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Singh J, Whitaker D, Thoma B, Islam S, Foden CS, Aliev AE, Sheppard TD, Powner MW. Prebiotic Catalytic Peptide Ligation Yields Proteinogenic Peptides by Intramolecular Amide Catalyzed Hydrolysis Facilitating Regioselective Lysine Ligation in Neutral Water. J Am Chem Soc 2022; 144:10151-10155. [PMID: 35640067 PMCID: PMC9204760 DOI: 10.1021/jacs.2c03486] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
![]()
The prebiotic origin
of catalyst-controlled peptide synthesis is
fundamental to understanding the emergence of life. Building on our
recent discovery that thiols catalyze the ligation of amino acids,
amides, and peptides with amidonitriles in neutral water, we demonstrate
the outcome of ligation depends on pH and that high pKa primary thiols are the ideal catalysts. While the most
rapid thiol catalyzed peptide ligation occurs at pH 8.5–9,
the most selective peptide ligation, that tolerates all proteinogenic
side chains, occurs at pH 7. We have also identified the highly selective
mechanism by which the intermediate peptidyl amidines undergo hydrolysis
to α-peptides while demonstrating that the hydrolysis of amidines
with nonproteinogenic structures, such as β- and γ-peptides,
displays poor selectivity. Notably, this discovery enables the highly
α-selective protecting-group-free ligation of lysine peptides
at neutral pH while leaving the functional ε-amine side chain
intact.
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Affiliation(s)
- Jyoti Singh
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Daniel Whitaker
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Benjamin Thoma
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Saidul Islam
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom.,Department of Chemistry, King's College London, 7 Trinity Street, London SE1 1DB, United Kingdom
| | - Callum S Foden
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Abil E Aliev
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Tom D Sheppard
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Matthew W Powner
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
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2
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Zeng J, Giese TJ, Ekesan Ş, York DM. Development of Range-Corrected Deep Learning Potentials for Fast, Accurate Quantum Mechanical/Molecular Mechanical Simulations of Chemical Reactions in Solution. J Chem Theory Comput 2021; 17:6993-7009. [PMID: 34644071 DOI: 10.1021/acs.jctc.1c00201] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We develop a new deep potential─range correction (DPRc) machine learning potential for combined quantum mechanical/molecular mechanical (QM/MM) simulations of chemical reactions in the condensed phase. The new range correction enables short-ranged QM/MM interactions to be tuned for higher accuracy, and the correction smoothly vanishes within a specified cutoff. We further develop an active learning procedure for robust neural network training. We test the DPRc model and training procedure against a series of six nonenzymatic phosphoryl transfer reactions in solution that are important in mechanistic studies of RNA-cleaving enzymes. Specifically, we apply DPRc corrections to a base QM model and test its ability to reproduce free-energy profiles generated from a target QM model. We perform these comparisons using the MNDO/d and DFTB2 semiempirical models because they differ in the way they treat orbital orthogonalization and electrostatics and produce free-energy profiles which differ significantly from each other, thereby providing us a rigorous stress test for the DPRc model and training procedure. The comparisons show that accurate reproduction of the free-energy profiles requires correction of the QM/MM interactions out to 6 Å. We further find that the model's initial training benefits from generating data from temperature replica exchange simulations and including high-temperature configurations into the fitting procedure, so the resulting models are trained to properly avoid high-energy regions. A single DPRc model was trained to reproduce four different reactions and yielded good agreement with the free-energy profiles made from the target QM/MM simulations. The DPRc model was further demonstrated to be transferable to 2D free-energy surfaces and 1D free-energy profiles that were not explicitly considered in the training. Examination of the computational performance of the DPRc model showed that it was fairly slow when run on CPUs but was sped up almost 100-fold when using NVIDIA V100 GPUs, resulting in almost negligible overhead. The new DPRc model and training procedure provide a potentially powerful new tool for the creation of next-generation QM/MM potentials for a wide spectrum of free-energy applications ranging from drug discovery to enzyme design.
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Affiliation(s)
- Jinzhe Zeng
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, and Department of Chemistry and Chemical Biology, Rutgers the State University of New Jersey, New Brunswick, New Jersey 08901-8554, United States
| | - Timothy J Giese
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, and Department of Chemistry and Chemical Biology, Rutgers the State University of New Jersey, New Brunswick, New Jersey 08901-8554, United States
| | - Şölen Ekesan
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, and Department of Chemistry and Chemical Biology, Rutgers the State University of New Jersey, New Brunswick, New Jersey 08901-8554, United States
| | - Darrin M York
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, and Department of Chemistry and Chemical Biology, Rutgers the State University of New Jersey, New Brunswick, New Jersey 08901-8554, United States
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3
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Harris ME, Piccirilli JA, York DM. Integration of kinetic isotope effect analyses to elucidate ribonuclease mechanism. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1801-8. [PMID: 25936517 DOI: 10.1016/j.bbapap.2015.04.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 04/17/2015] [Accepted: 04/21/2015] [Indexed: 01/21/2023]
Abstract
The well-studied mechanism of ribonuclease A is believed to involve concerted general acid-base catalysis by two histidine residues, His12 and His119. The basic features of this mechanism are often cited to explain rate enhancement by both protein and RNA enzymes that catalyze RNA 2'-O-transphosphorylation. Recent kinetic isotope effect analyses and computational studies are providing a more chemically detailed description of the mechanism of RNase A and the rate limiting transition state. Overall, the results support an asynchronous mechanism for both solution and ribonuclease catalyzed reactions in which breakdown of a transient dianoinic phosphorane intermediate by 5'OP bond cleavage is rate limiting. Relative to non-enzymatic reactions catalyzed by specific base, a smaller KIE on the 5'O leaving group and a less negative βLG are observed for RNase A catalysis. Quantum mechanical calculations consistent with these data support a model in which electrostatic and H-bonding interactions with the non-bridging oxygens and proton transfer from His119 render departure of the 5'O less advanced and stabilize charge buildup in the transition state. Both experiment and computation indicate advanced 2'OP bond formation in the rate limiting transition state. However, this feature makes it difficult to resolve the chemical steps involved in 2'O activation. Thus, modeling the transition state for RNase A catalysis underscores those elements of its chemical mechanism that are well resolved, as well as highlighting those where ambiguity remains. This article is part of a Special Issue entitled: Enzyme Transition States from Theory and Experiment.
