiliation(s)
- Christine E. Jennings
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Casey J. Zoss
- Medical Scientist Training Program, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Emma A. Morrison
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, United States
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8
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Kench T, Rakers V, Bouzada D, Gomez-González J, Robinson J, Kuimova MK, Vázquez López M, Vázquez ME, Vilar R. Dimeric Metal-Salphen Complexes Which Target Multimeric G-Quadruplex DNA. Bioconjug Chem 2023; 34:911-921. [PMID: 37119235 DOI: 10.1021/acs.bioconjchem.3c00114] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
G-Quadruplex DNA structures have attracted increasing attention due to their biological roles and potential as targets for the development of new drugs. While most guanine-rich sequences in the genome have the potential to form monomeric G-quadruplexes, certain sequences have enough guanine-tracks to give rise to multimeric quadruplexes. One of these sequences is the human telomere where tandem repeats of TTAGGG can lead to the formation of two or more adjacent G-quadruplexes. Herein we report on the modular synthesis via click chemistry of dimeric metal-salphen complexes (with NiII and PtII) bridged by either polyether or peptide linkers. We show by circular dichroism (CD) spectroscopy that they generally have higher selectivity for dimeric vs monomeric G-quadruplexes. The emissive properties of the PtII-salphen dimeric complexes have been used to study their interactions with monomeric and dimeric G-quadruplexes in vitro as well as to study their cellular uptake and localization.
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Affiliation(s)
- Timothy Kench
- Department of Chemistry, Imperial College London, White City Campus, 82 Wood Lane, London W12 0BZ, United Kingdom
| | - Viktoria Rakers
- Department of Chemistry, Imperial College London, White City Campus, 82 Wood Lane, London W12 0BZ, United Kingdom
| | - David Bouzada
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Jacobo Gomez-González
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Jenna Robinson
- Department of Chemistry, Imperial College London, White City Campus, 82 Wood Lane, London W12 0BZ, United Kingdom
| | - Marina K Kuimova
- Department of Chemistry, Imperial College London, White City Campus, 82 Wood Lane, London W12 0BZ, United Kingdom
| | - Miguel Vázquez López
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Inorgánica, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - M Eugenio Vázquez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Ramon Vilar
- Department of Chemistry, Imperial College London, White City Campus, 82 Wood Lane, London W12 0BZ, United Kingdom
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9
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Gupta S, Aggarwal S, Munde M. New Insights into the Role of Ligand-Binding Modes in GC-DNA Condensation through Thermodynamic and Spectroscopic Studies. ACS OMEGA 2023; 8:4554-4565. [PMID: 36777612 PMCID: PMC9909821 DOI: 10.1021/acsomega.2c01557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 09/20/2022] [Indexed: 06/18/2023]
Abstract
In biological systems, the unprompted assembly of DNA molecules by cationic ligands into condensed structures is ubiquitous. The ability of ligands to provoke DNA packaging is crucial to the molecular organization and functional control of DNA, yet their underlined physical roles have remained elusive. Here, we have examined the DNA condensation mechanism of four cationic ligands, including their primary DNA-binding modes through extensive biophysical studies. We observed contrasting changes for these ligands binding to poly[dGdC]:poly[dGdC] (GC-DNA) and poly[dAdT]:poly[dAdT] (AT-DNA). Based on a CD spectroscopic study, it was confirmed that only GC-DNA undergoes B- to Ψ-type DNA transformation in the presence of ligands. In the fluorescence displacement assay (FDA), the ability of ligands to displace GC-DNA-bound EtBr follows the order: protamine21+ > cohex3+ > Ni2+ > spermine4+, which indicates that there is no direct correlation between the ligand charge and its ability to displace the drug from the DNA, indicating that GC-DNA condensation is not just influenced by electrostatic interaction but ligand-specific interactions may also have played a crucial role. Furthermore, the detailed ITC-binding studies suggested that DNA-ligand interactions are generally driven by unfavorable enthalpy and favorable entropy. The correlations from various studies insinuate that cationic ligands show major groove binding as one of the preferred binding modes during GC-DNA condensation.
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Affiliation(s)
- Sakshi Gupta
- School
of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
- Department
of Applied Science, The NorthCap University, Sector 23-A, Gurgaon, Haryana 122017, India
| | - Soumya Aggarwal
- School
of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Manoj Munde
- School
of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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10
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Mondal M, Gao YQ. Sequence‐dependent clustering properties of nucleotides fragments in an ionic solution. J CHIN CHEM SOC-TAIP 2023. [DOI: 10.1002/jccs.202200425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Manas Mondal
- Institute of Systems and Physical Biology Shenzhen Bay Laboratory Shenzhen China
| | - Yi Qin Gao
- Institute of Systems and Physical Biology Shenzhen Bay Laboratory Shenzhen China
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering Peking University Beijing China
- Biomedical Pioneering Innovation Center Peking University Beijing China
- Beijing Advanced Innovation Center for Genomics Peking University Beijing China
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11
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Remodeling of algal photosystem I through phosphorylation. Biosci Rep 2023; 43:232211. [PMID: 36477263 PMCID: PMC9874419 DOI: 10.1042/bsr20220369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/29/2022] [Accepted: 12/07/2022] [Indexed: 12/12/2022] Open
Abstract
Photosystem I (PSI) with its associated light-harvesting system is the most important generator of reducing power in photosynthesis. The PSI core complex is highly conserved, whereas peripheral subunits as well as light-harvesting proteins (LHCI) reveal a dynamic plasticity. Moreover, in green alga, PSI-LHCI complexes are found as monomers, dimers, and state transition complexes, where two LHCII trimers are associated. Herein, we show light-dependent phosphorylation of PSI subunits PsaG and PsaH as well as Lhca6. Potential consequences of the dynamic phosphorylation of PsaG and PsaH are structurally analyzed and discussed in regard to the formation of the monomeric, dimeric, and LHCII-associated PSI-LHCI complexes.
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12
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Egli M, Zhang S. Ned Seeman and the prediction of amino acid-basepair motifs mediating protein-nucleic acid recognition. Biophys J 2022; 121:4777-4787. [PMID: 35711143 PMCID: PMC9808504 DOI: 10.1016/j.bpj.2022.06.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/04/2022] [Accepted: 06/10/2022] [Indexed: 01/07/2023] Open
Abstract
Fifty years ago, the first atomic-resolution structure of a nucleic acid double helix, the mini-duplex (ApU)2, revealed details of basepair geometry, stacking, sugar conformation, and backbone torsion angles, thereby superseding earlier models based on x-ray fiber diffraction, including the original DNA double helix proposed by Watson and Crick. Just 3 years later, in 1976, Ned Seeman, John Rosenberg, and Alex Rich leapt from their structures of mini-duplexes and H-bonding motifs between bases in small-molecule structures and transfer RNA to predicting how proteins could sequence specifically recognize double helix nucleic acids. They proposed interactions between amino acid side chains and nucleobases mediated by two hydrogen bonds in the major or minor grooves. One of these, the arginine-guanine pair, emerged as the most favored amino acid-base interaction in experimental structures of protein-nucleic acid complexes determined since 1986. In this brief review we revisit the pioneering work by Seeman et al. and discuss the importance of the arginine-guanine pairing motif.
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Affiliation(s)
- Martin Egli
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, Tennessee.
| | - Shuguang Zhang
- Media Lab, Massachusetts Institute of Technology, Cambridge, Massachusetts
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13
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Chhetri KB, Jang YH, Lansac Y, Maiti PK. Effect of phosphorylation of protamine-like cationic peptide on the binding affinity to DNA. Biophys J 2022; 121:4830-4839. [PMID: 36168289 PMCID: PMC9808561 DOI: 10.1016/j.bpj.2022.09.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/10/2022] [Accepted: 09/21/2022] [Indexed: 01/07/2023] Open
Abstract
Protamines are more arginine-rich and more basic than histones and are responsible for providing a highly compacted shape to the sperm heads in the testis. Phosphorylation and dephosphorylation are two events that occur in the late phase of spermatogenesis before the maturation of sperms. In this work, we have studied the effect of phosphorylation of protamine-like cationic peptides using all-atom molecular dynamics simulations. Through thermodynamic analyses, we found that phosphorylation reduces the binding efficiency of such cationic peptides on DNA duplexes. Peptide phosphorylation leads to a less efficient DNA condensation, due to a competition between DNA-peptide and peptide-peptide interactions. We hypothesize that the decrease of peptide bonds between DNA together with peptide self-assembly might allow an optimal re-organization of chromatin and an efficient condensation through subsequent peptide dephosphorylation. Based on the globular and compact conformations of phosphorylated peptides mediated by arginine-phosphoserine H-bonding, we furthermore postulate that phosphorylated protamines could more easily intrude into chromatin and participate to histone release through disruption of histone-histone and histone-DNA binding during spermatogenesis.
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Affiliation(s)
- Khadka B Chhetri
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India; Department of Physics, Prithvinarayan Campus, Tribhuvan University, Pokhara, Nepal
| | - Yun Hee Jang
- Department of Energy Science and Engineering, DGIST, Daegu 42988, Korea; GREMAN, CNRS UMR 7347, Université de Tours, 37200 Tours, France.
| | - Yves Lansac
- GREMAN, CNRS UMR 7347, Université de Tours, 37200 Tours, France; Laboratoire de Physique des Solides, CNRS UMR 8502, Université Paris Saclay, Orsay, France.
