1
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Meredith RJ, Yoon MK, Carmichael I, Serianni AS. MA'AT Analysis: Unbiased Multi-State Conformational Modeling of Exocyclic Hydroxymethyl Group Conformation in Methyl Aldohexopyranosides. J Phys Chem B 2024. [PMID: 38442069 DOI: 10.1021/acs.jpcb.3c08136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
MA'AT analysis (J. Chem. Inf. Model. 2022, 62, 3135-3141) has been applied to model exocyclic hydroxymethyl group conformation in methyl β-D-glucopyranoside (βGlcOMe), methyl β-D-galactopyranoside (βGalOMe), and methyl β-D-mannopyranoside (βManOMe) in an unbiased manner. Using up to eight NMR J-couplings sensitive to rotation about the C5-C6 bond (torsion angle ω), two-state models of ω were obtained that are qualitatively consistent with the relative populations of the gg, gt, and tg rotamers reported previously. MA'AT analysis gave consistent unbiased gt ⇌ tg models of ω in βGalOMe, with gt more populated than tg and mean values of ω for each population similar to those obtained from aqueous 1-μs MD simulation. Using different combinations of J-couplings had little effect on the βGalOMe model in terms of the mean values of ω and circular standard deviations (CSDs). In contrast, MA'AT analysis of ω in βGlcOMe and βManOMe produced more than one two-state model independent of the ensemble of J-values used in the analyses. These models were characterized by gg ⇌ gt conformer exchange as expected, but the mean values of ω in both conformers varied significantly in the different fits, especially for the gg rotamer. Constrained (biased) MA'AT analyses in which only staggered geometries about ω were allowed gave RMSDs slightly larger than those obtained from the unbiased fits, precluding an assignment of an unbiased model. It is unclear why MA'AT analysis gives consistent and predictable unbiased models of ω in βGalOMe but not in βGlcOMe and βManOMe. One possibility is that the distribution of ω in one or both of the gg and gt conformers in the latter does not conform to a von Mises function (i.e., is not Gaussian-like), but rather to a broad and/or flat distribution that cannot be fit by the current version of MA'AT. Nevertheless, the results of this study provide new evidence of the ability of MA'AT analysis to treat multi-state conformational exchange using only experimental NMR data, extending recent MA'AT applications to furanosyl ring pseudorotation (Biochemistry 2022, 61, 239-251).
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Affiliation(s)
- Reagan J Meredith
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556 ,United States
| | - Mi-Kyung Yoon
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556 ,United States
| | - Ian Carmichael
- Radiation Laboratory, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Anthony S Serianni
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556 ,United States
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2
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Krall JB, Nichols PJ, Henen MA, Vicens Q, Vögeli B. Structure and Formation of Z-DNA and Z-RNA. Molecules 2023; 28:843. [PMID: 36677900 PMCID: PMC9867160 DOI: 10.3390/molecules28020843] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/08/2023] [Accepted: 01/12/2023] [Indexed: 01/17/2023] Open
Abstract
Despite structural differences between the right-handed conformations of A-RNA and B-DNA, both nucleic acids adopt very similar, left-handed Z-conformations. In contrast to their structural similarities and sequence preferences, RNA and DNA exhibit differences in their ability to adopt the Z-conformation regarding their hydration shells, the chemical modifications that promote the Z-conformation, and the structure of junctions connecting them to right-handed segments. In this review, we highlight the structural and chemical properties of both Z-DNA and Z-RNA and delve into the potential factors that contribute to both their similarities and differences. While Z-DNA has been extensively studied, there is a gap of knowledge when it comes to Z-RNA. Where such information is lacking, we try and extend the principles of Z-DNA stability and formation to Z-RNA, considering the inherent differences of the nucleic acids.
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Affiliation(s)
- Jeffrey B. Krall
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Parker J. Nichols
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Morkos A. Henen
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Quentin Vicens
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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3
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Lönnberg H. Structural modifications as tools in mechanistic studies of the cleavage of RNA phosphodiester linkages. CHEM REC 2022; 22:e202200141. [PMID: 35832010 DOI: 10.1002/tcr.202200141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/28/2022] [Indexed: 11/06/2022]
Abstract
The cleavage of RNA phosphodiester bonds by RNase A and hammerhead ribozyme at neutral pH fundamentally differs from the spontaneous reactions of these bonds under the same conditions. While the predominant spontaneous reaction is isomerization of the 3',5'-phosphodiester linkages to their 2',5'-counterparts, this reaction has never been reported to compete with the enzymatic cleavage reaction, not even as a minor side reaction. Comparative kinetic measurements with structurally modified di-nucleoside monophosphates and oligomeric phosphodiesters have played an important role in clarification of mechanistic details of the buffer-independent and buffer-catalyzed reactions. More recently, heavy atom isotope effects and theoretical calculations have refined the picture. The primary aim of all these studies has been to form a solid basis for mechanistic analyses of the action of more complicated catalytic machineries. In other words, to contribute to conception of a plausible unified picture of RNA cleavage by biocatalysts, such as RNAse A, hammerhead ribozyme and DNAzymes. In addition, structurally modified trinucleoside monophosphates as transition state models for Group I and II introns have clarified some features of the action of large ribozymes.
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Affiliation(s)
- Harri Lönnberg
- Department of Chemistry, University of Turku, FI-20014 University of, Turku
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4
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Kusaka S, Yamamoto K, Shinohara M, Minato Y, Ichikawa S. Design, synthesis and conformation-activity relationship analysis of LNA/BNA-type 5'-O-aminoribosyluridine as MraY inhibitors. Bioorg Med Chem 2022; 65:116744. [PMID: 35500521 DOI: 10.1016/j.bmc.2022.116744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/03/2022] [Accepted: 04/05/2022] [Indexed: 11/02/2022]
Abstract
It is important to understand and control the biologically active conformation in medicinal chemistry. Muraymycins and caprazamycins, which are strong inhibitors of MraY, are promising antibacterial agents with a novel mode of action. Focusing on a sugar puckering and a dihedral angle ϕ of the uridine moiety of these natural products, LNA/BNA-type 5'-O-aminoribosyluridine analogues, whose puckering of the ribose moiety are completely restricted to the N-type, were designed and synthesized as simplified MraY inhibitors. Their conformation-activity relationship was further investigated in details. The conformation-activity relationship analysis investigated in this study could be a general guideline for simplification and rational drug design of MraY inhibitory nucleoside natural products.
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Affiliation(s)
- Shintaro Kusaka
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Kazuki Yamamoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Motoko Shinohara
- Department of Microbiology, Fujita Health University School of Medicine, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Yusuke Minato
- Department of Microbiology, Fujita Health University School of Medicine, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Satoshi Ichikawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan; Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan; Global Station for Biosurfaces and Drug Discovery, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan.
