1
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Roy A, Ray S. Traversing DNA-Protein Interactions Between Mesophilic and Thermophilic Bacteria: Implications from Their Cold Shock Response. Mol Biotechnol 2024; 66:824-844. [PMID: 36905463 DOI: 10.1007/s12033-023-00711-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 02/25/2023] [Indexed: 03/12/2023]
Abstract
Cold shock proteins (CSPs) are small, acidic proteins which contain a conserved nucleic acid-binding domain. These perform mRNA translation acting as "RNA chaperones" when triggered by low temperatures initiating their cold shock response. CSP- RNA interactions have been predominantly studied. Our focus will be CSP-DNA interaction examination, to analyse the diverse interaction patterns such as electrostatic, hydrogen and hydrophobic bonding in both thermophilic and mesophilic bacteria. The differences in the molecular mechanism of these contrasting bacterial proteins are studied. Computational techniques such as modelling, energy refinement, simulation and docking were operated to obtain data for comparative analysis. The thermostability factors which stabilise a thermophilic bacterium and their effect on their molecular regulation is investigated. Conformational deviation, atomic residual fluctuations, binding affinity, Electrostatic energy and Solvent Accessibility energy were determined during stimulation along with their conformational study. The study revealed that mesophilic bacteria E. coli CSP have higher binding affinity to DNA than thermophilic G. stearothermophilus. This was further evident by low conformation deviation and atomic fluctuations during simulation.
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Affiliation(s)
- Alankar Roy
- Amity Institute of Biotechnology, Amity University, Kolkata, India
| | - Sujay Ray
- Amity Institute of Biotechnology, Amity University, Kolkata, India.
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2
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Dhotre K, Dass D, Banerjee A, Nema V, Mukherjee A. A Computational Approach for Designing and Validating Small Interfering RNA against SARS-CoV-2 Variants. Curr Comput Aided Drug Des 2024; 20:876-887. [PMID: 37622690 DOI: 10.2174/1573409920666230825111406] [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: 04/17/2023] [Revised: 07/06/2023] [Accepted: 07/19/2023] [Indexed: 08/26/2023]
Abstract
AIMS The aim of this study is to develop a novel antiviral strategy capable of efficiently targeting a broad set of SARS-CoV-2 variants. BACKGROUND Since the first emergence of SARS-CoV-2, it has rapidly transformed into a global pandemic, posing an unprecedented threat to public health. SARS-CoV-2 is prone to mutation and continues to evolve, leading to the emergence of new variants capable of escaping immune protection achieved due to previous SARS-CoV-2 infections or by vaccination. OBJECTIVE RNA interference (RNAi) is a remarkable biological mechanism that can induce gene silencing by targeting complementary mRNA and inhibiting its translation. METHODS In this study, using the computational approach, we predicted the most efficient siRNA capable of inhibiting SARS-CoV-2 variants of concern (VoCs). RESULTS The presented siRNA was characterized and evaluated for its thermodynamic properties, offsite-target hits, and in silico validation by molecular docking and molecular dynamics simulations (MD) with Human AGO2 protein. CONCLUSION The study contributes to the possibility of designing and developing an effective response strategy against existing variants of concerns and preventing further.
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Affiliation(s)
- Kishore Dhotre
- Division of Virology, ICMR-National AIDS Research Institute, Pune, MH, India
| | - Debashree Dass
- Division of Virology, ICMR-National AIDS Research Institute, Pune, MH, India
| | - Anwesha Banerjee
- Division of Virology, ICMR-National AIDS Research Institute, Pune, MH, India
| | - Vijay Nema
- Division of Molecular Biology, ICMR-National AIDS Research Institute, Pune, MH, India
| | - Anupam Mukherjee
- Division of Virology, ICMR-National AIDS Research Institute, Pune, MH, India
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3
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Winkler L, Galindo-Murillo R, Cheatham TE. Assessment of A- to B- DNA Transitions Utilizing the Drude Polarizable Force Field. J Chem Theory Comput 2023; 19:8955-8966. [PMID: 38014857 PMCID: PMC10720382 DOI: 10.1021/acs.jctc.3c01002] [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: 09/13/2023] [Revised: 11/12/2023] [Accepted: 11/13/2023] [Indexed: 11/29/2023]
Abstract
In addition to the well-characterized B-form of DNA, duplex DNA can adopt various conformations, such as A or Z-DNA. Though less common, these structures can be induced biologically through protein or ligand interactions or experimentally with niche environmental conditions, such as high salt concentrations or in mixed water-ethanol. Reproducing these alternate structures through molecular dynamics simulations in recent years has been quite challenging with the currently available force fields, simulation techniques, and time scales. In this study, the Drude polarizable force field is tested for its ability to facilitate transitions between A-DNA and B-DNA or maintain A-DNA. Though transitions away from B-DNA were observed in high concentrations of ethanol, the resulting structures had hybrid properties taken from both B-DNA and A-DNA structures. This was also true for A-DNA in ethanol, which lost some of the A-DNA properties that it was expected to maintain. When B-DNA was tested in high salt environments, the resulting B-DNA structures showed no distinguishable differences with the increasing salt concentrations tested. These results with the Drude FF and recent results with additive force fields suggest that at present the current additive and polarizable force fields do not facilitate a complete transition between B- to A-DNA conformations under the conditions simulated. At present, the Drude FF favors A-B DNA hybrid structures when simulated in nonphysiological conditions.
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Affiliation(s)
- Lauren Winkler
- Department
of Medicinal Chemistry, College of Pharmacy, University of Utah, 2000 East 30 South Skaggs 306, Salt Lake City, Utah 84112,United States
| | - Rodrigo Galindo-Murillo
- Department
of Medicinal Chemistry, Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - 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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4
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Jonas F, Carmi M, Krupkin B, Steinberger J, Brodsky S, Jana T, Barkai N. The molecular grammar of protein disorder guiding genome-binding locations. Nucleic Acids Res 2023; 51:4831-4844. [PMID: 36938874 PMCID: PMC10250222 DOI: 10.1093/nar/gkad184] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 01/25/2023] [Accepted: 03/15/2023] [Indexed: 03/21/2023] Open
Abstract
Intrinsically disordered regions (IDRs) direct transcription factors (TFs) towards selected genomic occurrences of their binding motif, as exemplified by budding yeast's Msn2. However, the sequence basis of IDR-directed TF binding selectivity remains unknown. To reveal this sequence grammar, we analyze the genomic localizations of >100 designed IDR mutants, each carrying up to 122 mutations within this 567-AA region. Our data points at multivalent interactions, carried by hydrophobic-mostly aliphatic-residues dispersed within a disordered environment and independent of linear sequence motifs, as the key determinants of Msn2 genomic localization. The implications of our results for the mechanistic basis of IDR-based TF binding preferences are discussed.
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Affiliation(s)
- Felix Jonas
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Miri Carmi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Beniamin Krupkin
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Joseph Steinberger
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sagie Brodsky
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Tamar Jana
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Naama Barkai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
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5
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Dhotre K, Banerjee A, Dass D, Nema V, Mukherjee A. An In-silico Approach to Design and Validate siRNA against Monkeypox Virus. Curr Pharm Des 2023; 29:3060-3072. [PMID: 38062661 DOI: 10.2174/0113816128275065231103063935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 10/11/2023] [Indexed: 01/05/2024]
Abstract
INTRODUCTION The monkeypox virus has emerged as an uncommon zoonotic infection. The recent outbreak of MPXV in Europe and abroad in 2022 presented a major threat to individuals at risk. At present, no specific MPXV vaccinations or medications are available. METHODS In this study, we predicted the most effective siRNA against the conserved region of the MPXV and validated the activity by performing molecular docking studies. RESULTS Ultimately, the most efficient siRNA molecule was shortlisted against the envelope protein gene (B6R) based on its toxicity, effectivity, thermodynamic stability, molecular interaction, and molecular dynamics simulations (MD) with the Human Argonaute 2 protein. CONCLUSION Thus, the strategy may offer a platform for the development of potential antiviral RNA therapeutics that target MPXV at the genomic level.
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Affiliation(s)
- Kishore Dhotre
- Division of Virology, ICMR-National AIDS Research Institute, Pune 411026, Maharashtra, India
| | - Anwesha Banerjee
- Division of Virology, ICMR-National AIDS Research Institute, Pune 411026, Maharashtra, India
| | - Debashree Dass
- Division of Virology, ICMR-National AIDS Research Institute, Pune 411026, Maharashtra, India
| | - Vijay Nema
- Molecular Biology, National AIDS Research Institute, Pune 411026, India
| | - Anupam Mukherjee
- Division of Virology, ICMR-National AIDS Research Institute, Pune 411026, Maharashtra, India
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6
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Meredith RJ, McGurn M, Euell C, Rutkowski P, Cook E, Carmichael I, Serianni AS. MA'AT Analysis of Aldofuranosyl Rings: Unbiased Modeling of Conformational Equilibria and Dynamics in Solution. Biochemistry 2022; 61:239-251. [PMID: 35104120 DOI: 10.1021/acs.biochem.1c00630] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
MA'AT analysis has been applied to methyl β-d-ribofuranoside (3) and methyl 2-deoxy-β-d-erythro-pentofuranoside (4) to demonstrate the ability of this new experimental method to determine multi-state conformational equilibria in solution. Density functional theory (DFT) was used to obtain parameterized equations for >20 NMR spin-coupling constants sensitive to furanose ring conformation in 3 and 4, and these equations were used in conjunction with experimental spin-couplings to produce unbiased MA'AT models of ring pseudorotation. These models describe two-state north-south conformational exchange consistent with results obtained from traditional treatments of more limited sets of NMR spin-couplings (e.g., PSEUROT). While PSEUROT, MA'AT, and aqueous molecular dynamics models yielded similar two-state models, MA'AT analysis gives more reliable results since significantly more experimental observables are employed compared to PSEUROT, and no assumptions are needed to render the fitting tractable. MA'AT models indicate a roughly equal distribution of north and south ring conformers of 4 in aqueous (2H2O) solution compared to ∼80% north forms for 3. Librational motion about the mean pseudorotation phase angles P of the preferred north and south conformers of 3 in solution is more constrained than that for 4. The greater rigidity of the β-ribo ring may be caused by synergistic stereoelectronic effects and/or noncovalent (e.g., hydrogen-bonding) interactions in solution that preferentially stabilize north forms of 3. MA'AT analysis of oligonucleotides and other furanose ring-containing biomolecules promises to improve current experimental models of sugar ring behavior in solution and help reveal context effects on ring conformation in more complex biologically important systems.