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
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14
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A Biophysical Study of DNA Condensation Mediated by Histones and Protamines. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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15
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Islam R, Zhao L, Wang Y, Lu-Yao G, Liu LZ. Epigenetic Dysregulations in Arsenic-Induced Carcinogenesis. Cancers (Basel) 2022; 14:cancers14184502. [PMID: 36139662 PMCID: PMC9496897 DOI: 10.3390/cancers14184502] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/13/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
Arsenic is a crucial environmental metalloid whose high toxicity levels negatively impact human health. It poses significant health concerns to millions of people in developed and developing countries such as the USA, Canada, Bangladesh, India, China, and Mexico by enhancing sensitivity to various types of diseases, including cancers. However, how arsenic causes changes in gene expression that results in heinous conditions remains elusive. One of the proposed essential mechanisms that still has seen limited research with regard to causing disease upon arsenic exposure is the dysregulation of epigenetic components. In this review, we have extensively summarized current discoveries in arsenic-induced epigenetic modifications in carcinogenesis and angiogenesis. Importantly, we highlight the possible mechanisms underlying epigenetic reprogramming through arsenic exposure that cause changes in cell signaling and dysfunctions of different epigenetic elements.
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16
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D’haese S, Laeremans T, den Roover S, Allard SD, Vanham G, Aerts JL. Efficient Induction of Antigen-Specific CD8+ T-Cell Responses by Cationic Peptide-Based mRNA Nanoparticles. Pharmaceutics 2022; 14:pharmaceutics14071387. [PMID: 35890284 PMCID: PMC9321026 DOI: 10.3390/pharmaceutics14071387] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 06/24/2022] [Accepted: 06/28/2022] [Indexed: 11/16/2022] Open
Abstract
A major determinant for the success of mRNA-based vaccines is the composition of the nanoparticles (NPs) used for formulation and delivery. Cationic peptides represent interesting candidate carriers for mRNA, since they have been shown to efficiently deliver nucleic acids to eukaryotic cells. mRNA NPs based on arginine-rich peptides have previously been demonstrated to induce potent antigen-specific CD8+ T-cell responses. We therefore compared the histidine-rich amphipathic peptide LAH4-L1 (KKALLAHALHLLALLALHLAHALKKA) to the fully substituted arginine variant (LAH4-L1R) for their capacity to formulate mRNA and transfect dendritic cells (DCs). Although both peptides encapsulated mRNA to the same extent, and showed excellent uptake in DCs, the gene expression level was significantly higher for LAH4-L1. The LAH4-L1–mRNA NPs also resulted in enhanced antigen presentation in the context of MHC I compared to LAH4-L1R in primary murine CD103+ DCs. Both peptides induced DC maturation and inflammasome activation. Subsequent ex vivo stimulation of OT-I splenocytes with transfected CD103+ DCs resulted in a high proportion of polyfunctional CD8+ T cells for both peptides. In addition, in vivo immunization with LAH4-L1 or LAH4-L1R–mRNA NPs resulted in proliferation of antigen-specific T cells. In conclusion, although LAH4-L1 outperformed LAH4-L1R in terms of transfection efficiency, the immune stimulation ex vivo and in vivo was equally efficient.
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Affiliation(s)
- Sigrid D’haese
- Laboratory for Neuro-Aging and Viro-Immunotherapy (NAVI), Faculty of Pharmacy and Medicine, Vrije Universiteit Brussel, 1090 Brussels, Belgium; (S.D.); (T.L.); (S.d.R.)
| | - Thessa Laeremans
- Laboratory for Neuro-Aging and Viro-Immunotherapy (NAVI), Faculty of Pharmacy and Medicine, Vrije Universiteit Brussel, 1090 Brussels, Belgium; (S.D.); (T.L.); (S.d.R.)
| | - Sabine den Roover
- Laboratory for Neuro-Aging and Viro-Immunotherapy (NAVI), Faculty of Pharmacy and Medicine, Vrije Universiteit Brussel, 1090 Brussels, Belgium; (S.D.); (T.L.); (S.d.R.)
| | - Sabine D. Allard
- Department of Internal Medicine (IRG), Vrije Universiteit Brussel, Universitair Ziekenhuis Brussel, 1090 Brussels, Belgium;
| | - Guido Vanham
- Department of Virology, Institute of Tropical Medicine, University of Antwerp, 2000 Antwerp, Belgium;
| | - Joeri L. Aerts
- Laboratory for Neuro-Aging and Viro-Immunotherapy (NAVI), Faculty of Pharmacy and Medicine, Vrije Universiteit Brussel, 1090 Brussels, Belgium; (S.D.); (T.L.); (S.d.R.)
- Correspondence:
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17
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Dirisala A, Uchida S, Li J, Van Guyse JFR, Hayashi K, Vummaleti SVC, Kaur S, Mochida Y, Fukushima S, Kataoka K. Effective mRNA Protection by Poly(l-ornithine) Synergizes with Endosomal Escape Functionality of a Charge-Conversion Polymer toward Maximizing mRNA Introduction Efficiency. Macromol Rapid Commun 2022; 43:e2100754. [PMID: 35286740 DOI: 10.1002/marc.202100754] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 02/12/2022] [Indexed: 12/13/2022]
Abstract
For efficient delivery of messenger (m)RNA, delivery carriers need two major functions: protecting mRNA from nucleases and translocating mRNA from endolysosomes to the cytoplasm. Herein, these two complementary functionalities are integrated into a single polyplex by fine-tuning the catiomer chemical structure and incorporating the endosomal escape modality. The effect of the methylene spacer length on the catiomer side chain is evaluated by comparing poly(l-lysine) (PLL) with a tetramethylene spacer and poly(L-ornithine) (PLO) with a trimethylene spacer. Noteworthily, the nuclease stability of the mRNA/catiomer polyplexes is largely affected by the difference in one methylene group, with PLO/mRNA polyplex showing enhanced stability compared to PLL/mRNA polyplex. To introduce the endosomal escape function, the PLO/mRNA polyplex is wrapped with a charge-conversion polymer (CCP), which is negatively charged at extracellular pH but turns positive at endosomal acidic pH to disrupt the endosomal membrane. Compared to the parent PLO/mRNA polyplex, CCP facilitated the endosomal escape of the polyplex in cultured cells to improve the protein expression efficiency from mRNA by approximately 80-fold. Collectively, this system synergizes the protective effect of PLO against nucleases and the endosomal escape capability of CCP in mRNA delivery.
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Affiliation(s)
- Anjaneyulu Dirisala
- Innovation Center of NanoMedicine (iCONM), Kanagawa Institute of Industrial Promotion, 3-25-14 Tonomachi, Kawasaki-ku, Kawasaki, 210-0821, Japan
| | - Satoshi Uchida
- Innovation Center of NanoMedicine (iCONM), Kanagawa Institute of Industrial Promotion, 3-25-14 Tonomachi, Kawasaki-ku, Kawasaki, 210-0821, Japan.,Medical Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto, 606-0823, Japan
| | - Junjie Li
- Innovation Center of NanoMedicine (iCONM), Kanagawa Institute of Industrial Promotion, 3-25-14 Tonomachi, Kawasaki-ku, Kawasaki, 210-0821, Japan
| | - Joachim F R Van Guyse
- Innovation Center of NanoMedicine (iCONM), Kanagawa Institute of Industrial Promotion, 3-25-14 Tonomachi, Kawasaki-ku, Kawasaki, 210-0821, Japan
| | - Kotaro Hayashi
- Innovation Center of NanoMedicine (iCONM), Kanagawa Institute of Industrial Promotion, 3-25-14 Tonomachi, Kawasaki-ku, Kawasaki, 210-0821, Japan
| | - Sai V C Vummaleti
- Institute of High Performance Computing Agency for Science, Technology and Research, 1 Fusionopolis Way, 16-6 Connexis, 138632, Singapore
| | - Sarandeep Kaur
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, Johannisallee 29, Leipzig, 04103, Germany
| | - Yuki Mochida
- Innovation Center of NanoMedicine (iCONM), Kanagawa Institute of Industrial Promotion, 3-25-14 Tonomachi, Kawasaki-ku, Kawasaki, 210-0821, Japan
| | - Shigeto Fukushima
- Innovation Center of NanoMedicine (iCONM), Kanagawa Institute of Industrial Promotion, 3-25-14 Tonomachi, Kawasaki-ku, Kawasaki, 210-0821, Japan
| | - Kazunori Kataoka
- Innovation Center of NanoMedicine (iCONM), Kanagawa Institute of Industrial Promotion, 3-25-14 Tonomachi, Kawasaki-ku, Kawasaki, 210-0821, Japan
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18
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Chakraborty A, Ghosh S, Biswas B, Pramanik S, Nriagu J, Bhowmick S. Epigenetic modifications from arsenic exposure: A comprehensive review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 810:151218. [PMID: 34717984 DOI: 10.1016/j.scitotenv.2021.151218] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 10/19/2021] [Accepted: 10/21/2021] [Indexed: 06/13/2023]
Abstract
Arsenic is a notorious element with the potential to harm exposed individuals in ways that include cancerous and non-cancerous health complications. Millions of people across the globe (especially in South and Southeast Asian countries including China, Vietnam, India and Bangladesh) are currently being unknowingly exposed to precarious levels of arsenic. Among the diverse effects associated with such arsenic levels of exposure is the propensity to alter the epigenome. Although a large volume of literature exists on arsenic-induced genotoxicity, cytotoxicity, and inter-individual susceptibility due to active research on these subject areas from the last millennial, it is only recently that attention has turned on the ramifications and mechanisms of arsenic-induced epigenetic changes. The present review summarizes the possible mechanisms involved in arsenic induced epigenetic alterations. It focuses on the mechanisms underlying epigenome reprogramming from arsenic exposure that result in improper cell signaling and dysfunction of various epigenetic components. The mechanistic information articulated from the review is used to propose a number of novel therapeutic strategies with a potential for ameliorating the burden of worldwide arsenic poisoning.
