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Quintana-Feliciano R, Kottur J, Ni M, Ghosh R, Salas-Estrada L, Rechkoblit O, Filizola M, Fang G, Aggarwal AK. Burkholderia cenocepacia epigenetic regulator M.BceJIV simultaneously engages two DNA recognition sequences for methylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.20.576384. [PMID: 38328099 PMCID: PMC10849533 DOI: 10.1101/2024.01.20.576384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Burkholderia cenocepacia is an opportunistic and infective bacterium containing an orphan DNA methyltransferase (M.BceJIV) with roles in regulating gene expression and motility of the bacterium. M.BceJIV recognizes a GTWWAC motif (where W can be an adenine or a thymine) and methylates the N6 of the adenine at the fifth base position (GTWWAC). Here, we present a high-resolution crystal structure of M.BceJIV/DNA/sinefungin ternary complex and allied biochemical, computational, and thermodynamic analyses. Remarkably, the structure shows not one, but two DNA substrates bound to the M.BceJIV dimer, wherein each monomer contributes to the recognition of two recognition sequences. This unexpected mode of DNA binding and methylation has not been observed previously and sets a new precedent for a DNA methyltransferase. We also show that methylation at two recognition sequences occurs independently, and that GTWWAC motifs are enriched in intergenic regions of a strain of B. cenocepacia's genome. We further computationally assess the interactions underlying the affinities of different ligands (SAM, SAH, and sinefungin) for M.BceJIV, as a step towards developing selective inhibitors for limiting B. cenocepacia infection.
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Affiliation(s)
- Richard Quintana-Feliciano
- Department of Pharmacological Sciences Icahn School of Medicine at Mount Sinai 1425 Madison Avenue New York, New York, USA
| | - Jithesh Kottur
- Department of Pharmacological Sciences Icahn School of Medicine at Mount Sinai 1425 Madison Avenue New York, New York, USA
| | - Mi Ni
- Department of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai 1425 Madison Avenue New York, New York, USA
| | - Rikhia Ghosh
- Department of Pharmacological Sciences Icahn School of Medicine at Mount Sinai 1425 Madison Avenue New York, New York, USA
| | - Leslie Salas-Estrada
- Department of Pharmacological Sciences Icahn School of Medicine at Mount Sinai 1425 Madison Avenue New York, New York, USA
| | - Olga Rechkoblit
- Department of Pharmacological Sciences Icahn School of Medicine at Mount Sinai 1425 Madison Avenue New York, New York, USA
| | - Marta Filizola
- Department of Pharmacological Sciences Icahn School of Medicine at Mount Sinai 1425 Madison Avenue New York, New York, USA
| | - Gang Fang
- Department of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai 1425 Madison Avenue New York, New York, USA
| | - Aneel K. Aggarwal
- Department of Pharmacological Sciences Icahn School of Medicine at Mount Sinai 1425 Madison Avenue New York, New York, USA
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2
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Matienko LI, Mil EM, Albantova AA, Goloshchapov AN. The Role H-Bonding and Supramolecular Structures in Homogeneous and Enzymatic Catalysis. Int J Mol Sci 2023; 24:16874. [PMID: 38069195 PMCID: PMC10707003 DOI: 10.3390/ijms242316874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
The article analyzes the role of hydrogen bonds and supramolecular structures in enzyme catalysis and model systems. Hydrogen bonds play a crucial role in many enzymatic reactions. However, scientists have only recently attempted to harness the power of hydrogen bonds in homogeneous catalytic systems. One of the newest directions is associated with attempts to control the properties of catalysts by influencing the "second coordination sphere" of metal complexes. The role H-bonding, and the building of stable supramolecular nanostructures due to intermolecular H-bonds, based on catalytic active heteroligand iron (Fe) or nickel (Ni) complexes formed during hydrocarbon oxidations were assessed via the AFM (Atomic-force microscopy) method, which was proposed and applied by authors of this manuscript. Th is article also discusses the roles of hydrogen bonds and supramolecular structures in oxidation reactions catalyzed by heteroligand Ni and Fe complexes, which are not only effective homogeneous catalysts but also structural and functional models of Oxygenases.
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Affiliation(s)
- Ludmila I. Matienko
- N.M. Emanuel Institution of Biochemical Physics Russian Academy of Science, 4 Kosygin Str., 119334 Moscow, Russia; (E.M.M.); (A.A.A.); (A.N.G.)
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3
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Jurich C, Yang ZJ. High-throughput computational investigation of protein electrostatics and cavity for SAM-dependent methyltransferases. Protein Sci 2023; 32:e4690. [PMID: 37278582 PMCID: PMC10273352 DOI: 10.1002/pro.4690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/25/2023] [Accepted: 05/29/2023] [Indexed: 06/07/2023]
Abstract
S-adenosyl methionine (SAM)-dependent methyl transferases (MTases) are a ubiquitous class of enzymes catalyzing dozens of essential life processes. Despite targeting a large space of substrates with diverse intrinsic reactivity, SAM MTases have similar catalytic efficiency. While understanding of MTase mechanism has grown tremendously through the integration of structural characterization, kinetic assays, and multiscale simulations, it remains elusive how these enzymes have evolved to fit the diverse chemical needs of their respective substrates. In this work, we performed a high-throughput molecular modeling analysis of 91 SAM MTases to better understand how their properties (i.e., electric field [EF] strength and active site volumes) help achieve similar catalytic efficiency toward substrates of different reactivity. We found that EF strengths have largely adjusted to make the target atom a better methyl acceptor. For MTases that target RNA/DNA and histone proteins, our results suggest that EF strength accommodates formal hybridization state and variation in cavity volume trends with diversity of substrate classes. Metal ions in SAM MTases contribute negatively to EF strength for methyl donation and enzyme scaffolds tend to offset these contributions.
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Affiliation(s)
| | - Zhongyue J. Yang
- Department of ChemistryVanderbilt UniversityNashvilleTennesseeUSA
- Center for Structural BiologyVanderbilt UniversityNashvilleTennesseeUSA
- Vanderbilt Institute of Chemical Biology, Vanderbilt UniversityNashvilleTennesseeUSA
- Data Science InstituteVanderbilt UniversityNashvilleTennesseeUSA
- Department of Chemical and Biomolecular EngineeringVanderbilt UniversityNashvilleTennesseeUSA
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4
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Abstract
Quantum calculations study the potential of an intramolecular H-bond between the halogen atom (X) of a halobenzene and a substituent placed ortho to it, to amplify the ability of X to engage in a halogen bond (XB) with a Lewis base. H-bonding substituents NH2, CH2CH2OH, CH2OH, OH, and COOH were added to halobenzenes (X = Cl, Br, I). The amino group had little effect, but those containing OH increased the CX···N XB energy to a NH3 nucleophile by about 0.5 kcal/mol; the increment associated with COOH is larger, nearly 2 kcal/mol. These energy increments were approximately doubled if two such H-bonding substituents are present. Combining a pair of ortho COOH groups with an electron-withdrawing NO2 group in the para position has a particularly large effect, raising the XB energy by about 4 kcal/mol, which can amount to as much as a 4-fold magnification.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
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5
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Scheiner S. Does a halogen bond require positive potential on the acid and negative potential on the base? Phys Chem Chem Phys 2023; 25:7184-7194. [PMID: 36815530 DOI: 10.1039/d3cp00379e] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
It is usually expected that formation of a halogen bond (XB) requires that a region of positive electrostatic potential associated with a σ or π-hole on the Lewis acid will interact with the negative potential of the base, either a lone pair or π-bond region. Quantum calculations of model systems suggest this not to be necessary. The placement of electron-withdrawing substituents on the base can reverse the sign of the potential in its lone pair or π-bond region to positive, and this base can nonetheless engage in a XB with the positive σ-hole of a Lewis acid. The reverse scenario is also possible in certain circumstances, as a negatively charged σ-hole can form a XB with the negative lone pair region of a base. Despite these classical Coulombic repulsions, the overall electrostatic interaction is attractive in these XBs, albeit only weakly so. The strengths of these bonds are surprisingly insensitive to changes in the partner molecule. For example, even a wide range in the depth of the σ-hole of the approaching acid yields only a minimal change in the strength of the XB to a base with a positive potential.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry Utah State University Logan, Utah, USA, 84322-0300.
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6
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Faille A, Dent KC, Pellegrino S, Jaako P, Warren AJ. The chemical landscape of the human ribosome at 1.67 Å resolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.28.530191. [PMID: 36909531 PMCID: PMC10002709 DOI: 10.1101/2023.02.28.530191] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
The ability of ribosomes to translate the genetic code into protein requires a finely tuned ion and solvent ecosystem. However, the lack of high-resolution structures has precluded accurate positioning of all the functional elements of the ribosome and limited our understanding of the specific role of ribosomal RNA chemical modifications in modulating ribosome function in health and disease. Here, using a new sample preparation methodology based on functionalised pristine graphene-coated grids, we solve the cryo-EM structure of the human large ribosomal subunit to a resolution of 1.67 Å. The accurate assignment of water molecules, magnesium and potassium ions in our model highlights the fundamental biological role of ribosomal RNA methylation in harnessing unconventional carbon-oxygen hydrogen bonds to establish chemical interactions with the environment and fine-tune the functional interplay with tRNA. In addition, the structures of three translational inhibitors bound to the human large ribosomal subunit at better than 2 Å resolution provide mechanistic insights into how three key druggable pockets of the ribosome are targeted and illustrate the potential of this methodology to accelerate high-throughput structure-based design of anti-cancer therapeutics.
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Liu J, Zhou M, Deng R, Zheng P, Chi YR. Chalcogen bond-guided conformational isomerization enables catalytic dynamic kinetic resolution of sulfoxides. Nat Commun 2022; 13:4793. [PMID: 35970848 PMCID: PMC9378665 DOI: 10.1038/s41467-022-32428-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 08/01/2022] [Indexed: 11/29/2022] Open
Abstract
Conformational isomerization can be guided by weak interactions such as chalcogen bonding (ChB) interactions. Here we report a catalytic strategy for asymmetric access to chiral sulfoxides by employing conformational isomerization and chalcogen bonding interactions. The reaction involves a sulfoxide bearing two aldehyde moieties as the substrate that, according to structural analysis and DFT calculations, exists as a racemic mixture due to the presence of an intramolecular chalcogen bond. This chalcogen bond formed between aldehyde (oxygen atom) and sulfoxide (sulfur atom), induces a conformational locking effect, thus making the symmetric sulfoxide as a racemate. In the presence of N-heterocyclic carbene (NHC) as catalyst, the aldehyde moiety activated by the chalcogen bond selectively reacts with an alcohol to afford the corresponding chiral sulfoxide products with excellent optical purities. This reaction involves a dynamic kinetic resolution (DKR) process enabled by conformational locking and facile isomerization by chalcogen bonding interactions.
