1
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Love O, Winkler L, Cheatham TE. van der Waals Parameter Scanning with Amber Nucleic Acid Force Fields: Revisiting Means to Better Capture the RNA/DNA Structure through MD. J Chem Theory Comput 2024; 20:625-643. [PMID: 38157247 PMCID: PMC10809421 DOI: 10.1021/acs.jctc.3c01164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/11/2023] [Accepted: 12/14/2023] [Indexed: 01/03/2024]
Abstract
Molecular dynamics simulations can be used in combination with experimental techniques to uncover the intricacies of biomolecular structure, dynamics, and the resulting interactions. However, many noncanonical nucleic acid structures have proven to be challenging to replicate in accurate agreement with experimental data, often attributed to known force field deficiencies. A common force field criticism is the handling of van der Waals (vdW) parameters, which have not been updated since the regular use of Ewald's methods became routine. This work dives into the effects of minute vdW radii shifts on RNA tetranucleotide, B-DNA, and Z-DNA model systems described by commonly used Amber force fields. Using multidimensional replica exchange molecular dynamics (M-REMD), the GACC RNA tetranucleotide demonstrated changes in the structural distribution between the NMR minor and anomalous structure populations based on the O2' vdW radii scanning. However, no significant change in the NMR Major conformation population was observed. There were minimal changes in the B-DNA structure but there were more substantial improvements in Z-DNA structural descriptions, specifically with the Tumuc1 force field. This occurred with both LJbb vdW radii adjustments and incorporation of the CUFIX nonbonded parameter modifications. Though the limited vdW modifications tested did not provide a universal fix to the challenge of simulating the various known nucleic acid structures, they do provide direction and a greater understanding for future force field development efforts.
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Affiliation(s)
| | | | - Thomas E. Cheatham
- Department of Medicinal Chemistry,
College of Pharmacy, University of Utah, 2000 East 30 South Skaggs 306, Salt Lake City, Utah 84112, United States
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2
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Battistini F, Sala A, Hospital A, Orozco M. Sequence-Dependent Properties of the RNA Duplex. J Chem Inf Model 2023; 63:5259-5271. [PMID: 37577978 DOI: 10.1021/acs.jcim.3c00741] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Sequence-dependent properties of the DNA duplex have been accurately described using extensive molecular dynamics simulations. The RNA duplex meanwhile─which is typically represented as a sequence-averaged rigid rod─does not benefit from having equivalent molecular dynamics simulations. In this paper, we present a massive simulation effort using a set of ABC-optimized duplexes from which we derived tetramer-resolution properties of the RNA duplex and a simple mesoscopic model that can represent elastic properties of long RNA duplexes. Despite the extreme chemical similarity between DNA and RNA, the local and global elastic properties of the duplexes are very different. DNA duplexes show a complex and nonelastic pattern of flexibility, for instance, while RNA duplexes behave as an elastic system whose deformations can be represented by simple harmonic potentials. In RNA duplexes (RNA2), not only are intra- and interbase pair parameters (equilibrium and mechanical) different from those in the equivalent DNA duplex sequences (DNA2) but the correlations between movements also differ. Simple statements on the relative flexibility or stability of both polymers are meaningless and should be substituted by a more detailed description depending on the sequence and the type of deformation considered.
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Affiliation(s)
- Federica Battistini
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, Barcelona 08028, Spain
- Departament de Bioquímica i Biomedicina. Facultat de Biologia, Universitat de Barcelona, Avgda Diagonal 647, Barcelona 08028, Spain
| | - Alba Sala
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, Barcelona 08028, Spain
| | - Adam Hospital
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, Barcelona 08028, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, Barcelona 08028, Spain
- Departament de Bioquímica i Biomedicina. Facultat de Biologia, Universitat de Barcelona, Avgda Diagonal 647, Barcelona 08028, Spain
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3
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Parisis N, Dans PD, Jbara M, Singh B, Schausi-Tiffoche D, Molina-Serrano D, Brun-Heath I, Hendrychová D, Maity SK, Buitrago D, Lema R, Nait Achour T, Giunta S, Girardot M, Talarek N, Rofidal V, Danezi K, Coudreuse D, Prioleau MN, Feil R, Orozco M, Brik A, Wu PYJ, Krasinska L, Fisher D. Histone H3 serine-57 is a CHK1 substrate whose phosphorylation affects DNA repair. Nat Commun 2023; 14:5104. [PMID: 37607906 PMCID: PMC10444856 DOI: 10.1038/s41467-023-40843-4] [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: 11/10/2018] [Accepted: 08/12/2023] [Indexed: 08/24/2023] Open
Abstract
Histone post-translational modifications promote a chromatin environment that controls transcription, DNA replication and repair, but surprisingly few phosphorylations have been documented. We report the discovery of histone H3 serine-57 phosphorylation (H3S57ph) and show that it is implicated in different DNA repair pathways from fungi to vertebrates. We identified CHK1 as a major human H3S57 kinase, and disrupting or constitutively mimicking H3S57ph had opposing effects on rate of recovery from replication stress, 53BP1 chromatin binding, and dependency on RAD52. In fission yeast, mutation of all H3 alleles to S57A abrogated DNA repair by both non-homologous end-joining and homologous recombination, while cells with phospho-mimicking S57D alleles were partly compromised for both repair pathways, presented aberrant Rad52 foci and were strongly sensitised to replication stress. Mechanistically, H3S57ph loosens DNA-histone contacts, increasing nucleosome mobility, and interacts with H3K56. Our results suggest that dynamic phosphorylation of H3S57 is required for DNA repair and recovery from replication stress, opening avenues for investigating the role of this modification in other DNA-related processes.
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Affiliation(s)
- Nikolaos Parisis
- IGMM, CNRS, INSERM, University of Montpellier, Montpellier, France
- Equipe labellisée Ligue contre le Cancer, Paris, France
- BPMP, CNRS, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
- Institut Jacques Monod, CNRS, University Paris Diderot, Paris, France
| | - Pablo D Dans
- IRB Barcelona, BIST, Barcelona, Spain
- Bioinformatics Unit, Institute Pasteur of Montevideo, Montevideo, Uruguay
- Department of Biological Sciences, CENUR North Riverside, University of the Republic (UdelaR), Salto, Uruguay
| | - Muhammad Jbara
- Schulich Faculty of Chemistry, Technion Israel Institute of Technology, Haifa, Israel
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | | | | | | | | | - Denisa Hendrychová
- IGMM, CNRS, INSERM, University of Montpellier, Montpellier, France
- Equipe labellisée Ligue contre le Cancer, Paris, France
- Department of Experimental Biology, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - Suman Kumar Maity
- Schulich Faculty of Chemistry, Technion Israel Institute of Technology, Haifa, Israel
| | | | | | - Thiziri Nait Achour
- IGMM, CNRS, INSERM, University of Montpellier, Montpellier, France
- Equipe labellisée Ligue contre le Cancer, Paris, France
| | - Simona Giunta
- The Rockefeller University, New York, NY, USA
- Laboratory of Genome Evolution, Department of Biology and Biotechnology "Charles Darwin", University of Rome Sapienza, Rome, Italy
| | - Michael Girardot
- IGMM, CNRS, INSERM, University of Montpellier, Montpellier, France
| | - Nicolas Talarek
- IGMM, CNRS, INSERM, University of Montpellier, Montpellier, France
| | - Valérie Rofidal
- BPMP, CNRS, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Katerina Danezi
- IGMM, CNRS, INSERM, University of Montpellier, Montpellier, France
- Equipe labellisée Ligue contre le Cancer, Paris, France
| | - Damien Coudreuse
- IGDR, CNRS, University of Rennes, Rennes, France
- IBGC, CNRS, University of Bordeaux, Bordeaux, France
| | | | - Robert Feil
- IGMM, CNRS, INSERM, University of Montpellier, Montpellier, France
| | | | - Ashraf Brik
- Schulich Faculty of Chemistry, Technion Israel Institute of Technology, Haifa, Israel
| | - Pei-Yun Jenny Wu
- IGDR, CNRS, University of Rennes, Rennes, France
- IBGC, CNRS, University of Bordeaux, Bordeaux, France
| | - Liliana Krasinska
- IGMM, CNRS, INSERM, University of Montpellier, Montpellier, France.
- Equipe labellisée Ligue contre le Cancer, Paris, France.
| | - Daniel Fisher
- IGMM, CNRS, INSERM, University of Montpellier, Montpellier, France.
- Equipe labellisée Ligue contre le Cancer, Paris, France.
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4
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Rodriguez J, Battistini F, Learte-Aymamí S, Orozco M, Mascareñas JL. Molecular dynamics modelling of the interaction of a synthetic zinc-finger miniprotein with DNA. RSC Chem Biol 2023; 4:486-493. [PMID: 37415868 PMCID: PMC10320839 DOI: 10.1039/d3cb00053b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 05/09/2023] [Indexed: 07/08/2023] Open
Abstract
We report the modelling of the DNA complex of an artificial miniprotein composed of two zinc finger modules and an AT-hook linking peptide. The computational study provides for the first time a structural view of these types of complexes, dissecting interactions that are key to modulate their stability. The relevance of these interactions was validated experimentally. These results confirm the potential of this type of computational approach for studying peptide-DNA complexes and suggest that they could be very useful for the rational design of non-natural, DNA binding miniproteins.