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Affiliation(s)
- Arijit Chakraborty
- Kolkata Zonal Center, CSIR-National Environmental Engineering Research Institute (NEERI), Kolkata, West Bengal 700107, India
| | - Soma Ghosh
- Kolkata Zonal Center, CSIR-National Environmental Engineering Research Institute (NEERI), Kolkata, West Bengal 700107, India
| | - Bratisha Biswas
- Kolkata Zonal Center, CSIR-National Environmental Engineering Research Institute (NEERI), Kolkata, West Bengal 700107, India
| | - Sreemanta Pramanik
- Kolkata Zonal Center, CSIR-National Environmental Engineering Research Institute (NEERI), Kolkata, West Bengal 700107, India
| | - Jerome Nriagu
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, 109 Observatory Street, Ann Arbor, MI 48109-2029, USA
| | - Subhamoy Bhowmick
- Kolkata Zonal Center, CSIR-National Environmental Engineering Research Institute (NEERI), Kolkata, West Bengal 700107, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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19
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Wilburn DB, Kunkel CL, Feldhoff RC, Feldhoff PW, Searle BC. Recurrent Co-Option and Recombination of Cytokine and Three Finger Proteins in Multiple Reproductive Tissues Throughout Salamander Evolution. Front Cell Dev Biol 2022; 10:828947. [PMID: 35281090 PMCID: PMC8904931 DOI: 10.3389/fcell.2022.828947] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 02/01/2022] [Indexed: 11/13/2022] Open
Abstract
Reproductive proteins evolve at unparalleled rates, resulting in tremendous diversity of both molecular composition and biochemical function between gametes of different taxonomic clades. To date, the proteomic composition of amphibian gametes is largely a molecular mystery, particularly for Urodeles (salamanders and newts) for which few genomic-scale resources exist. In this study, we provide the first detailed molecular characterization of gametes from two salamander species (Plethodon shermani and Desmognathus ocoee) that are models of reproductive behavior. Long-read PacBio transcriptome sequencing of testis and ovary of both species revealed sex-specific expression of many genes common to vertebrate gametes, including a similar expression profile to the egg coat genes of Xenopus oocytes. In contrast to broad conservation of oocyte genes, major testis transcripts included paralogs of salamander-specific courtship pheromones (PRF, PMF, and SPF) that were confirmed as major sperm proteins by mass spectrometry proteomics. Sperm-specific paralogs of PMF and SPF are likely the most abundant secreted proteins in P. shermani and D. ocoee, respectively. In contrast, sperm PRF lacks a signal peptide and may be expressed in cytoplasm. PRF pheromone genes evolved independently multiple times by repeated gene duplication of sperm PRF genes with signal peptides recovered through recombination with PMF genes. Phylogenetic analysis of courtship pheromones and their sperm paralogs support that each protein family evolved for these two reproductive contexts at distinct evolutionary time points between 17 and 360 million years ago. Our combined phylogenetic, transcriptomic and proteomic analyses of plethodontid reproductive tissues support that the recurrent co-option and recombination of TFPs and cytokine-like proteins have been a novel driving force throughout salamander evolution and reproduction.
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Affiliation(s)
- Damien B. Wilburn
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, United States
- *Correspondence: Damien B. Wilburn,
| | - Christy L. Kunkel
- Department of Biology, John Carroll University, Cleveland Heights, OH, United States
| | - Richard C. Feldhoff
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY, United States
| | - Pamela W. Feldhoff
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY, United States
| | - Brian C. Searle
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, United States
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20
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Martin B, Dans PD, Wieczór M, Villegas N, Brun-Heath I, Battistini F, Terrazas M, Orozco M. Molecular basis of Arginine and Lysine DNA sequence-dependent thermo-stability modulation. PLoS Comput Biol 2022; 18:e1009749. [PMID: 35007284 PMCID: PMC8782489 DOI: 10.1371/journal.pcbi.1009749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 01/21/2022] [Accepted: 12/13/2021] [Indexed: 11/19/2022] Open
Abstract
We have used a variety of theoretical and experimental techniques to study the role of four basic amino acids-Arginine, Lysine, Ornithine and L-2,4-Diaminobutyric acid-on the structure, flexibility and sequence-dependent stability of DNA. We found that the presence of organic ions stabilizes the duplexes and significantly reduces the difference in stability between AT- and GC-rich duplexes with respect to the control conditions. This suggests that these amino acids, ingredients of the primordial soup during abiogenesis, could have helped to equalize the stability of AT- and GC-rich DNA oligomers, facilitating a general non-catalysed self-replication of DNA. Experiments and simulations demonstrate that organic ions have an effect that goes beyond the general electrostatic screening, involving specific interactions along the grooves of the double helix. We conclude that organic ions, largely ignored in the DNA world, should be reconsidered as crucial structural elements far from mimics of small inorganic cations.
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Affiliation(s)
- Benjamin Martin
- Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, Barcelona, Spain
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Pablo D. Dans
- Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Biological Sciences, CENUR Litoral Norte, Universidad de la República (UdelaR), Salto, Uruguay
- Functional Genomics Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Milosz Wieczór
- Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Nuria Villegas
- Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Isabelle Brun-Heath
- Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Federica Battistini
- Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Montserrat Terrazas
- Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Biochemistry and Biomedicine, Faculty of Biology, University of Barcelona, Barcelona, Spain
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21
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Crystal Structure-Guided Design of Bisubstrate Inhibitors and Photoluminescent Probes for Protein Kinases of the PIM Family. Molecules 2021; 26:molecules26144353. [PMID: 34299628 PMCID: PMC8307404 DOI: 10.3390/molecules26144353] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/09/2021] [Accepted: 07/14/2021] [Indexed: 11/23/2022] Open
Abstract
We performed an X-ray crystallographic study of complexes of protein kinase PIM-1 with three inhibitors comprising an adenosine mimetic moiety, a linker, and a peptide-mimetic (d-Arg)6 fragment. Guided by the structural models, simplified chemical structures with a reduced number of polar groups and chiral centers were designed. The developed inhibitors retained low-nanomolar potency and possessed remarkable selectivity toward the PIM kinases. The new inhibitors were derivatized with biotin or fluorescent dye Cy5 and then applied for the detection of PIM kinases in biochemical solutions and in complex biological samples. The sandwich assay utilizing a PIM-2-selective detection antibody featured a low limit of quantification (44 pg of active recombinant PIM-2). Fluorescent probes were efficiently taken up by U2OS cells and showed a high extent of co-localization with PIM-1 fused with a fluorescent protein. Overall, the developed inhibitors and derivatives represent versatile chemical tools for studying PIM function in cellular systems in normal and disease physiology.
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22
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Zhou L, Li QL, Wong HM. A Novel Strategy for Caries Management: Constructing an Antibiofouling and Mineralizing Dual-Bioactive Tooth Surface. ACS APPLIED MATERIALS & INTERFACES 2021; 13:31140-31152. [PMID: 34156831 DOI: 10.1021/acsami.1c06989] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Existing single-functional agents against dental caries are inadequate in antibacterial performance or mineralization balance. This problem can be resolved through a novel strategy, namely, the construction of an antibiofouling and mineralizing dual-bioactive tooth surface by grafting a dentotropic moiety to an antimicrobial peptide. The constructed bioactive peptide can strongly adsorb onto the tooth surface and has beneficial functions in a myriad of ways. It inhibits cariogenic bacteria Streptococcus mutans adhesion, kills planktonic S. mutans, and destroys the S. mutans biofilm on the tooth surface. It also protects teeth from demineralization in acidic environments, and induces self-healing regeneration in the remineralization environment. Molecular dynamics simulations elucidate the main adsorption mechanism that the positively charged amino acid residues in the bioactive peptide bind to phosphate groups on the tooth surface, and the main mineralization mechanism that the negative charges on the outermost layer of the bioactive peptide repel acetic acid ions and attract calcium ions as nucleation sites for remineralization. This study suggests that this in-house synthesized dual-bioactive peptide is a promising functional agent to prevent dental caries, and is effective in inducing in situ self-healing remineralization for the treatment of decayed teeth.
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Affiliation(s)
- Li Zhou
- Paediatric Dentistry and Orthodontics, Faculty of Dentistry, The University of Hong Kong, 34 Hospital Road, Hong Kong SAR 999077, China
| | - Quan Li Li
- Key Lab. of Oral Diseases Research of Anhui Province, College and Hospital of Stomatology, Anhui Medical University, Hefei 230000, China
| | - Hai Ming Wong
- Paediatric Dentistry and Orthodontics, Faculty of Dentistry, The University of Hong Kong, 34 Hospital Road, Hong Kong SAR 999077, China
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23
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Lafarga V, Sirozh O, Díaz-López I, Galarreta A, Hisaoka M, Zarzuela E, Boskovic J, Jovanovic B, Fernandez-Leiro R, Muñoz J, Stoecklin G, Ventoso I, Fernandez-Capetillo O. Widespread displacement of DNA- and RNA-binding factors underlies toxicity of arginine-rich cell-penetrating peptides. EMBO J 2021; 40:e103311. [PMID: 33978236 DOI: 10.15252/embj.2019103311] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 04/13/2021] [Accepted: 04/20/2021] [Indexed: 11/09/2022] Open
Abstract
Due to their capability to transport chemicals or proteins into target cells, cell-penetrating peptides (CPPs) are being developed as therapy delivery tools. However, and despite their interesting properties, arginine-rich CPPs often show toxicity for reasons that remain poorly understood. Using a (PR)n dipeptide repeat that has been linked to amyotrophic lateral sclerosis (ALS) as a model of an arginine-rich CPP, we here show that the presence of (PR)n leads to a generalized displacement of RNA- and DNA-binding proteins from chromatin and mRNA. Accordingly, any reaction involving nucleic acids, such as RNA transcription, translation, splicing and degradation, or DNA replication and repair, is impaired by the presence of the CPPs. Interestingly, the effects of (PR)n are fully mimicked by protamine, a small arginine-rich protein that displaces histones from chromatin during spermatogenesis. We propose that widespread coating of nucleic acids and consequent displacement of RNA- and DNA-binding factors from chromatin and mRNA accounts for the toxicity of arginine-rich CPPs, including those that have been recently associated with the onset of ALS.