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5
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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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6
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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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7
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Nester K, Plazinski W. Deciphering the conformational preferences of furanosides. A molecular dynamics study. J Biomol Struct Dyn 2020; 38:3359-3370. [DOI: 10.1080/07391102.2019.1656670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Karina Nester
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Krakow, Poland
| | - Wojciech Plazinski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Krakow, Poland
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8
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Maksimovic I, Zheng Q, Trujillo MN, Galligan JJ, David Y. An Azidoribose Probe to Track Ketoamine Adducts in Histone Ribose Glycation. J Am Chem Soc 2020; 142:9999-10007. [PMID: 32390412 PMCID: PMC8052992 DOI: 10.1021/jacs.0c01325] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Reactive cellular metabolites can modify macromolecules and form adducts known as nonenzymatic covalent modifications (NECMs). The dissection of the mechanisms, regulation, and consequences of NECMs, such as glycation, has been challenging due to the complex and often ambiguous nature of the adducts formed. Specific chemical tools are required to directly track the formation of these modifications on key targets in order to uncover their underlying physiological importance. Here, we present the novel chemoenzymatic synthesis of an active azido-modified ribose analog, 5-azidoribose (5-AR), as well as the synthesis of an inactive control derivative, 1-azidoribose (1-AR), and their application toward understanding protein ribose-glycation in vitro and in cellulo. With these new probes we found that, similar to methylglyoxal (MGO) glycation, ribose glycation specifically accumulates on histones. In addition to fluorescent labeling, we demonstrate the utility of the probe in enriching modified targets, which were identified by label-free quantitative proteomics and high-resolution MS/MS workflows. Finally, we establish that the known oncoprotein and hexose deglycase, fructosamine 3-kinase (FN3K), recognizes and facilitates the removal of 5-AR glycation adducts in live cells, supporting the dynamic regulation of ribose glycation as well as validating the probe as a new platform to monitor FN3K activity. Altogether, we demonstrate this probe's utilities to uncover ribose-glycation and deglycation events as well as track FN3K activity toward establishing its potential as a new cancer vulnerability.
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Affiliation(s)
- Igor Maksimovic
- Tri-Institutional PhD Program in Chemical Biology, New York, New York 10065, United States
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Qingfei Zheng
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Marissa N Trujillo
- Department of Pharmaocology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
| | - James J Galligan
- Department of Pharmaocology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
| | - Yael David
- Tri-Institutional PhD Program in Chemical Biology, New York, New York 10065, United States
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
- Department of Pharmacology, Weill Cornell Medicine, New York, New York 10065, United States
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, New York 10065, United States
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9
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The furanosidic scaffold of d-ribose: a milestone for cell life. Biochem Soc Trans 2020; 47:1931-1940. [PMID: 31697320 DOI: 10.1042/bst20190749] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 10/03/2019] [Accepted: 10/07/2019] [Indexed: 01/15/2023]
Abstract
The recruitment of the furanosidic scaffold of ribose as the crucial step for nucleotides and then for nucleic acids synthesis is presented. Based on the view that the selection of molecules to be used for relevant metabolic purposes must favor structurally well-defined molecules, the inadequacy of ribose as a preferential precursor for nucleotides synthesis is discussed. The low reliability of ribose in its furanosidic hemiacetal form must have played ab initio against the choice of d-ribose for the generation of d-ribose-5-phosphate, the fundamental precursor of the ribose moiety of nucleotides. The latter, which is instead generated through the 'pentose phosphate pathway' is strictly linked to the affordable and reliable pyranosidic structure of d-glucose.
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10
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Javed M, Ahmad MI, Javed H, Naseem S. D-ribose and pathogenesis of Alzheimer's disease. Mol Biol Rep 2020; 47:2289-2299. [PMID: 31933261 DOI: 10.1007/s11033-020-05243-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 01/02/2020] [Indexed: 12/29/2022]
Abstract
It is estimated that the global prevalence of dementia will rise as high as 24 million and predicted to be double in every 20 years which is attributed to the fact that the ageing population is increasing and so more individuals are at risk of developing neurodegenerative diseases like Alzheimer's. Many scientists favored glycation of proteins such as tau, amyloid beta (Aβ) etc. as one of the important risk factor in Alzheimer's disease (AD). Since, D-ribose shows highest glycation ability among other sugars hence, produces advanced glycation end products (AGEs) rapidly. However, there are several other mechanisms suggested by researchers through which D-ribose may cause cognitive impairments. There is a concern related to diabetic patients since they also suffer from D-ribose metabolism, may be more prone to AD risk. Thus, it is imperative that the pathogenesis and the pathways involved in AD progression are explored in the light of ribosylation and AGEs formation for identifying suitable diagnostics marker for early diagnosis or finding promising therapeutic outcomes.
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Affiliation(s)
- Mehjbeen Javed
- Aquatic Toxicology Research Laboratory, Department of Zoology, Aligarh Muslim University, Aligarh, U.P., India
| | - Md Irshad Ahmad
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, U.P., India.,Department of Biophysics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Hina Javed
- Department of Chemistry, Aligarh Muslim University, Aligarh, U.P., India
| | - Sufia Naseem
- Department of Biochemistry, Faculty of Medicine, Aligarh Muslim University, Aligarh, U.P., India.
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11
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Wagner JR, Demir Ö, Carpenter MA, Aihara H, Harki DA, Harris RS, Amaro RE. Determinants of Oligonucleotide Selectivity of APOBEC3B. J Chem Inf Model 2019; 59:2264-2273. [PMID: 30130104 PMCID: PMC6644697 DOI: 10.1021/acs.jcim.8b00427] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
APOBEC3B (A3B) is a prominent source of mutation in many cancers. To date, it has been difficult to capture the native protein-DNA interactions that confer A3B's substrate specificity by crystallography due to the highly dynamic nature of wild-type A3B active site. We use computational tools to restore a recent crystal structure of a DNA-bound A3B C-terminal domain mutant construct to its wild type sequence, and run molecular dynamics simulations to study its substrate recognition mechanisms. Analysis of these simulations reveal dynamics of the native A3Bctd-oligonucleotide interactions, including the experimentally inaccessible loop 1-oligonucleotide interactions. A second series of simulations in which the target cytosine nucleotide was computationally mutated from a deoxyribose to a ribose show a change in sugar ring pucker, leading to a rearrangement of the binding site and revealing a potential intermediate in the binding pathway. Finally, apo simulations of A3B, starting from the DNA-bound open state, experience a rapid and consistent closure of the binding site, reaching conformations incompatible with substrate binding. This study reveals a more realistic and dynamic view of the wild type A3B binding site and provides novel insights for structure-guided design efforts for A3B.
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Affiliation(s)
- Jeffrey R Wagner
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093-0340 , United States
| | - Özlem Demir
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093-0340 , United States
| | - Michael A Carpenter
- Department of Biochemistry, Molecular Biology and Biophysics , University of Minnesota , Minneapolis , Minnesota 55455 , United States
- Masonic Cancer Center , University of Minnesota , Minneapolis , Minnesota 55455 , United States
- Institute for Molecular Virology , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology and Biophysics , University of Minnesota , Minneapolis , Minnesota 55455 , United States
- Masonic Cancer Center , University of Minnesota , Minneapolis , Minnesota 55455 , United States
- Institute for Molecular Virology , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Daniel A Harki
- Department of Medicinal Chemistry , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology and Biophysics , University of Minnesota , Minneapolis , Minnesota 55455 , United States
- Masonic Cancer Center , University of Minnesota , Minneapolis , Minnesota 55455 , United States
- Institute for Molecular Virology , University of Minnesota , Minneapolis , Minnesota 55455 , United States
- Howard Hughes Medical Institute , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093-0340 , United States
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12
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Gaweda K, Plazinski W. The systematic influence of solvent on the conformational features of furanosides. Org Biomol Chem 2019; 17:2479-2485. [PMID: 30756110 DOI: 10.1039/c9ob00043g] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The endo- and exo-anomeric effects are the two most recognizable stereoelectronic effects exhibited by carbohydrates. Their presence relies on the interactions between ring substituent(s) and ring oxygen atoms. Here, we report the finding of a new effect that partially controls the conformational properties of furanose rings and can be ascribed to the influence of the solvent on the electronic structure of a molecule. In contrast to anomeric effects, it is not dependent on either presence or absence of ring substituents. Its origins lie in a solvent-induced flux of atomic charges that involves atoms forming the furanose ring. This systematically changes the energy of the whole molecular system and alters the ring-distortion free energies by ∼2.5-6.5 kJ mol-1, favoring the geometries close to the twist 3T2/2T3 conformers and disfavoring the envelope OE/EO-like shapes. This intriguing effect has never been reported before, although it is expected to exist in all furanose rings. Along with more recognized stereoelectronic effects, this phenomenon contributes to a wide applicability of the two-state (north vs. south) model of pseudorotation in furanosides and, in the case of extremely flexible furanose rings, may change the preferred conformation type in comparison with the gas-phase-oriented predictions.