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Affiliation(s)
- Jessica Rodriguez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), and Departamento de Química Orgánica, Universidade de Santiago de Compostela Rúa Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST) Baldiri Reixac 10-12 08028 Barcelona Spain
| | - Federica Battistini
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST) Baldiri Reixac 10-12 08028 Barcelona Spain
- Department of Biochemistry and Molecular Biology, University of Barcelona 08028 Barcelona Spain
| | - Soraya Learte-Aymamí
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), and Departamento de Química Orgánica, Universidade de Santiago de Compostela Rúa Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST) Baldiri Reixac 10-12 08028 Barcelona Spain
- Department of Biochemistry and Molecular Biology, University of Barcelona 08028 Barcelona Spain
| | - José L Mascareñas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), and Departamento de Química Orgánica, Universidade de Santiago de Compostela Rúa Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
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5
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Monsen RC, Chua ED, Hopkins J, Chaires J, Trent J. Structure of a 28.5 kDa duplex-embedded G-quadruplex system resolved to 7.4 Å resolution with cryo-EM. Nucleic Acids Res 2023; 51:1943-1959. [PMID: 36715343 PMCID: PMC9976903 DOI: 10.1093/nar/gkad014] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/16/2022] [Accepted: 01/04/2023] [Indexed: 01/31/2023] Open
Abstract
Genomic regions with high guanine content can fold into non-B form DNA four-stranded structures known as G-quadruplexes (G4s). Extensive in vivo investigations have revealed that promoter G4s are transcriptional regulators. Little structural information exists for these G4s embedded within duplexes, their presumed genomic environment. Here, we report the 7.4 Å resolution structure and dynamics of a 28.5 kDa duplex-G4-duplex (DGD) model system using cryo-EM, molecular dynamics, and small-angle X-ray scattering (SAXS) studies. The DGD cryo-EM refined model features a 53° bend induced by a stacked duplex-G4 interaction at the 5' G-tetrad interface with a persistently unstacked 3' duplex. The surrogate complement poly dT loop preferably stacks onto the 3' G-tetrad interface resulting in occlusion of both 5' and 3' tetrad interfaces. Structural analysis shows that the DGD model is quantifiably more druggable than the monomeric G4 structure alone and represents a new structural drug target. Our results illustrate how the integration of cryo-EM, MD, and SAXS can reveal complementary detailed static and dynamic structural information on DNA G4 systems.
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Affiliation(s)
- Robert C Monsen
- UofL Health Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA
| | - Eugene Y D Chua
- National Center for CryoEM Access and Training (NCCAT), Simons Electron Microscopy Center, New York Structural Biology Center, NY 10027, USA
| | - Jesse B Hopkins
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological, Chemical, and Physical Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Jonathan B Chaires
- UofL Health Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA
- Department of Medicine, University of Louisville, Louisville, KY 40202, USA
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY 40202, USA
| | - John O Trent
- UofL Health Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA
- Department of Medicine, University of Louisville, Louisville, KY 40202, USA
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY 40202, USA
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6
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Non-B DNA conformations analysis through molecular dynamics simulations. Biochim Biophys Acta Gen Subj 2022; 1866:130252. [DOI: 10.1016/j.bbagen.2022.130252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 03/13/2023]
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7
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Ghoshdastidar D, Bansal M. Flexibility of flanking DNA is a key determinant of transcription factor affinity for the core motif. Biophys J 2022; 121:3987-4000. [PMID: 35978548 PMCID: PMC9674967 DOI: 10.1016/j.bpj.2022.08.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 07/28/2022] [Accepted: 08/15/2022] [Indexed: 11/02/2022] Open
Abstract
Selective gene regulation is mediated by recognition of specific DNA sequences by transcription factors (TFs). The extremely challenging task of searching out specific cognate DNA binding sites among several million putative sites within the eukaryotic genome is achieved by complex molecular recognition mechanisms. Elements of this recognition code include the core binding sequence, the flanking sequence context, and the shape and conformational flexibility of the composite binding site. To unravel the extent to which DNA flexibility modulates TF binding, in this study, we employed experimentally guided molecular dynamics simulations of ternary complex of closely related Hox heterodimers Exd-Ubx and Exd-Scr with DNA. Results demonstrate that flexibility signatures embedded in the flanking sequences impact TF binding at the cognate binding site. A DNA sequence has intrinsic shape and flexibility features. While shape features are localized, our analyses reveal that flexibility features of the flanking sequences percolate several basepairs and allosterically modulate TF binding at the core. We also show that lack of flexibility in the motif context can render the cognate site resistant to protein-induced shape changes and subsequently lower TF binding affinity. Overall, this study suggests that flexibility-guided DNA shape, and not merely the static shape, is a key unexplored component of the complex DNA-TF recognition code.
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Affiliation(s)
| | - Manju Bansal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, Karnataka, India.
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8
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Tucker MR, Piana S, Tan D, LeVine MV, Shaw DE. Development of Force Field Parameters for the Simulation of Single- and Double-Stranded DNA Molecules and DNA-Protein Complexes. J Phys Chem B 2022; 126:4442-4457. [PMID: 35694853 PMCID: PMC9234960 DOI: 10.1021/acs.jpcb.1c10971] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
![]()
Although molecular
dynamics (MD) simulations have been used extensively
to study the structural dynamics of proteins, the role of MD simulation
in studies of nucleic acid based systems has been more limited. One
contributing factor to this disparity is the historically lower level
of accuracy of the physical models used in such simulations to describe
interactions involving nucleic acids. By modifying nonbonded and torsion
parameters of a force field from the Amber family of models, we recently
developed force field parameters for RNA that achieve a level of accuracy
comparable to that of state-of-the-art protein force fields. Here
we report force field parameters for DNA, which we developed by transferring
nonbonded parameters from our recently reported RNA force field and
making subsequent adjustments to torsion parameters. We have also
modified the backbone charges in both the RNA and DNA parameter sets
to make the treatment of electrostatics compatible with our recently
developed variant of the Amber protein and ion force field. We name
the force field resulting from the union of these three parameter
sets (the new DNA parameters, the revised RNA parameters, and the
existing protein and ion parameters) DES-Amber. Extensive
testing of DES-Amber indicates that it can describe the thermal stability
and conformational flexibility of single- and double-stranded DNA
systems with a level of accuracy comparable to or, especially for
disordered systems, exceeding that of state-of-the-art nucleic acid
force fields. Finally, we show that, in certain favorable cases, DES-Amber
can be used for long-timescale simulations of protein–nucleic
acid complexes.
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Affiliation(s)
| | - Stefano Piana
- D. E. Shaw Research, New York, New York 10036, United States
| | - Dazhi Tan
- D. E. Shaw Research, New York, New York 10036, United States
| | | | - David E Shaw
- D. E. Shaw Research, New York, New York 10036, United States.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, United States
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9
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Afanasyev AY, Onufriev AV. Stretching of Long Double-Stranded DNA and RNA Described by the Same Approach. J Chem Theory Comput 2022; 18:3911-3920. [PMID: 35544776 DOI: 10.1021/acs.jctc.1c01221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We propose an approach to help interpret polymer force-extension curves that exhibit plateau regimes. When coupled to a bead-spring dynamic model, the approach accurately reproduces a variety of experimental force-extension curves of long double-stranded DNA and RNA, including torsionally constrained and unconstrained DNA and negatively supercoiled DNA. A key feature of the model is a specific nonconvex energy function of the spring. We provide an algorithm to obtain the five required parameters of the model from experimental force-extension curves. The applicability of the approach to the force-extension curves of double-stranded (ds) DNA of variable GC content as well as to a DNA/RNA hybrid structure is explored and confirmed. We use the approach to explain counterintuitive sequence-dependent trends and make predictions. In the plateau region of the force-extension curves, our molecular dynamics simulations show that the polymer separates into a mix of weakly and strongly stretched states without forming macroscopically distinct phases. The distribution of these states is predicted to depend on the sequence.
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Affiliation(s)
- Alexander Y Afanasyev
- Department of Biomedical Engineering and Mechanics, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Alexey V Onufriev
- Departments of Computer Science and Physics, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
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10
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Schneider AL, Albrecht AV, Huang K, Germann MW, Poon GMK. Self-Consistent Parameterization of DNA Residues for the Non-Polarizable AMBER Force Fields. Life (Basel) 2022; 12:life12050666. [PMID: 35629334 PMCID: PMC9143812 DOI: 10.3390/life12050666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/27/2022] [Accepted: 04/27/2022] [Indexed: 11/22/2022] Open
Abstract
Fixed-charge (non-polarizable) forcefields are accurate and computationally efficient tools for modeling the molecular dynamics of nucleic acid polymers, particularly DNA, well into the µs timescale. The continued utility of these forcefields depends in part on expanding the residue set in step with advancing nucleic acid chemistry and biology. A key step in parameterizing new residues is charge derivation which is self-consistent with the existing residues. As atomic charges are derived by fitting against molecular electrostatic potentials, appropriate structural models are critical. Benchmarking against the existing charge set used in current AMBER nucleic acid forcefields, we report that quantum mechanical models of deoxynucleosides, even at a high level of theory, are not optimal structures for charge derivation. Instead, structures from molecular mechanics minimization yield charges with up to 6-fold lower RMS deviation from the published values, due to the choice of such an approach in the derivation of the original charge set. We present a contemporary protocol for rendering self-consistent charges as well as optimized charges for a panel of nine non-canonical residues that will permit comparison with literature as well as studying the dynamics of novel DNA polymers.
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Affiliation(s)
- Amelia L. Schneider
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; (A.L.S.); (A.V.A.); (K.H.)
| | - Amanda V. Albrecht
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; (A.L.S.); (A.V.A.); (K.H.)
| | - Kenneth Huang
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; (A.L.S.); (A.V.A.); (K.H.)
| | - Markus W. Germann
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; (A.L.S.); (A.V.A.); (K.H.)
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA
- Correspondence: (M.W.G.); (G.M.K.P.)
| | - Gregory M. K. Poon
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; (A.L.S.); (A.V.A.); (K.H.)
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
- Correspondence: (M.W.G.); (G.M.K.P.)
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11
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Yu B, Bien KG, Pletka CC, Iwahara J. Dynamics of Cations around DNA and Protein as Revealed by 23Na Diffusion NMR Spectroscopy. Anal Chem 2022; 94:2444-2452. [PMID: 35080384 PMCID: PMC8829827 DOI: 10.1021/acs.analchem.1c04197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Counterions are vital for the structure and function of biomolecules. However, the behavior of counterions remains elusive due to the difficulty in characterizing mobile ions. Here, we demonstrate that the dynamics of cations around biological macromolecules can be revealed by 23Na diffusion nuclear magnetic resonance (NMR) spectroscopy. NMR probe hardware capable of generating strong magnetic field gradients enables 23Na NMR-based diffusion measurements for Na+ ions in solutions of biological macromolecules and their complexes. The dynamic properties of Na+ ions interacting with the macromolecules can be investigated using apparent 23Na diffusion coefficients measured under various conditions. Our diffusion data clearly show that Na+ ions retain high mobility within the ion atmosphere around DNA. The 23Na diffusion NMR method also permits direct observation of the release of Na+ ions from nucleic acids upon protein-nucleic acid association. The entropy change due to the ion release can be estimated from the diffusion data.