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Affiliation(s)
- Vanesa Lafarga
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Oleksandra Sirozh
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Irene Díaz-López
- Centro de Biología Molecular 'Severo Ochoa' (CSIC-UAM), Departamento de Biología Molecular, Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Antonio Galarreta
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Misaru Hisaoka
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.,Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Eduardo Zarzuela
- ProteoRed-ISCIII, Proteomics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Jasminka Boskovic
- Electron Microscopy Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Bogdan Jovanovic
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.,Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Rafael Fernandez-Leiro
- Genomic Integrity and Structural Biology Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Jaime Muñoz
- ProteoRed-ISCIII, Proteomics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Georg Stoecklin
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.,Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Iván Ventoso
- Centro de Biología Molecular 'Severo Ochoa' (CSIC-UAM), Departamento de Biología Molecular, Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Oscar Fernandez-Capetillo
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.,Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
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24
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Lenton S, Hervø-Hansen S, Popov AM, Tully MD, Lund M, Skepö M. Impact of Arginine-Phosphate Interactions on the Reentrant Condensation of Disordered Proteins. Biomacromolecules 2021; 22:1532-1544. [PMID: 33730849 PMCID: PMC8045028 DOI: 10.1021/acs.biomac.0c01765] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Re-entrant condensation results in the formation of a condensed protein regime between two critical ion concentrations. The process is driven by neutralization and inversion of the protein charge by oppositely charged ions. Re-entrant condensation of cationic proteins by the polyvalent anions, pyrophosphate and tripolyphosphate, has previously been observed, but not for citrate, which has similar charge and size compared to the polyphosphates. Therefore, besides electrostatic interactions, other specific interactions between the polyphosphate ions and proteins must contribute. Here, we show that additional attractive interactions between arginine and tripolyphosphate determine the re-entrant condensation and decondensation boundaries of the cationic, intrinsically disordered saliva protein, histatin 5. Furthermore, we show by small-angle X-ray scattering (SAXS) that polyvalent anions cause compaction of histatin 5, as would be expected based solely on electrostatic interactions. Hence, we conclude that arginine-phosphate-specific interactions not only regulate solution properties but also influence the conformational ensemble of histatin 5, which is shown to vary with the number of arginine residues. Together, the results presented here provide further insight into an organizational mechanism that can be used to tune protein interactions in solution of both naturally occurring and synthetic proteins.
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Affiliation(s)
- Samuel Lenton
- Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Stefan Hervø-Hansen
- Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Anton M Popov
- BM29 BIOSAXS, European Synchroton Radiation Facility, 71 avenue des Martyrs, Grenoble, Isère 38043, France
| | - Mark D Tully
- BM29 BIOSAXS, European Synchroton Radiation Facility, 71 avenue des Martyrs, Grenoble, Isère 38043, France
| | - Mikael Lund
- Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden.,LINXS-Lund Institute of Advanced Neutron and X-ray Science, Scheelevägen 19, SE-223 70 Lund, Sweden
| | - Marie Skepö
- Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden.,LINXS-Lund Institute of Advanced Neutron and X-ray Science, Scheelevägen 19, SE-223 70 Lund, Sweden
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25
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Rabdano SO, Shannon MD, Izmailov SA, Gonzalez Salguero N, Zandian M, Purusottam RN, Poirier MG, Skrynnikov NR, Jaroniec CP. Histone H4 Tails in Nucleosomes: a Fuzzy Interaction with DNA. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202012046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Sevastyan O. Rabdano
- Laboratory of Biomolecular NMR St. Petersburg State University St. Petersburg 199034 Russian Federation
| | - Matthew D. Shannon
- Department of Chemistry and Biochemistry The Ohio State University Columbus OH 43210 USA
| | - Sergei A. Izmailov
- Laboratory of Biomolecular NMR St. Petersburg State University St. Petersburg 199034 Russian Federation
| | | | - Mohamad Zandian
- Department of Chemistry and Biochemistry The Ohio State University Columbus OH 43210 USA
| | - Rudra N. Purusottam
- Department of Chemistry and Biochemistry The Ohio State University Columbus OH 43210 USA
| | | | - Nikolai R. Skrynnikov
- Laboratory of Biomolecular NMR St. Petersburg State University St. Petersburg 199034 Russian Federation
- Department of Chemistry Purdue University West Lafayette IN 47906 USA
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26
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Rabdano SO, Shannon MD, Izmailov SA, Gonzalez Salguero N, Zandian M, Purusottam RN, Poirier MG, Skrynnikov NR, Jaroniec CP. Histone H4 Tails in Nucleosomes: a Fuzzy Interaction with DNA. Angew Chem Int Ed Engl 2021; 60:6480-6487. [PMID: 33522067 DOI: 10.1002/anie.202012046] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 12/15/2020] [Indexed: 12/21/2022]
Abstract
The interaction of positively charged N-terminal histone tails with nucleosomal DNA plays an important role in chromatin assembly and regulation, modulating their susceptibility to post-translational modifications and recognition by chromatin-binding proteins. Here, we report residue-specific 15 N NMR relaxation rates for histone H4 tails in reconstituted nucleosomes. These data indicate that H4 tails are strongly dynamically disordered, albeit with reduced conformational flexibility compared to a free peptide with the same sequence. Remarkably, the NMR observables were successfully reproduced in a 2-μs MD trajectory of the nucleosome. This is an important step toward resolving an apparent inconsistency where prior simulations were generally at odds with experimental evidence on conformational dynamics of histone tails. Our findings indicate that histone H4 tails engage in a fuzzy interaction with nucleosomal DNA, underpinned by a variable pattern of short-lived salt bridges and hydrogen bonds, which persists at low ionic strength (0-100 mM NaCl).
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Affiliation(s)
- Sevastyan O Rabdano
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg, 199034, Russian Federation
| | - Matthew D Shannon
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA
| | - Sergei A Izmailov
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg, 199034, Russian Federation
| | | | - Mohamad Zandian
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA
| | - Rudra N Purusottam
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA
| | - Michael G Poirier
- Department of Physics, The Ohio State University, Columbus, OH, 43210, USA
| | - Nikolai R Skrynnikov
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg, 199034, Russian Federation.,Department of Chemistry, Purdue University, West Lafayette, IN, 47906, USA
| | - Christopher P Jaroniec
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA
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27
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Gómez-González J, Pérez Y, Sciortino G, Roldan-Martín L, Martínez-Costas J, Maréchal JD, Alfonso I, Vázquez López M, Vázquez ME. Dynamic Stereoselection of Peptide Helicates and Their Selective Labeling of DNA Replication Foci in Cells*. Angew Chem Int Ed Engl 2021; 60:8859-8866. [PMID: 33290612 DOI: 10.1002/anie.202013039] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 11/12/2020] [Indexed: 01/03/2023]
Abstract
Although largely overlooked in peptide engineering, coordination chemistry offers a new set of interactions that opens unexplored design opportunities for developing complex molecular structures. In this context, we report new artificial peptide ligands that fold into chiral helicates in the presence of labile metal ions such as FeII and CoII . Heterochiral β-turn-promoting sequences encode the stereoselective folding of the peptide ligands and define the physicochemical properties of their corresponding metal complexes. Circular dichroism and NMR spectroscopy in combination with computational methods allowed us to identify and determine the structure of two isochiral ΛΛ-helicates, folded as topological isomers. Finally, in addition to the in-vitro characterization of their selective binding to DNA three-way junctions, cell-microscopy experiments demonstrated that a rhodamine-labeled FeII helicate was internalized and selectively stains DNA replication factories in functional cells.
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Affiliation(s)
- Jacobo Gómez-González
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Spain
| | - Yolanda Pérez
- NMR Facility, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, 08034, Barcelona, Spain
| | - Giuseppe Sciortino
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Cerdanyola, Spain.,Institute of Chemical Research of Catalonia (ICIQ), Avgda. Països Catalans, 16, 43007, Tarragona, Spain
| | - Lorena Roldan-Martín
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Cerdanyola, Spain
| | - José Martínez-Costas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Bioquímica y Biología Molecular, Universidade de Santiago de Compostela, Spain
| | - Jean-Didier Maréchal
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Cerdanyola, Spain
| | - Ignacio Alfonso
- Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, 08034, Barcelona, Spain
| | - Miguel Vázquez López
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Inorgánica, Universidade de Santiago de Compostela, Spain
| | - M Eugenio Vázquez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Spain
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28
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Enukashvily NI, Dobrynin MA, Chubar AV. RNA-seeded membraneless bodies: Role of tandemly repeated RNA. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 126:151-193. [PMID: 34090614 DOI: 10.1016/bs.apcsb.2020.12.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
Abstract
Membraneless organelles (bodies, granules, etc.) are spatially distinct sub-nuclear and cytoplasmic foci involved in all the processes in a living cell, such as development, cell death, carcinogenesis, proliferation, and differentiation. Today the list of the membraneless organelles includes a wide spectrum of intranuclear and cytoplasmic bodies. Proteins with intrinsically disordered regions are the key players in the membraneless body assembly. However, recent data assume an important role of RNA molecules in the process of the liquid-liquid phase separation. High-level expression of RNA above a critical concentration threshold is mandatory to nucleate interactions with specific proteins and for seeding membraneless organelles. RNA components are considered by many authors as the principal determinants of organelle identity. Tandemly repeated (TR) DNA of big satellites (a TR family that includes centromeric and pericentromeric DNA sequences) was believed to be transcriptionally silent for a long period. Now we know about the TR transcription upregulation during gameto- and embryogenesis, carcinogenesis, stress response. In the review, we summarize the recent data about the involvement of TR RNA in the formation of nuclear membraneless granules, bodies, etc., with different functions being in some cases an initiator of the structures assembly. These RNP structures sequestrate and inactivate different proteins and transcripts. The TR induced sequestration is one of the key principles of nuclear architecture and genome functioning. Studying the role of the TR-based membraneless organelles in stress and disease will bring some new ideas for translational medicine.