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Affiliation(s)
- Karolina Gaweda
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, ul. Niezapominajek 8, 30-239 Cracow, Poland.
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13
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Guo F, Yue Z, Trajkovski M, Zhou X, Cao D, Li Q, Wang B, Wen X, Plavec J, Peng Q, Xi Z, Zhou C. Effect of Ribose Conformation on RNA Cleavage via Internal Transesterification. J Am Chem Soc 2018; 140:11893-11897. [PMID: 30207719 DOI: 10.1021/jacs.8b06313] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
RNA cleavage via internal transesterification is a fundamental reaction involved in RNA processing and metabolism, and the regulation thereof. Herein, the influence of ribose conformation on this reaction was investigated with conformationally constrained ribonucleotides. RNA cleavage rates were found to decrease in the order South-constrained ribonucleotide > native ribonucleotide ≫ North-constrained counterpart, indicating that the ribose conformation plays an important role in modulating RNA cleavage via internal transesterification.
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Affiliation(s)
- Fengmin Guo
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry , Nankai University , Tianjin 300071 , China
| | - Zekun Yue
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry , Nankai University , Tianjin 300071 , China
| | - Marko Trajkovski
- Slovenian NMR Centre, National Institute of Chemistry , University of Ljubljana, Faculty of Chemistry and Chemical Technology, Ljubljana, EN-FIST Centre of Excellence , Hajdrihova 19 , Ljubljana 1000 , Slovenia
| | - Xiaoping Zhou
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry , Nankai University , Tianjin 300071 , China
| | - Dong Cao
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry , Nankai University , Tianjin 300071 , China
| | - Qiang Li
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry , Nankai University , Tianjin 300071 , China
| | - Baifan Wang
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry , Nankai University , Tianjin 300071 , China
| | - Xin Wen
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry , Nankai University , Tianjin 300071 , China
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry , University of Ljubljana, Faculty of Chemistry and Chemical Technology, Ljubljana, EN-FIST Centre of Excellence , Hajdrihova 19 , Ljubljana 1000 , Slovenia
| | - Qian Peng
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry , Nankai University , Tianjin 300071 , China
| | - Zhen Xi
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry , Nankai University , Tianjin 300071 , China
| | - Chuanzheng Zhou
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry , Nankai University , Tianjin 300071 , China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) , Tianjin 300071 , China
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14
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Hřebabecký H, Dračínský M, Procházková E, Šála M, Mackman R, Nencka R. Control of α/β Anomer Formation by a 2',5' Bridge: Toward Nucleoside Derivatives Locked in the South Conformation. J Org Chem 2017; 82:11337-11347. [PMID: 28972760 DOI: 10.1021/acs.joc.7b01000] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We describe a novel stereoselective synthesis of nucleoside derivatives with the ribose ring locked in the South conformation by a bridge between C2' and C5'. Despite the intrinsic constraints of the bicyclic structure, we demonstrate that their synthesis can be achieved by ring closing metathesis of readily accessible precursors. The obtained ribose derivatives are, however, very poor substrates for further installation of the nucleobases, and even simple nucleophiles, such as azido or cyano anions, react with unexpected stereo- or regioselectivity under standard glycosylation conditions. Here we explain this behavior by employing density functional theory (DFT) computations and devise an alternative approach resulting in isomers with the desired orientation of the nucleobase.
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Affiliation(s)
- Hubert Hřebabecký
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , v.v.i, Gilead Sciences & IOCB Research Centre, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , v.v.i, Gilead Sciences & IOCB Research Centre, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Eliška Procházková
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , v.v.i, Gilead Sciences & IOCB Research Centre, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Michal Šála
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , v.v.i, Gilead Sciences & IOCB Research Centre, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Richard Mackman
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Radim Nencka
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , v.v.i, Gilead Sciences & IOCB Research Centre, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
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15
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Clay MC, Ganser LR, Merriman DK, Al-Hashimi HM. Resolving sugar puckers in RNA excited states exposes slow modes of repuckering dynamics. Nucleic Acids Res 2017; 45:e134. [PMID: 28609788 PMCID: PMC5737546 DOI: 10.1093/nar/gkx525] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 06/01/2017] [Accepted: 06/05/2017] [Indexed: 11/15/2022] Open
Abstract
Recent studies have shown that RNAs exist in dynamic equilibrium with short-lived low-abundance 'excited states' that form by reshuffling base pairs in and around non-canonical motifs. These conformational states are proposed to be rich in non-canonical motifs and to play roles in the folding and regulatory functions of non-coding RNAs but their structure proves difficult to characterize given their transient nature. Here, we describe an approach for determining sugar pucker conformation in RNA excited states through nuclear magnetic resonance measurements of C1΄ and C4΄ rotating frame spin relaxation (R1ρ) in uniformly 13C/15N labeled RNA samples. Application to HIV-1 TAR exposed slow modes of sugar repuckering dynamics at the μs and ms timescale accompanying transitions between non-helical (C2΄-endo) to helical (C3΄-endo) conformations during formation of two distinct excited states. In contrast, we did not obtain any evidence for slow sugar repuckering dynamics for nucleotides in a variety of structural contexts that do not undergo non-helical to helical transitions. Our results outline a route for significantly improving the conformational characterization of RNA excited states and suggest that slow modes of repuckering dynamics gated by transient changes in secondary structure are quite common in RNA.
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Affiliation(s)
- Mary C. Clay
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Laura R. Ganser
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | | | - Hashim M. Al-Hashimi
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
- Department of Chemistry, Duke University, Durham, NC 27708, USA
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16
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Suárez-Ortiz GA, Cerda-García-Rojas CM, Fragoso-Serrano M, Pereda-Miranda R. Complementarity of DFT Calculations, NMR Anisotropy, and ECD for the Configurational Analysis of Brevipolides K-O from Hyptis brevipes. JOURNAL OF NATURAL PRODUCTS 2017; 80:181-189. [PMID: 28099005 DOI: 10.1021/acs.jnatprod.6b00953] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Brevipolides K-O (1-5), five new cytotoxic 6-(6'-cinnamoyloxy-2',5'-epoxy-1'-hydroxyheptyl)-5,6-dihydro-2H-pyran-2-ones (IC50 values against six cancer cell lines, 1.7-10 μM), were purified by recycling HPLC from Hyptis brevipes. The structures, containing a distinctive tetrahydrofuran ring, were established by comprehensive quantum mechanical calculations and experimental spectroscopic analysis of their NMR and ECD data. Detailed analysis of the experimental NMR 1H-1H vicinal coupling constants in comparison with the corresponding DFT-calculated values at the B3LYP/DGDZVP level confirmed the absolute configuration of 3 and revealed its conformational preferences, which were further strengthened by NOESY correlations. NMR anisotropy experiments by the application of Mosher's ester methodology and chemical correlations were also used to conclude that this novel brevipolide series (1-5) share the same absolute configuration corresponding to C-6(R), C-1'(S), C-2'(R), C-5'(S), and C-6'(S).