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Affiliation(s)
- Binhan Yu
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068 United States
| | - Karina G Bien
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068 United States
| | - Channing C Pletka
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068 United States
| | - Junji Iwahara
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068 United States
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12
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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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13
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Comparison of the ionic effects of Ca2+ and Mg2+ on nucleic acids in liquids. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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14
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Sequence-dependent structural properties of B-DNA: what have we learned in 40 years? Biophys Rev 2021; 13:995-1005. [DOI: 10.1007/s12551-021-00893-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 11/01/2021] [Indexed: 11/27/2022] Open
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15
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Battistini F, Dans PD, Terrazas M, Castellazzi CL, Portella G, Labrador M, Villegas N, Brun-Heath I, González C, Orozco M. The Impact of the HydroxyMethylCytosine epigenetic signature on DNA structure and function. PLoS Comput Biol 2021; 17:e1009547. [PMID: 34748533 PMCID: PMC8601608 DOI: 10.1371/journal.pcbi.1009547] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 11/18/2021] [Accepted: 10/10/2021] [Indexed: 12/30/2022] Open
Abstract
We present a comprehensive, experimental and theoretical study of the impact of 5-hydroxymethylation of DNA cytosine. Using molecular dynamics, biophysical experiments and NMR spectroscopy, we found that Ten-Eleven translocation (TET) dioxygenases generate an epigenetic variant with structural and physical properties similar to those of 5-methylcytosine. Experiments and simulations demonstrate that 5-methylcytosine (mC) and 5-hydroxymethylcytosine (hmC) generally lead to stiffer DNA than normal cytosine, with poorer circularization efficiencies and lower ability to form nucleosomes. In particular, we can rule out the hypothesis that hydroxymethylation reverts to unmodified cytosine physical properties, as hmC is even more rigid than mC. Thus, we do not expect dramatic changes in the chromatin structure induced by differences in physical properties between d(mCpG) and d(hmCpG). Conversely, our simulations suggest that methylated-DNA binding domains (MBDs), associated with repression activities, are sensitive to the substitution d(mCpG) ➔ d(hmCpG), while MBD3 which has a dual activation/repression activity is not sensitive to the d(mCpG) d(hmCpG) change. Overall, while gene activity changes due to cytosine methylation are the result of the combination of stiffness-related chromatin reorganization and MBD binding, those associated to 5-hydroxylation of methylcytosine could be explained by a change in the balance of repression/activation pathways related to differential MBD binding. In Eukaryotic cells, DNA epigenetic modifications play an important role in gene expression and regulation, and protein recognition. In this work we investigate the physical implications of cytosine 5-hydroxymethylation on DNA, its structural and flexibility differences with methylated and unmodified cytosine using molecular dynamics, biophysical experiments and NMR spectroscopy. In particular the effect of hydroxyl group on free energy of nucleosome and Methyl binding Protein (MBD) binding, comparing in silico and experimental data to shed light on the effect of the reduced flexibility and the direct protein-DNA recognition.
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Affiliation(s)
- Federica Battistini
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - 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 Lab., Institut Pasteur of Montevideo, Montevideo, Uruguay
| | - Montserrat Terrazas
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Chiara L. Castellazzi
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Guillem Portella
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology, Barcelona, Spain
- Chemistry Department, University of Cambridge, Cambridge, United Kingdom
| | - Mireia Labrador
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Núria 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
| | - Carlos González
- Instituto Química Física Rocasolano, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Biochemistry and Molecular Biology, University of Barcelona, Barcelona, Spain
- * E-mail:
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16
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Dohnalová H, Lankaš F. Deciphering the mechanical properties of
B‐DNA
duplex. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1575] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Hana Dohnalová
- Department of Informatics and Chemistry University of Chemistry and Technology Prague Praha 6 Czech Republic
| | - Filip Lankaš
- Department of Informatics and Chemistry University of Chemistry and Technology Prague Praha 6 Czech Republic
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17
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Molecular dynamics study of the competitive binding of hydrogen peroxide and water molecules with DNA phosphate groups. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2021; 50:759-770. [PMID: 33834265 DOI: 10.1007/s00249-021-01522-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 02/28/2021] [Accepted: 03/22/2021] [Indexed: 10/21/2022]
Abstract
The interaction of hydrogen peroxide molecules with the DNA double helix is of great interest for understanding the mechanisms of anticancer therapy utilising heavy ion beams. In the present work, a molecular dynamics study of competitive binding of hydrogen peroxide and water molecules with phosphate groups of the DNA double helix backbone was carried out. The system of DNA double helix in a water solution with hydrogen peroxide molecules and Na[Formula: see text] counterions was simulated. The results show that the hydrogen peroxide molecules bind to oxygen atoms of the phosphate groups of the double helix backbone replacing water molecules of its hydration shell. The complexes of hydrogen peroxide molecules with the phosphate groups are stabilized by one or two hydrogen bonds and by Na[Formula: see text] counterions, forming ion-mediated contacts between phosphate groups and hydrogen peroxide molecules. The complex characterized by one H-bond between the hydrogen peroxide molecule and phosphate group is dominant, the other complexes are rare. The hydrogen peroxide molecule bound to the phosphate group of the double helix backbone can inhibit the formation of hydrogen bonds indispensable for the DNA biological functioning.
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18
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Gheorghiu A, Coveney PV, Arabi AA. The influence of external electric fields on proton transfer tautomerism in the guanine-cytosine base pair. Phys Chem Chem Phys 2021; 23:6252-6265. [PMID: 33735350 PMCID: PMC8330266 DOI: 10.1039/d0cp06218a] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/23/2021] [Indexed: 12/28/2022]
Abstract
The Watson-Crick base pair proton transfer tautomers would be widely considered as a source of spontaneous mutations in DNA replication if not for their short lifetimes and thermodynamic instability. This work investigates the effects external electric fields have on the stability of the guanine-cytosine proton transfer tautomers within a realistic strand of aqueous DNA using a combination of ensemble-based classical molecular dynamics (MD) coupled to quantum mechanics/molecular mechanics (QM/MM). Performing an ensemble of calculations accounts for the stochastic aspects of the simulations while allowing for easier identification of systematic errors. The methodology applied in this work has previously been shown to estimate base pair proton transfer rate coefficients that are in good agreement with recent experimental data. A range of electric fields in the order of 104 to 109 V m-1 is investigated based on their real-life medicinal applications which include gene therapy and cancer treatments. The MD trajectories confirm that electric fields up to 1.00 × 109 V m-1 have a negligible influence on the structure of the base pairs within DNA. The QM/MM results show that the application of large external electric fields (1.00 × 109 V m-1) parallel to the hydrogen bonds increases the thermodynamic population of the tautomers by up to one order of magnitude; moreover, the lifetimes of the tautomers remain insignificant when compared to the timescale of DNA replication.
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Affiliation(s)
- Alexander Gheorghiu
- Centre for Computational Science, University College London, 20 Gordon St, London, WC1H 0AJ, UK.
| | - Peter V Coveney
- Centre for Computational Science, University College London, 20 Gordon St, London, WC1H 0AJ, UK. and Informatics Institute, University of Amsterdam, P.O. Box 94323 1090 GH, Amsterdam, The Netherlands
| | - Alya A Arabi
- Centre for Computational Science, University College London, 20 Gordon St, London, WC1H 0AJ, UK. and College of Medicine and Health Sciences, Biochemistry Department, United Arab Emirates University, AlAin, P. O. Box: 17666, United Arab Emirates.
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19
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Chawla M, Gorle S, Shaikh AR, Oliva R, Cavallo L. Replacing thymine with a strongly pairing fifth Base: A combined quantum mechanics and molecular dynamics study. Comput Struct Biotechnol J 2021; 19:1312-1324. [PMID: 33738080 PMCID: PMC7940798 DOI: 10.1016/j.csbj.2021.02.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/06/2021] [Accepted: 02/09/2021] [Indexed: 01/14/2023] Open
Abstract
The non-natural ethynylmethylpyridone C-nucleoside (W), a thymidine (T) analogue that can be incorporated in oligonucleotides by automated synthesis, has recently been reported to form a high fidelity base pair with adenosine (A) and to be well accommodated in B-DNA duplexes. The enhanced binding affinity for A of W, as compared to T, makes it an ideal modification for biotechnological applications, such as efficient probe hybridization for the parallel detection of multiple DNA strands. In order to complement the experimental study and rationalize the impact of the non-natural W nucleoside on the structure, stability and dynamics of DNA structures, we performed quantum mechanics (QM) calculations along with molecular dynamics (MD) simulations. Consistently with the experimental study, our QM calculations show that the A:W base pair has an increased stability as compared to the natural A:T pair, due to an additional CH-π interaction. Furthermore, we show that mispairing between W and guanine (G) causes a distortion in the planarity of the base pair, thus explaining the destabilization of DNA duplexes featuring a G:W pair. MD simulations show that incorporation of single or multiple consecutive A:W pairs in DNA duplexes causes minor changes to the intra- and inter-base geometrical parameters, while a moderate widening/shrinking of the major/minor groove of the duplexes is observed. QM calculations applied to selected stacks from the MD simulations also show an increased stacking energy for W, over T, with the neighboring bases.