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Affiliation(s)
- Jianjian Liu
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, 550025, China
| | - Mali Zhou
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, 550025, China
| | - Rui Deng
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, 550025, China
| | - Pengcheng Zheng
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, 550025, China.
| | - Yonggui Robin Chi
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, 550025, China.
- Division of Chemistry & Biological Chemistry, School of Physical & Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore.
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8
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Yang Z, Hajlasz N, Kulik HJ. Computational Modeling of Conformer Stability in Benenodin-1, a Thermally Actuated Lasso Peptide Switch. J Phys Chem B 2022; 126:3398-3406. [PMID: 35481742 DOI: 10.1021/acs.jpcb.2c00762] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Benenodin-1 is a thermally actuated lasso peptide rotaxane switch with two primary translational isomers that differ in the relative position of the residue Gln15. The conversion from one conformer to the other involves substantial enthalpy-entropy compensation: one conformer is energetically favored and the other is entropically favored. Here, we take a multi-scale quantum mechanical (QM) and classical molecular dynamic (MD) approach to reveal residue-specific sources of these differences in stability. QM reveals that the two benenodin-1 conformers involve distinct hydrogen bonding networks, with the enthalpically favored conformer having more intra-peptide hydrogen bonds between the Gln15 side chain and nearby residues. The evaluation of configurational entropy over the MD-sampled geometries reveals that the entropically favored conformer has enhanced conformational flexibility. By computing the by-residue-sum entropies, we identify the role of Gln15 and neighboring Glu14 in mediating the entropic variation during the switching process. These computational insights help explain the effects of Glu14Ala and Gln15Ala mutations on the conformational population of benenodin-1 observed experimentally.
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Affiliation(s)
- Zhongyue Yang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Natalia Hajlasz
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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9
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Abstract
Earlier, we established that nickel or iron heteroligand complexes, which include PhOH (nickel complexes) or tyrosine residue (nickel or iron complexes), are not only hydrocarbon oxidation catalysts (in the case of PhOH), but also simulate the active centers of enzymes (PhOH, tyrosine). The AFM method established the self-organization of nickel or iron heteroligand complexes, which included tyrosine residue or PhOH, into supramolecular structures on a modified silicon surface. Supramolecular structures were formed as a result of H-bonds and other non-covalent intermolecular interactions and, to a certain extent, reflected the structures involved in the mechanisms of reactions of homogeneous and enzymatic catalysis. Using the AFM method, we obtained evidence at the model level in favor of the involvement of the tyrosine fragment as one of the possible regulatory factors in the functioning of Ni(Fe)ARD dioxygenases or monooxygenases of the family of cytochrome P450. The principles of actions of these oxygenases were used to create highly efficient catalytic systems for the oxidation of hydrocarbons.
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10
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Jenepha Mary SJ, Pradhan S, James C. Molecular structure, NBO analysis of the hydrogen-bonded interactions, spectroscopic (FT-IR, FT-Raman), drug likeness and molecular docking of the novel anti COVID-2 molecule (2E)-N-methyl-2-[(4-oxo-4H-chromen-3-yl)methylidene]-hydrazinecarbothioamide (Dimer) - quantum chemical approach. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 251:119388. [PMID: 33503560 PMCID: PMC7834302 DOI: 10.1016/j.saa.2020.119388] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 12/04/2020] [Accepted: 12/24/2020] [Indexed: 05/14/2023]
Abstract
Prospective antiviral molecule (2E)-N-methyl-2-[(4-oxo-4H-chromen-3-yl)methylidene]-hydrazinecarbothioamide has been probed using Fourier transform infrared (FTIR), FT-Raman and quantum chemical computations. The geometry equilibrium and natural bond orbital analysis have been carried out with density functional theory employing Becke, 3-parameter, Lee-Yang-Parr method with the 6-311G++(d,p) basis set. The vibrational assignments pertaining to different modes of vibrations have been augmented by normal coordinate analysis, force constant and potential energy distributions. Drug likeness and oral activity have been carried out based on Lipinski's rule of five. The inhibiting potency of 2(2E)-methyl-2-[(4-oxo-4H-chromen-3-yl)methylidene]-hydrazinecarbothioamide has been investigated by docking simulation against SARS-CoV-2 protein. The optimized geometry shows a planar structure between the chromone and the side chain. Differences in the geometries due to the substitution of the electronegative atom and intermolecular contacts due to the chromone and hydrazinecarbothioamide were analyzed. NBO analysis confirms the presence of two strong stable hydrogen bonded NH⋯O intermolecular interactions and two weak hydrogen bonded CH⋯O interactions. The red shift in NH stretching frequency exposed from IR substantiates the formation of NH⋯O intermolecular hydrogen bond and the blue shift in CH stretching frequency substantiates the formation of CH⋯O intermolecular hydrogen bond. Drug likeness, absorption, distribution, metabolism, excretion and toxicity property gives an idea about the pharmacokinetic properties of the title molecule. The binding energy of the nonbonding interaction with Histidine 41 and Cysteine 145, present a clear view that 2(2E)-methyl-2-[(4-oxo-4H-chromen-3-yl)methylidene]-hydrazinecarbothioamide can irreversibly interact with SARS-CoV-2 protease.
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Affiliation(s)
- S J Jenepha Mary
- Department of Physics and Research Centre, Scott Christian College (Autonomous), Nagercoil 629003, Tamil Nadu, Affiliated to Manonmaniam Sundarnar University, Abishekapatti, Tirunelveli 627012, India
| | - Sayantan Pradhan
- Department of Chemistry, Jadavpur University, Kolkata 700 032, West Bengal, India
| | - C James
- Department of Physics and Research Centre, Scott Christian College (Autonomous), Nagercoil 629003, Tamil Nadu, Affiliated to Manonmaniam Sundarnar University, Abishekapatti, Tirunelveli 627012, India.
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11
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Potential Target Site for Inhibitors in MLS B Antibiotic Resistance. Antibiotics (Basel) 2021; 10:antibiotics10030264. [PMID: 33807634 PMCID: PMC7998614 DOI: 10.3390/antibiotics10030264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/24/2021] [Accepted: 02/24/2021] [Indexed: 11/17/2022] Open
Abstract
Macrolide-lincosamide-streptogramin B antibiotic resistance occurs through the action of erythromycin ribosome methylation (Erm) family proteins, causing problems due to their prevalence and high minimal inhibitory concentration, and feasibilities have been sought to develop inhibitors. Erms exhibit high conservation next to the N-terminal end region (NTER) as in ErmS, 64SQNF67. Side chains of homologous S, Q and F in ErmC' are surface-exposed, located closely together and exhibit intrinsic flexibility; these residues form a motif X. In S64 mutations, S64G, S64A and S64C exhibited 71%, 21% and 20% activity compared to the wild-type, respectively, conferring cell resistance. However, mutants harboring larger side chains did not confer resistance and retain the methylation activity in vitro. All mutants of Q65, Q65N, Q65E, Q65R, and Q65H lost their methyl group transferring activity in vivo and in vitro. At position F67, a size reduction of side-chain (F67A) or a positive charge (F67H) greatly reduced the activity to about 4% whereas F67L with a small size reduction caused a moderate loss, more than half of the activity. The increased size by F67Y and F67W reduced the activity by about 75%. In addition to stabilization of the cofactor, these amino acids could interact with substrate RNA near the methylatable adenine presumably to be catalytically well oriented with the SAM (S-adenosyl-L-methionine). These amino acids together with the NTER beside them could serve as unique potential inhibitor development sites. This region constitutes a divergent element due to the NTER which has variable length and distinct amino acids context in each Erm. The NTER or part of it plays critical roles in selective recognition of substrate RNA by Erms and this presumed target site might assume distinct local structure by induced conformational change with binding to substrate RNA and SAM, and contribute to the specific recognition of substrate RNA.
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12
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Li Y, Zhang Y, Cheng Y, Du T, Zhang J. Solvent inhibition profiles and inverse solvent isotope effects for enzymatic methyl transfer catalyzed by nicotinamide N‐methyltransferase. J PHYS ORG CHEM 2020. [DOI: 10.1002/poc.4093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Yuping Li
- School of Pharmaceutical Science and Technology Tianjin University Tianjin China
| | - Yali Zhang
- School of Pharmaceutical Science and Technology Tianjin University Tianjin China
| | - Yiting Cheng
- School of Pharmaceutical Science and Technology Tianjin University Tianjin China
| | - Tianshu Du
- School of Pharmaceutical Science and Technology Tianjin University Tianjin China
| | - Jianyu Zhang
- School of Pharmaceutical Science and Technology Tianjin University Tianjin China
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13
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Galle Kankanamge SR, Ma J, Mackin RT, Leonik FM, Taylor CM, Rubtsov IV, Kuroda DG. Proving and Probing the Presence of the Elusive C−H⋅⋅⋅O Hydrogen Bond in Liquid Solutions at Room Temperature. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
| | - Jianbo Ma
- Department of Chemistry Louisiana State University Baton Rouge LA 70803 USA
| | - Robert T. Mackin
- Department of Chemistry Tulane University New Orleans LA 70118 USA
| | - Fedra M. Leonik
- Department of Chemistry Louisiana State University Baton Rouge LA 70803 USA
| | - Carol M. Taylor
- Department of Chemistry Louisiana State University Baton Rouge LA 70803 USA
| | - Igor V. Rubtsov
- Department of Chemistry Tulane University New Orleans LA 70118 USA
| | - Daniel G. Kuroda
- Department of Chemistry Louisiana State University Baton Rouge LA 70803 USA
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14
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Galle Kankanamge SR, Ma J, Mackin RT, Leonik FM, Taylor CM, Rubtsov IV, Kuroda DG. Proving and Probing the Presence of the Elusive C-H⋅⋅⋅O Hydrogen Bond in Liquid Solutions at Room Temperature. Angew Chem Int Ed Engl 2020; 59:17012-17017. [PMID: 32559329 DOI: 10.1002/anie.202006210] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Indexed: 11/10/2022]
Abstract
Hydrogen bonds (H bonds) play a major role in defining the structure and properties of many substances, as well as phenomena and processes. Traditional H bonds are ubiquitous in nature, yet the demonstration of weak H bonds that occur between a highly polarized C-H group and an electron-rich oxygen atom, has proven elusive. Detailed here are linear and nonlinear IR spectroscopy experiments that reveal the presence of H bonds between the chloroform C-H group and an amide carbonyl oxygen atom in solution at room temperature. Evidence is provided for an amide solvation shell featuring two clearly distinguishable chloroform arrangements that undergo chemical exchange with a time scale of about 2 ps. Furthermore, the enthalpy of breaking the hydrogen bond is found to be 6-20 kJ mol-1 . Ab-initio computations support the findings of two distinct solvation shells formed by three chloroform molecules, where one thermally undergoes hydrogen-bond making and breaking.