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Affiliation(s)
- Natella I Enukashvily
- Institute of Cytology RAS, St. Petersburg, Russia; North-Western Medical State University named after I.I. Mechnikov, St. Petersburg, Russia.
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29
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Gómez‐González J, Pérez Y, Sciortino G, Roldan‐Martín L, Martínez‐Costas J, Maréchal J, Alfonso I, Vázquez López M, Vázquez ME. Dynamic Stereoselection of Peptide Helicates and Their Selective Labeling of DNA Replication Foci in Cells**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202013039] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Jacobo Gómez‐González
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS) Departamento de Química Orgánica Universidade de Santiago de Compostela Spain
| | - Yolanda Pérez
- NMR Facility Institute for Advanced Chemistry of Catalonia (IQAC-CSIC) Jordi Girona 18–26 08034 Barcelona Spain
| | - Giuseppe Sciortino
- Departament de Química Universitat Autònoma de Barcelona 08193 Cerdanyola Spain
- Institute of Chemical Research of Catalonia (ICIQ) Avgda. Països Catalans, 16 43007 Tarragona Spain
| | | | - José Martínez‐Costas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS) Departamento de Bioquímica y Biología Molecular Universidade de Santiago de Compostela Spain
| | | | - Ignacio Alfonso
- Department of Biological Chemistry Institute for Advanced Chemistry of Catalonia (IQAC-CSIC) Jordi Girona 18–26 08034 Barcelona Spain
| | - Miguel Vázquez López
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS) Departamento de Química Inorgánica Universidade de Santiago de Compostela Spain
| | - M. Eugenio Vázquez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS) Departamento de Química Orgánica Universidade de Santiago de Compostela Spain
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30
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Nanovesicle-Mediated Delivery Systems for CRISPR/Cas Genome Editing. Pharmaceutics 2020; 12:pharmaceutics12121233. [PMID: 33353099 PMCID: PMC7766488 DOI: 10.3390/pharmaceutics12121233] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/10/2020] [Accepted: 12/12/2020] [Indexed: 12/14/2022] Open
Abstract
Genome-editing technology has emerged as a potential tool for treating incurable diseases for which few therapeutic modalities are available. In particular, discovery of the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system together with the design of single-guide RNAs (sgRNAs) has sparked medical applications of genome editing. Despite the great promise of the CRISPR/Cas system, its clinical application is limited, in large part, by the lack of adequate delivery technology. To overcome this limitation, researchers have investigated various systems, including viral and nonviral vectors, for delivery of CRISPR/Cas and sgRNA into cells. Among nonviral delivery systems that have been studied are nanovesicles based on lipids, polymers, peptides, and extracellular vesicles. These nanovesicles have been designed to increase the delivery of CRISPR/Cas and sgRNA through endosome escape or using various stimuli such as light, pH, and environmental features. This review covers the latest research trends in nonviral, nanovesicle-based delivery systems that are being applied to genome-editing technology and suggests directions for future progress.
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31
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Johnston SD, López-Fernández C, Arroyo F, Roy R, Holt WV, Gosálvez J. Protamine composition of koala and wombat spermatozoa provides new insights into DNA stability following cryopreservation. Reprod Fertil Dev 2020; 31:1558-1566. [PMID: 31167697 DOI: 10.1071/rd18512] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 05/02/2019] [Indexed: 11/23/2022] Open
Abstract
To investigate differences in the post-thaw DNA stability of koala and wombat spermatozoa, protamine amino acid sequences were compared and it was found that there were three more arginine residues for the wombat. Koala and wombat spermatozoa, cryopreserved using identical protocols, were examined for changes in sperm DNA fragmentation (SDF) dynamics over 24h of post-thaw incubation. Following validation of a wombat sperm chromatin dispersion test, wombat DNA showed a rate of SDF that was 6-fold higher than for koala spermatozoa (P=0.038). Finally, we examined whether expected differences in chromatin compactness, associated with protamine sequence, had an effect on restriction site accessibility of sperm DNA. Thawed spermatozoa were exposed to Alu I and EcoR1 endonuclease restriction enzymes and the SDF dynamics were observed. Koala spermatozoa exposed to Alu I showed a greater rate of SDF (P=0.01), whereas wombat spermatozoa exposed to EcoR1 showed a greater rate of SDF (P=0.032). We conclude that restriction sites in these species are differentially present or exposed and potentially account for differences in SDF dynamics. Although differences in the arginine composition of protamine may explain relative differences in SDF following cryopreservation, they do not support the hypothesis that increased arginine composition increases DNA stability; rather, increased arginine composition in the wombat may reduce post-thaw chromatin swelling.
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Affiliation(s)
- S D Johnston
- School of Agriculture and Food Sciences, The University of Queensland, Gatton, Qld 4343, Australia; and Corresponding author.
| | - C López-Fernández
- Department of Biology, Autonomous University of Madrid, Cantoblanco, Madrid, 28049, Spain
| | - F Arroyo
- Department of Biology, Autonomous University of Madrid, Cantoblanco, Madrid, 28049, Spain
| | - R Roy
- Department of Biology, Autonomous University of Madrid, Cantoblanco, Madrid, 28049, Spain
| | - W V Holt
- Academic unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, S10 2TN, UK
| | - J Gosálvez
- Department of Biology, Autonomous University of Madrid, Cantoblanco, Madrid, 28049, Spain
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32
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Yoo J, Winogradoff D, Aksimentiev A. Molecular dynamics simulations of DNA-DNA and DNA-protein interactions. Curr Opin Struct Biol 2020; 64:88-96. [PMID: 32682257 DOI: 10.1016/j.sbi.2020.06.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 06/03/2020] [Accepted: 06/08/2020] [Indexed: 12/12/2022]
Abstract
The all-atom molecular dynamics method can characterize the molecular-level interactions in DNA and DNA-protein systems with unprecedented resolution. Recent advances in computational technologies have allowed the method to reveal the unbiased behavior of such systems at the microseconds time scale, whereas enhanced sampling approaches have matured enough to characterize the interaction free energy with quantitative precision. Here, we describe recent progress toward increasing the realism of such simulations by refining the accuracy of the molecular dynamics force field, and we highlight recent application of the method to systems of outstanding biological interest.
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Affiliation(s)
- Jejoong Yoo
- Department of Physics, Sungkyunkwan University, Suwon 16419, Republic of Korea; Center for Self-assembly and Complexity, Institute for Basic Science, Pohang 37673, Republic of Korea.
| | - David Winogradoff
- Department of Physics and the Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Aleksei Aksimentiev
- Department of Physics and the Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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33
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Brandariz-Nuñez A, Robinson SJ, Evilevitch A. Pressurized DNA state inside herpes capsids-A novel antiviral target. PLoS Pathog 2020; 16:e1008604. [PMID: 32702029 PMCID: PMC7377361 DOI: 10.1371/journal.ppat.1008604] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 05/05/2020] [Indexed: 01/25/2023] Open
Abstract
Drug resistance in viruses represents one of the major challenges of healthcare. As part of an effort to provide a treatment that avoids the possibility of drug resistance, we discovered a novel mechanism of action (MOA) and specific compounds to treat all nine human herpesviruses and animal herpesviruses. The novel MOA targets the pressurized genome state in a viral capsid, "turns off" capsid pressure, and blocks viral genome ejection into a cell nucleus, preventing viral replication. This work serves as a proof-of-concept to demonstrate the feasibility of a new antiviral target-suppressing pressure-driven viral genome ejection-that is likely impervious to developing drug resistance. This pivotal finding presents a platform for discovery of a new class of broad-spectrum treatments for herpesviruses and other viral infections with genome-pressure-dependent replication. A biophysical approach to antiviral treatment such as this is also a vital strategy to prevent the spread of emerging viruses where vaccine development is challenged by high mutation rates or other evasion mechanisms.
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Affiliation(s)
- Alberto Brandariz-Nuñez
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Scott J. Robinson
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Alex Evilevitch
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Experimental Medical Science, Lund University, Lund, Sweden
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34
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Viruses with different genome types adopt a similar strategy to pack nucleic acids based on positively charged protein domains. Sci Rep 2020; 10:5470. [PMID: 32214181 PMCID: PMC7096446 DOI: 10.1038/s41598-020-62328-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 03/02/2020] [Indexed: 11/17/2022] Open
Abstract
Capsid proteins often present a positively charged arginine-rich sequence at their terminal regions, which has a fundamental role in genome packaging and particle stability for some icosahedral viruses. These sequences show little to no conservation and are structurally dynamic such that they cannot be easily detected by common sequence or structure comparisons. As a result, the occurrence and distribution of positively charged domains across the viral universe are unknown. Based on the net charge calculation of discrete protein segments, we identified proteins containing amino acid stretches with a notably high net charge (Q > + 17), which are enriched in icosahedral viruses with a distinctive bias towards arginine over lysine. We used viral particle structural data to calculate the total electrostatic charge derived from the most positively charged protein segment of capsid proteins and correlated these values with genome charges arising from the phosphates of each nucleotide. We obtained a positive correlation (r = 0.91, p-value <0001) for a group of 17 viral families, corresponding to 40% of all families with icosahedral structures described to date. These data indicated that unrelated viruses with diverse genome types adopt a common underlying mechanism for capsid assembly based on R-arms.