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Affiliation(s)
- Reagan J Meredith
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana46556-5670, United States
| | - Margaret McGurn
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana46556-5670, United States
| | - Christopher Euell
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana46556-5670, United States
| | - Peter Rutkowski
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana46556-5670, United States
| | - Evan Cook
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana46556-5670, United States
| | - Ian Carmichael
- Radiation Laboratory, University of Notre Dame, Notre Dame, Indiana46556-5670, United States
| | - Anthony S Serianni
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana46556-5670, United States
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7
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Zhang X, Zheng Q. How DNA affects the hyperthermophilic protein Ape10b2 for oligomerization: an investigation using multiple short molecular dynamics simulations. Phys Chem Chem Phys 2021; 23:25841-25849. [PMID: 34763347 DOI: 10.1039/d1cp04341b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Alba2 is a hyperthermophilic DNA-binding protein, and DNA plays a crucial role in the Alba2 oligomerization process. It is a pity that there is limited research in terms of how DNA affects the conformational change of Alba2 in oligomerization. Herein, we complement the crystal structure of the Ape10b2 (belongs to Alba2)-dsDNA complex (PDB ID: 3U6Y) and employ multiple short molecular dynamics (MSMD) simulations to illuminate the influence of DNA on Ape10b2 at four temperatures (300, 343, 363, and 373 K). Our results indicate that DNA could cause the conformational changes of two important regions (loop1 and loop5), which may be beneficial for protein oligomerization. The results of hydrogen bond analysis show that the increasing number of hydrogen bonds between two monomers of Ape10b2 may also be a favorable factor for oligomerization. In addition, Ape10b2 can stabilize DNA by electrostatic interactions with an increase in temperature, and five residues (Arg40, Arg42, Asn43, Asn45, and Arg46) play a stabilizing role during protein binding to DNA. Our findings could help in understanding the favorable factors leading to protein oligomerization, which contributes to enzyme engineering research from an industrial perspective.
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Affiliation(s)
- Xue Zhang
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, 130023, People's Republic of China.
| | - Qingchuan Zheng
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, 130023, People's Republic of China. .,Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University, Changchun, 130023, People's Republic of China
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8
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Strelnikov IA, Kovaleva NA, Zubova EA. Variability of the DNA Backbone Geometry in DNA-Protein Complexes: Experimental Data Analysis. J Chem Inf Model 2021; 61:4783-4794. [PMID: 34529915 DOI: 10.1021/acs.jcim.1c00506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have analyzed and compared the available experimental data (PDB) on the backbone geometry of the DNA in solution (NMR), in crystals (X-rays), and in complexes with proteins (X-rays and cryo-electron microscopy). The deoxyribose (pseudorotational angle τ0) and ε/ζ (BI-BII transition in phosphates) flexibilities are practically the same in the four samples. The α/γ mobility is minimal in crystalline DNA: on the histograms, there is one canonical and one noncanonical t/t peak. The α/γ mobility increases in DNA solutions (three more noncanonical peaks) and is maximal in DNA-protein complexes (another additional peak). On a large amount of data, we have confirmed that the three main degrees of freedom of the sugar-phosphate backbone are "orthogonal": changes in any of the angles τ0, (ζ-ε), and (γ-α) occur, as a rule, at a constant (usually canonical) value of any other. In the DNA-protein complexes, none of the geometrical parameters commonly used to distinguish the A and B forms of DNA, except for Zp and its simpler analog Zp', show an unambiguous correlation with τ0. Proteins, binding to DNA, in 59% of cases change the local shape of the helix up to the characteristic of the A-form without switching the deoxyribose conformation from south to north. However, we have found simple local characteristics of one nucleotide that correlate with the angles τ0 and (ζ-ε). These are the angles C3'C1'N* and C4'C3'P(2), respectively. They are orthogonal in DNA-protein complexes exactly as the pair τ0 and (ζ-ε). Most characteristics of DNA in complexes with proteins are the same in X-ray and in cryo-EM data, except for the histogram for the angle τ0. We offer a possible explanation for this difference. We also discuss the artifacts on the ε/ζ histogram for DNA in solutions caused by the currently used NMR refinement protocols.
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Affiliation(s)
- Ivan A Strelnikov
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 4 Kosygin Street, Moscow 119991, Russia
| | - Natalya A Kovaleva
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 4 Kosygin Street, Moscow 119991, Russia
| | - Elena A Zubova
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 4 Kosygin Street, Moscow 119991, Russia
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9
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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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10
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Mozo-Villarías A, Cedano J, Querol E. The importance of hydrophobic interactions in the structure of transcription systems. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2021; 50:951-961. [PMID: 34131772 DOI: 10.1007/s00249-021-01557-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 12/01/2022]
Abstract
Hydrophobic forces play a crucial role in both the stability of B DNA and its interactions with proteins. In the present study, we postulate that the hydrophobic effect is an essential component in establishing specificity in the interaction transcription factor proteins with their consensus DNA sequence partners. The PDB coordinates of more than 50 transcription systems have been used to analyze the hydrophobic attraction of proteins towards their DNA consensus. This analysis includes computing the hydrophobic energy of the interacting molecules by means of their hydrophobic moments. Hydrophobic moments have successfully been used in previous studies involving self-assembly protein systems. In the present case, in spite of some variability, we found specificity in transcription factors when interacting with their respective consensus DNA sequences. By applying our model of biological membrane pattern for hydrophobic interactions, we postulate that hydrophobic forces constitute the necessary intermediate interaction between the unspecific electrostatic attraction for DNA phosphate groups and the very short-range interaction promoting hydrogen bonds. We conclude that hydrophobic interactions serve as the intermediate force guiding transcriptions factors towards the proper hydrogen bonds to their DNAs.
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Affiliation(s)
- Angel Mozo-Villarías
- Departament de Bioquímica i Biologia Molecular, Campus de Bellaterra, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.
| | - Juan Cedano
- Departament de Bioquímica i Biologia Molecular, Campus de Bellaterra, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Enrique Querol
- Departament de Bioquímica i Biologia Molecular, Campus de Bellaterra, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
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11
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Liu T, Yu T, Zhang S, Wang Y, Zhang W. Thermodynamic and kinetic properties of a single base pair in A-DNA and B-DNA. Phys Rev E 2021; 103:042409. [PMID: 34005973 DOI: 10.1103/physreve.103.042409] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 03/27/2021] [Indexed: 11/07/2022]
Abstract
Double stranded DNA can adopt different forms, the so-called A-, B-, and Z-DNA, which play different biological roles. In this work, the thermodynamic and the kinetic parameters for the base-pair closing and opening in A-DNA and B-DNA were calculated by all-atom molecular dynamics simulations at different temperatures. The thermodynamic parameters of the base pair in B-DNA were in good agreement with the experimental results. The free energy barrier of breaking a single base stack results from the enthalpy increase ΔH caused by the disruption of hydrogen bonding and base-stacking interactions, as well as water and base interactions. The free energy barrier of base pair closing comes from the unfavorable entropy loss ΔS caused by the restriction of torsional angles and hydration. It was found that the enthalpy change ΔH and the entropy change ΔS for the base pair in A-DNA are much larger than those in B-DNA, and the transition rates between the opening and the closing state for the base pair in A-DNA are much slower than those in B-DNA. The large difference of the enthalpy and entropy change for forming the base pair in A-DNA and B-DNA results from different hydration in A-DNA and B-DNA. The hydration pattern observed around DNA is an accompanying process for forming the base pair, rather than a follow-up of the conformation.
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Affiliation(s)
- Taigang Liu
- Department of Physics Wuhan University, Wuhan 430072, China
- School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China
| | - Ting Yu
- Department of Physics Wuhan University, Wuhan 430072, China
| | - Shuhao Zhang
- Department of Physics Wuhan University, Wuhan 430072, China
| | - Yujie Wang
- Department of Physics Wuhan University, Wuhan 430072, China
- Department of Physics and Telecommunication Engineering, Zhoukou Normal University, Zhoukou 466000, China
| | - Wenbing Zhang
- Department of Physics Wuhan University, Wuhan 430072, China
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12
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Kovaleva N, Strelnikov IA, Zubova EA. Kinetics of the Conformational Transformation between B- and A-Forms in the Drew-Dickerson Dodecamer. ACS OMEGA 2020; 5:32995-33006. [PMID: 33403261 PMCID: PMC7774075 DOI: 10.1021/acsomega.0c04247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 12/03/2020] [Indexed: 06/12/2023]
Abstract
Some DNA sequences in crystals and in complexes with proteins can exist in the forms intermediate between the B- and A-DNA. Based on this, it was implied that the B-to-A transition for any DNA molecule should go through these intermediate forms also in kinetics. More precisely, the helix parameter Slide has to change first, and the molecule should take the E-form. After that, the Roll parameter changes. In the present work, we simulated the kinetics of the B-A transition in the Drew-Dickerson dodecamer, a known B-philic DNA oligomer. We used the "sugar" coarse-grained model that reproduces ribose flexibility, preserves sequence specificity, employs implicit water and explicit ions, and offers the possibility to vary friction. As the control parameter of the transition, we chose the volume available for a counterion and considered the change from a large to a small volume. In the described system, the B-to-A conformational transformation proved to correspond to a first-order phase transition. The molecule behaves like a small cluster in the region of such a transition, jumping between the A- and B-forms in a wide range of available volumes. The viscosity of the solvent does not affect the midpoint of the transition but only the overall mobility of the system. All helix parameters change synchronously on average, we have not observed the sequence "Slide first, Roll later" in kinetics, and the E-DNA is not a necessary step for the transition between the B- and A-forms in the studied system. So, the existence of the intermediate DNA forms requires specific conditions, shifting the common balance of interactions: certain nucleotide sequence in specific solution or/and the interaction with some protein.