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Affiliation(s)
| | - Jianbo Ma
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Robert T Mackin
- Department of Chemistry, Tulane University, New Orleans, LA, 70118, USA
| | - Fedra M Leonik
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Carol M Taylor
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Igor V Rubtsov
- Department of Chemistry, Tulane University, New Orleans, LA, 70118, USA
| | - Daniel G Kuroda
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
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15
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Roca M, Williams IH. Transition-State Vibrational Analysis and Isotope Effects for COMT-Catalyzed Methyl Transfer. J Am Chem Soc 2020; 142:15548-15559. [PMID: 32812761 PMCID: PMC7498148 DOI: 10.1021/jacs.0c07344] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Isotopic partition-function ratios (IPFRs) computed for transition structures (TSs) of the methyl-transfer reaction catalyzed by catechol O-methyltransferase and modeled by hybrid QM/MM methods are analyzed. The ability of smaller Hessians to reproduce trends in α-3H3 and 14Cα IPFRs as obtained using the much larger subset QM/MM Hessians from which they are extracted is investigated critically. A 6-atom-extracted Hessian reproduces perfectly the α-T3 IPFR values from the full-subset Hessians of all the TSs but not the α-14CIPFRs. Average AM1/OPLS-AA harmonic frequencies and mean-square amplitudes are presented for the 12 normal modes of the α-CH3 moiety within the active site of several enzymic transition structures, together with QM/MM potential energy scans along each of these modes to assess the degree of anharmonicity. A novel investigation of ponderal effects upon IPFRs suggests that the value for α-14C tends toward a limiting minimum whereas that for α-T3 tends toward a limiting maximum as the mass of the rest of the system increases. The transition vector is dominated by motions of atoms within the donor and acceptor moieties and is very well described as a simple combination of Walden-inversion "umbrella" bending and asymmetric stretching of the SCα and CαO bonds. The contribution of atoms of the protein residues Met40, Tyr68, and Asp141 to the transition vector is extremely small. Average valence force constants for the COMT TS show significant differences from early BEBOVIB estimates which were used in support of the compression hypothesis for catalysis. There is no correlation between TS IPFRs and the nonbonded distances for close contacts between the S atom of SAM and Tyr68 or between any of the H atoms of the transferring methyl group and either Met40 or Asp141.
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Affiliation(s)
- Maite Roca
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain
| | - Ian H Williams
- Department of Chemistry, University of Bath, Bath BA2 7AY, United Kingdom
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16
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Zhao LN, Kaldis P. Cascading proton transfers are a hallmark of the catalytic mechanism of SAM-dependent methyltransferases. FEBS Lett 2020; 594:2128-2139. [PMID: 32353165 DOI: 10.1002/1873-3468.13799] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 04/20/2020] [Accepted: 04/22/2020] [Indexed: 11/10/2022]
Abstract
The S-adenosyl methionine (SAM)-dependent methyltransferases attach a methyl group to the deprotonated methyl lysine using SAM as a donor. An intriguing, yet unanswered, question is how the deprotonation takes place. PRDM9 with well-defined enzyme activity is a good representative of the methyltransferase family to study the deprotonation and subsequently the methyl transfer. Our study has found that the pKa of Tyr357 is low enough to make it an ideal candidate for proton abstraction from the methyl lysine. The partially deprontonated Tyr357 is able to change its H-bond pattern thus bridging two proton tunneling states and providing a cascading proton transfer. We have uncovered a new catalytic mechanism for the deprotonation of the methyl lysine in methyltransferases.
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Affiliation(s)
- Li Na Zhao
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Philipp Kaldis
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Department of Clinical Sciences, Lund University, Clinical Research Center (CRC), Malmö, Sweden
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17
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Ferreira de Freitas R, Ivanochko D, Schapira M. Methyltransferase Inhibitors: Competing with, or Exploiting the Bound Cofactor. Molecules 2019; 24:E4492. [PMID: 31817960 PMCID: PMC6943651 DOI: 10.3390/molecules24244492] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 12/03/2019] [Accepted: 12/04/2019] [Indexed: 12/11/2022] Open
Abstract
Protein methyltransferases (PMTs) are enzymes involved in epigenetic mechanisms, DNA repair, and other cellular machineries critical to cellular identity and function, and are an important target class in chemical biology and drug discovery. Central to the enzymatic reaction is the transfer of a methyl group from the cofactor S-adenosylmethionine (SAM) to a substrate protein. Here we review how the essentiality of SAM for catalysis is exploited by chemical inhibitors. Occupying the cofactor binding pocket to compete with SAM can be hindered by the hydrophilic nature of this site, but structural studies of compounds now in the clinic revealed that inhibitors could either occupy juxtaposed pockets to overlap minimally, but sufficiently with the bound cofactor, or induce large conformational remodeling leading to a more druggable binding site. Rather than competing with the cofactor, other inhibitors compete with the substrate and rely on bound SAM, either to allosterically stabilize the substrate binding site, or for direct SAM-inhibitor interactions.
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Affiliation(s)
- Renato Ferreira de Freitas
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Rua Arcturus 3, São Bernardo do Campo, SP 09606-070, Brazil
| | - Danton Ivanochko
- Structural Genomics Consortium, University of Toronto, MaRS Centre, South Tower, 101 College St., Suite 700, Toronto, ON M5G 1L7, Canada
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada
| | - Matthieu Schapira
- Structural Genomics Consortium, University of Toronto, MaRS Centre, South Tower, 101 College St., Suite 700, Toronto, ON M5G 1L7, Canada
- Department of Pharmacology and Toxicology, University of Toronto, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
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18
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Tewary SK, Zheng YG, Ho MC. Protein arginine methyltransferases: insights into the enzyme structure and mechanism at the atomic level. Cell Mol Life Sci 2019; 76:2917-2932. [PMID: 31123777 PMCID: PMC6741777 DOI: 10.1007/s00018-019-03145-x] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 05/10/2019] [Indexed: 02/06/2023]
Abstract
Protein arginine methyltransferases (PRMTs) catalyze the methyl transfer to the arginine residues of protein substrates and are classified into three major types based on the final form of the methylated arginine. Recent studies have shown a strong correlation between PRMT expression level and the prognosis of cancer patients. Currently, crystal structures of eight PRMT members have been determined. Kinetic and structural studies have shown that all PRMTs share similar, but unique catalytic and substrate recognition mechanism. In this review, we discuss the structural similarities and differences of different PRMT members, focusing on their overall structure, S-adenosyl-L-methionine-binding pocket, substrate arginine recognition and catalytic mechanisms. Since PRMTs are valuable targets for drug discovery, we also rationally classify the known PRMT inhibitors into five classes and discuss their mechanisms of action at the atomic level.
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Affiliation(s)
| | - Y George Zheng
- College of Pharmacy, University of Georgia, Athens, GA, 30602, USA
| | - Meng-Chiao Ho
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan.
- Institute of Biochemical Sciences, National Taiwan University, Taipei, 106, Taiwan.
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19
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Structural basis for stereoselective dehydration and hydrogen-bonding catalysis by the SAM-dependent pericyclase LepI. Nat Chem 2019; 11:812-820. [PMID: 31332284 PMCID: PMC6708486 DOI: 10.1038/s41557-019-0294-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 06/14/2019] [Indexed: 12/04/2022]
Abstract
LepI is an S-adenosylmethionine (SAM)-dependent pericyclase that catalyzes the formation of 2-pyridone natural product leporin C. Biochemical characterization showed LepI can catalyze the stereoselective dehydration to yield a reactive (E)-quinone methide that can undergo bifurcating intramolecular Diels-Alder (IMDA) and hetero-Diels-Alder (HDA) cyclizations from an ambimodal transition state, as well as a [3,3]-retro-Claisen rearrangement to recycle the IMDA product into leporin C. Here we solved the X-ray crystal structures of SAM-bound LepI and in complex with a substrate analog, the product leporin C, and a retro-Claisen reaction transition-state analog to understand the structural basis for the multitude of reactions. Structural and mutational analysis revealed how Nature evolves a classic methyltransferase active site into one that can serve as a dehydratase and a multifunctional pericyclase. Catalysis of both sets of reactions employs H133 and R295, two active site residues that are not found in canonical methyltransferases. An alternative role of SAM, which is not found to be in direct contact with the substrate, is also proposed.
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20
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Yang Z, Liu F, Steeves AH, Kulik HJ. Quantum Mechanical Description of Electrostatics Provides a Unified Picture of Catalytic Action Across Methyltransferases. J Phys Chem Lett 2019; 10:3779-3787. [PMID: 31244268 DOI: 10.1021/acs.jpclett.9b01555] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Methyl transferases (MTases) are a well-studied class of enzymes for which competing enzymatic enhancement mechanisms have been suggested, ranging from structural methyl group CH···X hydrogen bonds (HBs) to electrostatic- and charge-transfer-driven stabilization of the transition state (TS). We identified all Class I MTases for which reasonable resolution (<2.0 Å) crystal structures could be used to form catalytically competent ternary complexes for multiscale (i.e., quantum-mechanical/molecular-mechanical or QM/MM) simulation of the SN2 methyl transfer reaction coordinate. The four Class I MTases studied have both distinct functions (e.g., protein repair or biosynthesis) and substrate nucleophiles (i.e., C, N, or O). While CH···X HBs stabilize all reactant complexes, no universal TS stabilization role is found for these interactions in MTases. A consistent picture is instead obtained through analysis of charge transfer and electrostatics, wherein much of cofactor-substrate charge separation is maintained in the TS region, and electrostatic potential is correlated with substrate nucleophilicity (i.e., intrinsic reactivity).