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Affiliation(s)
- G Alejandra Suárez-Ortiz
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Circuito Exterior Ciudad Universitaria , Mexico City 04510, Mexico
| | - Carlos M Cerda-García-Rojas
- Departamento de Química, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional , A. P. 14-740, Mexico City 07000, Mexico
| | - Mabel Fragoso-Serrano
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Circuito Exterior Ciudad Universitaria , Mexico City 04510, Mexico
| | - Rogelio Pereda-Miranda
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Circuito Exterior Ciudad Universitaria , Mexico City 04510, Mexico
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17
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Dinda AK, Tripathy DR, Dasgupta S. Glycation of Ribonuclease A affects its enzymatic activity and DNA binding ability. Biochimie 2015; 118:162-72. [DOI: 10.1016/j.biochi.2015.09.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 09/08/2015] [Indexed: 11/30/2022]
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18
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Azofra LM, Quesada-Moreno MM, Alkorta I, Avilés-Moreno JR, Elguero J, López-González JJ. Understanding the Aldo-Enediolate Tautomerism of Glycolaldehyde in Basic Aqueous Solutions. Chemphyschem 2015; 16:2226-36. [DOI: 10.1002/cphc.201500139] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Indexed: 11/12/2022]
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19
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Govender KK, Naidoo KJ. Evaluating AM1/d-CB1 for Chemical Glycobiology QM/MM Simulations. J Chem Theory Comput 2014; 10:4708-17. [DOI: 10.1021/ct500373p] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Krishna K. Govender
- Scientific Computing
Research Unit and Department
of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Kevin J. Naidoo
- Scientific Computing
Research Unit and Department
of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
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20
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Ghosh S, Pandey NK, Singha Roy A, Tripathy DR, Dinda AK, Dasgupta S. Prolonged glycation of hen egg white lysozyme generates non amyloidal structures. PLoS One 2013; 8:e74336. [PMID: 24066139 PMCID: PMC3774808 DOI: 10.1371/journal.pone.0074336] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 08/02/2013] [Indexed: 11/18/2022] Open
Abstract
Glycation causes severe damage to protein structure that could lead to amyloid formation in special cases. Here in this report, we have shown for the first time that hen egg white lysozyme (HEWL) does not undergo amyloid formation even after prolonged glycation in the presence of D-glucose, D-fructose and D-ribose. Cross-linked oligomers were formed in all the cases and ribose was found to be the most potent among the three sugars. Ribose mediated oligomers, however, exhibit Thioflavin T binding properties although microscopic images clearly show amorphous and globular morphology of the aggregates. Our study demonstrates that the structural damage of hen egg white lysozyme due to glycation generates unstructured aggregates.
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Affiliation(s)
- Sudeshna Ghosh
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Nitin Kumar Pandey
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Atanu Singha Roy
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Debi Ranjan Tripathy
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Amit Kumar Dinda
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Swagata Dasgupta
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, India
- * E-mail:
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21
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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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22
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Mason PE, Neilson GW, Saboungi ML, Brady JW, Bush CA. The conformation of a ribose derivative in aqueous solution: a neutron-scattering and molecular dynamics study. Biopolymers 2013; 99:739-45. [PMID: 23828616 DOI: 10.1002/bip.22339] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2013] [Accepted: 06/19/2013] [Indexed: 11/10/2022]
Abstract
The structure of aqueous solutions of methyl β-D-ribofuranoside was investigated by coupling molecular dynamics (MD) simulations and neutron scattering measurements with isotopic substitution. Using a sample of the sugar isotopically-labeled at a single unique position, neutron scattering structure factors and radial distribution functions can be compared with MD simulations constrained to different conformations to determine which conformer best fits the experimental results. Three different simulations were performed with the methyl ether group of the sugar unconstrained and constrained in each of its staggered orientations. The results of the unconstrained simulation showed that the methyl ester group occupied predominantly the 300° position, which is in agreement with the diffraction experimental results. This result suggests that the molecular mechanics force field used in the simulation adequately describes the conformation of the 1-methyl ether group in the methyl β-D-ribofuranoside.
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Affiliation(s)
- Philip E Mason
- Department of Food Science, Stocking Hall, Cornell University, Ithaca, NY, 14853
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23
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Roe DR, Cheatham TE. PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data. J Chem Theory Comput 2013; 9:3084-95. [PMID: 26583988 DOI: 10.1021/ct400341p] [Citation(s) in RCA: 4572] [Impact Index Per Article: 415.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We describe PTRAJ and its successor CPPTRAJ, two complementary, portable, and freely available computer programs for the analysis and processing of time series of three-dimensional atomic positions (i.e., coordinate trajectories) and the data therein derived. Common tools include the ability to manipulate the data to convert among trajectory formats, process groups of trajectories generated with ensemble methods (e.g., replica exchange molecular dynamics), image with periodic boundary conditions, create average structures, strip subsets of the system, and perform calculations such as RMS fitting, measuring distances, B-factors, radii of gyration, radial distribution functions, and time correlations, among other actions and analyses. Both the PTRAJ and CPPTRAJ programs and source code are freely available under the GNU General Public License version 3 and are currently distributed within the AmberTools 12 suite of support programs that make up part of the Amber package of computer programs (see http://ambermd.org ). This overview describes the general design, features, and history of these two programs, as well as algorithmic improvements and new features available in CPPTRAJ.