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Affiliation(s)
- Mohit Chawla
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia
| | - Suresh Gorle
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Abdul Rajjak Shaikh
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia
| | - Romina Oliva
- Department of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, I-80143 Naples, Italy
| | - Luigi Cavallo
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia
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20
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Pal S, Paul S. An in silico investigation of the binding modes and pathway of APTO-253 on c-KIT G-quadruplex DNA. Phys Chem Chem Phys 2021; 23:3361-3376. [PMID: 33502401 DOI: 10.1039/d0cp05210h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The stability of c-KIT G-quadruplex DNA via ligands has been a significant concern in the growing field of cancer therapy. Thus, it is very important to understand the mechanism behind the high binding affinity of the small drug molecules on the c-KIT G-quadruplex DNA. In this study, we have investigated the binding mode and pathway of the APTO-253 ligand on the c-KIT G-quadruplex DNA employing a total of 10 μs all atom molecular dynamics simulations and further 8.82 μs simulations via the umbrella sampling method using both OL15 and BSC1 latest force fields for DNA structures. From the cluster structure analysis, mainly three binding pathways i.e., top, bottom and side loop stacking modes are identified. Moreover, RMSD, RMSF and 2D-RMSD values indicate that the c-KIT G-quadruplex DNA and APTO-253 molecules are stable throughout the simulation run. Furthermore, the number of hydrogen bonds in each tetrad and the distance between the two central K+ cations confirm that the c-KIT G-quadruplex DNA maintains its conformation in the process of complex formation with the APTO-253 ligand. The binding free energies and the minimum values in the potential of mean forces suggest that the binding processes are energetically favorable. Furthermore, we have found that the bottom stacking mode is the most favorable binding mode among all the three modes for the OL15 force field. However, for the BSC1 force field, both the top and bottom binding modes of the APTO-253 ligand in c-KIT G-quadruplex DNA are comparable to each other. To investigate the driving force for the complex formation, we have noticed that the van der Waals (vdW) and π-π stacking interactions are mainly responsible. Our detailed studies provide useful information for the discovery of novel drugs in the field of stabilization of G-quadruplex DNAs.
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Affiliation(s)
- Saikat Pal
- Department of Chemistry, Indian Institute of Technology, Guwahati Assam, 781039, India.
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21
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Zerze GH, Stillinger FH, Debenedetti PG. Thermodynamics of DNA Hybridization from Atomistic Simulations. J Phys Chem B 2021; 125:771-779. [PMID: 33434025 DOI: 10.1021/acs.jpcb.0c09237] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Studying DNA hybridization equilibrium at atomistic length scales, either via molecular dynamics (MD) or through commonly used advanced sampling approaches, is notoriously difficult. In this work, we describe an order-parameter-based advanced sampling technique to calculate the free energy of hybridization, and estimate the melting temperature of DNA oligomers at atomistic resolution. The free energy landscapes are reported as a function of a native-topology-based order parameter for the Drew-Dickerson dodecamer and for a range of DNA decamer sequences of different GC content. Our estimated melting temperatures match the experimental numbers within ±15 °C. As a test of the numerical reliability of the procedures employed, it was verified that the predicted free energy surfaces and melting temperatures of the d- and l-enantiomers of the Drew-Dickerson dodecamer were indistinguishable within numerical accuracy.
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Affiliation(s)
- Gül H Zerze
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Frank H Stillinger
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Pablo G Debenedetti
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
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22
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Gheorghiu A, Coveney PV, Arabi AA. The influence of base pair tautomerism on single point mutations in aqueous DNA. Interface Focus 2020; 10:20190120. [PMID: 33178413 PMCID: PMC7653342 DOI: 10.1098/rsfs.2019.0120] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2020] [Indexed: 12/11/2022] Open
Abstract
The relationship between base pair hydrogen bond proton transfer and the rate of spontaneous single point mutations at ambient temperatures and pressures in aqueous DNA is investigated. By using an ensemble-based multiscale computational modelling method, statistically robust rates of proton transfer for the A:T and G:C base pairs within a solvated DNA dodecamer are calculated. Several different proton transfer pathways are observed within the same base pair. It is shown that, in G:C, the double proton transfer tautomer is preferred, while the single proton transfer process is favoured in A:T. The reported range of rate coefficients for double proton transfer is consistent with recent experimental data. Notwithstanding the approximately 1000 times more common presence of single proton transfer products from A:T, observationally there is bias towards G:C to A:T mutations in a wide range of living organisms. We infer that the double proton transfer reactions between G:C base pairs have a negligible contribution towards this bias for the following reasons: (i) the maximum half-life of the G*:C* tautomer is in the range of picoseconds, which is significantly smaller than the milliseconds it takes for DNA to unwind during replication, (ii) statistically, the majority of G*:C* tautomers revert back to their canonical forms through a barrierless process, and (iii) the thermodynamic instability of the tautomers with respect to the canonical base pairs. Through similar reasoning, we also deduce that proton transfer in the A:T base pair does not contribute to single point mutations in DNA.
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Affiliation(s)
- A Gheorghiu
- Centre for Computational Science, University College London, London, UK
| | - P V Coveney
- Centre for Computational Science, University College London, London, UK.,Informatics Institute, University of Amsterdam, Amsterdam, The Netherlands
| | - A A Arabi
- Centre for Computational Science, University College London, London, UK.,College of Medicine and Health Sciences, Biochemistry Department, United Arab Emirates University, PO Box 17666, Al Ain, United Arab Emirates
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23
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Zdorevskyi OO, Perepelytsya SM. Dynamics of K + counterions around DNA double helix in the external electric field: A molecular dynamics study. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2020; 43:77. [PMID: 33306165 DOI: 10.1140/epje/i2020-12000-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 11/05/2020] [Indexed: 06/12/2023]
Abstract
The structure of DNA double helix is stabilized by metal counterions condensed to a diffuse layer around the macromolecule. The dynamics of counterions in real conditions is governed by the electric fields from DNA and other biological macromolecules. In the present work the molecular dynamics study was performed for the system of DNA double helix with neutralizing K+ counterions and for the system of KCl salt solution in an external electric field of different strength (up to 32mV/Å). The analysis of ionic conductivities of these systems has shown that the counterions around the DNA double helix are slowed down compared with the KCl salt solution. The calculated values of ion mobility are within (0.05-0.4)mS/cm depending on the orientation of the external electric field relatively to the double helix. Under the electric field parallel to the macromolecule K+ counterions move along the grooves of the double helix staying longer in the places with narrower minor groove. Under the electric field perpendicular to the macromolecule the dynamics of counterions is less affected by DNA atoms, and starting with the electric field values about 30mV/Å the double helix undergoes a phase transition from a double-stranded to a single-strand state.
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Affiliation(s)
- O O Zdorevskyi
- Bogolyubov Institute for Theoretical Physics of the National Academy of Sciences of Ukraine, 14-b, Metrolohichna Str., 03143, Kiev, Ukraine.
| | - S M Perepelytsya
- Bogolyubov Institute for Theoretical Physics of the National Academy of Sciences of Ukraine, 14-b, Metrolohichna Str., 03143, Kiev, Ukraine
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24
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Bouchal T, Durník I, Illík V, Réblová K, Kulhánek P. Importance of base-pair opening for mismatch recognition. Nucleic Acids Res 2020; 48:11322-11334. [PMID: 33080020 PMCID: PMC7672436 DOI: 10.1093/nar/gkaa896] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 09/09/2020] [Accepted: 09/30/2020] [Indexed: 01/04/2023] Open
Abstract
Mismatch repair is a highly conserved cellular pathway responsible for repairing mismatched dsDNA. Errors are detected by the MutS enzyme, which most likely senses altered mechanical property of damaged dsDNA rather than a specific molecular pattern. While the curved shape of dsDNA in crystallographic MutS/DNA structures suggests the role of DNA bending, the theoretical support is not fully convincing. Here, we present a computational study focused on a base-pair opening into the minor groove, a specific base-pair motion observed upon interaction with MutS. Propensities for the opening were evaluated in terms of two base-pair parameters: Opening and Shear. We tested all possible base pairs in anti/anti, anti/syn and syn/anti orientations and found clear discrimination between mismatches and canonical base-pairs only for the opening into the minor groove. Besides, the discrimination gap was also confirmed in hotspot and coldspot sequences, indicating that the opening could play a more significant role in the mismatch recognition than previously recognized. Our findings can be helpful for a better understanding of sequence-dependent mutability. Further, detailed structural characterization of mismatches can serve for designing anti-cancer drugs targeting mismatched base pairs.
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Affiliation(s)
- Tomáš Bouchal
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Ivo Durník
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Viktor Illík
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Kamila Réblová
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Petr Kulhánek
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
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25
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Rodríguez-Decuadro S, da Rosa G, Radío S, Barraco-Vega M, Benko-Iseppon AM, Dans PD, Smircich P, Cecchetto G. Antimicrobial peptides in the seedling transcriptome of the tree legume Peltophorum dubium. Biochimie 2020; 180:229-242. [PMID: 33197551 DOI: 10.1016/j.biochi.2020.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 09/14/2020] [Accepted: 11/03/2020] [Indexed: 10/23/2022]
Abstract
Antimicrobial peptides (AMPs) play an essential role in plant defense against invading pathogens. Due to their biological properties, these molecules have been considered useful for drug development, as novel agents in disease therapeutics, applicable to both agriculture and medicine. New technologies of massive sequencing open opportunities to discover novel AMP encoding genes in wild plant species. This work aimed to identify cysteine-rich AMPs from Peltophorum dubium, a legume tree from South America. We performed whole-transcriptome sequencing of P. dubium seedlings followed by de novo transcriptome assembly, uncovering 78 AMP transcripts classified into five families: hevein-like, lipid-transfer proteins (LTPs), alpha hairpinins, defensins, and snakin/GASA (Giberellic Acid Stimulated in Arabidopsis) peptides. No transcripts with similarity to cyclotide or thionin genes were identified. Genomic DNA analysis by PCR confirmed the presence of 18 genes encoding six putative defensins and 12 snakin/GASA peptides and allowed the characterization of their exon-intron structure. The present work demonstrates that AMP prediction from a wild species is possible using RNA sequencing and de novo transcriptome assembly, regarding a starting point for studies focused on AMP gene evolution and expression. Moreover, this study allowed the detection of strong AMP candidates for drug development and novel biotechnological products.
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Affiliation(s)
- Susana Rodríguez-Decuadro
- Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Garzón 780, Montevideo 12900, Uruguay.
| | - Gabriela da Rosa
- Departamento de Biociencias, Facultad de Química, Universidad de la República, General Flores 2124, Montevideo 11800, Uruguay.
| | - Santiago Radío
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable. MEC - Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo, 11400, Uruguay.
| | - Mariana Barraco-Vega
- Departamento de Biociencias, Facultad de Química, Universidad de la República, General Flores 2124, Montevideo 11800, Uruguay.
| | - Ana Maria Benko-Iseppon
- Universidade Federal de Pernambuco, Centro de Biociências, Av. Prof. Moraes Rego, 1235. CEP 50.670-420, Recife, PE, Brazil.
| | - Pablo D Dans
- Departamento de Ciencias Biológicas, CENUR Litoral Norte, Universidad de la República. General Fructuoso Rivera 1350, Laboratorio Genética Funcional, Institut Pasteur de Montevideo. Mataojo 2020, Salto 50000, Montevideo, 11400, Uruguay.
| | - Pablo Smircich
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable. MEC - Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo, 11400, Uruguay.
| | - Gianna Cecchetto
- Departamento de Biociencias, Facultad de Química, Universidad de la República, General Flores 2124, Montevideo 11800, Uruguay; Instituto de Química Biológica, Facultad de Ciencias - Facultad de Química, Universidad de la República, General Flores 2124, Montevideo, 11800, Uruguay.