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Affiliation(s)
- Michael E Harris
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44118, United States.
| | - Joseph A Piccirilli
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, United States; Department of Chemistry, University of Chicago, Chicago, IL 60637, United States
| | - Darrin M York
- Center for Integrative Proteomics Research, BioMaPS Institute for Quantitative Biology, Rutgers University, Piscataway, NJ 08854, United States; Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, United States
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4
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Xia F, Zhang Q, Tian K, Zhu H. Theoretical studies on the effect of sulfur substitution for the methanolysis of cyclic and acyclic phosphate esters. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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5
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Wong KY, Xu Y, York DM. Ab initio path-integral calculations of kinetic and equilibrium isotope effects on base-catalyzed RNA transphosphorylation models. J Comput Chem 2014; 35:1302-16. [PMID: 24841935 PMCID: PMC4096342 DOI: 10.1002/jcc.23628] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 04/06/2014] [Indexed: 12/16/2022]
Abstract
Detailed understandings of the reaction mechanisms of RNA catalysis in various environments can have profound importance for many applications, ranging from the design of new biotechnologies to the unraveling of the evolutionary origin of life. An integral step in the nucleolytic RNA catalysis is self-cleavage of RNA strands by 2'-O-transphosphorylation. Key to elucidating a reaction mechanism is determining the molecular structure and bonding characteristics of transition state. A direct and powerful probe of transition state is measuring isotope effects on biochemical reactions, particularly if we can reproduce isotope effect values from quantum calculations. This article significantly extends the scope of our previous joint experimental and theoretical work in examining isotope effects on enzymatic and nonenzymatic 2'-O-transphosphorylation reaction models that mimic reactions catalyzed by RNA enzymes (ribozymes), and protein enzymes such as ribonuclease A (RNase A). Native reactions are studied, as well as reactions with thio substitutions representing chemical modifications often used in experiments to probe mechanism. Here, we report and compare results from eight levels of electronic-structure calculations for constructing the potential energy surfaces in kinetic and equilibrium isotope effects (KIE and EIE) computations, including a "gold-standard" coupled-cluster level of theory [CCSD(T)]. In addition to the widely used Bigeleisen equation for estimating KIE and EIE values, internuclear anharmonicity and quantum tunneling effects were also computed using our recently developed ab initio path-integral method, that is, automated integration-free path-integral method. The results of this work establish an important set of benchmarks that serve to guide calculations of KIE and EIE for RNA catalysis.
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Affiliation(s)
- Kin-Yiu Wong
- Department of Physics, High Performance Cluster Computing Centre, Institute of Computational and Theoretical Studies, Hong Kong Baptist University, 224 Waterloo Road, Kowloon Tong, Hong Kong; Institute of Research and Continuing Education, Hong Kong Baptist University (Shenzhen), Shenzhen, China
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6
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Kaur M, Rob A, Caton-Williams J, Huang Z. Biochemistry of Nucleic Acids Functionalized with Sulfur, Selenium, and Tellurium: Roles of the Single-Atom Substitution. ACTA ACUST UNITED AC 2013. [DOI: 10.1021/bk-2013-1152.ch005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Affiliation(s)
- Manindar Kaur
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
| | - Abdur Rob
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
| | | | - Zhen Huang
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
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7
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Density functional calculations on alcoholysis and thiolysis of phosphate triesters: Stepwise or concerted? COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2013.05.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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8
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Abstract
SIGNIFICANCE Oxidative stress is widely invoked in inflammation, aging, and complex diseases. To avoid unwanted oxidations, the redox environment of cellular compartments needs to be tightly controlled. The complementary action of oxidoreductases and of high concentrations of low-molecular-weight (LMW) nonprotein thiols plays an essential role in maintaining the redox potential of the cell in balance. RECENT ADVANCES While LMW thiols are central players in an extensive range of redox regulation/metabolism processes, not all organisms use the same thiol cofactors to this effect, as evidenced by the recent discovery of mycothiol (MSH) and bacillithiol (BSH) among different gram-positive bacteria. CRITICAL ISSUES LMW thiol-disulfide exchange processes and their cellular implications are often oversimplified, as only the biology of the free thiols and their symmetrical disulfides is considered. In bacteria under oxidative stress, especially where concentrations of different LMW thiols are comparable [e.g., BSH, coenzyme A (CoA), and cysteine (Cys) in many low-G+C gram-positive bacteria (Firmicutes)], mixed disulfides (e.g., CoASSB and CySSCoA) must surely be major thiol-redox metabolites that need to be taken into consideration. FUTURE DIRECTIONS There are many microorganisms whose LMW thiol-redox buffers have not yet been identified (either bioinformatically or experimentally). Many elements of BSH and MSH redox biochemistry remain to be explored. The fundamental biophysical properties, thiol pK(a) and redox potential, have not yet been determined, and the protein interactome in which the biothiols MSH and BSH are involved needs further exploration.
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Affiliation(s)
- Koen Van Laer
- Department of Structural Biology, Vlaams Instituut voor Biotechnologie (VIB), Brussels, Belgium
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9
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Effect of sulfur substitution for methanolysis of paraoxon: CO vs. PO bond cleavage from density-functional theory. COMPUT THEOR CHEM 2012. [DOI: 10.1016/j.comptc.2011.11.052] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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10
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ZHANG ZHIQIANG, CHOW RAYMONDKWOKKEI, ZHOU HONGWEI, LI JIELIANG, CHEUNG HONYEUNG. AN AB INITIO STUDY ON THE STRUCTURE–CYTOTOXICITY RELATIONSHIP OF TERPENOID LACTONES BASED ON THE MICHAEL REACTION BETWEEN THEIR PHARMACOPHORES AND L-CYSTEINE-METHYLESTER-1. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633608003794] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The cytotoxic effects of terpenoid lactones are attributed to the alkylation of biological nucleophiles, especially sulfhydryl groups in proteins, by the α,β-unsaturated carbonyl moiety of lactones through Michael reaction. Therefore, the cytotoxicity could be reflected by the reactivity of the pharmacophores. In this work, the Michael reaction between 12 α,β-unsaturated-carbonyl-containing small species, i.e. 10 analogues of the alpha methylene gamma butyrolactone moiety of andrographolide, one cyclopentenone, and one methylene–pentanolide, and L-cysteine-methylester-1 were investigated by ab initio methods to mimic the alkylation of proteins by terpenoid lactones. The trend in the calculated reaction free energies of the small species is qualitatively in accordance with the reported cytotoxicity of corresponding terpenoid lactones.