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13
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Perret G, Boschetti E. Aptamer-Based Affinity Chromatography for Protein Extraction and Purification. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2020; 174:93-139. [PMID: 31485702 DOI: 10.1007/10_2019_106] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Aptamers are oligonucleotide molecules able to recognize very specifically proteins. Among the possible applications, aptamers have been used for affinity chromatography with effective results and advantages over most advanced protein separation technologies. This chapter first discusses the context of the affinity chromatography with aptamer ligands. With the adaptation of SELEX, the chemical modifications of aptamers to comply with the covalent coupling and the separation process are then extensively presented. A focus is then made about the most important applications for protein separation with real-life examples and the comparison with immunoaffinity chromatography. In spite of well-advanced demonstrations and the extraordinary potential developments, a significant optimization work is still due to deserve large-scale applications with all necessary validations. Graphical Abstract Aptamer-protein complexes by X-ray crystallography.
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14
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Faltejsková K, Jakubec D, Vondrášek J. Hydrophobic Amino Acids as Universal Elements of Protein-Induced DNA Structure Deformation. Int J Mol Sci 2020; 21:ijms21113986. [PMID: 32498246 PMCID: PMC7312683 DOI: 10.3390/ijms21113986] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/26/2020] [Accepted: 05/29/2020] [Indexed: 12/01/2022] Open
Abstract
Interaction with the DNA minor groove is a significant contributor to specific sequence recognition in selected families of DNA-binding proteins. Based on a statistical analysis of 3D structures of protein–DNA complexes, we propose that distortion of the DNA minor groove resulting from interactions with hydrophobic amino acid residues is a universal element of protein–DNA recognition. We provide evidence to support this by associating each DNA minor groove-binding amino acid residue with the local dimensions of the DNA double helix using a novel algorithm. The widened DNA minor grooves are associated with high GC content. However, some AT-rich sequences contacted by hydrophobic amino acids (e.g., phenylalanine) display extreme values of minor groove width as well. For a number of hydrophobic amino acids, distinct secondary structure preferences could be identified for residues interacting with the widened DNA minor groove. These results hold even after discarding the most populous families of minor groove-binding proteins.
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Affiliation(s)
- Kateřina Faltejsková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 542/2, 166 10 Prague 6, Czech Republic;
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, 128 00 Prague 2, Czech Republic
| | - David Jakubec
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 542/2, 166 10 Prague 6, Czech Republic;
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Hlavova 8, 128 40 Prague 2, Czech Republic
- Correspondence: (D.J.); (J.V.); Tel.: +420-220183267 (J.V.)
| | - Jiří Vondrášek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 542/2, 166 10 Prague 6, Czech Republic;
- Correspondence: (D.J.); (J.V.); Tel.: +420-220183267 (J.V.)
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15
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Vickers TA, Migawa MT, Seth PP, Crooke ST. Interaction of ASOs with PC4 Is Highly Influenced by the Cellular Environment and ASO Chemistry. J Am Chem Soc 2020; 142:9661-9674. [PMID: 32374993 DOI: 10.1021/jacs.0c01808] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The activity of PS-ASOs is strongly influenced by association with both inter- and intracellular proteins. The sequence, chemical nature, and structure of the ASO can have profound influences on the interaction of PS-ASOs with specific proteins. A more thorough understanding of how these pharmacological agents interact with various proteins and how chemical modifications, sequence, and structure influence interactions with proteins is needed to inform future ASO design efforts. To better understand the chemistry of PS-ASO interactions, we have focused on human positive cofactor 4 (PC4). Although several studies have investigated the in vitro binding properties of PC4 with endogenous nucleic acids, little is known about the chemistry of interaction of PS-ASOs with this protein. Here we examine in detail the impact of ASO backbone chemistry, 2'-modifications, and buffer environment on the binding affinity of PC4. In addition, using site-directed mutagenesis, we identify those amino acids that are specifically required for ASO binding interactions, and by substitution of abasic nucleotides we identify the positions on the ASO that most strongly influence affinity for PC4. Finally, to confirm that the interactions observed in vitro are biologically relevant, we use a recently developed complementation reporter system to evaluate the kinetics and subcellular localization of the interaction of ASO and PC4 in live cells.
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Affiliation(s)
- Timothy A Vickers
- Department of Core Antisense Research, IONIS Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Michael T Migawa
- Department of Medicinal ChemistryIONIS Pharmaceuticals, Inc.2855 Gazelle CourtCarlsbadCalifornia92010United States
| | - Punit P Seth
- Department of Medicinal ChemistryIONIS Pharmaceuticals, Inc.2855 Gazelle CourtCarlsbadCalifornia92010United States
| | - Stanley T Crooke
- Department of Core Antisense Research, IONIS Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, California 92010, United States
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16
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Vickers TA, Rahdar M, Prakash TP, Crooke ST. Kinetic and subcellular analysis of PS-ASO/protein interactions with P54nrb and RNase H1. Nucleic Acids Res 2020; 47:10865-10880. [PMID: 31495875 PMCID: PMC6846478 DOI: 10.1093/nar/gkz771] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 08/21/2019] [Accepted: 08/28/2019] [Indexed: 01/16/2023] Open
Abstract
The rapid RNase H1-dependent mislocalization of heterodimer proteins P54nrb and PSF to nucleoli is an early event in the pathway that explains the effects of most toxic phosphorothioate ASOs (PS-ASOs). Using a recently developed NanoLuciferace (NLuc)-based structural complementation reporter system which allows us to observe ASO/protein interactions in real time in live cells, we have determined that safe and toxic PS-ASOs associate with these proteins with kinetics and impact on subcellular localization that differ. Toxic PS-ASOs interact in a complex that includes RNase H1, P54nrb and PSF; but RNase H1/P54nrb complexes were observed in only the cells treated with toxic, but not safe PS-ASOs. In addition, experiments performed in vitro suggest that RNA is also a required component of the complex. The protein–protein interaction between P54nrb and RNase H1 requires the spacer region of RNAse H1, while the P54nrb core domains are required for association with RNase H1. In addition, we have determined that PS-ASOs bind P54nrb via RRM1 and RRM2, while they bind RNase H1 primarily via the hybrid binding domain, however catalytic domain interactions also contribute to overall affinity. These ASO–protein interactions are highly influenced by the chemistry of the PS-ASO binding environment, however little correlation between affinity for specific proteins and PS-ASO toxicity was observed.
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Affiliation(s)
- Timothy A Vickers
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, CA, USA
| | - Meghdad Rahdar
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, CA, USA
| | - Thazha P Prakash
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, CA, USA
| | - Stanley T Crooke
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, CA, USA
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17
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Humphreys SC, Thayer MB, Lade JM, Wu B, Sham K, Basiri B, Hao Y, Huang X, Smith R, Rock BM. Plasma and Liver Protein Binding of N-Acetylgalactosamine–Conjugated Small Interfering RNA. Drug Metab Dispos 2019; 47:1174-1182. [DOI: 10.1124/dmd.119.086967] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 05/06/2019] [Indexed: 12/20/2022] Open
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18
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Zhang C, Lu C, Jing Z, Wu C, Piquemal JP, Ponder JW, Ren P. AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids. J Chem Theory Comput 2018; 14:2084-2108. [PMID: 29438622 PMCID: PMC5893433 DOI: 10.1021/acs.jctc.7b01169] [Citation(s) in RCA: 152] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The AMOEBA polarizable atomic multipole force field for nucleic acids is presented. Valence and electrostatic parameters were determined from high-level quantum mechanical data, including structures, conformational energy, and electrostatic potentials, of nucleotide model compounds. Previously derived parameters for the phosphate group and nucleobases were incorporated. A total of over 35 μs of condensed-phase molecular dynamics simulations of DNA and RNA molecules in aqueous solution and crystal lattice were performed to validate and refine the force field. The solution and/or crystal structures of DNA B-form duplexes, RNA duplexes, and hairpins were captured with an average root-mean-squared deviation from NMR structures below or around 2.0 Å. Structural details, such as base pairing and stacking, sugar puckering, backbone and χ-torsion angles, groove geometries, and crystal packing interfaces, agreed well with NMR and/or X-ray. The interconversion between A- and B-form DNAs was observed in ethanol-water mixtures at 328 K. Crystal lattices of B- and Z-form DNA and A-form RNA were examined with simulations. For the RNA tetraloop, single strand tetramers, and HIV TAR with 29 residues, the simulated conformational states, 3 J-coupling, nuclear Overhauser effect, and residual dipolar coupling data were compared with NMR results. Starting from a totally unstacked/unfolding state, the rCAAU tetranucleotide was folded into A-form-like structures during ∼1 μs molecular dynamics simulations.