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26
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Abstract
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Molecular association of proteins with nucleic
acids is required
for many biological processes essential to life. Electrostatic interactions
via ion pairs (salt bridges) of nucleic acid phosphates and protein
side chains are crucial for proteins to bind to DNA or RNA. Counterions
around the macromolecules are also key constituents for the thermodynamics
of protein–nucleic acid association. Until recently, there
had been only a limited amount of experiment-based information about
how ions and ionic moieties behave in biological macromolecular processes.
In the past decade, there has been significant progress in quantitative
experimental research on ionic interactions with nucleic acids and
their complexes with proteins. The highly negatively charged surfaces
of DNA and RNA electrostatically attract and condense cations, creating
a zone called the ion atmosphere. Recent experimental studies were
able to examine and validate theoretical models on ions and their
mobility and interactions with macromolecules. The ionic interactions
are highly dynamic. The counterions rapidly diffuse within the ion
atmosphere. Some of the ions are released from the ion atmosphere
when proteins bind to nucleic acids, balancing the charge via intermolecular
ion pairs of positively charged side chains and negatively charged
backbone phosphates. Previously, the release of counterions had been
implicated indirectly by the salt-concentration dependence of the
association constant. Recently, direct detection of counterion
release by NMR spectroscopy
has become possible and enabled more accurate and quantitative analysis
of the counterion release and its entropic impact on the thermodynamics
of protein–nucleic acid association. Recent studies also revealed
the dynamic nature of ion pairs of protein side chains and nucleic
acid phosphates. These ion pairs undergo transitions between two major
states. In one of the major states, the cation and the anion are in
direct contact and form hydrogen bonds. In the other major state,
the cation and the anion are separated by water. Transitions between
these states rapidly occur on a picosecond to nanosecond time scale.
When proteins interact with nucleic acids, interfacial arginine (Arg)
and lysine (Lys) side chains exhibit considerably different behaviors.
Arg side chains show a higher propensity to form rigid contacts with
nucleotide bases, whereas Lys side chains tend to be more mobile at
the molecular interfaces. The dynamic ionic interactions may facilitate
adaptive molecular recognition and play both thermodynamic and kinetic
roles in protein–nucleic acid interactions.
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Affiliation(s)
- Binhan Yu
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, United States
| | - B. Montgomery Pettitt
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, United States
| | - Junji Iwahara
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, United States
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Colibactin DNA-damage signature indicates mutational impact in colorectal cancer. Nat Med 2020; 26:1063-1069. [PMID: 32483361 DOI: 10.1038/s41591-020-0908-2] [Citation(s) in RCA: 140] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 04/23/2020] [Indexed: 02/06/2023]
Abstract
The mucosal epithelium is a common target of damage by chronic bacterial infections and the accompanying toxins, and most cancers originate from this tissue. We investigated whether colibactin, a potent genotoxin1 associated with certain strains of Escherichia coli2, creates a specific DNA-damage signature in infected human colorectal cells. Notably, the genomic contexts of colibactin-induced DNA double-strand breaks were enriched for an AT-rich hexameric sequence motif, associated with distinct DNA-shape characteristics. A survey of somatic mutations at colibactin target sites of several thousand cancer genomes revealed notable enrichment of this motif in colorectal cancers. Moreover, the exact double-strand-break loci corresponded with mutational hot spots in cancer genomes, reminiscent of a trinucleotide signature previously identified in healthy colorectal epithelial cells3. The present study provides evidence for the etiological role of colibactin in human cancer.
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28
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Liebl K, Zacharias M. How global DNA unwinding causes non-uniform stress distribution and melting of DNA. PLoS One 2020; 15:e0232976. [PMID: 32413048 PMCID: PMC7228070 DOI: 10.1371/journal.pone.0232976] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 04/24/2020] [Indexed: 12/31/2022] Open
Abstract
DNA unwinding is an important process that controls binding of proteins, gene expression and melting of double-stranded DNA. In a series of all-atom MD simulations on two DNA molecules containing a transcription start TATA-box sequence we demonstrate that application of a global restraint on the DNA twisting dramatically changes the coupling between helical parameters and the distribution of deformation energy along the sequence. Whereas only short range nearest-neighbor coupling is observed in the relaxed case, long-range coupling is induced in the globally restrained case. With increased overall unwinding the elastic deformation energy is strongly non-uniformly distributed resulting ultimately in a local melting transition of only the TATA box segment during the simulations. The deformation energy tends to be stored more in cytidine/guanine rich regions associated with a change in conformational substate distribution. Upon TATA box melting the deformation energy is largely absorbed by the melting bubble with the rest of the sequences relaxing back to near B-form. The simulations allow us to characterize the structural changes and the propagation of the elastic energy but also to calculate the associated free energy change upon DNA unwinding up to DNA melting. Finally, we design an Ising model for predicting the local melting transition based on empirical parameters. The direct comparison with the atomistic MD simulations indicates a remarkably good agreement for the predicted necessary torsional stress to induce a melting transition, for the position and length of the melted region and for the calculated associated free energy change between both approaches.
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Affiliation(s)
- Korbinian Liebl
- Physics Department T38, Technical University of Munich, Garching, Germany
| | - Martin Zacharias
- Physics Department T38, Technical University of Munich, Garching, Germany
- * E-mail:
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29
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Molecular Dynamics Simulations of DNA Adsorption on Graphene Oxide and Reduced Graphene Oxide-PEG-NH2 in the Presence of Mg2+ and Cl− ions. COATINGS 2020. [DOI: 10.3390/coatings10030289] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Graphene and its functionalised derivatives are transforming the development of biosensors that are capable of detecting nucleic acid hybridization. Using a Molecular Dynamics (MD) approach, we explored single-stranded or double-stranded deoxyribose nucleic acid (ssDNA or dsDNA) adsorption on two graphenic species: graphene oxide (GO) and reduced graphene oxide functionalized with aminated polyethylene glycol (rGO-PEG-NH2). Innovatively, we included chloride (Cl−) and magnesium (Mg2+) ions that influenced both the ssDNA and dsDNA adsorption on GO and rGO-PEG-NH2 surfaces. Unlike Cl−, divalent Mg2+ ions formed bridges between the GO surface and DNA molecules, promoting adsorption through electrostatic interactions. For rGO-PEG-NH2, the Mg2+ ions were repulsed from the graphenic surface. The subsequent ssDNA adsorption, mainly influenced by electrostatic forces and hydrogen bonds, could be supported by π–π stacking interactions that were absent in the case of dsDNA. We provide a novel insight for guiding biosensor development.
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30
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Walther J, Dans PD, Balaceanu A, Hospital A, Bayarri G, Orozco M. A multi-modal coarse grained model of DNA flexibility mappable to the atomistic level. Nucleic Acids Res 2020; 48:e29. [PMID: 31956910 PMCID: PMC7049737 DOI: 10.1093/nar/gkaa015] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 12/10/2019] [Accepted: 01/04/2020] [Indexed: 12/13/2022] Open
Abstract
We present a new coarse grained method for the simulation of duplex DNA. The algorithm uses a generalized multi-harmonic model that can represent any multi-normal distribution of helical parameters, thus avoiding caveats of current mesoscopic models for DNA simulation and representing a breakthrough in the field. The method has been parameterized from accurate parmbsc1 atomistic molecular dynamics simulations of all unique tetranucleotide sequences of DNA embedded in long duplexes and takes advantage of the correlation between helical states and backbone configurations to derive atomistic representations of DNA. The algorithm, which is implemented in a simple web interface and in a standalone package reproduces with high computational efficiency the structural landscape of long segments of DNA untreatable by atomistic molecular dynamics simulations.
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Affiliation(s)
- Jürgen Walther
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Pablo D Dans
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
- Department of Biological Sciences, CENUR North Coast, University of the Republic, 50000 Salto, Uruguay
| | - Alexandra Balaceanu
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Adam Hospital
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Genís Bayarri
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
- Department of Biochemistry and Biomedicine, The University of Barcelona, 08028 Barcelona, Spain
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31
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Perepelytsya S, Uličný J, Laaksonen A, Mocci F. Pattern preferences of DNA nucleotide motifs by polyamines putrescine2+, spermidine3+ and spermine4. Nucleic Acids Res 2020; 47:6084-6097. [PMID: 31114917 PMCID: PMC6614828 DOI: 10.1093/nar/gkz434] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 04/10/2019] [Accepted: 05/08/2019] [Indexed: 12/25/2022] Open
Abstract
The interactions of natural polyamines (putrescine2+, spermidine3+ and spermine4+) with DNA double helix are studied to characterize their nucleotide sequence pattern preference. Atomistic Molecular Dynamics simulations have been carried out for three systems consisting of the same DNA fragment d(CGCGAATTCGCGAATTCGCG) with different polyamines. The results show that polyamine molecules are localized with well-recognized patterns along the double helix with different residence times. We observed a clear hierarchy in the residence times of the polyamines, with the longest residence time (ca 100ns) in the minor groove. The analysis of the sequence dependence shows that polyamine molecules prefer the A-tract regions of the minor groove - in its narrowest part. The preferable localization of putrescine2+, spermidine3+ and spermine4+ in the minor groove with A-tract motifs is correlated with modulation of the groove width by a specific nucleotide sequences. We did develop a theoretical model pointing to the electrostatic interactions as the main driving force in this phenomenon, making it even more prominent for polyamines with higher charges. The results of the study explain the specificity of polyamine interactions with A-tract region of the DNA double helix which is also observed in experiments.