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Affiliation(s)
- Zhongyue Yang
- Department of Chemical Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Fang Liu
- Department of Chemical Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Adam H Steeves
- Department of Chemical Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Heather J Kulik
- Department of Chemical Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
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21
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Chen S, Kapilashrami K, Senevirathne C, Wang Z, Wang J, Linscott JA, Luo M. Substrate-Differentiated Transition States of SET7/9-Catalyzed Lysine Methylation. J Am Chem Soc 2019; 141:8064-8067. [PMID: 31034218 DOI: 10.1021/jacs.9b02553] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Transition state stabilization is essential for rate acceleration of enzymatic reactions. Despite extensive studies on various transition state structures of enzymes, an intriguing puzzle is whether an enzyme can accommodate multiple transition states (TSs) to catalyze a chemical reaction. It is experimentally challenging to study this proposition in terms of the choices of suitable enzymes and the feasibility to distinguish multiple TSs. As a paradigm with the protein lysine methyltransferase (PKMT) SET7/9 paired with its physiological substrates H3 and p53, their TSs were solved with experimental kinetic isotope effects as computational constraints. Remarkably, SET7/9 adopts two structurally distinct TSs, a nearly symmetric SN2 and an extremely early SN2, for H3K4 and p53K372 methylation, respectively. The two TSs are also different from those previously revealed for other PKMTs. The setting of multiple TSs is expected to be essential for SET7/9 and likely other PKMTs to act on broad substrates with high efficiency.
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Affiliation(s)
| | | | | | - Zhen Wang
- Department of Biochemistry , Albert Einstein College of Medicine , Bronx , New York 10461 , United States
| | | | - Joshua A Linscott
- Program of Pharmacology, Weill Graduate School of Medical Science , Cornell University , New York , New York 10021 , United States
| | - Minkui Luo
- Program of Pharmacology, Weill Graduate School of Medical Science , Cornell University , New York , New York 10021 , United States
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22
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Matienko L, Binyukov V, Mil E, Zaikov G. Supramolecular Macrostructures in the Mechanisms of Catalysis with Nickel or Iron Heteroligand Complexes. CURRENT ORGANOCATALYSIS 2019. [DOI: 10.2174/2213337206666181231120410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
The AFM-techniques have been used for the research of the role of intermolecular
H-bonds and stable supramolecular nanostructures, based on effective catalysts of oxidation
processes, which are also models of Ni(Fe)ARD Dioxygenases, in mechanisms of catalysis.
Methods and Results:
The role of Histidine and Tyrosine ligands in the mechanisms of catalysis by
FeARD on model systems is discussed based on AFM and UV-Spectroscopy data.
Conclusion:
We first offer the new approach – method of atomic force microscopy (AFM) – to study
the possibility of the formation of supramolecular nanostructures, and also for assessing of role the
intermolecular hydrogen bonds (and the other intermolecular non-covalent interactions) in mechanisms
of homogeneous and enzymatic catalysis with nickel and iron complexes.
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Affiliation(s)
- L.I. Matienko
- The Federal State Budget Institution of Science N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygin str., Moscow, 119334, Russian Federation
| | - V.I. Binyukov
- The Federal State Budget Institution of Science N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygin str., Moscow, 119334, Russian Federation
| | - E.M. Mil
- The Federal State Budget Institution of Science N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygin str., Moscow, 119334, Russian Federation
| | - G.E. Zaikov
- The Federal State Budget Institution of Science N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygin str., Moscow, 119334, Russian Federation
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23
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Fick RJ, Horowitz S, McDole BG, Clay MC, Mehl RA, Al-Hashimi HM, Scheiner S, Trievel RC. Structural and Functional Characterization of Sulfonium Carbon-Oxygen Hydrogen Bonding in the Deoxyamino Sugar Methyltransferase TylM1. Biochemistry 2019; 58:2152-2159. [PMID: 30810306 DOI: 10.1021/acs.biochem.8b01141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The N-methyltransferase TylM1 from Streptomyces fradiae catalyzes the final step in the biosynthesis of the deoxyamino sugar mycaminose, a substituent of the antibiotic tylosin. The high-resolution crystal structure of TylM1 bound to the methyl donor S-adenosylmethionine (AdoMet) illustrates a network of carbon-oxygen (CH···O) hydrogen bonds between the substrate's sulfonium cation and residues within the active site. These interactions include hydrogen bonds between the methyl and methylene groups of the AdoMet sulfonium cation and the hydroxyl groups of Tyr14 and Ser120 in the enzyme. To examine the functions of these interactions, we generated Tyr14 to phenylalanine (Y14F) and Ser120 to alanine (S120A) mutations to selectively ablate the CH···O hydrogen bonding to AdoMet. The TylM1 S120A mutant exhibited a modest decrease in its catalytic efficiency relative to that of the wild type (WT) enzyme, whereas the Y14F mutation resulted in an approximately 30-fold decrease in catalytic efficiency. In contrast, site-specific substitution of Tyr14 by the noncanonical amino acid p-aminophenylalanine partially restored activity comparable to that of the WT enzyme. Correlatively, quantum mechanical calculations of the activation barrier energies of WT TylM1 and the Tyr14 mutants suggest that substitutions that abrogate hydrogen bonding with the AdoMet methyl group impair methyl transfer. Together, these results offer insights into roles of CH···O hydrogen bonding in modulating the catalytic efficiency of TylM1.
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Affiliation(s)
- Robert J Fick
- Department of Biological Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Scott Horowitz
- Department of Chemistry and Biochemistry, Knoebel Institute for Healthy Aging , University of Denver , Denver , Colorado 80208 , United States
| | - Brandon G McDole
- Department of Biological Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Mary C Clay
- Department of Biochemistry , Duke University , Durham , North Carolina 27710 , United States
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics , Oregon State University , Corvallis , Oregon 97331 , United States
| | - Hashim M Al-Hashimi
- Department of Biochemistry , Duke University , Durham , North Carolina 27710 , United States
| | - Steve Scheiner
- Department of Chemistry and Biochemistry , Utah State University , Logan , Utah 84322 , United States
| | - Raymond C Trievel
- Department of Biological Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
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24
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Rajakovich LJ, Pandelia ME, Mitchell AJ, Chang WC, Zhang B, Boal AK, Krebs C, Bollinger JM. A New Microbial Pathway for Organophosphonate Degradation Catalyzed by Two Previously Misannotated Non-Heme-Iron Oxygenases. Biochemistry 2019; 58:1627-1647. [PMID: 30789718 PMCID: PMC6503667 DOI: 10.1021/acs.biochem.9b00044] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The assignment of biochemical functions to hypothetical proteins is challenged by functional diversification within many protein structural superfamilies. This diversification, which is particularly common for metalloenzymes, renders functional annotations that are founded solely on sequence and domain similarities unreliable and often erroneous. Definitive biochemical characterization to delineate functional subgroups within these superfamilies will aid in improving bioinformatic approaches for functional annotation. We describe here the structural and functional characterization of two non-heme-iron oxygenases, TmpA and TmpB, which are encoded by a genomically clustered pair of genes found in more than 350 species of bacteria. TmpA and TmpB are functional homologues of a pair of enzymes (PhnY and PhnZ) that degrade 2-aminoethylphosphonate but instead act on its naturally occurring, quaternary ammonium analogue, 2-(trimethylammonio)ethylphosphonate (TMAEP). TmpA, an iron(II)- and 2-(oxo)glutarate-dependent oxygenase misannotated as a γ-butyrobetaine (γbb) hydroxylase, shows no activity toward γbb but efficiently hydroxylates TMAEP. The product, ( R)-1-hydroxy-2-(trimethylammonio)ethylphosphonate [( R)-OH-TMAEP], then serves as the substrate for the second enzyme, TmpB. By contrast to its purported phosphohydrolytic activity, TmpB is an HD-domain oxygenase that uses a mixed-valent diiron cofactor to enact oxidative cleavage of the C-P bond of its substrate, yielding glycine betaine and phosphate. The high specificities of TmpA and TmpB for their N-trimethylated substrates suggest that they have evolved specifically to degrade TMAEP, which was not previously known to be subject to microbial catabolism. This study thus adds to the growing list of known pathways through which microbes break down organophosphonates to harvest phosphorus, carbon, and nitrogen in nutrient-limited niches.
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Affiliation(s)
- Lauren J. Rajakovich
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Present address: Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Maria-Eirini Pandelia
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Present address: Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Andrew J. Mitchell
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Present address: Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142
| | - Wei-chen Chang
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Present address: Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Bo Zhang
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Present address: REG Life Sciences, LLC, South San Francisco, California 94080
| | - Amie K. Boal
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Carsten Krebs
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - J. Martin Bollinger
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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25
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Itoh Y, Nakashima Y, Tsukamoto S, Kurohara T, Suzuki M, Sakae Y, Oda M, Okamoto Y, Suzuki T. N +-C-H···O Hydrogen bonds in protein-ligand complexes. Sci Rep 2019; 9:767. [PMID: 30683882 PMCID: PMC6347603 DOI: 10.1038/s41598-018-36987-9] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 11/28/2018] [Indexed: 12/03/2022] Open
Abstract
In the context of drug design, C-H···O hydrogen bonds have received little attention so far, mostly because they are considered weak relative to other noncovalent interactions such as O-H···O hydrogen bonds, π/π interactions, and van der Waals interactions. Herein, we demonstrate the significance of hydrogen bonds between C-H groups adjacent to an ammonium cation and an oxygen atom (N+-C-H···O hydrogen bonds) in protein-ligand complexes. Quantum chemical calculations revealed details on the strength and geometrical requirements of these N+-C-H···O hydrogen bonds, and a subsequent survey of the Protein Data Bank (PDB) based on these criteria suggested that numerous protein-ligand complexes contain such N+-C-H···O hydrogen bonds. An ensuing experimental investigation into the G9a-like protein (GLP)-inhibitor complex demonstrated that N+-C-H···O hydrogen bonds affect the activity of the inhibitors against the target enzyme. These results should provide the basis for the use of N+-C-H···O hydrogen bonds in drug discovery.