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Affiliation(s)
- Changsheng Zhang
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
| | - Chao Lu
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, United States
| | - Zhifeng Jing
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
| | - Chuanjie Wu
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, United States
| | - Jean-Philip Piquemal
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC, UMR7616 CNRS, Paris, France
| | - Jay W. Ponder
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, United States
| | - Pengyu Ren
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
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19
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Zgarbová M, Jurečka P, Šponer J, Otyepka M. A- to B-DNA Transition in AMBER Force Fields and Its Coupling to Sugar Pucker. J Chem Theory Comput 2017; 14:319-328. [DOI: 10.1021/acs.jctc.7b00926] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Marie Zgarbová
- Regional Centre of Advanced
Technologies and Materials, Department of Physical Chemistry, Faculty
of Science, Palacky University, 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Petr Jurečka
- Regional Centre of Advanced
Technologies and Materials, Department of Physical Chemistry, Faculty
of Science, Palacky University, 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Jiří Šponer
- Regional Centre of Advanced
Technologies and Materials, Department of Physical Chemistry, Faculty
of Science, Palacky University, 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced
Technologies and Materials, Department of Physical Chemistry, Faculty
of Science, Palacky University, 17. listopadu 12, 77146 Olomouc, Czech Republic
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20
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Zhitnikova M, Shestopalova A. DNA minor groove electrostatic potential: influence of sequence-specific transitions of the torsion angle gamma and deoxyribose conformations. J Biomol Struct Dyn 2017; 35:3384-3397. [DOI: 10.1080/07391102.2016.1255259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- M.Y. Zhitnikova
- O. Ya. Usikov Institute for Radiophysics and Electronics, National Academy of Sciences of Ukraine, Acad. Proskury Street, 12 Kharkiv 61085, Ukraine
| | - A.V. Shestopalova
- O. Ya. Usikov Institute for Radiophysics and Electronics, National Academy of Sciences of Ukraine, Acad. Proskury Street, 12 Kharkiv 61085, Ukraine
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21
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Huang M, Dissanayake T, Kuechler E, Radak BK, Lee TS, Giese TJ, York DM. A Multidimensional B-Spline Correction for Accurate Modeling Sugar Puckering in QM/MM Simulations. J Chem Theory Comput 2017; 13:3975-3984. [PMID: 28768099 PMCID: PMC5839098 DOI: 10.1021/acs.jctc.7b00161] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The computational efficiency of approximate quantum mechanical methods allows their use for the construction of multidimensional reaction free energy profiles. It has recently been demonstrated that quantum models based on the neglect of diatomic differential overlap (NNDO) approximation have difficulty modeling deoxyribose and ribose sugar ring puckers and thus limit their predictive value in the study of RNA and DNA systems. A method has been introduced in our previous work to improve the description of the sugar puckering conformational landscape that uses a multidimensional B-spline correction map (BMAP correction) for systems involving intrinsically coupled torsion angles. This method greatly improved the adiabatic potential energy surface profiles of DNA and RNA sugar rings relative to high-level ab initio methods even for highly problematic NDDO-based models. In the present work, a BMAP correction is developed, implemented, and tested in molecular dynamics simulations using the AM1/d-PhoT semiempirical Hamiltonian for biological phosphoryl transfer reactions. Results are presented for gas-phase adiabatic potential energy surfaces of RNA transesterification model reactions and condensed-phase QM/MM free energy surfaces for nonenzymatic and RNase A-catalyzed transesterification reactions. The results show that the BMAP correction is stable, efficient, and leads to improvement in both the potential energy and free energy profiles for the reactions studied, as compared with ab initio and experimental reference data. Exploration of the effect of the size of the quantum mechanical region indicates the best agreement with experimental reaction barriers occurs when the full CpA dinucleotide substrate is treated quantum mechanically with the sugar pucker correction.
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Affiliation(s)
- Ming Huang
- Center for Integrative Proteomics Research, Laboratory for Biomolecular Simulation Research and Department of Chemistry and Chemical Biology, Rutgers University, 174 Frelinghuysen Road, Piscataway, New Jersey 08854, United States
| | - Thakshila Dissanayake
- Center for Integrative Proteomics Research, Laboratory for Biomolecular Simulation Research and Department of Chemistry and Chemical Biology, Rutgers University, 174 Frelinghuysen Road, Piscataway, New Jersey 08854, United States
| | - Erich Kuechler
- Center for Integrative Proteomics Research, Laboratory for Biomolecular Simulation Research and Department of Chemistry and Chemical Biology, Rutgers University, 174 Frelinghuysen Road, Piscataway, New Jersey 08854, United States
| | - Brian K. Radak
- Center for Integrative Proteomics Research, Laboratory for Biomolecular Simulation Research and Department of Chemistry and Chemical Biology, Rutgers University, 174 Frelinghuysen Road, Piscataway, New Jersey 08854, United States
| | - Tai-Sung Lee
- Center for Integrative Proteomics Research, Laboratory for Biomolecular Simulation Research and Department of Chemistry and Chemical Biology, Rutgers University, 174 Frelinghuysen Road, Piscataway, New Jersey 08854, United States
| | - Timothy J. Giese
- Center for Integrative Proteomics Research, Laboratory for Biomolecular Simulation Research and Department of Chemistry and Chemical Biology, Rutgers University, 174 Frelinghuysen Road, Piscataway, New Jersey 08854, United States
| | - Darrin M. York
- Center for Integrative Proteomics Research, Laboratory for Biomolecular Simulation Research and Department of Chemistry and Chemical Biology, Rutgers University, 174 Frelinghuysen Road, Piscataway, New Jersey 08854, United States
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22
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Vickers TA, Crooke ST. Development of a Quantitative BRET Affinity Assay for Nucleic Acid-Protein Interactions. PLoS One 2016; 11:e0161930. [PMID: 27571227 PMCID: PMC5003356 DOI: 10.1371/journal.pone.0161930] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 08/15/2016] [Indexed: 11/25/2022] Open
Abstract
Protein-nucleic acid interactions play a crucial role in the regulation of diverse biological processes. Elucidating the roles that protein-nucleic acid complexes play in the regulation of transcription, translation, DNA replication, repair and recombination, and RNA processing continues to be a crucial aspect of understanding of cell biology and the mechanisms of disease. In addition, proteins have been demonstrated to interact with antisense oligonucleotide therapeutics in a sequence and chemistry dependent manner, influencing ASO potency and distribution in cells and in vivo. While many assays have been developed to measure protein-nucleic acid interactions, many suffer from lack of throughput and sensitivity, or challenges with protein purification and scalability. In this report we present a new BRET assay for the analysis of DNA-protein interactions which makes use of an extremely bright luciferase as a tag for the binding protein, along with a long-wavelength fluorophore conjugated to the nucleic acid. The resulting assay is high throughput, sensitive, does not require protein purification, and even allows for quantitative characterization of these interactions within the biologically relevant context of whole cells.
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Affiliation(s)
- Timothy A. Vickers
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA, 92010, United States of America
- * E-mail:
| | - Stanley T. Crooke
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA, 92010, United States of America
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23
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Deiana M, Pokladek Z, Olesiak-Banska J, Młynarz P, Samoc M, Matczyszyn K. Photochromic switching of the DNA helicity induced by azobenzene derivatives. Sci Rep 2016; 6:28605. [PMID: 27339811 PMCID: PMC4919647 DOI: 10.1038/srep28605] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 06/03/2016] [Indexed: 01/08/2023] Open
Abstract
The photochromic properties of azobenzene, involving conformational changes occurring upon interaction with light, provide an excellent tool to establish new ways of selective regulation applied to biosystems. We report here on the binding of two water-soluble 4-(phenylazo)benzoic acid derivatives (Azo-2N and Azo-3N) with double stranded DNA and demonstrate that the photoisomerization of Azo-3N leads to changes in DNA structure. In particular, we show that stabilization and destabilization of the B-DNA secondary structure can be photochemically induced in situ by light. This photo-triggered process is fully reversible and could be an alternative pathway to control a broad range of biological processes. Moreover, we found that the bicationic Azo-3N exhibited a higher DNA-binding constant than the monocationic Azo-2N pointing out that the number of positive charges along the photosensitive polyamines chain plays a pivotal role in stabilizing the photochrome-DNA complex.
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Affiliation(s)
- Marco Deiana
- Advanced Materials Engineering and Modelling Group, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Ziemowit Pokladek
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Joanna Olesiak-Banska
- Advanced Materials Engineering and Modelling Group, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Piotr Młynarz
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Marek Samoc
- Advanced Materials Engineering and Modelling Group, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Katarzyna Matczyszyn
- Advanced Materials Engineering and Modelling Group, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
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24
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High-resolution biophysical analysis of the dynamics of nucleosome formation. Sci Rep 2016; 6:27337. [PMID: 27263658 PMCID: PMC4897087 DOI: 10.1038/srep27337] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Indexed: 12/14/2022] Open
Abstract
We describe a biophysical approach that enables changes in the structure of DNA to be followed during nucleosome formation in in vitro reconstitution with either the canonical "Widom" sequence or a judiciously mutated sequence. The rapid non-perturbing photochemical analysis presented here provides 'snapshots' of the DNA configuration at any given moment in time during nucleosome formation under a very broad range of reaction conditions. Changes in DNA photochemical reactivity upon protein binding are interpreted as being mainly induced by alterations in individual base pair roll angles. The results strengthen the importance of the role of an initial (H3/H4)2 histone tetramer-DNA interaction and highlight the modulation of this early event by the DNA sequence. (H3/H4)2 binding precedes and dictates subsequent H2A/H2B-DNA interactions, which are less affected by the DNA sequence, leading to the final octameric nucleosome. Overall, our results provide a novel, exciting way to investigate those biophysical properties of DNA that constitute a crucial component in nucleosome formation and stabilization.