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Affiliation(s)
- Daniel R Roe
- Department of Medicinal Chemistry, College of Pharmacy, 2000 South 30 East Room 105, University of Utah, Salt Lake City, Utah 84112, United States
| | - Thomas E Cheatham
- Department of Medicinal Chemistry, College of Pharmacy, 2000 South 30 East Room 105, University of Utah, Salt Lake City, Utah 84112, United States
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24
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Taha HA, Richards MR, Lowary TL. Conformational Analysis of Furanoside-Containing Mono- and Oligosaccharides. Chem Rev 2012; 113:1851-76. [DOI: 10.1021/cr300249c] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Hashem A. Taha
- Alberta Glycomics Centre and Department of Chemistry, Gunning−Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2
| | - Michele R. Richards
- Alberta Glycomics Centre and Department of Chemistry, Gunning−Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2
| | - Todd L. Lowary
- Alberta Glycomics Centre and Department of Chemistry, Gunning−Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2
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25
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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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26
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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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27
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Gore KR, Nawale GN, Harikrishna S, Chittoor VG, Pandey SK, Höbartner C, Patankar S, Pradeepkumar PI. Synthesis, gene silencing, and molecular modeling studies of 4'-C-aminomethyl-2'-O-methyl modified small interfering RNAs. J Org Chem 2012; 77:3233-45. [PMID: 22372696 DOI: 10.1021/jo202666m] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The linear syntheses of 4'-C-aminomethyl-2'-O-methyl uridine and cytidine nucleoside phosphoramidites were achieved using glucose as the starting material. The modified RNA building blocks were incorporated into small interfering RNAs (siRNAs) by employing solid phase RNA synthesis. Thermal melting studies showed that the modified siRNA duplexes exhibited slightly lower T(m) (∼1 °C/modification) compared to the unmodified duplex. Molecular dynamics simulations revealed that the 4'-C-aminomethyl-2'-O-methyl modified nucleotides adopt South-type conformation in a siRNA duplex, thereby altering the stacking and hydrogen-bonding interactions. These modified siRNAs were also evaluated for their gene silencing efficiency in HeLa cells using a luciferase-based reporter assay. The results indicate that the modifications are well tolerated in various positions of the passenger strand and at the 3' end of the guide strand but are less tolerated in the seed region of the guide strand. The modified siRNAs exhibited prolonged stability in human serum compared to unmodified siRNA. This work has implications for the use of 4'-C-aminomethyl-2'-O-methyl modified nucleotides to overcome some of the challenges associated with the therapeutic utilities of siRNAs.
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Affiliation(s)
- Kiran R Gore
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
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28
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Han C, Lu Y, Wei Y, Liu Y, He R. D-ribose induces cellular protein glycation and impairs mouse spatial cognition. PLoS One 2011; 6:e24623. [PMID: 21966363 PMCID: PMC3169629 DOI: 10.1371/journal.pone.0024623] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Accepted: 08/14/2011] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND D-ribose, an important reducing monosaccharide, is highly active in the glycation of proteins, and results in the rapid production of advanced glycation end products (AGEs) in vitro. However, whether D-ribose participates in glycation and leads to production of AGEs in vivo still requires investigation. METHODOLOGY/PRINCIPAL FINDINGS Here we treated cultured cells and mice with D-ribose and D-glucose to compare ribosylation and glucosylation for production of AGEs. Treatment with D-ribose decreased cell viability and induced more AGE accumulation in cells. C57BL/6J mice intraperitoneally injected with D-ribose for 30 days showed high blood levels of glycated proteins and AGEs. Administration of high doses D-ribose also accelerated AGE formation in the mouse brain and induced impairment of spatial learning and memory ability according to the performance in Morris water maze test. CONCLUSIONS/SIGNIFICANCE These data demonstrate that D-ribose but not D-glucose reacts rapidly with proteins and produces significant amounts of AGEs in both cultured cells and the mouse brain, leading to accumulation of AGEs which may impair mouse spatial cognition.
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Affiliation(s)
- Chanshuai Han
- State Key Laboratory of Brain and Cognitive Sciences, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Graduate University of the Chinese Academy of Sciences, Beijing, China
| | - Yang Lu
- State Key Laboratory of Brain and Cognitive Sciences, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- School of Life Sciences, University of Science and Technology of China, Anhui, China
| | - Yan Wei
- State Key Laboratory of Brain and Cognitive Sciences, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Ying Liu
- State Key Laboratory of Brain and Cognitive Sciences, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Rongqiao He
- State Key Laboratory of Brain and Cognitive Sciences, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing, China
- * E-mail:
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29
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Barnett CB, Naidoo KJ. Ring puckering: a metric for evaluating the accuracy of AM1, PM3, PM3CARB-1, and SCC-DFTB carbohydrate QM/MM simulations. J Phys Chem B 2010; 114:17142-54. [PMID: 21138284 DOI: 10.1021/jp107620h] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The puckered conformations of furanose and pyranose carbohydrate rings are central to analyzing the action of enzymes on carbohydrates. Enzyme reaction mechanisms are generally inaccessible to experiments and so have become the focus of QM(semiempirical)/MM simulations. We show that the complete free energy of puckering is required to evaluate the accuracy of semiempirical methods used to study reactions involving carbohydrates. Interestingly, we find that reducing the free energy space to lower dimensions results in near meaningless minimum energy pathways. We analyze the furanose and pyranose free energy pucker surfaces and volumes using AM1, PM3, PM3CARB-1, and SCC-DFTB. A comparison with DFT optimized structures and a HF free energy surface reveals that SCC-DFTB provides the best semiempirical description of five- and six-membered carbohydrate ring deformation.
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Affiliation(s)
- Christopher B Barnett
- Scientific Computing Research Unit and Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
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30
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Koole LH, Buck HM, Kuijpers WHA, Balgobin N, Nyilas A, Remaud G, Vial JM, Chattopadhyaya J. Lariat formation in splicing of pre-messenger RNA. Conformation and base stacking at the lariat branch point studied using 500-MHz 1H NMR and CD spectroscopy. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19881071203] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Williams AA, Darwanto A, Theruvathu JA, Burdzy A, Neidigh JW, Sowers LC. Impact of sugar pucker on base pair and mispair stability. Biochemistry 2009; 48:11994-2004. [PMID: 19899814 PMCID: PMC2814217 DOI: 10.1021/bi9014133] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The selection of nucleoside triphosphates by a polymerase is controlled by several energetic and structural features, including base pairing geometry as well as sugar structure and conformation. Whereas base pairing has been considered exhaustively, substantially less is known about the role of sugar modifications for both nucleotide incorporation and primer extension. In this study, we synthesized oligonucleotides containing 2'-fluoro-modified nucleosides with constrained sugar pucker in an internucleotide position and, for the first time, at a primer 3'-end. The thermodynamic stability of these duplexes was examined. The nucleoside 2'-deoxy-2'-fluoroarabinofuranosyluracil [U(2'F(ara))] favors the 2'-endo conformation (DNA-like), while 2'-deoxy-2'-fluororibofuranosyluracil [U(2'F(ribo))] favors the 3'-endo conformation (RNA-like). Oligonucleotides containing U(2'F(ara)) have slightly higher melting temperatures (T(m)) than those containing U(2'F(ribo)) when located in internucleotide positions or at the 3'-end and when correctly paired with adenine or mispaired with guanine. However, both modifications decrease the magnitude of DeltaH degrees and DeltaS degrees for duplex formation in all sequence contexts. In examining the thermodynamic properties for this set of oligonucleotides, we find entropy-enthalpy compensation is apparent. Our thermodynamic findings led to a series of experiments with DNA ligase that reveal, contrary to expectation based upon observed T(m) values, that the duplex containing the U(2'F(ribo)) analogue is more easily ligated. The 2'-fluoro-2'-deoxynucleosides examined here are valuable probes of the impact of sugar constraint and are also members of an important class of antitumor and antiviral agents. The data reported here may facilitate an understanding of the biological properties of these agents, as well as the contribution of sugar conformation to replication fidelity.