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Affiliation(s)
- Yukihiro Itoh
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto, 606-0823, Japan
| | - Yusuke Nakashima
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto, 606-0823, Japan
| | - Shuichiro Tsukamoto
- Department of Physics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Takashi Kurohara
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto, 606-0823, Japan
| | - Miki Suzuki
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto, 606-0823, Japan
| | - Yoshitake Sakae
- Department of Physics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Masayuki Oda
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto, 606-8522, Japan
| | - Yuko Okamoto
- Department of Physics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan.,CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Takayoshi Suzuki
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto, 606-0823, Japan. .,CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan.
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26
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Tang B, Li B, Li B, Qin J, Zhao J, Xu J, Qiu Y, Wu Z, Fang M. Insights into the stereoselectivity of human SETD7 methyltransferase. RSC Adv 2019; 9:9218-9227. [PMID: 35517649 PMCID: PMC9062083 DOI: 10.1039/c9ra00190e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 03/04/2019] [Indexed: 12/31/2022] Open
Abstract
Human SETD7 methyltransferase (hSETD7) is involved in a wide range of physiological processes, and has been considered as a significant target to develop new drugs. (R)-PFI-2, one hSETD7 inhibitor, could bind to the pocket of substrates with potent (low nanomolar) activity and high selectivity, while its enantiomer (S)-PFI-2 showed 500-fold less activity in IC50 determination. Why do this pair of enantiomers, with nearly identical structures, exert tremendously different inhibitory activity? We performed a total of 900 ns long-timescale molecular dynamics (MD) simulations and 80 ps hybrid quantum mechanics/molecular mechanics (QM/MM) MD simulations to understand the molecular mechanism of the stereoselectivity of hSETD7. For each SAM/hSETD7/PFI-2 system, we characterized and compared the residual fluctuation of hSETD7, and generated molecular interaction fingerprints (IFP) to exemplify the propensities of SAM/hSETD7-inhibitor interactions. Based on the QM/MM MD, we accurately captured the difference of hydrogen bonds between the SAM/hSETD7/(R)-PFI-2 and SAM/hSETD7/(S)-PFI-2 systems. Especially the strength of the hydrogen bond between G336 and two inhibitors, which determines the stability of the post-SET loop. The energy barrier for (S)-PFI-2 was much bigger than (R)-PFI-2 from global minimum to bioactive conformation as the potential energy surface scanning (PES) showed. Moreover, by estimating the binding affinity and phylogenetic tree analysis, we discovered 16 hotspots were essential for binding both enantiomers but the specific mode of interaction between these hotspots and enantiomorphs is different. Our findings reveal the effect of chirality on the inhibition activity of hSETD7 in detail, and provide valuable information for hSETD7 structure-based drug development. This work clearly reveals the interaction of SAM/hSET7/(R/S)-PFI-2 systems, and confirms that the different bioactive energy barriers of (R)-PFI-2 and (S)-PFI-2 lead to the tremendously different inhibitory activities between these two antipodes.![]()
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Affiliation(s)
- Bowen Tang
- School of Pharmaceutical Sciences
- Fujian Provincial Key Laboratory of Innovative Drug Target Research
- Xiamen University
- Xiamen 361000
- China
| | - Baicun Li
- School of Pharmaceutical Sciences
- Fujian Provincial Key Laboratory of Innovative Drug Target Research
- Xiamen University
- Xiamen 361000
- China
| | - Boqun Li
- School of Pharmaceutical Sciences
- Fujian Provincial Key Laboratory of Innovative Drug Target Research
- Xiamen University
- Xiamen 361000
- China
| | - Jingbo Qin
- School of Pharmaceutical Sciences
- Fujian Provincial Key Laboratory of Innovative Drug Target Research
- Xiamen University
- Xiamen 361000
- China
| | - Junming Zhao
- School of Pharmaceutical Sciences
- Fujian Provincial Key Laboratory of Innovative Drug Target Research
- Xiamen University
- Xiamen 361000
- China
| | - Jianwenn Xu
- School of Pharmaceutical Sciences
- Fujian Provincial Key Laboratory of Innovative Drug Target Research
- Xiamen University
- Xiamen 361000
- China
| | - Yingkun Qiu
- School of Pharmaceutical Sciences
- Fujian Provincial Key Laboratory of Innovative Drug Target Research
- Xiamen University
- Xiamen 361000
- China
| | - Zhen Wu
- School of Pharmaceutical Sciences
- Fujian Provincial Key Laboratory of Innovative Drug Target Research
- Xiamen University
- Xiamen 361000
- China
| | - Meijuan Fang
- School of Pharmaceutical Sciences
- Fujian Provincial Key Laboratory of Innovative Drug Target Research
- Xiamen University
- Xiamen 361000
- China
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27
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Sen S, Patwari GN. Electrostatics and Dispersion in X-H···Y (X = C, N, O; Y = N, O) Hydrogen Bonds and Their Role in X-H Vibrational Frequency Shifts. ACS OMEGA 2018; 3:18518-18527. [PMID: 31458423 PMCID: PMC6644087 DOI: 10.1021/acsomega.8b01802] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 11/19/2018] [Indexed: 06/10/2023]
Abstract
The frequency shifts of donor stretching vibration in X-H···Y (X = C, N, O; Y = N, O) hydrogen-bonded complexes of phenylacetylene, indole, and phenol are linearly correlated with the electrostatic component of the interaction energy. This linear correlation suggests that the electrostatic component, which is the first-order perturbative correction to the stabilization energy, is essentially localized on the X-H group. The linear correlation suggests that the electrostatic tuning rate, which is a measure of the X-H oscillator to undergo shifts upon hydrogen bonding per unit increase in the electrostatic component of the stabilization energy, was found to be in the order of O-H > N-H > C-H. Interestingly, for each of the donor groups, viz., C-H, N-H, and O-H, the vibrational frequency shifts were inversely correlated to the dipole moment of the acceptor separately, which is counterintuitive vis-à-vis the electrostatic component. This implies that extrapolation to zero dipole moment of the acceptor will yield very large shifts in the hydrogen-bonded X-H stretching frequencies. The trends in the variation of the dispersion and exchange-repulsion components and the total interaction energy vis-à-vis frequency shifts of donor stretching vibration are similar for hydrogen-bonded complexes of phenylacetylene, indole, and phenol. Furthermore, it was observed that the vibrational frequency shifts of all of the complexes are linearly correlated with the charge transfer from the filled orbital of the hydrogen acceptor to the vacant antibonding (σ*) orbital of the X-H donor group on the basis of natural bonding orbital calculations.
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Affiliation(s)
| | - G. Naresh Patwari
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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28
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Meinke JL, Mehaffey MR, Wagner DT, Sun N, Zhang Z, Brodbelt JS, Keatinge-Clay AT. Structural and Functional Studies of a gem-Dimethylating Methyltransferase from a trans-Acyltransferase Assembly Line. ACS Chem Biol 2018; 13:3306-3314. [PMID: 30371052 DOI: 10.1021/acschembio.8b00733] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The methyl substituents in products of trans-acyltransferase assembly lines are usually incorporated by S-adenosyl-methionine (SAM)-dependent methyltransferase (MT) domains. The gem-dimethyl moieties within the polyketide disorazol are installed through the iterative action of an MT in the third module of its assembly line. The 1.75-Å-resolution crystal structure of this MT helps elucidate how it catalyzes the addition of two methyl groups. Activity assays of point mutants on β-ketoacyl chains linked to an acyl carrier protein and N-acetylcysteamine provide additional insights into the roles of active site residues. The replacement of an alanine with a phenylalanine at an apparent gatekeeping position resulted in more monomethylation than dimethylation. MTs may form an interface with ketoreductases (KRs) and even mediate the docking of trans-acyltransferase assembly line polypeptides through this association.
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Affiliation(s)
- Jessica L. Meinke
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - M. Rachel Mehaffey
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Drew T. Wagner
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Ningze Sun
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Zhicheng Zhang
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jennifer S. Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Adrian T. Keatinge-Clay
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
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29
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Kim HJ, Pei M, Ko JS, Ma MH, Park GE, Baek J, Yang H, Cho MJ, Choi DH. Influence of Branched Alkyl Ester-Labeled Side Chains on Specific Chain Arrangement and Charge-Transport Properties of Diketopyrrolopyrrole-Based Conjugated Polymers. ACS APPLIED MATERIALS & INTERFACES 2018; 10:40681-40691. [PMID: 30381941 DOI: 10.1021/acsami.8b13292] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A series of diketopyrrolopyrrole (DPP)-based copolymers, with DPP and bithiophene (BT) as the electron-acceptor and donor backbone units, respectively, are synthesized with branched alkyl side chains that are either directly coupled to the N-positions of DPP or separated by an alkyl ester group. The ester moieties in the side chains induce specific cohesive molecular interactions between these side chains, as compared to the alkyl-only side chains with weak van der Waals interactions. Structure analysis of the DPPBT-based copolymers demonstrated that the introduction of a proper alkyl ester spacer to the branched alkyl chains can shorten the π-π stacking distance between the DPPBT backbones down to 3.61 Å and promote the development of two-dimensionally extended domains. DPPBT-based copolymers, including different branched alkyl ester-labeled side chains, are spun-cast on polymer-treated SiO2 dielectrics from dilute chloroform solutions for organic thin-film transistors. A DPPBT-based copolymer with properly engineered side chains (i.e., 2-decyltetradecyl ester-labeled side chains) shows the highest hole mobility of 2.30 cm2 V-1 s-1 and an on/off current ratio of above 106.