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35
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Pelassa I, Cibelli M, Villeri V, Lilliu E, Vaglietti S, Olocco F, Ghirardi M, Montarolo PG, Corà D, Fiumara F. Compound Dynamics and Combinatorial Patterns of Amino Acid Repeats Encode a System of Evolutionary and Developmental Markers. Genome Biol Evol 2020; 11:3159-3178. [PMID: 31589292 PMCID: PMC6839033 DOI: 10.1093/gbe/evz216] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2019] [Indexed: 01/05/2023] Open
Abstract
Homopolymeric amino acid repeats (AARs) like polyalanine (polyA) and polyglutamine (polyQ) in some developmental proteins (DPs) regulate certain aspects of organismal morphology and behavior, suggesting an evolutionary role for AARs as developmental "tuning knobs." It is still unclear, however, whether these are occasional protein-specific phenomena or hints at the existence of a whole AAR-based regulatory system in DPs. Using novel approaches to trace their functional and evolutionary history, we find quantitative evidence supporting a generalized, combinatorial role of AARs in developmental processes with evolutionary implications. We observe nonrandom AAR distributions and combinations in HOX and other DPs, as well as in their interactomes, defining elements of a proteome-wide combinatorial functional code whereby different AARs and their combinations appear preferentially in proteins involved in the development of specific organs/systems. Such functional associations can be either static or display detectable evolutionary dynamics. These findings suggest that progressive changes in AAR occurrence/combination, by altering embryonic development, may have contributed to taxonomic divergence, leaving detectable traces in the evolutionary history of proteomes. Consistent with this hypothesis, we find that the evolutionary trajectories of the 20 AARs in eukaryotic proteomes are highly interrelated and their individual or compound dynamics can sharply mark taxonomic boundaries, or display clock-like trends, carrying overall a strong phylogenetic signal. These findings provide quantitative evidence and an interpretive framework outlining a combinatorial system of AARs whose compound dynamics mark at the same time DP functions and evolutionary transitions.
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Affiliation(s)
- Ilaria Pelassa
- Department of Neuroscience Rita Levi Montalcini, University of Torino, Italy
| | - Marica Cibelli
- Department of Neuroscience Rita Levi Montalcini, University of Torino, Italy
| | - Veronica Villeri
- Department of Neuroscience Rita Levi Montalcini, University of Torino, Italy
| | - Elena Lilliu
- Department of Neuroscience Rita Levi Montalcini, University of Torino, Italy
| | - Serena Vaglietti
- Department of Neuroscience Rita Levi Montalcini, University of Torino, Italy
| | - Federica Olocco
- Department of Neuroscience Rita Levi Montalcini, University of Torino, Italy
| | - Mirella Ghirardi
- Department of Neuroscience Rita Levi Montalcini, University of Torino, Italy.,National Institute of Neuroscience (INN), Torino, Italy
| | - Pier Giorgio Montarolo
- Department of Neuroscience Rita Levi Montalcini, University of Torino, Italy.,National Institute of Neuroscience (INN), Torino, Italy
| | - Davide Corà
- Department of Translational Medicine, Piemonte Orientale University, Novara, Italy.,Center for Translational Research on Autoimmune and Allergic Disease (CAAD), Novara, Italy
| | - Ferdinando Fiumara
- Department of Neuroscience Rita Levi Montalcini, University of Torino, Italy.,National Institute of Neuroscience (INN), Torino, Italy
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36
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Perry CC, Ramos-Méndez J, Milligan JR. DNA Condensation with a Boron-Containing Cationic Peptide for Modeling Boron Neutron Capture Therapy. Radiat Phys Chem Oxf Engl 1993 2019; 166. [PMID: 32454570 DOI: 10.1016/j.radphyschem.2019.108521] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The amino acid derivative 4-borono-L-phenylalanine (BPA) has been used in the radiation medicine technique boron neutron capture therapy (BNCT). Here we have characterized its interaction with DNA when incorporated into a positively charged hexa-L-arginine peptide. This ligand binds strongly to DNA and induces its condensation, an effect which is attenuated at higher ionic strengths. The use of an additional tetra-L-arginine ligand enables the preparation of a DNA condensate in the presence of a negligible concentration of unbound boron. Under these conditions, Monte Carlo simulation indicates that >85% of energy deposition events resulting from thermal neutron irradiation derive from boron fission. The combination of experimental model systems and simulations that we describe here provides a valuable tool for accurate track structure modeling of the DNA damage produced by the high LET particles involved in BNCT.
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Affiliation(s)
- Chris C Perry
- Department of Basic Sciences, School of Medicine, Loma Linda University, 11085 Campus Street, Loma Linda, CA 92350, USA
| | - Jose Ramos-Méndez
- Department of Radiation Oncology, University of California San Francisco, 1600 Divisadero Street, San Francisco, CA 94115, USA
| | - Jamie R Milligan
- Department of Basic Sciences, School of Medicine, Loma Linda University, 11085 Campus Street, Loma Linda, CA 92350, USA
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37
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Danilevich VN, Kozlov SA, Shevchuk TV, Oleinikov VA, Sizova SV, Khodarovich YM, Mulyukin AL. Ribonucleic acid (RNA) condensation by thermal cycling with metal cations: yield of nanoparticles and their applicability for transfection. J Biomol Struct Dyn 2019; 38:3959-3971. [PMID: 31543001 DOI: 10.1080/07391102.2019.1671228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
To the present, different efficient but expensive, multistage, and time-consuming technologies have been developed to deliver ribonucleic acids (RNA) into eukaryotic cells. Here, we report a simple and feasible solution to design RNA nanocarriers based on nucleic acid condensation by bi- and trivalent metal ions during thermal cycling. Efficient RNA conversion to nanoparticles with small size (10-50 nm) suitable for transfection was achieved using cations Ni2+, Co2+ or Cu2+ alone or in combination with Ca2+ at the specially selected concentrations (2.0 mM-3.5 mM), low ionic strength, and narrow pH range (8.0-8.5). Other ions - Mn2+, Zn2+, Tb3+, or Gd3+ - caused RNA-cleaving effect that was abolished in the presence of Ni2+, Co2+, Zn2+, or Cu2+. Naked RNA-metal ion nanoparticles were extremely unstable in phosphate buffer and sensitive to serum ribonucleases (RNases), and this problem was solved by treatment with polyarginines-16 and 8. Polyarginine-stabilized nanoparticles, containing malachite green (MG) aptamer RNA and metal cations, crossed the cell membrane, dissociated in the cytoplasm, and preserved the functionality of transported RNA, as judged from efficient transfection of human embryonic kidney 293 cells. The technology, involving RNA condensation by metal cations, can be used as a cheap alternative to produce nanoscale carriers to deliver various RNAs into cells in vitro and in vivo.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vasily N Danilevich
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia
| | - Sergey A Kozlov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia
| | - Taras V Shevchuk
- Branch of the M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Moscow, Russia
| | - Vladimir A Oleinikov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia
| | - Svetlana V Sizova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia
| | - Yuriy M Khodarovich
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia
| | - Andrey L Mulyukin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
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38
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Kang H, Yoo J, Sohn BK, Lee SW, Lee HS, Ma W, Kee JM, Aksimentiev A, Kim H. Sequence-dependent DNA condensation as a driving force of DNA phase separation. Nucleic Acids Res 2019; 46:9401-9413. [PMID: 30032232 PMCID: PMC6182145 DOI: 10.1093/nar/gky639] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 07/04/2018] [Indexed: 02/06/2023] Open
Abstract
The physical properties of DNA have been suggested to play a central role in spatio-temporal organization of eukaryotic chromosomes. Experimental correlations have been established between the local nucleotide content of DNA and the frequency of inter- and intra-chromosomal contacts but the underlying physical mechanism remains unknown. Here, we combine fluorescence resonance energy transfer (FRET) measurements, precipitation assays, and molecular dynamics simulations to characterize the effect of DNA nucleotide content, sequence, and methylation on inter-DNA association and its correlation with DNA looping. First, we show that the strength of DNA condensation mediated by poly-lysine peptides as a reduced model of histone tails depends on the DNA’s global nucleotide content but also on the local nucleotide sequence, which turns out to be qualitatively same as the condensation by spermine. Next, we show that the presence and spatial arrangement of C5 methyl groups determines the strength of inter-DNA attraction, partially explaining why RNA resists condensation. Interestingly, multi-color single molecule FRET measurements reveal strong anti-correlation between DNA looping and DNA–DNA association, suggesting that a common biophysical mechanism underlies them. We propose that the differential affinity between DNA regions of varying sequence pattern may drive the phase separation of chromatin into chromosomal subdomains.
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Affiliation(s)
- Hyunju Kang
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Jejoong Yoo
- Department of Physics and the Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Center for Self-assembly and Complexity, Institute for Basic Science, Pohang, Republic of Korea
| | - Byeong-Kwon Sohn
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Seung-Won Lee
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Hong Soo Lee
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Wenjie Ma
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Jung-Min Kee
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Aleksei Aksimentiev
- Department of Physics and the Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Hajin Kim
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea.,Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea
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39
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Lysine/RNA-interactions drive and regulate biomolecular condensation. Nat Commun 2019; 10:2909. [PMID: 31266957 PMCID: PMC6606616 DOI: 10.1038/s41467-019-10792-y] [Citation(s) in RCA: 149] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 05/28/2019] [Indexed: 02/08/2023] Open
Abstract
Cells form and use biomolecular condensates to execute biochemical reactions. The molecular properties of non-membrane-bound condensates are directly connected to the amino acid content of disordered protein regions. Lysine plays an important role in cellular function, but little is known about its role in biomolecular condensation. Here we show that protein disorder is abundant in protein/RNA granules and lysine is enriched in disordered regions of proteins in P-bodies compared to the entire human disordered proteome. Lysine-rich polypeptides phase separate into lysine/RNA-coacervates that are more dynamic and differ at the molecular level from arginine/RNA-coacervates. Consistent with the ability of lysine to drive phase separation, lysine-rich variants of the Alzheimer's disease-linked protein tau undergo coacervation with RNA in vitro and bind to stress granules in cells. Acetylation of lysine reverses liquid-liquid phase separation and reduces colocalization of tau with stress granules. Our study establishes lysine as an important regulator of cellular condensation.