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Affiliation(s)
- ZHI QIANG ZHANG
- Research Group for Bioactive Products, Department of Biology and Chemistry, City University of Hong Kong, Hong Kong SAR, China
| | - RAYMOND KWOK KEI CHOW
- Research Group for Bioactive Products, Department of Biology and Chemistry, City University of Hong Kong, Hong Kong SAR, China
| | - HONG WEI ZHOU
- Research Group for Bioactive Products, Department of Biology and Chemistry, City University of Hong Kong, Hong Kong SAR, China
| | - JIE LIANG LI
- Research Group for Bioactive Products, Department of Biology and Chemistry, City University of Hong Kong, Hong Kong SAR, China
| | - HON-YEUNG CHEUNG
- Research Group for Bioactive Products, Department of Biology and Chemistry, City University of Hong Kong, Hong Kong SAR, China
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11
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Xia F, Zhu H. Density functional calculations on the effect of sulfur substitution for 2'-hydroxypropyl-p-nitrophenyl phosphate: C-O vs. P-O bond cleavage. Bioorg Chem 2011; 40:99-107. [PMID: 22000806 DOI: 10.1016/j.bioorg.2011.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Accepted: 09/10/2011] [Indexed: 10/17/2022]
Abstract
Density functional theory calculations have been used to investigate the intra-molecular attack of 2'-hydroxypropyl-p-nitrophenyl phosphate (HPpNP) and its analogous compound 2-thiouridyl-p-nitrophenyl phosphate (s-2'pNP). Bulk solvent effect has been tested at the geometry optimization level with the polarized continuum model. It is found that the P-path involving the intra-molecular attack at the phosphorus atom and C-path involving the attack at the beta carbon atom proceed through the S(N)2-type mechanism for HPpNP and s-2'pNP. The calculated results indicate that the P-path with the free energy barrier of about 11 kcal/mol is more accessible than the C-path for the intra-molecular attack of HPpNP, which favors the formation of the five-membered phosphate diester. While for s-2'pNP, the C-path with the free energy barrier of about 21 kcal/mol proceeds more favorably than the P-path. The calculated energy barriers of the favorable pathways for HPpNP and s-2'pNP are both in agreement with the experimental results.
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Affiliation(s)
- Futing Xia
- School of Chemistry, Sichuan University, Chengdu 610064, China
| | - Hua Zhu
- School of Chemistry, Sichuan University, Chengdu 610064, China; State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610064, China.
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12
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McAnoy AM, Williams J, Paine MRL, Rogers ML, Blanksby SJ. Ion−Molecule Reactions of O,S-Dimethyl Methylphosphonothioate: Evidence for Intramolecular Sulfur Oxidation during VX Perhydrolysis. J Org Chem 2009; 74:9319-27. [DOI: 10.1021/jo901944p] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Andrew M. McAnoy
- Human Protection and Performance Division, Defence Science and Technology Organisation, 506 Lorimer St., Fishermans Bend, Victoria 3207, Australia
| | - Jilliarne Williams
- Human Protection and Performance Division, Defence Science and Technology Organisation, 506 Lorimer St., Fishermans Bend, Victoria 3207, Australia
| | - Martin R. L. Paine
- School of Chemistry, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Michael L. Rogers
- Human Protection and Performance Division, Defence Science and Technology Organisation, 506 Lorimer St., Fishermans Bend, Victoria 3207, Australia
| | - Stephen J. Blanksby
- School of Chemistry, University of Wollongong, Wollongong, New South Wales 2522, Australia
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13
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Frederiksen JK, Piccirilli JA. Identification of catalytic metal ion ligands in ribozymes. Methods 2009; 49:148-66. [PMID: 19651216 DOI: 10.1016/j.ymeth.2009.07.005] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2009] [Revised: 07/20/2009] [Accepted: 07/29/2009] [Indexed: 01/05/2023] Open
Abstract
Site-bound metal ions participate in the catalytic mechanisms of many ribozymes. Understanding these mechanisms therefore requires knowledge of the specific ligands on both substrate and ribozyme that coordinate these catalytic metal ions. A number of different structural and biochemical strategies have been developed and refined for identifying metal ion binding sites within ribozymes, and for assessing the catalytic contributions of the metal ions bound at those sites. We review these approaches and provide examples of their application, focusing in particular on metal ion rescue experiments and their roles in the construction of the transition state models for the Tetrahymena group I and RNase P ribozymes.
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Affiliation(s)
- John K Frederiksen
- The Pritzker School of Medicine, The University of Chicago, Chicago, IL 60637, USA
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14
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Huang KS, Carrasco N, Pfund E, Strobel SA. Transition state chirality and role of the vicinal hydroxyl in the ribosomal peptidyl transferase reaction. Biochemistry 2008; 47:8822-7. [PMID: 18672893 DOI: 10.1021/bi800299u] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ribosomal peptidyl transferase is a biologically essential catalyst responsible for protein synthesis. The reaction is expected to proceed through a transition state approaching tetrahedral geometry with a specific chirality. To establish that stereospecificity, we synthesized two diastereomers of a transition state inhibitor with mimics for each of the four ligands around the reactive chiral center. Preferential binding of the inhibitor that mimics a transition state with S chirality establishes the spatial position of the nascent peptide and the oxyanion and places the amine near the critical A76 2'-OH group on the P-site tRNA. Another inhibitor series with 2'-NH 2 and 2'-SH substitutions at the critical 2'-OH group was used to test the neutrality of the 2'-OH group as predicted if the hydroxyl functions as a proton shuttle in the transition state. The lack of significant pH-dependent binding by these inhibitors argues that the 2'-OH group remains neutral in the transition state. Both of these observations are consistent with a proton shuttle mechanism for the peptidyl transferase reaction.
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Affiliation(s)
- Kevin S Huang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, USA
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15
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Iyer S, Hengge AC. The effects of sulfur substitution for the nucleophile and bridging oxygen atoms in reactions of hydroxyalkyl phosphate esters. J Org Chem 2008; 73:4819-29. [PMID: 18533704 PMCID: PMC2575009 DOI: 10.1021/jo8002198] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The effects of sulfur substitution on the reactions of hydroxyalkyl phosphate esters are examined. These compounds are models for the intramolecular phosphoryl transfer reaction involved in the cleavage of the internucleotide bond in RNA. The models studied here lack the ribose ring and their conformational flexibility results in greater stability and the availability of different reaction pathways. Sulfur in the nucleophilic position shows no nucleophilic reaction at phosphorus, instead rapidly attacking at the beta carbon atom, forming thiirane with departure of a phosphomonoester. Sulfur substitution at either of the two bridging positions leads to cleavage of the diester via formation of a cyclic intermediate, but with significant rate acceleration when compared to the oxygen analogues. The bridge-substituted models react substantially slower than the analogous ribose compounds with sulfur substitution at comparable positions. Kinetic isotope effects reveal significant differences in the transition state depending on which bridging position sulfur occupies. When sulfur is in the scissile bridging position, a highly associative transition state is indicated, with a largely formed bond to the nucleophile and the scissile P-S bond is little changed. When sulfur occupies the other bridging position, the isotope effects imply a very early transition state in a concerted reaction.