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Affiliation(s)
- Hyung Jong Kim
- Department of Chemistry, Research Institute for Natural Sciences , Korea University , Seoul 02841 , South Korea
| | - Mingyuan Pei
- Department of Applied Organic Materials Engineering , Inha University , Incheon 22212 , South Korea
| | - Joong Se Ko
- Department of Applied Organic Materials Engineering , Inha University , Incheon 22212 , South Korea
| | - Min Hee Ma
- Department of Chemistry, Research Institute for Natural Sciences , Korea University , Seoul 02841 , South Korea
| | - Gi Eun Park
- Department of Chemistry, Research Institute for Natural Sciences , Korea University , Seoul 02841 , South Korea
| | - Jimin Baek
- Department of Applied Organic Materials Engineering , Inha University , Incheon 22212 , South Korea
| | - Hoichang Yang
- Department of Applied Organic Materials Engineering , Inha University , Incheon 22212 , South Korea
| | - Min Ju Cho
- Department of Chemistry, Research Institute for Natural Sciences , Korea University , Seoul 02841 , South Korea
| | - Dong Hoon Choi
- Department of Chemistry, Research Institute for Natural Sciences , Korea University , Seoul 02841 , South Korea
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30
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Crystallographic and Computational Characterization of Methyl Tetrel Bonding in S-Adenosylmethionine-Dependent Methyltransferases. Molecules 2018; 23:molecules23112965. [PMID: 30428636 PMCID: PMC6278250 DOI: 10.3390/molecules23112965] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 10/19/2018] [Accepted: 10/20/2018] [Indexed: 11/17/2022] Open
Abstract
Tetrel bonds represent a category of non-bonding interaction wherein an electronegative atom donates a lone pair of electrons into the sigma antibonding orbital of an atom in the carbon group of the periodic table. Prior computational studies have implicated tetrel bonding in the stabilization of a preliminary state that precedes the transition state in SN2 reactions, including methyl transfer. Notably, the angles between the tetrel bond donor and acceptor atoms coincide with the prerequisite geometry for the SN2 reaction. Prompted by these findings, we surveyed crystal structures of methyltransferases in the Protein Data Bank and discovered multiple instances of carbon tetrel bonding between the methyl group of the substrate S-adenosylmethionine (AdoMet) and electronegative atoms of small molecule inhibitors, ions, and solvent molecules. The majority of these interactions involve oxygen atoms as the Lewis base, with the exception of one structure in which a chlorine atom of an inhibitor functions as the electron donor. Quantum mechanical analyses of a representative subset of the methyltransferase structures from the survey revealed that the calculated interaction energies and spectral properties are consistent with the values for bona fide carbon tetrel bonds. The discovery of methyl tetrel bonding offers new insights into the mechanism underlying the SN2 reaction catalyzed by AdoMet-dependent methyltransferases. These findings highlight the potential of exploiting these interactions in developing new methyltransferase inhibitors.
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31
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Scheiner S. Ability of IR and NMR Spectral Data to Distinguish between a Tetrel Bond and a Hydrogen Bond. J Phys Chem A 2018; 122:7852-7862. [DOI: 10.1021/acs.jpca.8b07631] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
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32
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Saez DA, Zinovjev K, Tuñón I, Vöhringer-Martinez E. Catalytic Reaction Mechanism in Native and Mutant Catechol-O-methyltransferase from the Adaptive String Method and Mean Reaction Force Analysis. J Phys Chem B 2018; 122:8861-8871. [DOI: 10.1021/acs.jpcb.8b07339] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- David Adrian Saez
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, 4070371 Concepcion, Chile
| | - Kirill Zinovjev
- Departament de Química Física, Universitat de València, 46100 Burjassot, Spain
| | - Iñaki Tuñón
- Departament de Química Física, Universitat de València, 46100 Burjassot, Spain
| | - Esteban Vöhringer-Martinez
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, 4070371 Concepcion, Chile
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33
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Abstract
Protein lysine methylation is a distinct posttranslational modification that causes minimal changes in the size and electrostatic status of lysine residues. Lysine methylation plays essential roles in regulating fates and functions of target proteins in an epigenetic manner. As a result, substrates and degrees (free versus mono/di/tri) of protein lysine methylation are orchestrated within cells by balanced activities of protein lysine methyltransferases (PKMTs) and demethylases (KDMs). Their dysregulation is often associated with neurological disorders, developmental abnormalities, or cancer. Methyllysine-containing proteins can be recognized by downstream effector proteins, which contain methyllysine reader domains, to relay their biological functions. While numerous efforts have been made to annotate biological roles of protein lysine methylation, limited work has been done to uncover mechanisms associated with this modification at a molecular or atomic level. Given distinct biophysical and biochemical properties of methyllysine, this review will focus on chemical and biochemical aspects in addition, recognition, and removal of this posttranslational mark. Chemical and biophysical methods to profile PKMT substrates will be discussed along with classification of PKMT inhibitors for accurate perturbation of methyltransferase activities. Semisynthesis of methyllysine-containing proteins will also be covered given the critical need for these reagents to unambiguously define functional roles of protein lysine methylation.
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Affiliation(s)
- Minkui Luo
- Chemical Biology Program , Memorial Sloan Kettering Cancer Center , New York , New York 10065 , United States.,Program of Pharmacology, Weill Graduate School of Medical Science , Cornell University , New York , New York 10021 , United States
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34
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Skiba MA, Sikkema AP, Moss NA, Lowell AN, Su M, Sturgis RM, Gerwick L, Gerwick WH, Sherman DH, Smith JL. Biosynthesis of t-Butyl in Apratoxin A: Functional Analysis and Architecture of a PKS Loading Module. ACS Chem Biol 2018; 13:1640-1650. [PMID: 29701944 PMCID: PMC6003868 DOI: 10.1021/acschembio.8b00252] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The unusual feature of a t-butyl group is found in several marine-derived natural products including apratoxin A, a Sec61 inhibitor produced by the cyanobacterium Moorea bouillonii PNG 5-198. Here, we determine that the apratoxin A t-butyl group is formed as a pivaloyl acyl carrier protein (ACP) by AprA, the polyketide synthase (PKS) loading module of the apratoxin A biosynthetic pathway. AprA contains an inactive "pseudo" GCN5-related N-acetyltransferase domain (ΨGNAT) flanked by two methyltransferase domains (MT1 and MT2) that differ distinctly in sequence. Structural, biochemical, and precursor incorporation studies reveal that MT2 catalyzes unusually coupled decarboxylation and methylation reactions to transform dimethylmalonyl-ACP, the product of MT1, to pivaloyl-ACP. Further, pivaloyl-ACP synthesis is primed by the fatty acid synthase malonyl acyltransferase (FabD), which compensates for the ΨGNAT and provides the initial acyl-transfer step to form AprA malonyl-ACP. Additionally, images of AprA from negative stain electron microscopy reveal multiple conformations that may facilitate the individual catalytic steps of the multienzyme module.
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Affiliation(s)
- Meredith A Skiba
- Life Sciences Institute , University of Michigan , Ann Arbor , Michigan 48109 , United States
- Department of Biological Chemistry , University of Michigan , Ann Arbor Michigan 48109 , United States
| | - Andrew P Sikkema
- Life Sciences Institute , University of Michigan , Ann Arbor , Michigan 48109 , United States
- Department of Biological Chemistry , University of Michigan , Ann Arbor Michigan 48109 , United States
| | - Nathan A Moss
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California, San Diego , La Jolla , California 92093 , United States
| | - Andrew N Lowell
- Life Sciences Institute , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Min Su
- Life Sciences Institute , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Rebecca M Sturgis
- Life Sciences Institute , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California, San Diego , La Jolla , California 92093 , United States
| | - William H Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California, San Diego , La Jolla , California 92093 , United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California, San Diego , La Jolla , California 92093 , United States
| | - David H Sherman
- Life Sciences Institute , University of Michigan , Ann Arbor , Michigan 48109 , United States
- Department of Medicinal Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
- Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
- Department of Microbiology and Immunology , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Janet L Smith
- Life Sciences Institute , University of Michigan , Ann Arbor , Michigan 48109 , United States
- Department of Biological Chemistry , University of Michigan , Ann Arbor Michigan 48109 , United States
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35
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Fick RJ, Clay MC, Vander Lee L, Scheiner S, Al-Hashimi H, Trievel RC. Water-Mediated Carbon–Oxygen Hydrogen Bonding Facilitates S-Adenosylmethionine Recognition in the Reactivation Domain of Cobalamin-Dependent Methionine Synthase. Biochemistry 2018; 57:3733-3740. [DOI: 10.1021/acs.biochem.8b00375] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Robert J. Fick
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Mary C. Clay
- Department of Biochemistry, Duke University, Durham, North Carolina 27710, United States
| | - Lucas Vander Lee
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Hashim Al-Hashimi
- Department of Biochemistry, Duke University, Durham, North Carolina 27710, United States
| | - Raymond C. Trievel
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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36
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Wategaonkar S, Bhattacherjee A. N–H···S Interaction Continues To Be an Enigma: Experimental and Computational Investigations of Hydrogen-Bonded Complexes of Benzimidazole with Thioethers. J Phys Chem A 2018; 122:4313-4321. [DOI: 10.1021/acs.jpca.8b01943] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sanjay Wategaonkar
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India
| | - Aditi Bhattacherjee
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India
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37
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Diagouraga B, Clément JAJ, Duret L, Kadlec J, de Massy B, Baudat F. PRDM9 Methyltransferase Activity Is Essential for Meiotic DNA Double-Strand Break Formation at Its Binding Sites. Mol Cell 2018; 69:853-865.e6. [PMID: 29478809 DOI: 10.1016/j.molcel.2018.01.033] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 01/09/2018] [Accepted: 01/24/2018] [Indexed: 01/06/2023]
Abstract
The programmed formation of hundreds of DNA double-strand breaks (DSBs) is essential for proper meiosis and fertility. In mice and humans, the location of these breaks is determined by the meiosis-specific protein PRDM9, through the DNA-binding specificity of its zinc-finger domain. PRDM9 also has methyltransferase activity. Here, we show that this activity is required for H3K4me3 and H3K36me3 deposition and for DSB formation at PRDM9-binding sites. By analyzing mice that express two PRDM9 variants with distinct DNA-binding specificities, we show that each variant generates its own set of H3K4me3 marks independently from the other variant. Altogether, we reveal several basic principles of PRDM9-dependent DSB site determination, in which an excess of sites are designated through PRDM9 binding and subsequent histone methylation, from which a subset is selected for DSB formation.