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40
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Zink M, Hotzel K, Schubert US, Heinze T, Fischer D. Amino Acid–Substituted Dextran‐Based Non‐Viral Vectors for Gene Delivery. Macromol Biosci 2019; 19:e1900085. [DOI: 10.1002/mabi.201900085] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 05/08/2019] [Indexed: 11/07/2022]
Affiliation(s)
- Matthias Zink
- Institute of PharmacyFriedrich Schiller University Jena Lessingstrasse 8 D‐07743 Jena Germany
| | - Konrad Hotzel
- Friedrich Schiller University Jena Humboldtstraße 10 D‐07743 Jena Germany
- Friedrich Schiller University Jena Humboldtstraße 10 D‐07743 Jena Germany
| | - Ulrich S. Schubert
- Friedrich Schiller University Jena Humboldtstraße 10 D‐07743 Jena Germany
- Friedrich Schiller University Jena Philosophenweg 7 D‐07743 Jena Germany
| | - Thomas Heinze
- Friedrich Schiller University Jena Humboldtstraße 10 D‐07743 Jena Germany
- Friedrich Schiller University Jena Humboldtstraße 10 D‐07743 Jena Germany
- Friedrich Schiller University Jena Philosophenweg 7 D‐07743 Jena Germany
| | - Dagmar Fischer
- Institute of PharmacyFriedrich Schiller University Jena Lessingstrasse 8 D‐07743 Jena Germany
- Friedrich Schiller University Jena Philosophenweg 7 D‐07743 Jena Germany
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41
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Zinchenko A, Hiramatsu H, Yamaguchi H, Kubo K, Murata S, Kanbe T, Hazemoto N, Yoshikawa K, Akitaya T. Amino Acid Sequence of Oligopeptide Causes Marked Difference in DNA Compaction and Transcription. Biophys J 2019; 116:1836-1844. [PMID: 31076102 PMCID: PMC6531782 DOI: 10.1016/j.bpj.2019.04.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 03/04/2019] [Accepted: 04/12/2019] [Indexed: 02/04/2023] Open
Abstract
Compaction of T4 phage DNA (166 kbp) by short oligopeptide octamers composed of two types of amino acids, four cationic lysine (K), and four polar nonionic serine (S) having different sequence order was studied by single-molecule fluorescent microscopy. We found that efficient DNA compaction by oligopeptide octamers depends on the geometrical match between phosphate groups of DNA and cationic amines. The amino acid sequence order in octamers dramatically affects the mechanism of DNA compaction, which changes from a discrete all-or-nothing coil-globule transition induced by a less efficient (K4S4) octamer to a continuous compaction transition induced by a (KS)4 octamer with a stronger DNA-binding character. This difference in the DNA compaction mechanism dramatically changes the packaging density, and the morphology of T4 DNA condensates: DNA is folded into ordered toroidal or rod morphologies during all-or-nothing compaction, whereas disordered DNA condensates are formed as a result of the continuous DNA compaction. Furthermore, the difference in DNA compaction mechanism has a certain effect on the inhibition scenario of the DNA transcription activity, which is gradual for the continuous DNA compaction and abrupt for the all-or-nothing DNA collapse.
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Affiliation(s)
- Anatoly Zinchenko
- Graduate School of Environmental Studies, Nagoya University, Furocho, Chikusa-ku, Nagoya, Japan.
| | - Hiroyuki Hiramatsu
- Faculty of Pharmaceutical Science, Nagoya City University, Mizuho-ku, Nagoya, Japan
| | | | - Koji Kubo
- Graduate School of Environmental Studies, Nagoya University, Furocho, Chikusa-ku, Nagoya, Japan
| | - Shizuaki Murata
- Graduate School of Environmental Studies, Nagoya University, Furocho, Chikusa-ku, Nagoya, Japan
| | - Toshio Kanbe
- Laboratory of Medical Mycology, Research Institute for Disease Mechanism and Control, School of Medicine, Nagoya University, Tsurumai-cho, Showa-ku, Nagoya, Japan
| | - Norio Hazemoto
- Faculty of Pharmaceutical Science, Nagoya City University, Mizuho-ku, Nagoya, Japan
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Japan
| | - Tatsuo Akitaya
- Department of Chemistry, Asahikawa Medical University, Asahikawa, Hokkaido, Japan.
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42
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Lone SA, Sadhu KK. Gold Nanoflower for Selective Detection of Single Arginine Effect in α-Helix Conformational Change over Lysine in 310-Helix Peptide. Bioconjug Chem 2019; 30:1781-1787. [DOI: 10.1021/acs.bioconjchem.9b00301] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Shahbaz Ahmad Lone
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Kalyan K. Sadhu
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
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Gupta S, Tiwari N, Munde M. A Comprehensive Biophysical Analysis of the Effect of DNA Binding Drugs on Protamine-induced DNA Condensation. Sci Rep 2019; 9:5891. [PMID: 30971720 PMCID: PMC6458161 DOI: 10.1038/s41598-019-41975-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 03/13/2019] [Indexed: 11/21/2022] Open
Abstract
DNA condensation is a ubiquitous phenomenon in biology, yet the physical basis for it has remained elusive. Here, we have explored the mechanism of DNA condensation through the protamine-DNA interaction, and by examining on it the influence of DNA binding drugs. We observed that the DNA condensation is accompanied by B to Ψ-DNA transition as a result of DNA base pair distortions due to protamine binding, bringing about the formation of toroidal structure through coil-globule transition. The binding energetics suggested that electrostatic energy, bending energy and hydration energy must play crucial roles in DNA condensation. EtBr intercalation interferes with the protamine-DNA interaction, challenging the distortion of the DNA helix and separation of DNA base pairs by protamine. Thus, EtBr, by competing directly with protamine, resists the phenomenon of DNA condensation. On the contrary, netropsin impedes the DNA condensation by an allosteric mechanism, by resisting the probable DNA major groove bending by protamine. In summary, we demonstrate that drugs with distinct binding modes use different mechanism to interfere with DNA condensation.
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Affiliation(s)
- Sakshi Gupta
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Neha Tiwari
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Manoj Munde
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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Wan H, Li J, Chang S, Lin S, Tian Y, Tian X, Wang M, Hu J. Probing the Behaviour of Cas1-Cas2 upon Protospacer Binding in CRISPR-Cas Systems using Molecular Dynamics Simulations. Sci Rep 2019; 9:3188. [PMID: 30816277 PMCID: PMC6395717 DOI: 10.1038/s41598-019-39616-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 01/29/2019] [Indexed: 12/26/2022] Open
Abstract
Adaptation in CRISPR-Cas systems enables the generation of an immunological memory to defend against invading viruses. This process is driven by foreign DNA spacer (termed protospacer) selection and integration mediated by Cas1-Cas2 protein. Recently, different states of Cas1-Cas2, in its free form and in complex with protospacer DNAs, were solved by X-ray crystallography. In this paper, molecular dynamics (MD) simulations are employed to study crystal structures of one free and two protospacer-bound Cas1-Cas2 complexes. The simulated results indicate that the protospacer binding markedly increases the system stability, in particular when the protospacer containing the PAM-complementary sequence. The hydrogen bond and binding free energy calculations explain that PAM recognition introduces more specific interactions to increase the cleavage activity of Cas1. By using principal component analysis (PCA) and intramolecular angle calculation, this study observes two dominant slow motions associated with the binding of Ca1-Cas2 to the protospacer and potential target DNAs respectively. The comparison of DNA structural deformation further implies a cooperative conformational change of Cas1-Cas2 and protospacer for the target DNA capture. We propose that this cooperativity is the intrinsic requirement of the CRISPR integration complex formation. This study provides some new insights into the understanding of CRISPR-Cas adaptation.
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Affiliation(s)
- Hua Wan
- College of Mathematics and Informatics, South China Agricultural University, Guangzhou, 510642, China
| | - Jianming Li
- College of Mathematics and Informatics, South China Agricultural University, Guangzhou, 510642, China
| | - Shan Chang
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, 213001, China
| | - Shuoxin Lin
- Department of Electrical and Computer Engineering, James Clark School of Engineering, University of Maryland, College Park, MD, 20742, USA
| | - Yuanxin Tian
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Xuhong Tian
- College of Mathematics and Informatics, South China Agricultural University, Guangzhou, 510642, China
| | - Meihua Wang
- College of Mathematics and Informatics, South China Agricultural University, Guangzhou, 510642, China.
| | - Jianping Hu
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Chengdu University, Chengdu, 610106, China.
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45
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Yoo J, Aksimentiev A. New tricks for old dogs: improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions. Phys Chem Chem Phys 2018; 20:8432-8449. [PMID: 29547221 DOI: 10.1039/c7cp08185e] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In contrast to ordinary polymers, the vast majority of biological macromolecules adopt highly ordered three-dimensional structures that define their functions. The key to folding of a biopolymer into a unique 3D structure or to an assembly of several biopolymers into a functional unit is a delicate balance between the attractive and repulsive forces that also makes such self-assembly reversible under physiological conditions. The all-atom molecular dynamics (MD) method has emerged as a powerful tool for studies of individual biomolecules and their functional assemblies, encompassing systems of ever increasing complexity. However, advances in parallel computing technology have outpaced the development of the underlying theoretical models-the molecular force fields, pushing the MD method into an untested territory. Recent tests of the MD method have found the most commonly used molecular force fields to be out of balance, overestimating attractive interactions between charged and hydrophobic groups, which can promote artificial aggregation in MD simulations of multi-component protein, nucleic acid, and lipid systems. One route towards improving the force fields is through the NBFIX corrections method, in which the intermolecular forces are calibrated against experimentally measured quantities such as osmotic pressure by making atom pair-specific adjustments to the non-bonded interactions. In this article, we review development of the NBFIX (Non-Bonded FIX) corrections to the AMBER and CHARMM force fields and discuss their implications for MD simulations of electrolyte solutions, dense DNA systems, Holliday junctions, protein folding, and lipid bilayer membranes.