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25
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Cole HA, Cui F, Ocampo J, Burke TL, Nikitina T, Nagarajavel V, Kotomura N, Zhurkin VB, Clark DJ. Novel nucleosomal particles containing core histones and linker DNA but no histone H1. Nucleic Acids Res 2015; 44:573-81. [PMID: 26400169 PMCID: PMC4737182 DOI: 10.1093/nar/gkv943] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 09/09/2015] [Indexed: 11/12/2022] Open
Abstract
Eukaryotic chromosomal DNA is assembled into regularly spaced nucleosomes, which play a central role in gene regulation by determining accessibility of control regions. The nucleosome contains ∼147 bp of DNA wrapped ∼1.7 times around a central core histone octamer. The linker histone, H1, binds both to the nucleosome, sealing the DNA coils, and to the linker DNA between nucleosomes, directing chromatin folding. Micrococcal nuclease (MNase) digests the linker to yield the chromatosome, containing H1 and ∼160 bp, and then converts it to a core particle, containing ∼147 bp and no H1. Sequencing of nucleosomal DNA obtained after MNase digestion (MNase-seq) generates genome-wide nucleosome maps that are important for understanding gene regulation. We present an improved MNase-seq method involving simultaneous digestion with exonuclease III, which removes linker DNA. Remarkably, we discovered two novel intermediate particles containing 154 or 161 bp, corresponding to 7 bp protruding from one or both sides of the nucleosome core. These particles are detected in yeast lacking H1 and in H1-depleted mouse chromatin. They can be reconstituted in vitro using purified core histones and DNA. We propose that these ‘proto-chromatosomes’ are fundamental chromatin subunits, which include the H1 binding site and influence nucleosome spacing independently of H1.
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Affiliation(s)
- Hope A Cole
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Feng Cui
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USA
| | - Josefina Ocampo
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tara L Burke
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tatiana Nikitina
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - V Nagarajavel
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Naoe Kotomura
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Victor B Zhurkin
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David J Clark
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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26
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The 3D structure of Kaposi sarcoma herpesvirus LANA C-terminal domain bound to DNA. Proc Natl Acad Sci U S A 2015; 112:6694-9. [PMID: 25947153 DOI: 10.1073/pnas.1421804112] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Kaposi sarcoma herpesvirus (KSHV) persists as a latent nuclear episome in dividing host cells. This episome is tethered to host chromatin to ensure proper segregation during mitosis. For duplication of the latent genome, the cellular replication machinery is recruited. Both of these functions rely on the constitutively expressed latency-associated nuclear antigen (LANA) of the virus. Here, we report the crystal structure of the KSHV LANA DNA-binding domain (DBD) in complex with its high-affinity viral target DNA, LANA binding site 1 (LBS1), at 2.9 Å resolution. In contrast to homologous proteins such as Epstein-Barr virus nuclear antigen 1 (EBNA-1) of the related γ-herpesvirus Epstein-Barr virus, specific DNA recognition by LANA is highly asymmetric. In addition to solving the crystal structure, we found that apart from the two known LANA binding sites, LBS1 and LBS2, LANA also binds to a novel site, denoted LBS3. All three sites are located in a region of the KSHV terminal repeat subunit previously recognized as a minimal replicator. Moreover, we show that the LANA DBD can coat DNA of arbitrary sequence by virtue of a characteristic lysine patch, which is absent in EBNA-1 of the Epstein-Barr virus. Likely, these higher-order assemblies involve the self-association of LANA into supermolecular spirals. One such spiral assembly was solved as a crystal structure of 3.7 Å resolution in the absence of DNA. On the basis of our data, we propose a model for the controlled nucleation of higher-order LANA oligomers that might contribute to the characteristic subnuclear KSHV microdomains ("LANA speckles"), a hallmark of KSHV latency.
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27
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Whelan DR, Hiscox TJ, Rood JI, Bambery KR, McNaughton D, Wood BR. Detection of an en masse and reversible B- to A-DNA conformational transition in prokaryotes in response to desiccation. J R Soc Interface 2014; 11:20140454. [PMID: 24898023 PMCID: PMC4208382 DOI: 10.1098/rsif.2014.0454] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 05/12/2014] [Indexed: 02/02/2023] Open
Abstract
The role that DNA conformation plays in the biochemistry of cells has been the subject of intensive research since DNA polymorphism was discovered. B-DNA has long been considered the native form of DNA in cells although alternative conformations of DNA are thought to occur transiently and along short tracts. Here, we report the first direct observation of a fully reversible en masse conformational transition between B- and A-DNA within live bacterial cells using Fourier transform infrared (FTIR) spectroscopy. This biospectroscopic technique allows for non-invasive and reagent-free examination of the holistic biochemistry of samples. For this reason, we have been able to observe the previously unknown conformational transition in all four species of bacteria investigated. Detection of this transition is evidence of a previously unexplored biological significance for A-DNA and highlights the need for new research into the role that A-DNA plays as a cellular defence mechanism and in stabilizing the DNA conformation. Such studies are pivotal in understanding the role of A-DNA in the evolutionary pathway of nucleic acids. Furthermore, this discovery demonstrates the exquisite capabilities of FTIR spectroscopy and opens the door for further investigations of cell biochemistry with this under-used technique.
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Affiliation(s)
- Donna R Whelan
- Centre for Biospectroscopy, School of Chemistry, Monash University, Victoria 3800, Australia
| | - Thomas J Hiscox
- Department of Microbiology, School of Biomedical Sciences, Monash University, Victoria 3800, Australia
| | - Julian I Rood
- Department of Microbiology, School of Biomedical Sciences, Monash University, Victoria 3800, Australia
| | - Keith R Bambery
- Centre for Biospectroscopy, School of Chemistry, Monash University, Victoria 3800, Australia Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Don McNaughton
- Centre for Biospectroscopy, School of Chemistry, Monash University, Victoria 3800, Australia
| | - Bayden R Wood
- Centre for Biospectroscopy, School of Chemistry, Monash University, Victoria 3800, Australia
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28
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Schneider B, Černý J, Svozil D, Čech P, Gelly JC, de Brevern AG. Bioinformatic analysis of the protein/DNA interface. Nucleic Acids Res 2014; 42:3381-94. [PMID: 24335080 PMCID: PMC3950675 DOI: 10.1093/nar/gkt1273] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 11/14/2013] [Accepted: 11/14/2013] [Indexed: 01/04/2023] Open
Abstract
To investigate the principles driving recognition between proteins and DNA, we analyzed more than thousand crystal structures of protein/DNA complexes. We classified protein and DNA conformations by structural alphabets, protein blocks [de Brevern, Etchebest and Hazout (2000) (Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks. Prots. Struct. Funct. Genet., 41:271-287)] and dinucleotide conformers [Svozil, Kalina, Omelka and Schneider (2008) (DNA conformations and their sequence preferences. Nucleic Acids Res., 36:3690-3706)], respectively. Assembling the mutually interacting protein blocks and dinucleotide conformers into 'interaction matrices' revealed their correlations and conformer preferences at the interface relative to their occurrence outside the interface. The analyzed data demonstrated important differences between complexes of various types of proteins such as transcription factors and nucleases, distinct interaction patterns for the DNA minor groove relative to the major groove and phosphate and importance of water-mediated contacts. Water molecules mediate proportionally the largest number of contacts in the minor groove and form the largest proportion of contacts in complexes of transcription factors. The generally known induction of A-DNA forms by complexation was more accurately attributed to A-like and intermediate A/B conformers rare in naked DNA molecules.
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Affiliation(s)
- Bohdan Schneider
- Institute of Biotechnology AS CR, Videnska 1083, CZ-142 20 Prague, Czech Republic, Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, Institute of Chemical Technology Prague, Technická 5, CZ-166 28 Prague, Czech Republic, INSERM, U665, DSIMB, F-75739 Paris, France, University of Paris Diderot, Sorbonne Paris Cité, UMR_S 665, F-75739 Paris, France, Institut National de la Transfusion Sanguine (INTS), F-75739 Paris, France and Laboratoire d’Excellence GR-Ex, F-75739 Paris, France
| | - Jiří Černý
- Institute of Biotechnology AS CR, Videnska 1083, CZ-142 20 Prague, Czech Republic, Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, Institute of Chemical Technology Prague, Technická 5, CZ-166 28 Prague, Czech Republic, INSERM, U665, DSIMB, F-75739 Paris, France, University of Paris Diderot, Sorbonne Paris Cité, UMR_S 665, F-75739 Paris, France, Institut National de la Transfusion Sanguine (INTS), F-75739 Paris, France and Laboratoire d’Excellence GR-Ex, F-75739 Paris, France
| | - Daniel Svozil
- Institute of Biotechnology AS CR, Videnska 1083, CZ-142 20 Prague, Czech Republic, Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, Institute of Chemical Technology Prague, Technická 5, CZ-166 28 Prague, Czech Republic, INSERM, U665, DSIMB, F-75739 Paris, France, University of Paris Diderot, Sorbonne Paris Cité, UMR_S 665, F-75739 Paris, France, Institut National de la Transfusion Sanguine (INTS), F-75739 Paris, France and Laboratoire d’Excellence GR-Ex, F-75739 Paris, France
| | - Petr Čech
- Institute of Biotechnology AS CR, Videnska 1083, CZ-142 20 Prague, Czech Republic, Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, Institute of Chemical Technology Prague, Technická 5, CZ-166 28 Prague, Czech Republic, INSERM, U665, DSIMB, F-75739 Paris, France, University of Paris Diderot, Sorbonne Paris Cité, UMR_S 665, F-75739 Paris, France, Institut National de la Transfusion Sanguine (INTS), F-75739 Paris, France and Laboratoire d’Excellence GR-Ex, F-75739 Paris, France
| | - Jean-Christophe Gelly
- Institute of Biotechnology AS CR, Videnska 1083, CZ-142 20 Prague, Czech Republic, Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, Institute of Chemical Technology Prague, Technická 5, CZ-166 28 Prague, Czech Republic, INSERM, U665, DSIMB, F-75739 Paris, France, University of Paris Diderot, Sorbonne Paris Cité, UMR_S 665, F-75739 Paris, France, Institut National de la Transfusion Sanguine (INTS), F-75739 Paris, France and Laboratoire d’Excellence GR-Ex, F-75739 Paris, France
| | - Alexandre G. de Brevern
- Institute of Biotechnology AS CR, Videnska 1083, CZ-142 20 Prague, Czech Republic, Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, Institute of Chemical Technology Prague, Technická 5, CZ-166 28 Prague, Czech Republic, INSERM, U665, DSIMB, F-75739 Paris, France, University of Paris Diderot, Sorbonne Paris Cité, UMR_S 665, F-75739 Paris, France, Institut National de la Transfusion Sanguine (INTS), F-75739 Paris, France and Laboratoire d’Excellence GR-Ex, F-75739 Paris, France
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Zhitnikova MY, Boryskina OP, Shestopalova AV. Sequence-specific transitions of the torsion angle gamma change the polar-hydrophobic profile of the DNA grooves: implication for indirect protein-DNA recognition. J Biomol Struct Dyn 2013; 32:1670-85. [PMID: 23998351 DOI: 10.1080/07391102.2013.830579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Variations of the shape and polarity of the DNA grooves caused by changes of the DNA conformation play an important role in the DNA readout. Despite the fact that non-canonical trans and gauche- conformations of the DNA backbone angle γ (O5'-C5'-C4'-C3') are frequently found in the DNA crystal structures, their possible role in the DNA recognition has not been studied systematically. In order to fill in this gap, we analyze the available high-resolution crystal structures of the naked and complexed DNA. The analysis shows that the non-canonical γ angle conformations are present both in the naked and bound DNA, more often in the bound vs. naked DNA, and in the nucleotides with the A-like vs. the B-like sugar pucker. The alternative angle γ torsions are more frequently observed in the purines with the A-like sugar pucker and in the pyrimidines with the B-like sugar conformation. The minor groove of the nucleotides with non-canonical γ angle conformation is more polar, while the major groove is more hydrophobic than in the nucleotides with the classical γ torsions due to variations in exposure of the polar and hydrophobic groups of the DNA backbone. The propensity of the nucleotides with different γ angle conformations to participate in the protein-nucleic acid contacts in the minor and major grooves is connected with their sugar pucker and sequence-specific. Our findings imply that the angle γ transitions contribute to the process of the protein-DNA recognition due to modification of the polar/hydrophobic profile of the DNA grooves.