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Affiliation(s)
- Subashree Iyer
- Utah State University, Department of Chemistry and Biochemistry, Logan, Utah 84322-0300, USA
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16
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Stivers JT, Nagarajan R. Probing enzyme phosphoester interactions by combining mutagenesis and chemical modification of phosphate ester oxygens. Chem Rev 2007; 106:3443-67. [PMID: 16895336 PMCID: PMC2729714 DOI: 10.1021/cr050317n] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- James T Stivers
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205, USA.
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17
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Liu Y, Gregersen BA, Lopez X, York DM. Density functional study of the in-line mechanism of methanolysis of cyclic phosphate and thiophosphate esters in solution: insight into thio effects in RNA transesterification. J Phys Chem B 2007; 109:19987-20003. [PMID: 16853584 DOI: 10.1021/jp053146z] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Density functional calculations of thio effects on the in-line mechanism of methanolysis of ethylene phosphate (a reverse reaction model for RNA phosphate transesterification) are presented. A total of 12 reaction mechanisms are examined using the B3LYP functional with large basis sets, and the effects of solvation were treated using the PCM, CPCM, and SM5 solvation models. Single thio substitutions at all of the distinct phosphoryl oxygen positions (2', 3', 5', pro-R) and a double thio substitution at the nonbridging (pro-R/pro-S) positions were considered. Profiles for each reaction were calculated in the dianionic and monoanionic/monoprotic states, corresponding to reaction models under alkaline and nonalkaline conditions, respectively. These models provide insight into the mechanisms of RNA transesterification thio effects and serve as a set of high-level quantum data that can be used in the design of new semiempirical quantum models for hybrid quantum mechanical/molecular mechanical simulations and linear-scaling electronic structure calculations.
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Affiliation(s)
- Yun Liu
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455-0431, USA
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18
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Arantes GM, Chaimovich H. Thiolysis and alcoholysis of phosphate tri- and monoesters with alkyl and aryl leaving groups. An ab initio study in the gas phase. J Phys Chem A 2007; 109:5625-35. [PMID: 16833895 DOI: 10.1021/jp0449556] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Phosphate esters are important compounds in living systems. Their biological reactions with alcohol and thiol nucleophiles are catalyzed by a large superfamily of phosphatase enzymes. However, very little is known about the intrinsic reactivity of these nucleophiles with phosphorus centers. We have performed ab initio calculations on the thiolysis and alcoholysis at phosphorus of trimethyl phosphate, dimethyl phenyl phosphate, methyl phosphate, and phenyl phosphate. Results in the gas phase are a reference for the study of the intrinsic reactivity of these compounds. Thiolysis of triesters was much slower and less favorable than the corresponding alcoholysis. Triesters reacted through an associative mechanism. Monoesters can react by both associative and dissociative mechanisms. The basicity of the attacking and leaving groups and the possibility of proton transfers can modulate the reaction mechanisms. Intermediates formed along associative reactions did not follow empirically proposed rules for ligand positioning. Our calculations also allow re-interpretation of some experimental results, and new experiments are proposed to trace reactions that are normally not observed, both in the gas phase and in solution.
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Affiliation(s)
- Guilherme Menegon Arantes
- Instituto de Química, Universidade de São Paulo, Av. Lineu Prestes 748, 05508-900, São Paulo, SP, Brasil.
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19
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Gordon PM, Fong R, Piccirilli JA. A Second Divalent Metal Ion in the Group II Intron Reaction Center. ACTA ACUST UNITED AC 2007; 14:607-12. [PMID: 17584608 DOI: 10.1016/j.chembiol.2007.05.008] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2006] [Revised: 05/14/2007] [Accepted: 05/15/2007] [Indexed: 10/23/2022]
Abstract
Group II introns are mobile genetic elements that have been implicated as agents of genetic diversity, and serve as important model systems for investigating RNA catalysis and pre-mRNA splicing. In the absence of an atomic-resolution structure of the intron, detailed understanding of its catalytic mechanism has remained elusive. Previous identification of a divalent metal ion stabilizing the leaving group in both splicing steps suggested that the group II intron may employ a "two-metal ion" mechanism, a catalytic strategy used by a number of protein phosphoester transfer enzymes. Using metal rescue experiments, we now reveal the presence of a second metal ion required for nucleophile activation in the exon-ligation step of group II intron splicing. Coupled with biochemical and structural evidence of at least two metal ions at the group I intron reaction center, these results suggest a mechanistic paradigm for describing catalysis by large ribozymes.
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Affiliation(s)
- Peter M Gordon
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
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Sam M, Pierce K, Szostak JW, McLaughlin LW. 2‘,3‘-Dideoxy-3‘-thionucleoside Triphosphates: Syntheses and Polymerase Substrate Activities. Org Lett 2007; 9:1161-3. [PMID: 17319676 DOI: 10.1021/ol070147w] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
All four 2',3'-dideoxy-3'-thio-nucleosides (ddtNTPs) function as substrates for the Y410F mutant of Deep Vent (exo-) DNA polymerase. Not only are the ddtNTPs incorporated to form the N + 1 product, but further elongations are observed in which the key step is attack of the 3'-thiol on the 5'-triphosphate. Although other polymerases are likely to differ in their use of the ddtNTPs, there does not appear to be a fundamental prohibition against using a thiol nucleophile on a phosphate anhydride electrophile. The syntheses of four ddtNTPs (C, T, A, G) are described. [structure: see text]
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21
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Arantes GM. Free-energy profiles for catalysis by dual-specificity phosphatases. Biochem J 2006; 399:343-50. [PMID: 16784417 PMCID: PMC1609924 DOI: 10.1042/bj20060637] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2006] [Revised: 06/19/2006] [Accepted: 06/20/2006] [Indexed: 11/17/2022]
Abstract
PTPs (protein tyrosine phosphatases) are fundamental enzymes for cell signalling and have been linked to the pathogenesis of several diseases, including cancer. Hence, PTPs are potential drug targets and inhibitors have been designed as possible therapeutic agents for Type II diabetes and obesity. However, a complete understanding of the detailed catalytic mechanism in PTPs is still lacking. Free-energy profiles, obtained by computer simulations of catalysis by a dual-specificity PTP, are shown in the present study and are used to shed light on the catalytic mechanism. A highly accurate hybrid potential of quantum mechanics/molecular mechanics calibrated specifically for PTP reactions was used. Reactions of alkyl and aryl substrates, with different protonation states and PTP active-site mutations, were simulated. Calculated reaction barriers agree well with experimental rate measurements. Results show the PTP substrate reacts as a bi-anion, with an ionized nucleophile. This protonation state has been a matter of debate in the literature. The inactivity of Cys-->Ser active-site mutants is also not fully understood. It is shown that mutants are inactive because the serine nucleophile is protonated. Results also clarify the interpretation of experimental data, particularly kinetic isotope effects. The simulated mechanisms presented here are better examples of the catalysis carried out by PTPs.