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Affiliation(s)
- Adides A. Williams
- Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, California 92350
| | - Agus Darwanto
- Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, California 92350
| | - Jacob A. Theruvathu
- Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, California 92350
| | - Artur Burdzy
- Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, California 92350
| | - Jonathan W. Neidigh
- Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, California 92350
| | - Lawrence C. Sowers
- Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, California 92350
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Johnson JE, Hoogstraten CG. Extensive backbone dynamics in the GCAA RNA tetraloop analyzed using 13C NMR spin relaxation and specific isotope labeling. J Am Chem Soc 2009; 130:16757-69. [PMID: 19049467 DOI: 10.1021/ja805759z] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Conformational dynamics play a key role in the properties and functions of proteins and nucleic acids. Heteronuclear NMR spin relaxation is a uniquely powerful site-specific probe of dynamics in proteins and has found increasing applications to nucleotide base side chains and anomeric sites in RNA. Applications to the nucleic acid ribose backbone, however, have been hampered by strong magnetic coupling among ring carbons in uniformly 13C-labeled samples. In this work, we apply a recently developed, metabolically directed isotope labeling scheme that places 13C with high efficiency and specificity at the nucleotide ribose C2' and C4' sites. We take advantage of this scheme to explore backbone dynamics in the well-studied GCAA RNA tetraloop. Using a combination of CPMG (Carr-Purcell-Meiboom-Gill) and R(1rho) relaxation dispersion spectroscopy to explore exchange processes on the microsecond to millisecond time scale, we find an extensive pattern of dynamic transitions connecting a set of relatively well-defined conformations. In many cases, the observed transitions appear to be linked to C3'-endo/C2'-endo sugar pucker transitions of the corresponding nucleotides, and may also be correlated across multiple nucleotides within the tetraloop. These results demonstrate the power of NMR spin relaxation based on alternate-site isotope labeling to open a new window into the dynamic properties of ribose backbone groups in RNA.
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Affiliation(s)
- James E Johnson
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
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Consequence of hydrogen atom abstraction from 5’-hydroxyl group of 2’-deoxyadenosine. Theoretical quantum mechanics study. OPEN CHEM 2008. [DOI: 10.2478/s11532-008-0038-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
AbstractReactive oxygen species (ROS) may generate different nucleoside/nucleotide radicals in a cell environment. In this study, the possibility of cyclic-2’-deoxyadenosines formation by a rearrangement of their free radicals was investigated. It seems that for cyclic-nucleosides formation, adoption of an O4’-exo conformation by the sugar moiety is necessary. However, this is the energetically unfavoured form of the 2-deoxyribose ring. Moreover, the creation of a O5’, C8 bond in purine deoxy-nucleosides/nucleotides leads to the termination of the DNA elongation process.
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Buděšínský M, Daněček P, Bednárová L, Kapitán J, Baumruk V, Bouř P. Comparison of Quantitative Conformer Analyses by Nuclear Magnetic Resonance and Raman Optical Activity Spectra for Model Dipeptides. J Phys Chem A 2008; 112:8633-40. [DOI: 10.1021/jp806181q] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Miloš Buděšínský
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo nám. 2, 16610, Prague 6, Czech Republic, and Charles University, Faculty of Mathematics and Physics, Institute of Physics, Ke Karlovu 5, 12116, Prague 2, Czech Republic
| | - Petr Daněček
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo nám. 2, 16610, Prague 6, Czech Republic, and Charles University, Faculty of Mathematics and Physics, Institute of Physics, Ke Karlovu 5, 12116, Prague 2, Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo nám. 2, 16610, Prague 6, Czech Republic, and Charles University, Faculty of Mathematics and Physics, Institute of Physics, Ke Karlovu 5, 12116, Prague 2, Czech Republic
| | - Josef Kapitán
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo nám. 2, 16610, Prague 6, Czech Republic, and Charles University, Faculty of Mathematics and Physics, Institute of Physics, Ke Karlovu 5, 12116, Prague 2, Czech Republic
| | - Vladimír Baumruk
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo nám. 2, 16610, Prague 6, Czech Republic, and Charles University, Faculty of Mathematics and Physics, Institute of Physics, Ke Karlovu 5, 12116, Prague 2, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo nám. 2, 16610, Prague 6, Czech Republic, and Charles University, Faculty of Mathematics and Physics, Institute of Physics, Ke Karlovu 5, 12116, Prague 2, Czech Republic
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Karwowski BT, Gaillard J, Grand A, Cadet J. Effect of (5'S)-5',8-cyclo-2'-deoxyadenosine on the conformation of di and trinucleotides. A NMR and DFT study. Org Biomol Chem 2008; 6:3408-13. [PMID: 18802649 DOI: 10.1039/b807046f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
5',8-Purine cyclonucleosides constitute an important class of oxidatively generated tandem lesions whose formation involves initial hydroxyl radical-mediated hydrogen atom abstraction from the 5-hydroxymethyl group of 2-deoxyribose followed by intramolecular cyclization. The present study deals with the synthesis of the 5'S diastereomer of 5',8-cyclo-2'-deoxyadenosine containing di- and tri-oligodeoxynucleotides as an attempt to delineate the conformational changes induced in the DNA fragments by the presence of a rigid modified nucleoside. For this purpose, extensive 1D and 2D NMR measurements that were completed by DFT theoretical calculations were performed. As a striking result, it was found that the covalent bond between C(5') and C(8) in the investigated purine cyclonucleoside induces an unusual West ((0)T(1)) conformation of the furanose ring. Thus it can be postulated that the rigid structure of the tandem lesion would strongly perturb the global geometry of oligonucleotides at the site of the modification and therefore affect the enzymatic activity of DNA polymerases and repair enzymes.
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Affiliation(s)
- Boleslaw T Karwowski
- Laboratoire des Lésions des Acides Nucléiques, INAC/SCIB-UMR-E n degrees 3 CEA-UJF, Condensée, CEA Grenoble, 17 avenue des Martyrs, F-38054, Grenoble Cedex 9, France.
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Ohnishi YY, Nakao Y, Sato H, Sakaki S. Frontier Orbital Consistent Quantum Capping Potential (FOC-QCP) for Bulky Ligand of Transition Metal Complexes. J Phys Chem A 2008; 112:1946-55. [DOI: 10.1021/jp710310s] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yu-ya Ohnishi
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan, and ‡Fukui Institute for Fundamental Chemistry, Kyoto University, Nishihiraki-cho, Takano, Sakyo-ku, Kyoto 606-8103, Japan
| | - Yoshihide Nakao
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan, and ‡Fukui Institute for Fundamental Chemistry, Kyoto University, Nishihiraki-cho, Takano, Sakyo-ku, Kyoto 606-8103, Japan
| | - Hirofumi Sato
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan, and ‡Fukui Institute for Fundamental Chemistry, Kyoto University, Nishihiraki-cho, Takano, Sakyo-ku, Kyoto 606-8103, Japan
| | - Shigeyoshi Sakaki
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan, and ‡Fukui Institute for Fundamental Chemistry, Kyoto University, Nishihiraki-cho, Takano, Sakyo-ku, Kyoto 606-8103, Japan
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Keith JA, Behenna DC, Mohr JT, Ma S, Marinescu SC, Oxgaard J, Stoltz BM, Goddard WA. The inner-sphere process in the enantioselective Tsuji allylation reaction with (S)-t-Bu-phosphinooxazoline ligands. J Am Chem Soc 2007; 129:11876-7. [PMID: 17824701 DOI: 10.1021/ja070516j] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- John A Keith
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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Aleman C, Zanuy D, Casanovas J, Cativiela C, Nussinov R. Backbone conformational preferences and pseudorotational ring puckering of 1-aminocyclopentane-1-carboxylic acid. J Phys Chem B 2007; 110:21264-71. [PMID: 17048955 DOI: 10.1021/jp062804s] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We have used quantum mechanical calculations at the B3LYP/6-311G(d,p) level to determine the conformational preferences of the N-acetyl-N'-methylamide derivative of 1-aminocyclopentane-1-carboxylic acid in the gas phase, chloroform solution, and water solution. The backbone conformation of this dipeptide has been described through the dihedral angles varphi and psi, while the pseudorotational phase angle was used to define the conformation of the cyclopentane ring. Results indicate that the backbone flexibility of this amino acid is restricted by the cyclic nature of the side chain, the relative stability of the different conformations depending on the polarity of the environment. The potential energy of the pseudorotation was also studied as a function of the backbone conformation. Interestingly, the conformation of the cyclic side chain depends on the backbone arrangement. Furthermore, the number of pseudorotational states accessible at room temperature is high in all the investigated environments, especially in aqueous solution. Finally, a set of force-field parameters for classical molecular mechanics calculations was developed for the investigated amino acid. Molecular dynamics simulations in both chloroform and aqueous solutions were performed to demonstrate the reliability of such parameters.