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Affiliation(s)
- Mariia Yu Zhitnikova
- a O. Ya. Usikov Institute for Radiophysics and Electronics of the National Academy of Sciences of Ukraine , Acad. Proskura Street, 12, Kharkiv , 61085 , Ukraine
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30
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Chu WT, Zheng QC. Conformational changes of enzymes and DNA in molecular dynamics: influenced by pH, temperature, and ligand. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2013; 92:179-217. [PMID: 23954102 DOI: 10.1016/b978-0-12-411636-8.00005-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Protein conformation, which has been a research hotspot for human diseases, is an important factor of protein properties. Recently, a series of approaches have been utilized to investigate the conformational changes under different conditions. Some of them have gained promising achievements, but it is still deficient in the detail researches at the atomic level. In this chapter, a series of computational examples of protein conformational changes under different pH environment, temperature, and ligand binding are described. We further show some useful methods, such as constant pH molecular dynamics simulations, molecular docking, and molecular mechanics Poisson-Boltzmann surface area/generalized Born surface area calculations. In comparison with the experimental results, the methods mentioned above are reasonable to detect and predict the interaction between residue and residue, residue and DNA, and residue and ligand. Additionally, some crucial interactions that cause protein conformational changes are discovered and discussed in this chapter. In summary, our work can give penetrating information to understand the pH-, temperature-, and ligand-induced conformational change mechanisms.
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Affiliation(s)
- Wen-Ting Chu
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, PR China
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31
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Čech P, Kukal J, Černý J, Schneider B, Svozil D. Automatic workflow for the classification of local DNA conformations. BMC Bioinformatics 2013; 14:205. [PMID: 23800225 PMCID: PMC3694522 DOI: 10.1186/1471-2105-14-205] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 05/28/2013] [Indexed: 12/03/2022] Open
Abstract
Background A growing number of crystal and NMR structures reveals a considerable structural polymorphism of DNA architecture going well beyond the usual image of a double helical molecule. DNA is highly variable with dinucleotide steps exhibiting a substantial flexibility in a sequence-dependent manner. An analysis of the conformational space of the DNA backbone and the enhancement of our understanding of the conformational dependencies in DNA are therefore important for full comprehension of DNA structural polymorphism. Results A detailed classification of local DNA conformations based on the technique of Fourier averaging was published in our previous work. However, this procedure requires a considerable amount of manual work. To overcome this limitation we developed an automatic classification method consisting of the combination of supervised and unsupervised approaches. A proposed workflow is composed of k-NN method followed by a non-hierarchical single-pass clustering algorithm. We applied this workflow to analyze 816 X-ray and 664 NMR DNA structures released till February 2013. We identified and annotated six new conformers, and we assigned four of these conformers to two structurally important DNA families: guanine quadruplexes and Holliday (four-way) junctions. We also compared populations of the assigned conformers in the dataset of X-ray and NMR structures. Conclusions In the present work we developed a machine learning workflow for the automatic classification of dinucleotide conformations. Dinucleotides with unassigned conformations can be either classified into one of already known 24 classes or they can be flagged as unclassifiable. The proposed machine learning workflow permits identification of new classes among so far unclassifiable data, and we identified and annotated six new conformations in the X-ray structures released since our previous analysis. The results illustrate the utility of machine learning approaches in the classification of local DNA conformations.
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Affiliation(s)
- Petr Čech
- Laboratory of Informatics and Chemistry, ICT Prague, Technická 5, Prague 6, 166 28, Czech Republic
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32
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Chen L, Zhang JL, Yu LY, Zheng QC, Chu WT, Xue Q, Zhang HX, Sun CC. Influence of hyperthermophilic protein Cren7 on the stability and conformation of DNA: insights from molecular dynamics simulation and free energy analysis. J Phys Chem B 2012; 116:12415-25. [PMID: 23013198 DOI: 10.1021/jp305860h] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cren7, a novel chromatin protein highly conserved among crenarchaea, plays an important role in genome packaging and gene regulation. However, the detail dynamical structural characteristic of the Cren7-DNA complex and the detail study of the DNA in the complex have not been done. Focused on two specific Cren7-DNA complexes (PDB codes 3LWH and 3LWI ), we applied molecular dynamics (MD) simulations at four different temperatures (300, 350, 400, and 450 K) and the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) free energy calculation at 300 and 350 K to examine the role of Cren7 protein in enhancing the stability of DNA duplexes via protein-DNA interactions, and to study the structural transition in DNA. The simulation results indicate that Cren7 stabilizes DNA duplex in a certain temperature range in the binary complex compared with the unbound DNA molecules. At the same time, DNA molecules were found to undergo B-like to A-like form transitions with increased temperature. The results of statistical analyses of the H-bond and hydrophobic contacts show that some residues have significant influence on the structure of DNA molecules. Our work can give important information to understand the interactions of proteins with nucleic acids and other ligands.
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Affiliation(s)
- Lin Chen
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, People's Republic of China
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33
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Babbitt GA, Schulze KV. Codons support the maintenance of intrinsic DNA polymer flexibility over evolutionary timescales. Genome Biol Evol 2012; 4:954-65. [PMID: 22936074 PMCID: PMC3468960 DOI: 10.1093/gbe/evs073] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/21/2012] [Indexed: 01/02/2023] Open
Abstract
Despite our long familiarity with how the genetic code specifies the amino acid sequence, we still know little about why it is organized in the way that it is. Contrary to the view that the organization of the genetic code is a "frozen accident" of evolution, recent studies have demonstrated that it is highly nonrandom, with implications for both codon assignment and usage. We hypothesize that this inherent nonrandomness may facilitate the coexistence of both sequence and structural information in DNA. Here, we take advantage of a simple metric of intrinsic DNA flexibility to analyze mutational effects on the four phosphate linkages present in any given codon. Application of a simple evolutionary neutral model of substitution to random sequences, translated with alternative genetic codes, reveals that the standard code is highly optimized to favor synonymous substitutions that maximize DNA polymer flexibility, potentially counteracting neutral evolutionary drift toward stiffer DNA caused by spontaneous deamination. Comparison to existing mutational patterns in yeast also demonstrates evidence of strong selective constraint on DNA flexibility, especially at so-called "silent" sites. We also report a fundamental relationship between DNA flexibility, codon usage bias, and several important evolutionary descriptors of comparative genomics (e.g., base composition, transition/transversion ratio, and nonsynonymous vs. synonymous substitution rate). Recent advances in structural genomics have emphasized the role of the DNA polymer's flexibility in both gene function and whole genome folding, thereby implicating possible reasons for codons to facilitate the multiplexing of both genetic and structural information within the same molecular context.
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Affiliation(s)
- G A Babbitt
- TH Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USA.
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34
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Chen L, Zheng QC, Yu LY, Chu WT, Zhang JL, Xue Q, Zhang HX, Sun CC. Insights into the thermal stabilization and conformational transitions of DNA by hyperthermophile protein Sso7d: molecular dynamics simulations and MM-PBSA analysis. J Biomol Struct Dyn 2012; 30:716-27. [PMID: 22731116 DOI: 10.1080/07391102.2012.689702] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In the assembly of DNA-protein complex, the DNA kinking plays an important role in nucleoprotein structures and gene regulation. Molecular dynamics (MD) simulations were performed on specific protein-DNA complexes in this study to investigate the stability and structural transitions of DNA depending on temperature. Furthermore, we introduced the molecular mechanics/Poisson-Boltzmann surface area (MM-PBSA) approach to analyze the interactions between DNA and protein in hyperthermophile. Focused on two specific Sso7d-DNA complexes (PDB codes: 1BNZ and 1BF4), we performed MD simulations at four temperatures (300, 360, 420, and 480 K) and MM-PBSA at 300 and 360 K to illustrate detailed information on the changes of DNA. Our results show that Sso7d stabilizes DNA duplex over a certain temperature range and DNA molecules undergo B-like to A-like form transitions in the binary complex with the temperature increasing, which are consistent with the experimental data. Our work will contribute to a better understanding of protein-DNA interaction.