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Key Words
- computer simulation
- enzyme mechanism
- hybrid potential
- phosphate ester
- protein phosphatase
- ds-ptp, dual-specificity protein tyrosine phosphatase
- kie, kinetic isotope effect
- lm-ptp, low-molecular-mass protein tyrosine phosphatase
- mc, michaelis complex
- ph, phenyl
- ptp, protein tyrosine phosphatase
- qm/mm, quantum mechanical/molecular mechanical
- rmsd, root mean squared deviation
- ts, transition state
- vhr, vaccinia vh1-related
- wt, wild-type
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Affiliation(s)
- Guilherme M Arantes
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Lineu Prestes 748, 05508-900, São Paulo, SP, Brazil.
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Liu Y, Gregersen BA, Hengge A, York DM. Transesterification thio effects of phosphate diesters: free energy barriers and kinetic and equilibrium isotope effects from density-functional theory. Biochemistry 2006; 45:10043-53. [PMID: 16906762 DOI: 10.1021/bi060869f] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Primary and secondary kinetic and equilibrium isotope effects are calculated with density-functional methods for the in-line dianionic methanolysis of the native (unsubstituted) and thio-substituted cyclic phosphates. These reactions represent reverse reaction models for RNA transesterification under alkaline conditions. The effect of solvent is treated with explicit (single and double) water molecules and self-consistently with an implicit (continuum) solvation model. Singly substituted reactions at the nonbridging O(P1) position and bridging O(2)('), O(3)('), and O(5)(') positions and a doubly substituted reaction at the O(P1) and O(P2) positions were considered. Aqueous free energy barriers are calculated, and the structures and bond orders of the rate-controlling transition states are characterized. The results are consistent with available experimental data and provide useful information for the interpretation of measured isotope and thio effects used to probe mechanism in phosphoryl transfer reactions catalyzed by enzymes and ribozymes.
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Affiliation(s)
- Yun Liu
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, USA
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23
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Roos G, Loverix S, Brosens E, Van Belle K, Wyns L, Geerlings P, Messens J. The Activation of Electrophile, Nucleophile and Leaving Group during the Reaction Catalysed by pI258 Arsenate Reductase. Chembiochem 2006; 7:981-9. [PMID: 16607668 DOI: 10.1002/cbic.200500507] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The reduction of arsenate to arsenite by pI258 arsenate reductase (ArsC) combines a nucleophilic displacement reaction with a unique intramolecular disulfide cascade. Within this reaction mechanism, the oxidative equivalents are translocated from the active site to the surface of ArsC. The first reaction step in the reduction of arsenate by pI258 ArsC consists of a nucleophilic displacement reaction carried out by Cys10 on dianionic arsenate. The second step involves the nucleophilic attack of Cys82 on the Cys10-arseno intermediate formed during the first reaction step. The onset of the second step is studied here by using quantum chemical calculations in a density functional theory context. The optimised geometry of the Cys10-arseno adduct in the ArsC catalytic site (sequence motif: Cys10-Thr11-Gly12-Asn13-Ser14-Cys15-Arg16-Ser17) forms the starting point for all subsequent calculations. Thermodynamic data and a hard and soft acids and bases (HSAB) reactivity analysis show a preferential nucleophilic attack on a monoanionic Cys10-arseno adduct, which is stabilised by Ser17. The P-loop active site of pI258 ArsC activates first a hydroxy group and subsequently arsenite as the leaving group, as is clear from an increase in the calculated nucleofugality of these groups upon going from the gas phase to the solvent phase to the enzymatic environment. Furthermore, the enzymatic environment stabilises the thiolate form of the nucleophile Cys82 by 3.3 pH units through the presence of the eight-residue alpha helix flanked by Cys82 and Cys89 (redox helix) and through a hydrogen bond with Thr11. The importance of Thr11 in the pKa regulation of Cys82 was confirmed by the observed decrease in the kcat value of the Thr11Ala mutant as compared to that of wild-type ArsC. During the final reaction step, Cys89 is activated as a nucleophile by structural alterations of the redox helix that functions as a pKa control switch for Cys89; this final step is necessary to expose a Cys82-Cys89 disulfide.
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Affiliation(s)
- Goedele Roos
- Vrije Universiteit Brussel, Algemene Chemie, Pleinlaan 2, 1050, Brussels, Belgium.
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24
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Gordon PM, Fong R, Deb SK, Li NS, Schwans JP, Ye JD, Piccirilli JA. New strategies for exploring RNA's 2'-OH expose the importance of solvent during group II intron catalysis. ACTA ACUST UNITED AC 2004; 11:237-46. [PMID: 15123285 DOI: 10.1016/j.chembiol.2004.02.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2002] [Revised: 10/28/2003] [Accepted: 11/24/2003] [Indexed: 10/21/2022]
Abstract
The 2'-hydroxyl group contributes inextricably to the functional behavior of many RNA molecules, fulfilling numerous essential chemical roles. To assess how hydroxyl groups impart functional behavior to RNA, we developed a series of experimental strategies using an array of nucleoside analogs. These strategies provide the means to investigate whether a hydroxyl group influences function directly (via hydrogen bonding or metal ion coordination), indirectly (via space-filling capacity, inductive effects, and sugar conformation), or through interactions with solvent. The nucleoside analogs span a broad range of chemical diversity, such that quantitative structure activity relationships (QSAR) now become possible in the exploration of RNA biology. We employed these strategies to investigate the spliced exons reopening (SER) reaction of the group II intron. Our results suggest that the cleavage site 2'-hydroxyl may mediate an interaction with a water molecule.