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Affiliation(s)
- Sergiy Perepelytsya
- Bogolyubov Institute for Theoretical Physics of the National Academy of Sciences of Ukraine, 03143 Kyiv, Ukraine.,Department of Theoretical and Mathematical Physics, Kyiv Academic University, 03142 Kyiv, Ukraine
| | - Jozef Uličný
- Department of Biophysics, Institute of Physics, P. J. Šafárik University, 041 54 Košice, Slovakia
| | - Aatto Laaksonen
- State Key Laboratory of Materials-Oriented and Chemical Engineering, Nanjing Tech University, 210009 Nanjing, China.,Division of Physical Chemistry, Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, 10691 Stockholm, Sweden.,Centre of Advanced Research in Bionanoconjugates and Biopolymers, Petru Poni Institute of Macromolecular Chemistry, Iasi, 700487, Romania
| | - Francesca Mocci
- Centre of Advanced Research in Bionanoconjugates and Biopolymers, Petru Poni Institute of Macromolecular Chemistry, Iasi, 700487, Romania.,Department of Chemical and Geological Sciences, University of Cagliari, I-09042 Monserrato, Italy
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32
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Dans PD, Balaceanu A, Pasi M, Patelli AS, Petkevičiūtė D, Walther J, Hospital A, Bayarri G, Lavery R, Maddocks JH, Orozco M. The static and dynamic structural heterogeneities of B-DNA: extending Calladine-Dickerson rules. Nucleic Acids Res 2019; 47:11090-11102. [PMID: 31624840 PMCID: PMC6868377 DOI: 10.1093/nar/gkz905] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 09/25/2019] [Accepted: 10/06/2019] [Indexed: 12/12/2022] Open
Abstract
We present a multi-laboratory effort to describe the structural and dynamical properties of duplex B-DNA under physiological conditions. By processing a large amount of atomistic molecular dynamics simulations, we determine the sequence-dependent structural properties of DNA as expressed in the equilibrium distribution of its stochastic dynamics. Our analysis includes a study of first and second moments of the equilibrium distribution, which can be accurately captured by a harmonic model, but with nonlocal sequence-dependence. We characterize the sequence-dependent choreography of backbone and base movements modulating the non-Gaussian or anharmonic effects manifested in the higher moments of the dynamics of the duplex when sampling the equilibrium distribution. Contrary to prior assumptions, such anharmonic deformations are not rare in DNA and can play a significant role in determining DNA conformation within complexes. Polymorphisms in helical geometries are particularly prevalent for certain tetranucleotide sequence contexts and are always coupled to a complex network of coordinated changes in the backbone. The analysis of our simulations, which contain instances of all tetranucleotide sequences, allow us to extend Calladine-Dickerson rules used for decades to interpret the average geometry of DNA, leading to a set of rules with quantitative predictive power that encompass nonlocal sequence-dependence and anharmonic fluctuations.
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Affiliation(s)
- Pablo D Dans
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology. Baldiri Reixac 10–12, 08028 Barcelona, Spain
- Department of Biological Sciences, University of the Republic (UdelaR), CENUR Gral. Rivera 1350, 50000 Salto, Uruguay
| | - Alexandra Balaceanu
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology. Baldiri Reixac 10–12, 08028 Barcelona, Spain
| | - Marco Pasi
- LBPA, École normale supérieure Paris-Saclay, 61 Av. du Pdt Wilson, Cachan 94235, France
- Bases Moléculaires et Structurales des Systèmes Infectieux, Univ. Lyon I/CNRS UMR 5086, IBCP, 7 Passage du Vercors, Lyon 69367, France
| | - Alessandro S Patelli
- Institute of Mathematics, Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland
| | - Daiva Petkevičiūtė
- Institute of Mathematics, Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland
- Faculty of Mathematics and Natural Sciences, Kaunas University of Technology, Studentų g. 50, 51368 Kaunas, Lithuania
| | - Jürgen Walther
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology. Baldiri Reixac 10–12, 08028 Barcelona, Spain
| | - Adam Hospital
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology. Baldiri Reixac 10–12, 08028 Barcelona, Spain
| | - Genís Bayarri
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology. Baldiri Reixac 10–12, 08028 Barcelona, Spain
| | - Richard Lavery
- Bases Moléculaires et Structurales des Systèmes Infectieux, Univ. Lyon I/CNRS UMR 5086, IBCP, 7 Passage du Vercors, Lyon 69367, France
| | - John H Maddocks
- Institute of Mathematics, Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology. Baldiri Reixac 10–12, 08028 Barcelona, Spain
- Department of Biochemistry and Molecular Biology. University of Barcelona, 08028 Barcelona, Spain
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33
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Hospital A, Battistini F, Soliva R, Gelpí JL, Orozco M. Surviving the deluge of biosimulation data. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2019. [DOI: 10.1002/wcms.1449] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Adam Hospital
- Institut de Recerca Biomèdica, IRB Barcelona, The Barcelona Institute of Science and Technology Joint IRB‐BSC Program in Computational Biology Barcelona Spain
| | - Federica Battistini
- Institut de Recerca Biomèdica, IRB Barcelona, The Barcelona Institute of Science and Technology Joint IRB‐BSC Program in Computational Biology Barcelona Spain
| | | | - Josep Lluis Gelpí
- Barcelona Supercomputing Center Join IRB‐BSC Program in Computational Biology Barcelona Spain
- Departament de Bioquímica i Biomedicina Universitat de Barcelona Barcelona Spain
| | - Modesto Orozco
- Institut de Recerca Biomèdica, IRB Barcelona, The Barcelona Institute of Science and Technology Joint IRB‐BSC Program in Computational Biology Barcelona Spain
- Departament de Bioquímica i Biomedicina Universitat de Barcelona Barcelona Spain
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34
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Balaceanu A, Buitrago D, Walther J, Hospital A, Dans PD, Orozco M. Modulation of the helical properties of DNA: next-to-nearest neighbour effects and beyond. Nucleic Acids Res 2019; 47:4418-4430. [PMID: 30957854 PMCID: PMC6511876 DOI: 10.1093/nar/gkz255] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 03/23/2019] [Accepted: 03/30/2019] [Indexed: 12/21/2022] Open
Abstract
We used extensive molecular dynamics simulations to study the structural and dynamic properties of the central d(TpA) step in the highly polymorphic d(CpTpApG) tetranucleotide. Contrary to the assumption of the dinucleotide-model and its nearest neighbours (tetranucleotide-model), the properties of the central d(TpA) step change quite significantly dependent on the next-to-nearest (hexanucleotide) sequence context and in a few cases are modulated by even remote neighbours (beyond next-to-nearest from the central TpA). Our results highlight the existence of previously undescribed dynamical mechanisms for the transmission of structural information into the DNA and demonstrate the existence of certain sequences with special physical properties that can impact on the global DNA structure and dynamics.
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Affiliation(s)
- Alexandra Balaceanu
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Diana Buitrago
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Jürgen Walther
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Adam Hospital
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Pablo D Dans
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain.,Department of Biochemistry and Biomedicine, University of Barcelona, 08028 Barcelona, Spain
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35
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Rodríguez-Decuadro S, Dans PD, Borba MA, Benko-Iseppon AM, Cecchetto G. Gene isolation and structural characterization of a legume tree defensin with a broad spectrum of antimicrobial activity. PLANTA 2019; 250:1757-1772. [PMID: 31428874 DOI: 10.1007/s00425-019-03260-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/09/2019] [Indexed: 06/10/2023]
Abstract
The recombinant EcgDf1 defensin has an antimicrobial effect against both plant and human pathogens. In silico analyses predict that EcgDf1 is prone to form dimers capable of interacting with the membranes of microorganisms. Plant defensins comprise a large family of antimicrobial peptides (AMP) with a wide range of biological functions. They are cysteine-rich molecules, highly sequence diverse but with a conserved and stable structure. In this work, a defensin gene (EcgDf1) was isolated from Erythrina crista-galli, a legume tree native from South America. The predicted peptide presents eight cysteines, with a γ-core motif GXCX3-9C and six cysteines distributed like the typical defensin αβ motif. The mature EcgDf1 coding sequence was heterologously expressed in Escherichia coli strains and purified by affinity chromatography. Possible dimer and oligomers of EcgDf1 were visible in SDS electrophoresis. Moreover, its 3D structure, determined by homology modeling, docking, and molecular dynamics simulations, was found to be compatible with the formation of homodimers between the β3 and β1-loop-α1, leaving the β2-loop-β3 free to interact with lipid membranes. The purified recombinant peptide inhibited the growth of several critical plant and human pathogens, like the opportunistic fungi Candida albicans and Aspergillus niger and the plant pathogens Clavibacter michiganensis ssp. michiganensis, Penicillium expansum, Botrytis cinerea, and Alternaria alternata. EcgDf1 is a promising candidate for the development of antimicrobial products for use in agriculture and medicine.
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Affiliation(s)
- Susana Rodríguez-Decuadro
- Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Garzón 780, 12900, Montevideo, Uruguay
| | - Pablo D Dans
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028, Barcelona, Spain
- Joint BSC-IRB Research Program in Computational Biology, Baldiri Reixac 10-12, 08028, Barcelona, Spain
| | - María Alejandra Borba
- Instituto de Química Biológica, Facultad de Ciencias-Facultad de Química, Universidad de la República, General Flores 2124, 11800, Montevideo, Uruguay
| | - Ana Maria Benko-Iseppon
- Universidade Federal de Pernambuco, Centro de Biociências, Av. Prof. Moraes Rego, 1235, Recife, PE, CEP 50.670-420, Brazil
| | - Gianna Cecchetto
- Departamento de Biociencias, Facultad de Química, Universidad de la República, General Flores 2124, 11800, Montevideo, Uruguay.
- Instituto de Química Biológica, Facultad de Ciencias-Facultad de Química, Universidad de la República, General Flores 2124, 11800, Montevideo, Uruguay.
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36
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Schauss J, Kundu A, Fingerhut BP, Elsaesser T. Contact Ion Pairs of Phosphate Groups in Water: Two-Dimensional Infrared Spectroscopy of Dimethyl Phosphate and ab Initio Simulations. J Phys Chem Lett 2019; 10:6281-6286. [PMID: 31560211 DOI: 10.1021/acs.jpclett.9b02157] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The interaction of phosphate groups with ions in an aqueous environment has a strong impact on the structure and folding processes of DNA and RNA. The dynamic variety of ionic arrangements, including both contact pairs and water separated ions, and the molecular coupling mechanisms are far from being understood. In a combined experimental and theoretical approach, we address the properties of contact ion pairs of the prototypical system dimethyl phosphate with Na+, Ca2+, and Mg2+ ions in water. Linear and femtosecond two-dimensional infrared (2D-IR) spectroscopy of the asymmetric (PO2)- stretching vibration separates and characterizes the different species via their blue-shifted vibrational signatures and 2D-IR line shapes. Phosphate-magnesium contact pairs stand out as the most compact geometry while the contact pairs with Ca2+ and Na+ display a wider structural variation. Microscopic density functional theory simulations rationalize the observed frequency shifts and reveal distinct differences between the contact geometries.