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Affiliation(s)
- Jejoong Yoo
- Center for the Physics of Living Cells, Department of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL 61801, USA. and Center for Self-assembly and Complexity, Institute for Basic Science, Pohang, 37363, Republic of Korea
| | - Aleksei Aksimentiev
- Center for the Physics of Living Cells, Department of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL 61801, USA.
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46
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Collapse of DNA in packaging and cellular transport. Int J Biol Macromol 2017; 109:36-48. [PMID: 29247730 DOI: 10.1016/j.ijbiomac.2017.12.076] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 12/11/2017] [Accepted: 12/12/2017] [Indexed: 01/02/2023]
Abstract
The dawn of molecular biology and recombinant DNA technology arose from our ability to manipulate DNA, including the process of collapse of long extended DNA molecules into nanoparticles of approximately 100 nm diameter. This condensation process is important for the packaging of DNA in the cell and for transporting DNA through the cell membrane for gene therapy. Multivalent cations, such as natural polyamines (spermidine and spermine), were initially recognized for their ability to provoke DNA condensation. Current research is targeted on molecules such as linear and branched polymers, oligopeptides, polypeptides and dendrimers that promote collapse of DNA to nanometric particles for gene therapy and on the energetics of DNA packaging.
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47
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Grasso G, Deriu MA, Patrulea V, Borchard G, Möller M, Danani A. Free energy landscape of siRNA-polycation complexation: Elucidating the effect of molecular geometry, polymer flexibility, and charge neutralization. PLoS One 2017; 12:e0186816. [PMID: 29088239 PMCID: PMC5663398 DOI: 10.1371/journal.pone.0186816] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 10/09/2017] [Indexed: 12/16/2022] Open
Abstract
The success of medical threatments with DNA and silencing interference RNA is strongly related to the design of efficient delivery technologies. Cationic polymers represent an attractive strategy to serve as nucleic-acid carriers with the envisioned advantages of efficient complexation, low cost, ease of production, well-defined size, and low polydispersity index. However, the balance between efficacy and toxicity (safety) of these polymers is a challenge and in need of improvement. With the aim of designing more effective polycationic-based gene carriers, many parameters such as carrier morphology, size, molecular weight, surface chemistry, and flexibility/rigidity ratio need to be taken into consideration. In the present work, the binding mechanism of three cationic polymers (polyarginine, polylysine and polyethyleneimine) to a model siRNA target is computationally investigated at the atomistic level. In order to better understand the polycationic carrier-siRNA interactions, replica exchange molecular dynamic simulations were carried out to provide an exhaustive exploration of all the possible binding sites, taking fully into account the siRNA flexibility together with the presence of explicit solvent and ions. Moreover, well-tempered metadynamics simulations were employed to elucidate how molecular geometry, polycation flexibility, and charge neutralization affect the siRNA-polycations free energy landscape in term of low-energy binding modes and unbinding free energy barriers. Significant differences among polymer binding modes have been detected, revealing the advantageous binding properties of polyarginine and polylysine compared to polyethyleneimine.
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Affiliation(s)
- Gianvito Grasso
- Istituto Dalle Molle di Studi Sull'Intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale della Svizzera Italiana (SUPSI), Università della Svizzera Italiana (USI), Centro Galleria 2, Manno, Switzerland
| | - Marco Agostino Deriu
- Istituto Dalle Molle di Studi Sull'Intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale della Svizzera Italiana (SUPSI), Università della Svizzera Italiana (USI), Centro Galleria 2, Manno, Switzerland
| | - Viorica Patrulea
- School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, Geneva, Switzerland
| | - Gerrit Borchard
- School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, Geneva, Switzerland
| | - Michael Möller
- School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, Geneva, Switzerland
| | - Andrea Danani
- Istituto Dalle Molle di Studi Sull'Intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale della Svizzera Italiana (SUPSI), Università della Svizzera Italiana (USI), Centro Galleria 2, Manno, Switzerland
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48
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An M, Tonga GY, Parkin SR, Rotello VM, DeRouchey JE. Tuning DNA Condensation with Zwitterionic Polyamidoamine (zPAMAM) Dendrimers. Macromolecules 2017; 50:8202-8211. [PMID: 30700915 DOI: 10.1021/acs.macromol.7b01470] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cationic dendrimers are promising vectors for non-viral gene due to their well-defined size and chemistry. We have synthesized a series of succinylated fourth generation (G4) PAMAM dendrimers to control the DNA packaging in dendriplexes, allowing us to probe the role of charge on DNA packaging. The self-assembly of DNA induced by these zwitterionic PAMAM (zPAMAM) was investigated using small-angle x-ray scattering (SAXS). We demonstrate that changing the degree of modification in zPAMAM-DNA significantly alters the packing density of the resulting dendriplexes. Salt sensitivities and pH dependence on the inter-DNA spacing were also examined. The swelling and stability to salt is reduced with increasing degree of PAMAM modification. Lowering the pH leads to significantly tighter hexagonal DNA packaging. In combination, these results show zPAMAM is an effective means to modulate nucleic acid packaging in a deterministic manner.
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Affiliation(s)
- Min An
- Department of Chemistry, University of Kentucky, Lexington, KY 40506, USA
| | | | - Sean R Parkin
- Department of Chemistry, University of Kentucky, Lexington, KY 40506, USA
| | - Vincent M Rotello
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Jason E DeRouchey
- Department of Chemistry, University of Kentucky, Lexington, KY 40506, USA
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49
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Muramatsu A, Shimizu Y, Yoshikawa Y, Fukuda W, Umezawa N, Horai Y, Higuchi T, Fujiwara S, Imanaka T, Yoshikawa K. Naturally occurring branched-chain polyamines induce a crosslinked meshwork structure in a giant DNA. J Chem Phys 2017; 145:235103. [PMID: 28010109 DOI: 10.1063/1.4972066] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
We studied the effect of branched-chain polyamines on the folding transition of genome-sized DNA molecules in aqueous solution by the use of single-molecule observation with fluorescence microcopy. Detailed morphological features of polyamine/DNA complexes were characterized by atomic force microscopy (AFM). The AFM observations indicated that branched-chain polyamines tend to induce a characteristic change in the higher-order structure of DNA by forming bridges or crosslinks between the segments of a DNA molecule. In contrast, natural linear-chain polyamines cause a parallel alignment between DNA segments. Circular dichroism measurements revealed that branched-chain polyamines induce the A-form in the secondary structure of DNA, while linear-chain polyamines have only a minimum effect. This large difference in the effects of branched- and linear-chain polyamines is discussed in relation to the difference in the manner of binding of these polyamines to negatively charged double-stranded DNA.
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Affiliation(s)
- Akira Muramatsu
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe 610-0394, Japan
| | - Yuta Shimizu
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe 610-0394, Japan
| | - Yuko Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe 610-0394, Japan
| | - Wakao Fukuda
- College of Life Sciences, Ritsumeikan University, Kusatsu 525-8577, Japan
| | - Naoki Umezawa
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan
| | - Yuhei Horai
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan
| | - Tsunehiko Higuchi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan
| | - Shinsuke Fujiwara
- School of Science and Technology, Kwansei-Gakuin University, Sanda 669-1337, Japan
| | - Tadayuki Imanaka
- College of Life Sciences, Ritsumeikan University, Kusatsu 525-8577, Japan
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe 610-0394, Japan
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50
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Wieczorek R, Adamala K, Gasperi T, Polticelli F, Stano P. Small and Random Peptides: An Unexplored Reservoir of Potentially Functional Primitive Organocatalysts. The Case of Seryl-Histidine. Life (Basel) 2017; 7:E19. [PMID: 28397774 PMCID: PMC5492141 DOI: 10.3390/life7020019] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Revised: 04/03/2017] [Accepted: 04/05/2017] [Indexed: 12/11/2022] Open
Abstract
Catalysis is an essential feature of living systems biochemistry, and probably, it played a key role in primordial times, helping to produce more complex molecules from simple ones. However, enzymes, the biocatalysts par excellence, were not available in such an ancient context, and so, instead, small molecule catalysis (organocatalysis) may have occurred. The best candidates for the role of primitive organocatalysts are amino acids and short random peptides, which are believed to have been available in an early period on Earth. In this review, we discuss the occurrence of primordial organocatalysts in the form of peptides, in particular commenting on reports about seryl-histidine dipeptide, which have recently been investigated. Starting from this specific case, we also mention a peptide fragment condensation scenario, as well as other potential roles of peptides in primordial times. The review actually aims to stimulate further investigation on an unexplored field of research, namely one that specifically looks at the catalytic activity of small random peptides with respect to reactions relevant to prebiotic chemistry and early chemical evolution.
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Affiliation(s)
- Rafal Wieczorek
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
| | - Katarzyna Adamala
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Tecla Gasperi
- Department of Science, Roma Tre University, Viale G. Marconi 446, 00146 Rome, Italy.
| | - Fabio Polticelli
- Department of Science, Roma Tre University, Viale G. Marconi 446, 00146 Rome, Italy.
- National Institute of Nuclear Physics, Roma Tre Section, Via della Vasca Navale 84, 00146 Rome, Italy.
| | - Pasquale Stano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Campus Ecotekne (S.P. 6 Lecce-Monteroni), 73100 Lecce, Italy.
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