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Affiliation(s)
- Peter M Gordon
- Department of Biochemistry and Molecular Biology, The University of Chicago, 5841 South Maryland Avenue, MC1028, Chicago, IL 60637, USA
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25
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Gregersen BA, Lopez X, York DM. Hybrid QM/MM study of thio effects in transphosphorylation reactions: the role of solvation. J Am Chem Soc 2004; 126:7504-13. [PMID: 15198597 DOI: 10.1021/ja031815l] [Citation(s) in RCA: 52] [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
Transphosphorylation thio effects in solution are studied using hybrid QM/MM calculations with a d-orbital semiempirical Hamiltonian. Activated dynamics simulations were performed for a 3' ribose-phosphate model in an explicit 20 A sphere of TIP3P water surrounded by a solvent boundary potential, and free energy analysis was performed using the weighted histogram analysis method. Single thio-substitutions at all of the phosphoryl oxygen positions and a double thio-substitution at the nonbridging positions were considered. The reaction free energy profiles are compared with available experimental data, and the role of solvation on the barrier heights and reaction coordinate is discussed. These results provide an important step in the characterization of thio effects in reactions of biological phosphates that may aid in the interpretation of kinetic data and ultimately help to unravel the catalytic mechanisms of ribozymes.
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Affiliation(s)
- Brent A Gregersen
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, USA
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26
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27
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Schwans JP, Cortez CN, Olvera JM, Piccirilli JA. 2'-mercaptonucleotide interference reveals regions of close packing within folded RNA molecules. J Am Chem Soc 2003; 125:10012-8. [PMID: 12914464 DOI: 10.1021/ja035175y] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The 2'-hydroxyl group makes essential contributions to RNA structure and function. As an approach to assess the ability of a mercapto group to serve as a functional analogue for the 2'-hydroxyl group, we synthesized 2'-mercaptonucleotides for use in nucleotide analogue interference mapping. To correlate the observed interference effects with tertiary structure, we used the independently folding DeltaC209 P4-P6 domain from the Tetrahymena group I intron. We generated populations of DeltaC209 P4-P6 molecules containing 2'-mercaptonucleotides located randomly throughout the domain and separated the folded molecules from the unfolded molecules by nondenaturing gel electrophoresis. Iodine-induced cleavage of the RNA molecules revealed the sites at which 2'-mercaptonucleotides interfere with folding. These interferences cluster in the most densely packed regions of the tertiary structure, occurring only at sites that lack the space and flexibility to accommodate a sulfur atom. Interference mapping with 2'-mercaptonucleotides therefore provides a method by which to identify structurally rigid and densely packed regions within folded RNA molecules.
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Affiliation(s)
- Jason P Schwans
- Howard Hughes Medical Institute, Department of Biochemistry, The University of Chicago, Chicago, IL 60637, USA
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28
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Roos G, Loverix S, De Proft F, Wyns L, Geerlings P. A Computational and Conceptual DFT Study of the Reactivity of Anionic Compounds: Implications for Enzymatic Catalysis. J Phys Chem A 2003. [DOI: 10.1021/jp034376l] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- G. Roos
- Vrije Universiteit Brussel (VUB), Eenheid Algemene Chemie (ALGC), Pleinlaan 2, B-1050, Brussels, Belgium and Vrije Universiteit Brussel (VUB), Dienst Ultrastructuur, Vlaams interuniversitair Instituut voor Biotechnologie (VIB), Pleinlaan 2, B-1050, Brussels, Belgium
| | - S. Loverix
- Vrije Universiteit Brussel (VUB), Eenheid Algemene Chemie (ALGC), Pleinlaan 2, B-1050, Brussels, Belgium and Vrije Universiteit Brussel (VUB), Dienst Ultrastructuur, Vlaams interuniversitair Instituut voor Biotechnologie (VIB), Pleinlaan 2, B-1050, Brussels, Belgium
| | - F. De Proft
- Vrije Universiteit Brussel (VUB), Eenheid Algemene Chemie (ALGC), Pleinlaan 2, B-1050, Brussels, Belgium and Vrije Universiteit Brussel (VUB), Dienst Ultrastructuur, Vlaams interuniversitair Instituut voor Biotechnologie (VIB), Pleinlaan 2, B-1050, Brussels, Belgium
| | - L. Wyns
- Vrije Universiteit Brussel (VUB), Eenheid Algemene Chemie (ALGC), Pleinlaan 2, B-1050, Brussels, Belgium and Vrije Universiteit Brussel (VUB), Dienst Ultrastructuur, Vlaams interuniversitair Instituut voor Biotechnologie (VIB), Pleinlaan 2, B-1050, Brussels, Belgium
| | - P. Geerlings
- Vrije Universiteit Brussel (VUB), Eenheid Algemene Chemie (ALGC), Pleinlaan 2, B-1050, Brussels, Belgium and Vrije Universiteit Brussel (VUB), Dienst Ultrastructuur, Vlaams interuniversitair Instituut voor Biotechnologie (VIB), Pleinlaan 2, B-1050, Brussels, Belgium
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29
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Menegon G, Loos M, Chaimovich H. Ab Initio Study of the Thiolysis of Trimethyl Phosphate Ester in the Gas Phase. J Phys Chem A 2002. [DOI: 10.1021/jp026083i] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Guilherme Menegon
- Instituto de Química, Universidade de São Paulo, Av. Lineu Prestes 748, 05508-900, São Paulo, SP, Brazil
| | - Michel Loos
- Instituto de Química, Universidade de São Paulo, Av. Lineu Prestes 748, 05508-900, São Paulo, SP, Brazil
| | - Hernan Chaimovich
- Instituto de Química, Universidade de São Paulo, Av. Lineu Prestes 748, 05508-900, São Paulo, SP, Brazil
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30
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Chambert S, Décout JL. RECENT DEVELOPMENTS IN THE SYNTHESIS, CHEMICAL MODIFICATIONS AND BIOLOGICAL APPLICATIONS OF SULFUR MODIFIED NUCLEOSIDES, NUCLEOTIDES AND OLIGONUCLEOTIDES. ORG PREP PROCED INT 2002. [DOI: 10.1080/00304940209355745] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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31
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Hamm ML, Nikolic D, van Breemen RB, Piccirilli JA. Unconventional Origin of Metal Ion Rescue in the Hammerhead Ribozyme Reaction: Mn2+-Assisted Redox Conversion of 2‘-Mercaptocytidine to Cytidine. J Am Chem Soc 2000. [DOI: 10.1021/ja000379p] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michelle L. Hamm