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Affiliation(s)
- Lin Chen
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, 130023, P.R. China
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35
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Chirgadze YN, Sivozhelezov VS, Polozov RV, Stepanenko VA, Ivanov VV. Recognition Rules for Binding of Homeodomains to Operator DNA. J Biomol Struct Dyn 2012; 29:715-31. [DOI: 10.1080/073911012010525019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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36
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Whelan DR, Bambery KR, Heraud P, Tobin MJ, Diem M, McNaughton D, Wood BR. Monitoring the reversible B to A-like transition of DNA in eukaryotic cells using Fourier transform infrared spectroscopy. Nucleic Acids Res 2011; 39:5439-48. [PMID: 21447564 PMCID: PMC3141270 DOI: 10.1093/nar/gkr175] [Citation(s) in RCA: 140] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The ability to detect DNA conformation in eukaryotic cells is of paramount importance in understanding how some cells retain functionality in response to environmental stress. It is anticipated that the B to A transition might play a role in resistance to DNA damage such as heat, desiccation and toxic damage. To this end, conformational detail about the molecular structure of DNA has been derived primarily from in vitro experiments on extracted or synthetic DNA. Here, we report that a B- to A-like DNA conformational change can occur in the nuclei of intact cells in response to dehydration. This transition is reversible upon rehydration in air-dried cells. By systematically monitoring the dehydration and rehydration of single and double-stranded DNA, RNA, extracted nuclei and three types of eukaryotic cells including chicken erythrocytes, mammalian lymphocytes and cancerous rodent fibroblasts using Fourier transform infrared (FTIR) spectroscopy, we unequivocally assign the important DNA conformation marker bands within these cells. We also demonstrate that by applying FTIR spectroscopy to hydrated samples, the DNA bands become sharper and more intense. This is anticipated to provide a methodology enabling differentiation of cancerous from non-cancerous cells based on the increased DNA content inherent to dysplastic and neoplastic tissue.
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Affiliation(s)
- Donna R Whelan
- Center for Biospectroscopy and School of Chemistry, Monash Immunology and Stem Cell Laboratories, Monash University, Clayton, Victoria, 3800 Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia
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37
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Boryskina OP, Tkachenko MY, Shestopalova AV. Protein-DNA complexes: specificity and DNA readout mechanisms. ACTA ACUST UNITED AC 2011. [DOI: 10.7124/bc.00007c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- O. P. Boryskina
- O. Ya. Usikov Institute for Radio Physics and Electronics, National Academy of Sciences of Ukraine
| | - M. Yu. Tkachenko
- O. Ya. Usikov Institute for Radio Physics and Electronics, National Academy of Sciences of Ukraine
| | - A. V. Shestopalova
- O. Ya. Usikov Institute for Radio Physics and Electronics, National Academy of Sciences of Ukraine
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38
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Bazzi A, Zargarian L, Chaminade F, Boudier C, De Rocquigny H, René B, Mély Y, Fossé P, Mauffret O. Structural insights into the cTAR DNA recognition by the HIV-1 nucleocapsid protein: role of sugar deoxyriboses in the binding polarity of NC. Nucleic Acids Res 2011; 39:3903-16. [PMID: 21227929 PMCID: PMC3089453 DOI: 10.1093/nar/gkq1290] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
An essential step of the reverse transcription of the HIV-1 genome is the first strand transfer that requires the annealing of the TAR RNA hairpin to the cTAR DNA hairpin. HIV-1 nucleocapsid protein (NC) plays a crucial role by facilitating annealing of the complementary hairpins. Using nuclear magnetic resonance and gel retardation assays, we investigated the interaction between NC and the top half of the cTAR DNA (mini-cTAR). We show that NC(11-55) binds the TGG sequence in the lower stem that is destabilized by the adjacent internal loop. The 5′ thymine interacts with residues of the N-terminal zinc knuckle and the 3′ guanine is inserted in the hydrophobic plateau of the C-terminal zinc knuckle. The TGG sequence is preferred relative to the apical and internal loops containing unpaired guanines. Investigation of the DNA–protein contacts shows the major role of hydrophobic interactions involving nucleobases and deoxyribose sugars. A similar network of hydrophobic contacts is observed in the published NC:DNA complexes, whereas NC contacts ribose differently in NC:RNA complexes. We propose that the binding polarity of NC is related to these contacts that could be responsible for the preferential binding to single-stranded nucleic acids.
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Affiliation(s)
- Ali Bazzi
- LBPA, ENS de Cachan, CNRS, Cachan, Faculté de Pharmacie, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
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39
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Oguey C, Foloppe N, Hartmann B. Understanding the sequence-dependence of DNA groove dimensions: implications for DNA interactions. PLoS One 2010; 5:e15931. [PMID: 21209967 PMCID: PMC3012109 DOI: 10.1371/journal.pone.0015931] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Accepted: 11/30/2010] [Indexed: 01/05/2023] Open
Abstract
Background The B-DNA major and minor groove dimensions are crucial for DNA-protein interactions. It has long been thought that the groove dimensions depend on the DNA sequence, however this relationship has remained elusive. Here, our aim is to elucidate how the DNA sequence intrinsically shapes the grooves. Methodology/Principal Findings The present study is based on the analysis of datasets of free and protein-bound DNA crystal structures, and from a compilation of NMR 31P chemical shifts measured on free DNA in solution on a broad range of representative sequences. The 31P chemical shifts can be interpreted in terms of the BI↔BII backbone conformations and dynamics. The grooves width and depth of free and protein-bound DNA are found to be clearly related to the BI/BII backbone conformational states. The DNA propensity to undergo BI↔BII backbone transitions is highly sequence-dependent and can be quantified at the dinucleotide level. This dual relationship, between DNA sequence and backbone behavior on one hand, and backbone behavior and groove dimensions on the other hand, allows to decipher the link between DNA sequence and groove dimensions. It also firmly establishes that proteins take advantage of the intrinsic DNA groove properties. Conclusions/Significance The study provides a general framework explaining how the DNA sequence shapes the groove dimensions in free and protein-bound DNA, with far-reaching implications for DNA-protein indirect readout in both specific and non specific interactions.
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Affiliation(s)
- Christophe Oguey
- Laboratoire de Physique Théorique et Modélisation, UMR-8089, Centre National de la Recherche Scientifique et Université de Cergy-Pontoise, Cergy-Pontoise, France
| | - Nicolas Foloppe
- UMR-S665, Institut National de la Santé et de la Recherche Médicale et Université Paris Diderot, Institut National de la Transfusion Sanguine, Paris, France
- * E-mail: (BH); (NF)
| | - Brigitte Hartmann
- UMR-S665, Institut National de la Santé et de la Recherche Médicale et Université Paris Diderot, Institut National de la Transfusion Sanguine, Paris, France
- * E-mail: (BH); (NF)
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40
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Priyakumar UD, Harika G, Suresh G. Molecular simulations on the thermal stabilization of DNA by hyperthermophilic chromatin protein Sac7d, and associated conformational transitions. J Phys Chem B 2010; 114:16548-57. [PMID: 21086967 DOI: 10.1021/jp101583d] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Sac7d belongs to a family of chromosomal proteins, which are crucial for thermal stabilization of DNA at higher growth temperatures. It is capable of binding DNA nonspecifically, and is responsible for the increase in the melting temperature of DNA in the bound form up to 85 °C. Molecular dynamics (MD) simulations were performed at different temperatures on two protein-DNA complexes of Sac7d. Various structural and energetic parameters were calculated to examine the DNA stability and to investigate the conformational changes in DNA and the protein-DNA interactions. Room temperature simulations indicated very good agreement with the experimental structures. The protein structure is nearly unchanged at both 300 and 360 K, and only up to five base pairs of the DNA are stabilized by Sac7d at 360 K. However, the MD simulations on DNA alone systems show that they lose their helical structures at 360 K further supporting the role of Sac7d in stabilizing the oligomers. At higher temperatures (420 and 480 K), DNA undergoes denaturation in the presence and the absence of the protein. The DNA molecules were found to undergo B- to A-form transitions consistent with experimental studies, and the extent of these transitions are examined in detail. The extent of sampling B- and A-form regions was found to show temperature and sequence dependence. Multiple MD simulations yielded similar results validating the proposed model. Interaction energy calculations corresponding to protein-DNA binding indicates major contribution due to DNA backbone, explaining the nonspecific interactions of Sac7d.
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Affiliation(s)
- U Deva Priyakumar
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India.