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Affiliation(s)
| | | | - Laurent Duret
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villeurbanne, France
| | - Jan Kadlec
- Université Grenoble Alpes, CNRS, CEA, IBS, F-38000 Grenoble, France
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38
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Wilson PB, Williams IH. Computational Modeling of a Caged Methyl Cation: Structure, Energetics, and Vibrational Analysis. J Phys Chem A 2018; 122:1432-1438. [DOI: 10.1021/acs.jpca.7b11836] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Philippe B. Wilson
- Department
of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
- Leicester
School of Pharmacy, De Montfort University, The Gateway, Leicester LE1 9BH, United Kingdom
| | - Ian H. Williams
- Department
of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
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39
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Atomic structure of the eukaryotic intramembrane RAS methyltransferase ICMT. Nature 2018; 553:526-529. [PMID: 29342140 PMCID: PMC5785467 DOI: 10.1038/nature25439] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 12/07/2017] [Indexed: 11/08/2022]
Abstract
The maturation of RAS GTPases and approximately 200 other cellular CAAX proteins involves three enzymatic steps: addition of a farnesyl or geranylgeranyl prenyl lipid to the cysteine (C) in the C-terminal CAAX motif, proteolytic cleavage of the AAX residues and methylation of the exposed prenylcysteine residue at its terminal carboxylate. This final step is catalysed by isoprenylcysteine carboxyl methyltransferase (ICMT), a eukaryote-specific integral membrane enzyme that resides in the endoplasmic reticulum. ICMT is the only cellular enzyme that is known to methylate prenylcysteine substrates; methylation is important for the biological functions of these substrates, such as the membrane localization and subsequent activity of RAS, prelamin A and RAB. Inhibition of ICMT has potential for combating progeria and cancer. Here we present an X-ray structure of ICMT, in complex with its cofactor, an ordered lipid molecule and a monobody inhibitor, at 2.3 Å resolution. The active site spans cytosolic and membrane-exposed regions, indicating distinct entry routes for the cytosolic methyl donor, S-adenosyl-l-methionine, and for prenylcysteine substrates, which are associated with the endoplasmic reticulum membrane. The structure suggests how ICMT overcomes the topographical challenge and unfavourable energetics of bringing two reactants that have different cellular localizations together in a membrane environment-a relatively uncharacterized but defining feature of many integral membrane enzymes.
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40
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Moore KB, Sadeghian K, Sherrill CD, Ochsenfeld C, Schaefer HF. C-H···O Hydrogen Bonding. The Prototypical Methane-Formaldehyde System: A Critical Assessment. J Chem Theory Comput 2017; 13:5379-5395. [PMID: 29039941 DOI: 10.1021/acs.jctc.7b00753] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Distinguishing the functionality of C-H···O hydrogen bonds (HBs) remains challenging, because their properties are difficult to quantify reliably. Herein, we present a study of the model methane-formaldehyde complex (MFC). Six stationary points on the MFC potential energy surface (PES) were obtained at the CCSD(T)/ANO2 level. The CCSDT(Q)/CBS interaction energies of the conformers range from only -1.12 kcal mol-1 to -0.33 kcal mol-1, denoting a very flat PES. Notably, only the lowest energy stationary point (MFC1) corresponds to a genuine minimum, whereas all other stationary points-including the previously studied ideal case of ae(C-H···O) = 180°-exhibit some degree of freedom that leads to MFC1. Despite the flat PES, we clearly see that the HB properties of MFC1 align with those of the prototypical water dimer O-H···O HB. Each HB property generally becomes less prominent in the higher-energy conformers. Only the MFC1 conformer prominently exhibits (1) elongated C-H donor bonds, (2) attractive C-H···O═C interactions, (3) n(O) → σ*(C-H) hyperconjugation, (4) critical points in the electron density from Bader's method and from the noncovalent interactions method, (5) positively charged donor hydrogen, and (6) downfield NMR chemical shifts and nonzero 2J(CM-HM···OF) coupling constants. Based on this research, some issues merit further study. The flat PES hinders reliable determinations of the HB-induced shifts of the C-H stretches; a similarly difficult challenge is observed for the experiment. The role of charge transfer in HBs remains an intriguing open question, although our BLW and NBO computations suggest that it is relevant to the C-H···O HB geometries. These issues notwithstanding, the prominence of the HB properties in MFC1 serves as clear evidence that the MFC is predominantly bound by a C-H···O HB.
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Affiliation(s)
- Kevin B Moore
- Center for Computational Quantum Chemistry, University of Georgia , Athens, Georgia 30602, United States
| | - Keyarash Sadeghian
- Department of Chemistry, Ludwig-Maximilians University (LMU) , Munich D-81377, Germany
| | - C David Sherrill
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
| | - Christian Ochsenfeld
- Department of Chemistry, Ludwig-Maximilians University (LMU) , Munich D-81377, Germany
| | - Henry F Schaefer
- Center for Computational Quantum Chemistry, University of Georgia , Athens, Georgia 30602, United States
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41
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Backman LRF, Funk MA, Dawson CD, Drennan CL. New tricks for the glycyl radical enzyme family. Crit Rev Biochem Mol Biol 2017; 52:674-695. [PMID: 28901199 DOI: 10.1080/10409238.2017.1373741] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Glycyl radical enzymes (GREs) are important biological catalysts in both strict and facultative anaerobes, playing key roles both in the human microbiota and in the environment. GREs contain a backbone glycyl radical that is post-translationally installed, enabling radical-based mechanisms. GREs function in several metabolic pathways including mixed acid fermentation, ribonucleotide reduction and the anaerobic breakdown of the nutrient choline and the pollutant toluene. By generating a substrate-based radical species within the active site, GREs enable C-C, C-O and C-N bond breaking and formation steps that are otherwise challenging for nonradical enzymes. Identification of previously unknown family members from genomic data and the determination of structures of well-characterized GREs have expanded the scope of GRE-catalyzed reactions as well as defined key features that enable radical catalysis. Here, we review the structures and mechanisms of characterized GREs, classifying members into five categories. We consider the open questions about each of the five GRE classes and evaluate the tools available to interrogate uncharacterized GREs.
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Affiliation(s)
- Lindsey R F Backman
- a Department of Chemistry , Massachusetts Institute of Technology , Cambridge , MA , USA
| | - Michael A Funk
- a Department of Chemistry , Massachusetts Institute of Technology , Cambridge , MA , USA.,b Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , IL , USA
| | - Christopher D Dawson
- c Department of Biology , Massachusetts Institute of Technology , Cambridge , MA , USA
| | - Catherine L Drennan
- a Department of Chemistry , Massachusetts Institute of Technology , Cambridge , MA , USA.,c Department of Biology , Massachusetts Institute of Technology , Cambridge , MA , USA.,d Howard Hughes Medical Institute , Massachusetts Institute of Technology , Cambridge , MA , USA
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42
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Bratkowski M, Yang X, Liu X. Polycomb repressive complex 2 in an autoinhibited state. J Biol Chem 2017; 292:13323-13332. [PMID: 28607149 DOI: 10.1074/jbc.m117.787572] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 05/24/2017] [Indexed: 01/23/2023] Open
Abstract
Polycomb-group proteins control many fundamental biological processes, such as anatomical development in mammals and vernalization in plants. Polycomb repressive complex 2 (PRC2) is responsible for methylation of histone H3 lysine 27 (H3K27), and trimethylated H3K27 (H3K27me3) is implicated in epigenetic gene silencing. Recent genomic, biochemical, and structural data indicate that PRC2 is broadly conserved from yeast to human in many aspects. Here, we determined the crystal structure of an apo-PRC2 from the fungus Chaetomium thermophilum captured in a bona fide autoinhibited state, which represents a novel conformation of PRC2 associated with enzyme regulation in light of the basal and stimulated states that we reported previously. We found that binding by the cofactor S-adenosylmethionine mitigates this autoinhibited structural state. Using steady-state enzyme kinetics, we also demonstrated that disrupting the autoinhibition results in a vastly activated enzyme complex. Autoinhibition provides a novel structural platform that may enable control of PRC2 activity in response to diverse transcriptional states and chromatin contexts and set a ground state to allow PRC2 activation by other cellular mechanisms as well.
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Affiliation(s)
- Matthew Bratkowski
- From the Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Research, Department of Obstetrics and Gynecology, Department of Biophysics, UT Southwestern Medical Center, Dallas, Texas 75390
| | - Xin Yang
- From the Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Research, Department of Obstetrics and Gynecology, Department of Biophysics, UT Southwestern Medical Center, Dallas, Texas 75390
| | - Xin Liu
- From the Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Research, Department of Obstetrics and Gynecology, Department of Biophysics, UT Southwestern Medical Center, Dallas, Texas 75390
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43
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Qian P, Guo H, Wang L, Guo H. QM/MM Investigation of Substrate and Product Specificities of Suv4-20h2: How Does This Enzyme Generate Dimethylated H4K20 from Monomethylated Substrate? J Chem Theory Comput 2017; 13:2977-2986. [PMID: 28489369 DOI: 10.1021/acs.jctc.7b00069] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein lysine methyltransferases (PKMTs) catalyze the methylation of lysine residues on histone proteins in the regulation of chromatin structure and gene expression. In contrast to many other PKMTs for which unmodified lysine is the methylation target, the enzymes in the Suv4-20 family are able to generate dimethylated product (H4K20me2) based exclusively on the monomethylated H4K20 substrate (H4K20me1). The origin of such substrate/product specificity is still not clear. Here, molecular dynamics (MD) and free energy (potential of mean force) simulations are undertaken using quantum mechanical/molecular mechanical (QM/MM) potentials to understand the substrate/product specificities of Suv4-20h2, a member of the Suv4-20 family. The free energy barriers for mono-, di-, and trimethylation in Suv4-20h2 obtained from the simulations are found to be well correlated with the specificities observed experimentally with the allowed dimethylation based on the H4K20me1 substrate and prohibited monomethylation and trimethylation based on H4K20 and H4K20me2, respectively. It is demonstrated that the reason for the relatively efficient dimethylation is an effective transition state (TS) stabilization through strengthening the CH···O interactions as well as the presence of a cation-π interaction at the transition state. The simulations also show that the failures of Suv4-20h2 to catalyze monomethylation and trimethylation are due, respectively, to a less effective TS stabilization and inability of the reactant complex containing H4K20me2 to adopt a reactive (near attack) configuration for methyl transfer. The results suggest that care must be exercised in the prediction of the substrate specificity based only on the existence of near attack configurations in substrate complexes.