- Contribution from the Howard Hughes Medical Institute, The University of Chicago, Departments of Biochemistry and Molecular Biology, and Chemistry, 5841 South Maryland Avenue MC1028, Chicago, Illinois 60637, University of Illinois at Chicago, College of Pharmacy, Department of Medicinal Chemistry and Pharmacognosy, 833 South Wood Street, Chicago, Illinois 60612-7231
| | - Dejan Nikolic
- Contribution from the Howard Hughes Medical Institute, The University of Chicago, Departments of Biochemistry and Molecular Biology, and Chemistry, 5841 South Maryland Avenue MC1028, Chicago, Illinois 60637, University of Illinois at Chicago, College of Pharmacy, Department of Medicinal Chemistry and Pharmacognosy, 833 South Wood Street, Chicago, Illinois 60612-7231
| | - Richard B. van Breemen
- Contribution from the Howard Hughes Medical Institute, The University of Chicago, Departments of Biochemistry and Molecular Biology, and Chemistry, 5841 South Maryland Avenue MC1028, Chicago, Illinois 60637, University of Illinois at Chicago, College of Pharmacy, Department of Medicinal Chemistry and Pharmacognosy, 833 South Wood Street, Chicago, Illinois 60612-7231
| | - Joseph A. Piccirilli
- Contribution from the Howard Hughes Medical Institute, The University of Chicago, Departments of Biochemistry and Molecular Biology, and Chemistry, 5841 South Maryland Avenue MC1028, Chicago, Illinois 60637, University of Illinois at Chicago, College of Pharmacy, Department of Medicinal Chemistry and Pharmacognosy, 833 South Wood Street, Chicago, Illinois 60612-7231
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32
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Messmore JM, Raines RT. Pentavalent Organo-Vanadates as Transition State Analogues for Phosphoryl Transfer Reactions. J Am Chem Soc 2000; 122:9911-9916. [PMID: 21423825 PMCID: PMC3058181 DOI: 10.1021/ja0021058] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pentavalent organo-vanadates have been put forth as transition state analogues for a variety of phosphoryl transfer reactions. In particular, uridine 2',3'-cyclic vanadate (U>v) has been proposed to resemble the transition state during catalysis by ribonuclease A (RNase A). Here, this hypothesis is tested. Lys41 of RNase A is known to donate a hydrogen bond to a nonbridging phosphoryl oxygen in the transition state during catalysis. Site-directed mutagenesis and semisynthesis were used to create enzymes with natural and nonnatural amino acid residues at position 41. These variants differ by 10(5)-fold in their k(cat)/K(m) values for catalysis, but <40-fold in their K(i) values for inhibition of catalysis by U>v. Plots of logK(i) vs log(K(m)/k(cat)) for three distinct substrates [poly(cytidylic acid), uridine 3'-(p-nitrophenyl phosphate), and cytidine 2',3'-cyclic phosphate] have slopes that range from 0.25 and 0.36. These plots would have a slope of unity if U>v were a perfect transition state analogue. Values of K(i) for U>v correlate weakly with the equilibrium dissociation constant for the enzymic complexes with substrate or product, indicating that U>v bears some resemblance to the substrate and product as well as the transition state. Thus, U>v is a transition state analogue for RNase A, but only a marginal one. This finding indicates that a pentavalent organo-vanadate cannot necessarily be the basis for a rigorous analysis of the transition state for a phosphoryl transfer reaction.
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Affiliation(s)
| | - Ronald T. Raines
- To whom all correspondence should be addressed. Tel.: (608) 262-8588. Fax: (608) 262-3453.
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33
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Hamm ML, Schwans JP, Piccirilli JA. The Hammerhead Ribozyme Catalyzes the Deglycosylation of 2‘-Mercaptocytidine. J Am Chem Soc 2000. [DOI: 10.1021/ja993027v] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michelle L. Hamm
- The University of Chicago Department of Biochemistry and Molecular Biology Department of Chemistry 5841 S. Maryland Avenue MC1028 Chicago, Illinois 60637
| | - Jason P. Schwans
- The University of Chicago Department of Biochemistry and Molecular Biology Department of Chemistry 5841 S. Maryland Avenue MC1028 Chicago, Illinois 60637
| | - Joseph A. Piccirilli
- The University of Chicago Department of Biochemistry and Molecular Biology Department of Chemistry 5841 S. Maryland Avenue MC1028 Chicago, Illinois 60637
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34
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Elzagheid MI, Oivanen M, Klika KD, Jones BCNM, Cosstick R, Lönnberg H. Hydrolytic Reactions of 3′-Deoxy-3′-thioinosylyl-(3′→ >5′)-uridine; An RNA Dinucleotide Containing a 3′-S-Phosphorothiolate Linkage. ACTA ACUST UNITED AC 1999. [DOI: 10.1080/07328319908044866] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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35
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Hamm ML, Piccirilli JA. Synthesis and Characterization of Oligonucleotides Containing 2'-S,3'-O-Cyclic Phosphorothiolate Termini. J Org Chem 1999; 64:5700-5704. [PMID: 11674644 DOI: 10.1021/jo9903508] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michelle L. Hamm
- Howard Hughes Medical Institute and Departments of Biochemistry and Molecular Biology, and Chemistry, The University of Chicago, 5841 South Maryland Avenue, MC 1028, Chicago, Illinois 60637
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36
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Abstract
Accurate excision of intervening sequences (introns) from messenger RNA precursors is accomplished by a very large and complicated ribonucleoprotein complex called the spliceosome. Elucidating the mechanisms of the two phosphotransesterification reactions that result in intron removal is important for our understanding of the molecular evolution of early genetic systems, as well as our knowledge of contemporary eukaryotic gene expression. The functional consequences of systematic alterations in the reactive groups can be invaluable for understanding catalytic mechanisms, especially for enzymes, such as the spliceosome, whose size and complexity place them beyond the reach of crystallographic and spectroscopic analysis. One type of modification that can be incorporated into a scissile phosphate linkage is the phosphorothiolate, in which a bridging phosphate oxygen is substituted with sulfur. Phosphorothiolate substitutions can be used to detect metal ion-ligand interactions by a "metal specificity switch" strategy. I review recent advances in the synthesis, incorporation, and manipulation of nucleoside phosphorothiolates (with an emphasis on 3'-S-phosphorothiolates), and describe their utility in the study of pre-mRNA splicing.