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Affiliation(s)
- Jakob Schauss
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , Berlin 12489 , Germany
| | - Achintya Kundu
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , Berlin 12489 , Germany
| | - Benjamin P Fingerhut
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , Berlin 12489 , Germany
| | - Thomas Elsaesser
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , Berlin 12489 , Germany
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37
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How B-DNA Dynamics Decipher Sequence-Selective Protein Recognition. J Mol Biol 2019; 431:3845-3859. [DOI: 10.1016/j.jmb.2019.07.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 07/09/2019] [Accepted: 07/10/2019] [Indexed: 11/23/2022]
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38
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Liebl K, Zacharias M. How methyl-sugar interactions determine DNA structure and flexibility. Nucleic Acids Res 2019; 47:1132-1140. [PMID: 30541032 PMCID: PMC6379717 DOI: 10.1093/nar/gky1237] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/26/2018] [Accepted: 11/30/2018] [Indexed: 12/18/2022] Open
Abstract
The sequence dependent structure and flexibility of the DNA double helix is of key importance for gene expression and DNA packing and it can be modulated by DNA modifications. The presence of a C5′-methyl group in thymine or the frequent C5′-methylated-cytosine affects the DNA fine structure, however, the underlying mechanism and steric origins have remained largely unexplained. Employing Molecular Dynamics free energy simulations that allow switching on or off interactions with the methyl groups in several DNA sequences, we systematically identified the physical origin of the coupling between methyl groups and DNA backbone fine structure. Whereas methyl-solvent and methyl–nucleobase interactions were found to be of minor importance, the methyl group interaction with the 5′ neighboring sugar was identified as main cause for influencing the population of backbone substates. The sterical methyl sugar clash prevents the formation of unconventional stabilizing hydrogen bonds between nucleobase and backbone. The technique was also used to study the contribution of methyl groups to DNA flexibility and served to explain why the presence of methyl sugar clashes in thymine and methyl-cytosine can result in an overall local increase of DNA flexibility.
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Affiliation(s)
- Korbinian Liebl
- Physics Department T38, Technical University of Munich, James-Franck-Str. 1, 85748 Garching, Germany
| | - Martin Zacharias
- Physics Department T38, Technical University of Munich, James-Franck-Str. 1, 85748 Garching, Germany
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39
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Sun Z, Wang X, Zhang JZH, He Q. Sulfur-substitution-induced base flipping in the DNA duplex. Phys Chem Chem Phys 2019; 21:14923-14940. [PMID: 31233058 DOI: 10.1039/c9cp01989h] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Base flipping is widely observed in a number of important biological processes. The genetic codes deposited inside the DNA duplex become accessible to external agents upon base flipping. The sulfur substitution of guanine leads to thioguanine, which alters the thermodynamic stability of the GC base pairs and the GT mismatches. Experimental studies conclude that the sulfur substitution decreases the lifetime of the GC base pair. In this work, under three AMBER force fields for nucleotide systems, we firstly performed equilibrium and nonequilibrium free energy simulations to investigate the variation of the thermodynamic profiles in base flipping upon sulfur substitution. It is found that the bsc0 modification, the bsc1 modification and the OL15 modification of AMBER force fields are able to qualitatively describe the sulfur-substitution dependent behavior of the thermodynamics. However, only the two last-generation AMBER force fields are able to provide quantitatively correct predictions. The second computational study on the sulfur substitutions focused on the relative stability of the S6G-C base pair and the S6G-T mismatch. Two conflicting experimental observations were reported by the same authors. One suggested that the S6G-C base pair was more stable, while the other concludes that the S6G-T mismatch was more stable. We answered this question by constructing the free energy profiles along the base flipping pathway computationally.
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Affiliation(s)
- Zhaoxi Sun
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China and Computational Biomedicine (IAS-5/INM-9), Forschungszentrum Jülich, Jülich 52425, Germany.
| | - Xiaohui Wang
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China and Institute of Computational Science, Università della Svizzera italiana (USI), Via Giuseppe Buffi 13, CH-6900, Lugano, Ticino, Switzerland
| | - John Z H Zhang
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China and NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China and Department of Chemistry, New York University, NY, NY 10003, USA
| | - Qiaole He
- Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, Wilhelm-Johnen-Str. 1, 52425 Jülich, Germany. and State Key Laboratory of Bioreactor Engineering, R&D Center of Separation and Extraction Technology in Fermentation Industry, East China University of Science and Technology, Shanghai 200237, China
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40
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Wang X, Sun Z. Determination of Base-Flipping Free-Energy Landscapes from Nonequilibrium Stratification. J Chem Inf Model 2019; 59:2980-2994. [PMID: 31124677 DOI: 10.1021/acs.jcim.9b00263] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Correct calculation of the variation of free energy upon base flipping is crucial in understanding the dynamics of DNA systems. The free-energy landscape along the flipping pathway gives the thermodynamic stability and the flexibility of base-paired states. Although numerous free-energy simulations are performed in the base flipping cases, no theoretically rigorous nonequilibrium techniques are devised and employed to investigate the thermodynamics of base flipping. In the current work, we report a general nonequilibrium stratification scheme for the efficient calculation of the free-energy landscape of base flipping in DNA duplex. We carefully monitor the convergence behavior of the equilibrium sampling based free-energy simulation and the nonequilibrium stratification and determine the empirical length of time blocks required for converged sampling. Comparison between the performances of the equilibrium umbrella sampling and the nonequilibrium stratification is given. The results show that nonequilibrium free-energy simulation achieves similar accuracy and efficiency compared with the equilibrium enhanced sampling technique in the base flipping cases. We further test a convergence criterion we previously proposed and it comes out that the convergence determined by this criterion agrees with those given by the time-invariant behavior of PMF and the nonlinear dependence of standard deviation on the sample size.
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Affiliation(s)
- Xiaohui Wang
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering , East China Normal University , Shanghai 200062 , China.,Institute of Computational Science , Università della Svizzera Italiana (USI) , Via Giuseppe Buffi 13 , CH-6900 , Lugano , Ticino , Switzerland
| | - Zhaoxi Sun
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering , East China Normal University , Shanghai 200062 , China.,Computational Biomedicine (IAS-5/INM-9) , Forschungszentrum Jülich , Jülich 52425 , Germany
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41
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Jakubec D, Vondrášek J. Can All-Atom Molecular Dynamics Simulations Quantitatively Describe Homeodomain-DNA Binding Equilibria? J Chem Theory Comput 2019; 15:2635-2648. [PMID: 30807142 DOI: 10.1021/acs.jctc.8b01144] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
We systematically investigate the applicability of a molecular dynamics-based setup for the calculations of standard binding free energies of biologically relevant protein-DNA complexes. The free energies are extracted from a potential of mean force calculated using umbrella sampling simulations. Two protein-DNA systems derived from a homeodomain transcription factor complex are studied in order to investigate the binding of both disordered and globular proteins. Free energies and trajectories obtained using two modern molecular mechanical force fields are compared to each other and to experimental data. The temperature dependence of the calculated standard binding free energies is investigated by performing all simulations over a range of temperatures. We show that the values of standard binding free energies obtained from these simulations are overestimated compared to experimental results. Significant differences are observed between the two protein-DNA systems and between the two force fields, which are explained by different propensities to form inter- and intramolecular contacts. The number of protein-DNA contacts increases with increasing temperature, in agreement with the experimentally known temperature dependence of enthalpies of binding. However, conclusions about the temperature dependence of the standard binding free energies cannot be made with confidence, as the differences among the values are on the order of statistical uncertainty.
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Affiliation(s)
- David Jakubec
- Bioinformatics Group, Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , 166 10 Praha 6, Czech Republic.,Department of Physical and Macromolecular Chemistry, Faculty of Science , Charles University , 128 43 Praha 2, Czech Republic
| | - Jiří Vondrášek
- Bioinformatics Group, Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , 166 10 Praha 6, Czech Republic
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42
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43
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Li MR, Zhang N, Zhang FS. Computational investigation of the conformation transitions of DNA in modified water models. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.08.129] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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44
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Jaiswal AK, Srivastava R, Pandey P, Bandyopadhyay P. Microscopic picture of water-ethylene glycol interaction near a model DNA by computer simulation: Concentration dependence, structure, and localized thermodynamics. PLoS One 2018; 13:e0206359. [PMID: 30427849 PMCID: PMC6235303 DOI: 10.1371/journal.pone.0206359] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 10/11/2018] [Indexed: 01/03/2023] Open
Abstract
It is known that crowded molecular environment affects the structure, thermodynamics, and dynamics of macromolecules. Most of the previous works on molecular crowding have majorly focused on the behavior of the macromolecule with less emphasis on the behavior of the crowder and water molecules. In the current study, we have precisely focused on the behavior of the crowder, (ethylene glycol (EG)), salt ions, and water in the presence of a DNA with the increase of the EG concentration. We have probed the behavior of water and crowder using molecular dynamics (MD) simulation and by calculating localized thermodynamic properties. Our results show an interesting competition between EG and water molecules to make hydrogen bonds (H-bond) with DNA. Although the total number of H-bonds involving DNA with both EG and water remains essentially same irrespective of the increase in EG concentration, there is a proportional change in the H-bonding pattern between water-water, EG-EG, and EG-water near DNA and in bulk. At low concentrations of EG, the displacement of water molecules near DNA is relatively easy. However, the displacement of water becomes more difficult as the concentration of EG increases. The density of Na+ (Cl-) near DNA increases (decreases) as the concentration of EG is increased. The density of Cl- near Na+ increases with the increase in EG concentration. It was also found that the average free energy per water in the first solvation shell increases with the increase in EG concentration. Putting all these together, a microscopic picture of EG, water, salt interaction in the presence of DNA, as a function of EG concentration, has emerged.