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41
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Boryskina OP, Tkachenko MY, Shestopalova AV. Variability of DNA structure and protein-nucleic acid reconginition. ACTA ACUST UNITED AC 2010. [DOI: 10.7124/bc.00016a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- O. P. Boryskina
- A. Usikov Institute of Radio Physics and Electronics, National Academy of Sciences of Ukraine
| | - M. Yu. Tkachenko
- A. Usikov Institute of Radio Physics and Electronics, National Academy of Sciences of Ukraine
| | - A. V. Shestopalova
- A. Usikov Institute of Radio Physics and Electronics, National Academy of Sciences of Ukraine
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42
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Rohs R, Jin X, West SM, Joshi R, Honig B, Mann RS. Origins of specificity in protein-DNA recognition. Annu Rev Biochem 2010; 79:233-69. [PMID: 20334529 DOI: 10.1146/annurev-biochem-060408-091030] [Citation(s) in RCA: 656] [Impact Index Per Article: 46.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Specific interactions between proteins and DNA are fundamental to many biological processes. In this review, we provide a revised view of protein-DNA interactions that emphasizes the importance of the three-dimensional structures of both macromolecules. We divide protein-DNA interactions into two categories: those when the protein recognizes the unique chemical signatures of the DNA bases (base readout) and those when the protein recognizes a sequence-dependent DNA shape (shape readout). We further divide base readout into those interactions that occur in the major groove from those that occur in the minor groove. Analogously, the readout of the DNA shape is subdivided into global shape recognition (for example, when the DNA helix exhibits an overall bend) and local shape recognition (for example, when a base pair step is kinked or a region of the minor groove is narrow). Based on the >1500 structures of protein-DNA complexes now available in the Protein Data Bank, we argue that individual DNA-binding proteins combine multiple readout mechanisms to achieve DNA-binding specificity. Specificity that distinguishes between families frequently involves base readout in the major groove, whereas shape readout is often exploited for higher resolution specificity, to distinguish between members within the same DNA-binding protein family.
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Affiliation(s)
- Remo Rohs
- Howard Hughes Medical Institute, Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10032, USA
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43
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Thomas MS, Nuñez V, Upadhyayula S, Zielins ER, Bao D, Vasquez JM, Bahmani B, Vullev VI. Kinetics of bacterial fluorescence staining with 3,3'-diethylthiacyanine. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:9756-9765. [PMID: 20481488 DOI: 10.1021/la1013279] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
For more than a century, colorimetric and fluorescence staining have been the foundation of a broad range of key bioanalytical techniques. The dynamics of such staining processes, however, still remains largely unexplored. We investigated the kinetics of fluorescence staining of two gram-negative and two gram-positive species with 3,3'-diethylthiacyanine (THIA) iodide. An increase in the THIA fluorescence quantum yield, induced by the bacterial dye uptake, was the principal reason for the observed emission enhancement. The fluorescence quantum yield of THIA depended on the media viscosity and not on the media polarity, which suggested that the microenvironment of the dye molecules taken up by the cells was restrictive. The kinetics of fluorescence staining did not manifest a statistically significant dependence neither on the dye concentration, nor on the cell count. In the presence of surfactant additives, however, the fluorescence-enhancement kinetic patterns manifested species specificity with statistically significant discernibility.
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Affiliation(s)
- Marlon S Thomas
- Department of Bioengineering, University of California, Riverside, California 92521, USA
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44
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Tang ZQ, Lin HH, Zhang HL, Han LY, Chen X, Chen YZ. Prediction of functional class of proteins and peptides irrespective of sequence homology by support vector machines. Bioinform Biol Insights 2009; 1:19-47. [PMID: 20066123 PMCID: PMC2789692 DOI: 10.4137/bbi.s315] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Various computational methods have been used for the prediction of protein and peptide function based on their sequences. A particular challenge is to derive functional properties from sequences that show low or no homology to proteins of known function. Recently, a machine learning method, support vector machines (SVM), have been explored for predicting functional class of proteins and peptides from amino acid sequence derived properties independent of sequence similarity, which have shown promising potential for a wide spectrum of protein and peptide classes including some of the low- and non-homologous proteins. This method can thus be explored as a potential tool to complement alignment-based, clustering-based, and structure-based methods for predicting protein function. This article reviews the strategies, current progresses, and underlying difficulties in using SVM for predicting the functional class of proteins. The relevant software and web-servers are described. The reported prediction performances in the application of these methods are also presented.
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Affiliation(s)
- Zhi Qun Tang
- Department of Pharmacy and Department of Computational Science, National University of Singapore, Republic of Singapore, 117543
| | - Hong Huang Lin
- Department of Pharmacy and Department of Computational Science, National University of Singapore, Republic of Singapore, 117543
| | - Hai Lei Zhang
- Department of Pharmacy and Department of Computational Science, National University of Singapore, Republic of Singapore, 117543
| | - Lian Yi Han
- Department of Pharmacy and Department of Computational Science, National University of Singapore, Republic of Singapore, 117543
| | - Xin Chen
- Department of Biotechnology, Zhejiang University, Hang Zhou, Zhejiang Province, P. R. China, 310029
| | - Yu Zong Chen
- Department of Pharmacy and Department of Computational Science, National University of Singapore, Republic of Singapore, 117543
- Shanghai Center for Bioinformatics Technology, Shanghai, P. R. China, 201203
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Abstract
An analysis of cavities present in protein–DNA and protein–RNA complexes is presented. In terms of the number of cavities and their total volume, the interfaces formed in these complexes are akin to those in transient protein–protein heterocomplexes. With homodimeric proteins protein–DNA interfaces may contain cavities involving both the protein subunits and DNA, and these are more than twice as large as cavities involving a single protein subunit and DNA. A parameter, cavity index, measuring the degree of surface complementarity, indicates that the packing of atoms in protein–protein/DNA/RNA is very similar, but it is about two times less efficient in the permanent interfaces formed between subunits in homodimers. As within the tertiary structure and protein–protein interfaces, protein–DNA interfaces have a higher inclination to be lined by β-sheet residues; from the DNA side, base atoms, in particular those in minor grooves, have a higher tendency to be located in cavities. The larger cavities tend to be less spherical and solvated. A small fraction of water molecules are found to mediate hydrogen-bond interactions with both the components, suggesting their primary role is to fill in the void left due to the local non-complementary nature of the surface patches.
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Affiliation(s)
- Shrihari Sonavane
- Department of Biochemistry and Bioinformatics Centre, Bose Institute, P-1/12 CIT Scheme VIIM, Calcutta 700 054, India
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Marathe A, Karandur D, Bansal M. Small local variations in B-form DNA lead to a large variety of global geometries which can accommodate most DNA-binding protein motifs. BMC STRUCTURAL BIOLOGY 2009; 9:24. [PMID: 19393049 PMCID: PMC2687451 DOI: 10.1186/1472-6807-9-24] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2008] [Accepted: 04/24/2009] [Indexed: 01/01/2023]
Abstract
BACKGROUND An important question of biological relevance is the polymorphism of the double-helical DNA structure in its free form, and the changes that it undergoes upon protein-binding. We have analysed a database of free DNA crystal structures to assess the inherent variability of the free DNA structure and have compared it with a database of protein-bound DNA crystal structures to ascertain the protein-induced variations. RESULTS Most of the dinucleotide steps in free DNA display high flexibility, assuming different conformations in a sequence-dependent fashion. With the exception of the AA/TT and GA/TC steps, which are 'A-phobic', and the GG/CC step, which is 'A-philic', the dinucleotide steps show no preference for A or B forms of DNA. Protein-bound DNA adopts the B-conformation most often. However, in certain cases, protein-binding causes the DNA backbone to take up energetically unfavourable conformations. At the gross structural level, several protein-bound DNA duplexes are observed to assume a curved conformation in the absence of any large distortions, indicating that a series of normal structural parameters at the dinucleotide and trinucleotide level, similar to the ones in free B-DNA, can give rise to curvature at the overall level. CONCLUSION The results illustrate that the free DNA molecule, even in the crystalline state, samples a large amount of conformational space, encompassing both the A and the B-forms, in the absence of any large ligands. A-form as well as some non-A, non-B, distorted geometries are observed for a small number of dinucleotide steps in DNA structures bound to the proteins belonging to a few specific families. However, for most of the bound DNA structures, across a wide variety of protein families, the average step parameters for various dinucleotide sequences as well as backbone torsion angles are observed to be quite close to the free 'B-like' DNA oligomer values, highlighting the flexibility and biological significance of this structural form.
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Affiliation(s)
- Arvind Marathe
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.
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Gan H, Tang K, Sun T, Hirtz M, Li Y, Chi L, Butz S, Fuchs H. Selective Adsorption of DNA on Chiral Surfaces: Supercoiled or Relaxed Conformation. Angew Chem Int Ed Engl 2009; 48:5282-6. [DOI: 10.1002/anie.200806295] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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48
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Gan H, Tang K, Sun T, Hirtz M, Li Y, Chi L, Butz S, Fuchs H. Selective Adsorption of DNA on Chiral Surfaces: Supercoiled or Relaxed Conformation. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200806295] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Biswas S, Guharoy M, Chakrabarti P. Dissection, residue conservation, and structural classification of protein-DNA interfaces. Proteins 2009; 74:643-54. [PMID: 18704949 DOI: 10.1002/prot.22180] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The basic DNA-binding modules of 128 protein-DNA interfaces have been analyzed. Although these are less planar, like the protein-protein interfaces, the protein-DNA interfaces can also be dissected into core regions in which all the fully-buried atoms are located, and rim regions having atoms with residual accessibilities. The sequence entropy of the core residues is smaller than those in the rim, indicating that the former are better conserved and possibly contribute more towards the binding free energy, as has been implicated in protein-protein interactions. On the protein side, 1014 A(2) of the surface is buried of which 63% belong to the core. There are some differences in the propensities of residues to occur in the core and the rim. In the DNA strands, the nucleotide(s) containing fully-buried atoms in all three components usually occupy central positions of the binding region. A new classification scheme for the interfaces has been introduced based on the composition of secondary structural elements of residues and the results compared with the conventional classification of DNA-binding proteins, as well as the protein class of the molecule. It appears that a common framework may be developed to understand both protein-protein and protein-DNA interactions.
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Affiliation(s)
- Sumit Biswas
- Department of Biochemistry, Bose Institute, Kolkata 700 054, India
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50
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Barbe S, Le Bret M. Ab initiodetermination of the flexibility of 2′-aminoribonucleosides and 2′-aminoarabinonucleosides inserted in duplexes. J Comput Chem 2008; 29:1353-63. [DOI: 10.1002/jcc.20890] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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