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Affiliation(s)
- E J Sontheimer
- Howard Hughes Medical Institute, The University of Chicago, 5841 South Maryland Avenue, MC 1028, Chicago, Illinois 60637, USA
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37
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Abstract
Synthetic oligonucleotide analogs have greatly aided our understanding of several biochemical processes. Efficient solid-phase and enzyme-assisted synthetic methods and the availability of modified base analogs have added to the utility of such oligonucleotides. In this review, we discuss the applications of synthetic oligonucleotides that contain backbone, base, and sugar modifications to investigate the mechanism and stereochemical aspects of biochemical reactions. We also discuss interference mapping of nucleic acid-protein interactions; spectroscopic analysis of biochemical reactions and nucleic acid structures; and nucleic acid cross-linking studies. The automation of oligonucleotide synthesis, the development of versatile phosphoramidite reagents, and efficient scale-up have expanded the application of modified oligonucleotides to diverse areas of fundamental and applied biological research. Numerous reports have covered oligonucleotides for which modifications have been made of the phosphodiester backbone, of the purine and pyrimidine heterocyclic bases, and of the sugar moiety; these modifications serve as structural and mechanistic probes. In this chapter, we review the range, scope, and practical utility of such chemically modified oligonucleotides. Because of space limitations, we discuss only those oligonucleotides that contain phosphate and phosphate analogs as internucleotidic linkages.
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Affiliation(s)
- S Verma
- Max-Planck-Institut für Experimentelle Medizin, Göttingen, Germany
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38
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Affiliation(s)
- Ronald T. Raines
- Departments of Biochemistry and Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
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39
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Oivanen M, Kuusela S, Lönnberg H. Kinetics and Mechanisms for the Cleavage and Isomerization of the Phosphodiester Bonds of RNA by Brønsted Acids and Bases. Chem Rev 1998; 98:961-990. [PMID: 11848921 DOI: 10.1021/cr960425x] [Citation(s) in RCA: 358] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mikko Oivanen
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland
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40
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Zhou DM, Taira K. The Hydrolysis of RNA: From Theoretical Calculations to the Hammerhead Ribozyme-Mediated Cleavage of RNA. Chem Rev 1998; 98:991-1026. [PMID: 11848922 DOI: 10.1021/cr9604292] [Citation(s) in RCA: 158] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- De-Min Zhou
- Institute of Applied Biochemistry, University of Tsukuba, Tennoudai 1-1-1, Tsukuba Science City 305-8572, Japan, National Institute for Advanced Interdisciplinary Research, 1-1-4 Higashi, Tsukuba Science City 305-8562, Japan, and National Institute of Bioscience & Human Technology, 1-1 Higashi, Tsukuba Science City 305-8566, Japan
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41
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Wittschieben J, Petersen BO, Shuman S. Replacement of the active site tyrosine of vaccinia DNA topoisomerase by glutamate, cysteine or histidine converts the enzyme into a site-specific endonuclease. Nucleic Acids Res 1998; 26:490-6. [PMID: 9421505 PMCID: PMC147276 DOI: 10.1093/nar/26.2.490] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Vaccinia topoisomerase forms a covalent protein-DNA intermediate at 5'-CCCTT downward arrow sites in duplex DNA. The T downward arrow nucleotide is linked via a 3'-phosphodiester bond to Tyr-274 of the enzyme. Here, we report that mutant enzymes containing glutamate, cysteine or histidine in lieu of Tyr-274 catalyze endonucleolytic cleavage of a 60 bp duplex DNA at the CCCTT downward arrow site to yield a 3' phosphate-terminated product. The Cys-274 mutant forms trace levels of a covalent protein-DNA complex, suggesting that the DNA cleavage reaction may proceed through a cysteinyl-phosphate intermediate. However, the His-274 and Glu-274 mutants evince no detectable accumulation of a covalent protein-DNA adduct. Glu-274 is the most active of the mutants tested. The pH dependence of the endonuclease activity of Glu-274 (optimum pH = 6.5) is distinct from that of the wild-type enzyme in hydrolysis of the covalent adduct (optimum pH = 9.5). At pH 6.5, the Glu-274 endonuclease reaction is slower by 5-6 orders of magnitude than the rate of covalent adduct formation by the wild-type topoisomerase, but is approximately 20 times faster than the rate of hydrolysis by the wild-type covalent adduct. We discuss two potential mechanisms to account for the apparent conversion of a topoisomerase into an endonuclease.
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Affiliation(s)
- J Wittschieben
- Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10021, USA
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42
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Sontheimer EJ, Sun S, Piccirilli JA. Metal ion catalysis during splicing of premessenger RNA. Nature 1997; 388:801-5. [PMID: 9285595 DOI: 10.1038/42068] [Citation(s) in RCA: 137] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The removal of intervening sequences from premessenger RNA is essential for the expression of most eukaryotic genes. The spliceosome ribonucleoprotein complex catalyses intron removal by two sequential phosphotransesterification reactions, but the catalytic mechanisms are unknown. It has been proposed that two divalent metal ions may mediate catalysis of both reaction steps, activating the 2'- or 3'-hydroxyl groups for nucleophilic attack and stabilizing the 3'-oxyanion leaving groups by direct coordination. Here we show that in splicing reactions with a precursor RNA containing a 3'-sulphur substitution at the 5' splice site, interaction between metal ion and leaving group is essential for catalysis of the first reaction step. This establishes that the spliceosome is a metalloenzyme and demonstrates a direct parallel with the catalytic strategy used by the self-splicing group I intron from Tetrahymena. In contrast, 3'-sulphur substitution at the 3' splice site provides no evidence for a metal ion-leaving group interaction in the second reaction step, suggesting that the two steps of splicing proceed by different catalytic mechanisms and therefore in distinct active sites.
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Affiliation(s)
- E J Sontheimer
- Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biology, The University of Chicago, Illinois 60637, USA
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Hamm ML, Piccirilli JA. Incorporation of 2'-Deoxy-2'-mercaptocytidine into Oligonucleotides via Phosphoramidite Chemistry. J Org Chem 1997; 62:3415-3420. [PMID: 11671734 DOI: 10.1021/jo970096o] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michelle L. Hamm
- Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biology, and Department of Chemistry, The University of Chicago, 5841 South Maryland Avenue, Room N104, Chicago, Illinois 60637
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