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Affiliation(s)
- Carlos Aleman
- Departament d'Enginyeria Química, E. T. S. d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, Barcelona E-08028, Spain.
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Kapitán J, Baumruk V, Kopecký V, Pohl R, Bour P. Proline Zwitterion Dynamics in Solution, Glass, and Crystalline State. J Am Chem Soc 2006; 128:13451-62. [PMID: 17031958 DOI: 10.1021/ja062958l] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Raman and Raman optical activity spectra of L- and D-proline zwitterionic (PROZW) forms were recorded for H(2)O and D(2)O solutions in a wide frequency range and analyzed with respect to the motion of the proline ring and rotation of the carbonyl group. The solution spectra were additionally compared to Raman scattering of glass and crystalline powder proline. Solution and glass spectral band broadenings are similar and reveal information about the extent of internal molecular motion. Two distinct but equally populated flexible forms were found in the glass and the solution. The equal population is consistent with NMR data, temperature, and concentration dependencies. The molecular flexibility is reduced significantly in the crystal, however, where only one conformer is present. Consequently, the crystal bands are narrow and exhibit minor frequency shifts. The spectra were interpreted with the aid of density functional theory computations involving both continuum and explicit solvent. A two-dimensional potential energy surface pertaining to the five-member ring puckering coordinates was constructed and used for dynamical averaging of spectral properties. Comparison of the computed and experimental bandwidths suggests that the puckering is strongly correlated with the carbonyl rotation. An averaging over these two motions produces similar results. The interpretation of the Raman experiments with the aid of the simulation techniques also indicates that the environment modulates properties of the hydrophobic part of the molecule indirectly by interacting with the ionic group. Such behavior may be important for the reactivity and biological activity of proline-containing peptides and proteins.
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Affiliation(s)
- Josef Kapitán
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
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41
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López-Serrano J, Duckett SB, Lledós A. Palladium-Catalyzed Hydrogenation: Detection of Palladium Hydrides. A Joint Study Using Para-Hydrogen-Enhanced NMR Spectroscopy and Density Functional Theory. J Am Chem Soc 2006; 128:9596-7. [PMID: 16866490 DOI: 10.1021/ja0630137] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pd(PEt3)2(OTf)2, acting as an in situ source of Pd(PEt3)2, reacts with an alkyne and hydrogen via phosphine loss to form the detectable hydride-containing species Pd(PEt3)2(H)(CHPhCH2Ph), cis- and trans-Pd(PEt3)2(H)(CPh=CHPh), and Pd2(PEt3)3(H)(CHPhCH2Ph)2+, which map onto the reaction scheme predicted by density functional theory.
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Affiliation(s)
- Joaquín López-Serrano
- Department of Chemistry, University of York, Heslington, YO10 5DD York, United Kingdom
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42
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Zhao Y, Kormos BL, Beveridge DL, Baranger AM. Molecular dynamics simulation studies of a protein-RNA complex with a selectively modified binding interface. Biopolymers 2006; 81:256-69. [PMID: 16278830 DOI: 10.1002/bip.20408] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The RNA recognition motif (RRM) is one of the most common RNA binding domains. We have investigated the contribution of three highly conserved aromatic amino acids to RNA binding by the N-terminal RRM of the U1A protein. Recently, we synthesized a modified base (A-4CPh) in which a phenyl group is tethered to adenine using a linker of 4 methylene groups. The substitution of this base for adenine in the target RNA selectively stabilizes the complex formed with a U1A protein in which one of the conserved aromatic amino acids is replaced with Ala (Phe56Ala). In this article, we report molecular dynamics (MD) simulations that probe the structural consequences of the substitution of A-4CPh for adenine in the wild type and Phe56Ala U1A-RNA complexes and in the free RNA. The simulations suggest that A-4CPh stabilizes the complex formed with Phe56Ala by adopting a folded conformation in which the tethered phenyl group fills the site occupied by the phenyl group of Phe56 in the wild-type complex. In contrast, an extended conformation of A-4CPh is predicted to be most stable in the complex formed with the wild-type protein. The calculations indicate A-4CPh is in an extended conformation in the free RNA. Therefore, preorganizing the structure of the phenyl-tethered base for binding may improve both the affinity and specificity of the RNA containing A-4CPh for the Phe56Ala U1A protein. Taken together, the previous experimental work and the calculations reported here suggest a general design strategy for altering RRM-RNA complex stability.
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Affiliation(s)
- Ying Zhao
- Chemistry Department and Molecular Biophysics Program, Wesleyan University, Middletown, CT 06459, USA
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43
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Kapitán J, Baumruk V, Bour P. Demonstration of the ring conformation in polyproline by the Raman optical activity. J Am Chem Soc 2006; 128:2438-43. [PMID: 16478200 DOI: 10.1021/ja057337r] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Raman and Raman optical activity (ROA) spectra of poly-L-proline were recorded in a wide frequency range and analyzed with respect to the proline side chain conformation. The analysis was based on comparison to ab initio simulations of spectral band positions and intensities. The presence of two conformer states of the five-member ring was found, approximately equally populated in the polypeptide. Additionally, Raman and ROA spectral shapes indicated that the peptide adopts the polyproline II helical conformation, in both aqueous and TFE solutions. The helix, however, is perturbed by fluctuations, which affects the vibrational coupling among amino acid residues and broadens the ROA bands. Contributions of the side and main peptide chains to the polyproline ROA intensities have comparable magnitudes. Thus understanding of the origins of both signals is important for determination of the peptide structure by ROA.
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Affiliation(s)
- Josef Kapitán
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo nám 2, 16610 Prague, Czech Republic
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44
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Banavali NK, Roux B. Free energy landscape of A-DNA to B-DNA conversion in aqueous solution. J Am Chem Soc 2005; 127:6866-76. [PMID: 15869310 DOI: 10.1021/ja050482k] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The interconversion between the well-characterized A- and B-forms of DNA is a structural transition for which the intermediate states and the free energy difference between the two endpoints are not known precisely. In the present study, the difference between the Root Mean Square Distance (RMSD) from canonical A-form and B-form DNA is used as an order parameter to characterize this free energy difference using umbrella sampling molecular dynamics (MD) simulations with explicit solvent. The constraint imposed along this order parameter allows relatively unrestricted evolution of the intermediate structures away from both canonical A- and B-forms. The free energy difference between the A- and B-forms for the hexamer DNA sequence CTCGAG in aqueous solution is conservatively estimated to be at least 2.8 kcal/mol. A continuum of intermediate structures with no well-defined local minima links the two forms. The absence of any major barriers in the free energy surface is consistent with spontaneous conversion of the A-form DNA to B-form DNA in unconstrained simulations. The extensive sampling in the MD simulations (>0.1 mus) also allowed quantitative energetic characterization of local backbone conformational variables such as sugar pseudorotation angles and BI/BII state equilibria and their dependence on base identity. The absolute minimum in the calculated free energy profile corresponds closely to the crystal structure of the hexamer sequence, indicating that the present method has the potential to identify the most stable state for an arbitrary DNA sequence in water.