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Affiliation(s)
- Atul Kumar Jaiswal
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Rakesh Srivastava
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Preeti Pandey
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Pradipta Bandyopadhyay
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
- * E-mail:
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45
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Balaceanu A, Pérez A, Dans PD, Orozco M. Allosterism and signal transfer in DNA. Nucleic Acids Res 2018; 46:7554-7565. [PMID: 29905860 PMCID: PMC6125689 DOI: 10.1093/nar/gky549] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 05/11/2018] [Accepted: 06/06/2018] [Indexed: 12/14/2022] Open
Abstract
We analysed the basic mechanisms of signal transmission in DNA and the origins of the allostery exhibited by systems such as the ternary complex BAMHI-DNA-GRDBD. We found that perturbation information generated by a primary protein binding event travels as a wave to distant regions of DNA following a hopping mechanism. However, such a structural perturbation is transient and does not lead to permanent changes in the DNA geometry and interaction properties at the secondary binding site. The BAMHI-DNA-GRDBD allosteric mechanism does not occur through any traditional models: direct (protein-protein), indirect (reorganization of the secondary site) readout or solvent-release. On the contrary, it is generated by a subtle and less common entropy-mediated mechanism, which might have an important role to explain other DNA-mediated cooperative effects.
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Affiliation(s)
- Alexandra Balaceanu
- Joint IRB-BSC Program on Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Alberto Pérez
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Pablo D Dans
- Joint IRB-BSC Program on Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Modesto Orozco
- Joint IRB-BSC Program on Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
- Department of Biochemistry and Biomedicine, University of Barcelona, 08028 Barcelona, Spain
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46
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Ghoshdastidar D, Bansal M. Dynamics of physiologically relevant noncanonical DNA structures: an overview from experimental and theoretical studies. Brief Funct Genomics 2018; 18:192-204. [DOI: 10.1093/bfgp/ely026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 06/23/2018] [Accepted: 07/09/2018] [Indexed: 12/23/2022] Open
Abstract
Abstract
DNA is a complex molecule with phenomenal inherent plasticity and the ability to form different hydrogen bonding patterns of varying stabilities. These properties enable DNA to attain a variety of structural and conformational polymorphic forms. Structurally, DNA can exist in single-stranded form or as higher-order structures, which include the canonical double helix as well as the noncanonical duplex, triplex and quadruplex species. Each of these structural forms in turn encompasses an ensemble of dynamically heterogeneous conformers depending on the sequence composition and environmental context. In vivo, the widely populated canonical B-DNA attains these noncanonical polymorphs during important cellular processes. While several investigations have focused on the structure of these noncanonical DNA, studying their dynamics has remained nontrivial. Here, we outline findings from some recent advanced experimental and molecular simulation techniques that have significantly contributed toward understanding the complex dynamics of physiologically relevant noncanonical forms of DNA.
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Affiliation(s)
| | - Manju Bansal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
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Peters JP, Kowal EA, Pallan PS, Egli M, Maher LJ. Comparative analysis of inosine-substituted duplex DNA by circular dichroism and X-ray crystallography. J Biomol Struct Dyn 2018; 36:2753-2772. [PMID: 28818035 PMCID: PMC6251417 DOI: 10.1080/07391102.2017.1369164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Leveraging structural biology tools, we report the results of experiments seeking to determine if the different mechanical properties of DNA polymers with base analog substitutions can be attributed, at least in part, to induced changes from classical B-form DNA. The underlying hypothesis is that different inherent bending and twisting flexibilities may characterize non-canonical B-DNA, so that it is inappropriate to interpret mechanical changes caused by base analog substitution as resulting simply from 'electrostatic' or 'base stacking' influences without considering the larger context of altered helical geometry. Circular dichroism spectra of inosine-substituted oligonucleotides and longer base-substituted DNAs in solution indicated non-canonical helical conformations, with the degree of deviation from a standard B-form geometry depending on the number of I⋅C pairs. X-ray diffraction of a highly inosine-substituted DNA decamer crystal (eight I⋅C and two A⋅T pairs) revealed an A-tract-like conformation with a uniformly narrow minor groove, reduced helical rise, and the majority of sugars adopting a C1'-exo (southeastern) conformation. This contrasts with the standard B-DNA geometry with C2'-endo sugar puckers (south conformation). In contrast, the crystal structure of a decamer with only four I⋅C pairs has a geometry similar to that of the reference duplex with eight G⋅C and two A⋅T pairs. The unique crystal geometry of the inosine-rich duplex is noteworthy given its unusual CD signature in solution and the altered mechanical properties of some inosine-containing DNAs.
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Affiliation(s)
- Justin P. Peters
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, 200 First St. SW, Rochester, MN 55905, USA
| | - Ewa A. Kowal
- Department of Biochemistry, Vanderbilt University School of Medicine, 607 Light Hall, Nashville, TN 37232, USA
| | - Pradeep S. Pallan
- Department of Biochemistry, Vanderbilt University School of Medicine, 607 Light Hall, Nashville, TN 37232, USA
| | - Martin Egli
- Department of Biochemistry, Vanderbilt University School of Medicine, 607 Light Hall, Nashville, TN 37232, USA
| | - L. James Maher
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, 200 First St. SW, Rochester, MN 55905, USA,To whom correspondence should be addressed at
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Sweeny EA, Singh AB, Chakravarti R, Martinez-Guzman O, Saini A, Haque MM, Garee G, Dans PD, Hannibal L, Reddi AR, Stuehr DJ. Glyceraldehyde-3-phosphate dehydrogenase is a chaperone that allocates labile heme in cells. J Biol Chem 2018; 293:14557-14568. [PMID: 30012884 DOI: 10.1074/jbc.ra118.004169] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 07/05/2018] [Indexed: 11/06/2022] Open
Abstract
Cellular heme is thought to be distributed between a pool of sequestered heme that is tightly bound within hemeproteins and a labile heme pool required for signaling and transfer into proteins. A heme chaperone that can hold and allocate labile heme within cells has long been proposed but never been identified. Here, we show that the glycolytic protein glyceraldehyde-3-phosphate dehydrogenase (GAPDH) fulfills this role by acting as an essential repository and allocator of bioavailable heme to downstream protein targets. We identified a conserved histidine in GAPDH that is needed for its robust heme binding both in vitro and in mammalian cells. Substitution of this histidine, and the consequent decreases in GAPDH heme binding, antagonized heme delivery to both cytosolic and nuclear hemeprotein targets, including inducible nitric-oxide synthase (iNOS) in murine macrophages and the nuclear transcription factor Hap1 in yeast, even though this GAPDH variant caused cellular levels of labile heme to rise dramatically. We conclude that by virtue of its heme-binding property, GAPDH binds and chaperones labile heme to create a heme pool that is bioavailable to downstream proteins. Our finding solves a fundamental question in cell biology and provides a new foundation for exploring heme homeostasis in health and disease.
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Affiliation(s)
- Elizabeth A Sweeny
- From the Department of Inflammation and Immunity, Lerner Research Institute, The Cleveland Clinic, Cleveland, Ohio 44195
| | - Anuradha Bharara Singh
- From the Department of Inflammation and Immunity, Lerner Research Institute, The Cleveland Clinic, Cleveland, Ohio 44195
| | - Ritu Chakravarti
- From the Department of Inflammation and Immunity, Lerner Research Institute, The Cleveland Clinic, Cleveland, Ohio 44195
| | - Osiris Martinez-Guzman
- the School of Chemistry and Biochemistry and Parker Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Arushi Saini
- the School of Chemistry and Biochemistry and Parker Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Mohammad Mahfuzul Haque
- From the Department of Inflammation and Immunity, Lerner Research Institute, The Cleveland Clinic, Cleveland, Ohio 44195
| | - Greer Garee
- From the Department of Inflammation and Immunity, Lerner Research Institute, The Cleveland Clinic, Cleveland, Ohio 44195
| | - Pablo D Dans
- the Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Balidiri Reixac 10-12, Barcelona 08028, Spain, and
| | - Luciana Hannibal
- the Laboratory of Clinical Biochemistry and Metabolism, Center of Pediatrics, Medical Center, University of Freiburg, D-79106 Freiburg, Germany
| | - Amit R Reddi
- the School of Chemistry and Biochemistry and Parker Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Dennis J Stuehr
- From the Department of Inflammation and Immunity, Lerner Research Institute, The Cleveland Clinic, Cleveland, Ohio 44195,
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49
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Špačková N, Réblová K. Role of Inosine⁻Uracil Base Pairs in the Canonical RNA Duplexes. Genes (Basel) 2018; 9:genes9070324. [PMID: 29958383 PMCID: PMC6070904 DOI: 10.3390/genes9070324] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/13/2018] [Accepted: 06/26/2018] [Indexed: 01/09/2023] Open
Abstract
Adenosine to inosine (A–I) editing is the most common modification of double-stranded RNA (dsRNA). This change is mediated by adenosine deaminases acting on RNA (ADARs) enzymes with a preference of U>A>C>G for 5′ neighbor and G>C=A>U or G>C>U=A for 3′ neighbor. A–I editing occurs most frequently in the non-coding regions containing repetitive elements such as ALUs. It leads to disruption of RNA duplex structure, which prevents induction of innate immune response. We employed standard and biased molecular dynamics (MD) simulations to analyze the behavior of RNA duplexes with single and tandem inosine–uracil (I–U) base pairs in different sequence context. Our analysis showed that the I–U pairs induce changes in base pair and base pair step parameters and have different dynamics when compared with standard canonical base pairs. In particular, the first I–U pair from tandem I–U/I–U systems exhibited increased dynamics depending on its neighboring 5′ base. We discovered that UII sequence, which is frequently edited, has lower flexibility compared with other sequences (AII, GII, CII), hence it only modestly disrupts dsRNA. This might indicate that the UAA motifs in ALUs do not have to be sufficiently effective in preventing immune signaling.
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Affiliation(s)
- Naďa Špačková
- Department of Condensed Matter Physics, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic.
| | - Kamila Réblová
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.
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50
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Hydration of counterions interacting with DNA double helix: a molecular dynamics study. J Mol Model 2018; 24:171. [DOI: 10.1007/s00894-018-3704-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 06/06/2018] [Indexed: 12/12/2022]
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