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Affiliation(s)
- Nilesh K Banavali
- Department of Physiology, Biophysics, and Systems Biology, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10021, USA.
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45
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Zuidema E, van Leeuwen PWNM, Bo C. Reductive Elimination of Organic Molecules from Palladium−Diphosphine Complexes. Organometallics 2005. [DOI: 10.1021/om050113x] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Erik Zuidema
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands, Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Campus Sescelades, Marcel·lí Domingo s/n, 43007 Tarragona, Spain, and Catalan Intitute of Chemical Research, ICIQ, Avda. Països Catalans, s/n, 43007 Tarragona, Spain
| | - Piet W. N. M. van Leeuwen
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands, Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Campus Sescelades, Marcel·lí Domingo s/n, 43007 Tarragona, Spain, and Catalan Intitute of Chemical Research, ICIQ, Avda. Països Catalans, s/n, 43007 Tarragona, Spain
| | - Carles Bo
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands, Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Campus Sescelades, Marcel·lí Domingo s/n, 43007 Tarragona, Spain, and Catalan Intitute of Chemical Research, ICIQ, Avda. Països Catalans, s/n, 43007 Tarragona, Spain
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Villamena FA, Merle JK, Hadad CM, Zweier JL. Superoxide Radical Anion Adduct of 5,5-Dimethyl-1-pyrroline N-Oxide (DMPO). 2. The Thermodynamics of Decay and EPR Spectral Properties. J Phys Chem A 2005; 109:6089-98. [PMID: 16833946 DOI: 10.1021/jp0524330] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The formation of the superoxide radical anion (O2*-) adduct of the nitrone 5,5-dimethyl-1-pyrroline N-oxide (DMPO) as detected by electron paramagnetic resonance (EPR) spectroscopy is one of the most common techniques for O2*- detection in chemical and biological systems. However, the nature of DMPO-O2H has confounded spin-trapping investigators over the years, since there has been no independently synthesized DMPO-O2H to date. A density functional theory (DFT) approach was used to predict the isotropic hyperfine coupling constants arising from the N, beta-H, and gamma-H nuclei of DMPO-O2H using explicit interactions with water molecules as well as via a bulk dielectric effect employing the polarizable continuum model (PCM). Theoretical calculation on the thermodynamics of DMPO-O2H decay shows favorable intramolecular rearrangement to form a nitrosoaldehyde and a hydroxyl radical as products, consistent with experimental observations. Some pathways for the bimolecular decomposition of DMPO-O2H and DMPO-OH have also been computed.
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Affiliation(s)
- Frederick A Villamena
- Center for Biomedical EPR Spectroscopy and Imaging, The Davis Heart and Lung Research Institute, College of Medicine, The Ohio State University, Columbus, Ohio 43210, USA.
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Suzuki T, Kawashima H, Kotoku H, Sota T. Structural Fluctuation and Dynamics of Ribose Puckering in Aqueous Solution from First Principles. J Phys Chem B 2005; 109:12997-3005. [PMID: 16852613 DOI: 10.1021/jp050475i] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Using the method of ab initio molecular dynamics, we examine the structural fluctuation and the low-frequency dynamics of beta-ribofuranose puckering in aqueous solution. Our analysis suggests that the distance between the anomeric and hydroxymethyl oxygens is a simple relevant geometrical parameter that dynamically correlates with the phase angle in the north region. The time-frequency analysis using the Hilbert-Huang transform also confirms the correlation, and most of the instantaneous frequencies for the phase angle and the above distance are found to be concentrated on the region below about 100 cm(-1). Our analysis of ab initio molecular dynamics trajectories suggests that the molecular origin of the hydration effects on the low-frequency dynamics of beta-ribofuranose puckering is closely related to this correlation and thus primarily attributed to the relatively local interactions among the anomeric and hydroxymethyl oxygens and the surrounding water molecules near them. Additionally, we discuss the difference in the low-frequency dynamics of beta-ribofuranose puckering between two hydroxymethyl rotamers.
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Affiliation(s)
- Teppei Suzuki
- Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan.
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Hunziker J, Roth HJ, Böhringer M, Giger A, Diederichsen U, Göbel M, Krishnan R, Jaun B, Leumann C, Eschenmoser A. Warum pentose-und nicht hexose-nucleinsäuren? Teil III. Oligo(2′,3′-dideoxy-β-D-glucopyranosyl) nucleotide (‘homo-DNS’): Paarungesigenschaften. Helv Chim Acta 2004. [DOI: 10.1002/hlca.19930760119] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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49
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Shekhar S, Hartwig JF. Distinct Electronic Effects on Reductive Eliminations of Symmetrical and Unsymmetrical Bis-Aryl Platinum Complexes. J Am Chem Soc 2004; 126:13016-27. [PMID: 15469300 DOI: 10.1021/ja0480365] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Symmetrical bis-aryl platinum complexes (DPPF)Pt(C(6)H(4)-4-R)(2) (R = NMe(2), OMe, CH(3), H, Cl, CF(3)) and electronically unsymmetrical bis-aryl platinum complexes (DPPF)Pt(C(6)H(4)-4-R)(C(6)H(4)-4-X) (R = CH(3), X = NMe(2), OMe, H, Cl, F, CF(3); R = OMe, X = NMe(2), H, Cl, F, CF(3); R = CF(3), X = H, Cl, NMe(2); and R = NMe(2), X = H, Cl) were prepared, and the rates of reductive elimination of these complexes in the presence of excess PPh(3) are reported. The platinum complexes reductively eliminated biaryl compounds in quantitative yields with first-order rate constants that were independent of the concentration of PPh(3). Plots of Log(k(obs)/k(obs(H))) vs Hammett substituent constants (sigma) of the para substituents R and X showed that the rates of reductive elimination reactions depended on two different electronic properties. The reductive elimination from symmetrical bis-aryl platinum complexes occurred faster from complexes with more electron-donating para substituents R. However, reductive elimination from a series of electronically unsymmetrical bis-aryl complexes was not faster from complexes with the more electron-donating substituents. Instead, reductive elimination was faster from complexes with a larger difference in the electronic properties of the substituents on the two platinum-bound aryl groups. The two electronic effects can complement or cancel each other. Thus, this combination of electronic effects gives rise to complex, but now more interpretable, free energy relationships for reductive elimination.
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Affiliation(s)
- Shashank Shekhar
- Contribution from the Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT 06520-8107, USA
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50
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Gabb HA, Lavery R, Prévost C. Efficient conformational space sampling for nucleosides using internal coordinate Monte Carlo simulations and a modified furanose description. J Comput Chem 2004. [DOI: 10.1002/jcc.540160603] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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