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Affiliation(s)
- Ping Qian
- Chemistry and Material Science Faculty, Shandong Agricultural University , Tai'an 271018, Shandong, Peoples Republic of China
| | - Haobo Guo
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Liang Wang
- Chemistry and Material Science Faculty, Shandong Agricultural University , Tai'an 271018, Shandong, Peoples Republic of China
| | - Hong Guo
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee , Knoxville, Tennessee 37996, United States.,UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37830, United States
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44
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Linscott JA, Kapilashrami K, Wang Z, Senevirathne C, Bothwell IR, Blum G, Luo M. Kinetic isotope effects reveal early transition state of protein lysine methyltransferase SET8. Proc Natl Acad Sci U S A 2016; 113:E8369-E8378. [PMID: 27940912 PMCID: PMC5206543 DOI: 10.1073/pnas.1609032114] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Protein lysine methyltransferases (PKMTs) catalyze the methylation of protein substrates, and their dysregulation has been linked to many diseases, including cancer. Accumulated evidence suggests that the reaction path of PKMT-catalyzed methylation consists of the formation of a cofactor(cosubstrate)-PKMT-substrate complex, lysine deprotonation through dynamic water channels, and a nucleophilic substitution (SN2) transition state for transmethylation. However, the molecular characters of the proposed process remain to be elucidated experimentally. Here we developed a matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) method and corresponding mathematic matrix to determine precisely the ratios of isotopically methylated peptides. This approach may be generally applicable for examining the kinetic isotope effects (KIEs) of posttranslational modifying enzymes. Protein lysine methyltransferase SET8 is the sole PKMT to monomethylate histone 4 lysine 20 (H4K20) and its function has been implicated in normal cell cycle progression and cancer metastasis. We therefore implemented the MS-based method to measure KIEs and binding isotope effects (BIEs) of the cofactor S-adenosyl-l-methionine (SAM) for SET8-catalyzed H4K20 monomethylation. A primary intrinsic 13C KIE of 1.04, an inverse intrinsic α-secondary CD3 KIE of 0.90, and a small but statistically significant inverse CD3 BIE of 0.96, in combination with computational modeling, revealed that SET8-catalyzed methylation proceeds through an early, asymmetrical SN2 transition state with the C-N and C-S distances of 2.35-2.40 Å and 2.00-2.05 Å, respectively. This transition state is further supported by the KIEs, BIEs, and steady-state kinetics with the SAM analog Se-adenosyl-l-selenomethionine (SeAM) as a cofactor surrogate. The distinct transition states between protein methyltransferases present the opportunity to design selective transition-state analog inhibitors.
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Affiliation(s)
- Joshua A Linscott
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Program of Pharmacology, Weill Graduate School of Medical Science, Cornell University, New York, NY 10021
| | - Kanishk Kapilashrami
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Zhen Wang
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Chamara Senevirathne
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Ian R Bothwell
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Gil Blum
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Minkui Luo
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065;
- Program of Pharmacology, Weill Graduate School of Medical Science, Cornell University, New York, NY 10021
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45
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Skiba MA, Sikkema AP, Fiers WD, Gerwick WH, Sherman DH, Aldrich CC, Smith JL. Domain Organization and Active Site Architecture of a Polyketide Synthase C-methyltransferase. ACS Chem Biol 2016; 11:3319-3327. [PMID: 27723289 PMCID: PMC5224524 DOI: 10.1021/acschembio.6b00759] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Polyketide metabolites produced by modular type I polyketide synthases (PKS) acquire their chemical diversity through the variety of catalytic domains within modules of the pathway. Methyltransferases are among the least characterized of the catalytic domains common to PKS systems. We determined the domain boundaries and characterized the activity of a PKS C-methyltransferase (C-MT) from the curacin A biosynthetic pathway. The C-MT catalyzes S-adenosylmethionine-dependent methyl transfer to the α-position of β-ketoacyl substrates linked to acyl carrier protein (ACP) or a small-molecule analog but does not act on β-hydroxyacyl substrates or malonyl-ACP. Key catalytic residues conserved in both bacterial and fungal PKS C-MTs were identified in a 2 Å crystal structure and validated biochemically. Analysis of the structure and the sequences bordering the C-MT provides insight into the positioning of this domain within complete PKS modules.
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Affiliation(s)
- Meredith A. Skiba
- Life Sciences Institute, University of Michigan, Ann Arbor, MI
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI
| | - Andrew P. Sikkema
- Life Sciences Institute, University of Michigan, Ann Arbor, MI
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI
| | - William D. Fiers
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN
| | - William H. Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA
- School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA
| | - David H. Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI
- Department of Chemistry, University of Michigan, Ann Arbor, MI
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI
| | | | - Janet L. Smith
- Life Sciences Institute, University of Michigan, Ann Arbor, MI
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI
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46
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Bodea S, Funk MA, Balskus EP, Drennan CL. Molecular Basis of C-N Bond Cleavage by the Glycyl Radical Enzyme Choline Trimethylamine-Lyase. Cell Chem Biol 2016; 23:1206-1216. [PMID: 27642068 DOI: 10.1016/j.chembiol.2016.07.020] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 07/07/2016] [Accepted: 07/25/2016] [Indexed: 01/16/2023]
Abstract
Deamination of choline catalyzed by the glycyl radical enzyme choline trimethylamine-lyase (CutC) has emerged as an important route for the production of trimethylamine, a microbial metabolite associated with both human disease and biological methane production. Here, we have determined five high-resolution X-ray structures of wild-type CutC and mechanistically informative mutants in the presence of choline. Within an unexpectedly polar active site, CutC orients choline through hydrogen bonding with a putative general base, and through close interactions between phenolic and carboxylate oxygen atoms of the protein scaffold and the polarized methyl groups of the trimethylammonium moiety. These structural data, along with biochemical analysis of active site mutants, support a mechanism that involves direct elimination of trimethylamine. This work broadens our understanding of radical-based enzyme catalysis and will aid in the rational design of inhibitors of bacterial trimethylamine production.
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Affiliation(s)
- Smaranda Bodea
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Michael A Funk
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts, Avenue 68-680, Cambridge, MA 02139, USA
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.
| | - Catherine L Drennan
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts, Avenue 68-680, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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47
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Schapira M. Chemical Inhibition of Protein Methyltransferases. Cell Chem Biol 2016; 23:1067-1076. [PMID: 27569753 DOI: 10.1016/j.chembiol.2016.07.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 07/08/2016] [Accepted: 07/15/2016] [Indexed: 01/16/2023]
Abstract
Protein methyltransferases (PMTs) participate in the epigenetic control of cell fate and other signaling pathways that are deregulated in disease, and the first PMT inhibitors have entered clinical trials in oncology. This review discusses structural studies that recently uncovered the mode of action of compounds in the clinic, as well as challenges and opportunities in the development of PMT inhibitors. It examines inhibitors that compete with the highly polar cofactor but preserve cell penetrance, and allosteric modes of inhibition. Vectors of optimization at the substrate-binding site and the potential of fragment screening approaches are discussed. Finally, the review presents strategies focused on targeting non-catalytic domains of PMTs or scaffolding subunits of chromatin complexes. Overall, although targeting PMTs remains a challenge, recent successes in the field are diverse and encouraging.
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Affiliation(s)
- Matthieu Schapira
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S 1A8, Canada.
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48
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Zhang J, Klinman JP. Convergent Mechanistic Features between the Structurally Diverse N- and O-Methyltransferases: Glycine N-Methyltransferase and Catechol O-Methyltransferase. J Am Chem Soc 2016; 138:9158-65. [PMID: 27355841 PMCID: PMC5270642 DOI: 10.1021/jacs.6b03462] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
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Although an enormous and still growing
number of biologically diverse
methyltransferases have been reported and identified, a comprehensive
understanding of the enzymatic methyl transfer mechanism is still
lacking. Glycine N-methyltransferase (GNMT), a member
of the family that acts on small metabolites as the substrate, catalyzes
methyl transfer from S-adenosyl-l-methionine
(AdoMet) to glycine to form S-adenosyl-l-homocysteine and sarcosine. We report primary carbon (12C/14C) and secondary (1H3/3H3) kinetic isotope effects at the transferred methyl
group, together with 1H3/3H3 binding isotope effects for wild-type GNMT and a series of Tyr21
mutants. The data implicate a compaction effect in the methyl transfer
step that is conferred by the protein structure. Furthermore, a remarkable
similarity of properties is observed between GNMT and catechol O-methyltransferase, despite significant differences between
these enzymes with regard to their active site structures and catalyzed
reactions. We attribute these results to a catalytically relevant
reduction in the methyl donor–acceptor distance that is dependent
on a tyrosine side chain positioned behind the methyl-bearing sulfur
of AdoMet.
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Affiliation(s)
- Jianyu Zhang
- Department of Chemistry, ‡Department of Molecular and Cell Biology, and §California Institute for Quantitative Biosciences, University of California , Berkeley, California 94720, United States
| | - Judith P Klinman
- Department of Chemistry, ‡Department of Molecular and Cell Biology, and §California Institute for Quantitative Biosciences, University of California , Berkeley, California 94720, United States
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49
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Poulin MB, Schneck JL, Matico RE, Hou W, McDevitt PJ, Holbert M, Schramm VL. Nucleosome Binding Alters the Substrate Bonding Environment of Histone H3 Lysine 36 Methyltransferase NSD2. J Am Chem Soc 2016; 138:6699-702. [PMID: 27183271 PMCID: PMC6702673 DOI: 10.1021/jacs.6b01612] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Nuclear receptor-binding SET domain protein 2 (NSD2) is a histone H3 lysine 36 (H3K36)-specific methyltransferase enzyme that is overexpressed in a number of cancers, including multiple myeloma. NSD2 binds to S-adenosyl-l-methionine (SAM) and nucleosome substrates to catalyze the transfer of a methyl group from SAM to the ε-amino group of histone H3K36. Equilibrium binding isotope effects and density functional theory calculations indicate that the SAM methyl group is sterically constrained in complex with NSD2, and that this steric constraint is released upon nucleosome binding. Together, these results show that nucleosome binding to NSD2 induces a significant change in the chemical environment of enzyme-bound SAM.
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Affiliation(s)
- Myles B. Poulin
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Jessica L. Schneck
- Biological Sciences, Platform Technology and Science, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Rosalie E. Matico
- Biological Sciences, Platform Technology and Science, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Wangfang Hou
- Biological Sciences, Platform Technology and Science, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Patrick J. McDevitt
- Biological Sciences, Platform Technology and Science, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Marc Holbert
- Biological Sciences, Platform Technology and Science, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Vern L. Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
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50
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Blazer LL, Lima-Fernandes E, Gibson E, Eram MS, Loppnau P, Arrowsmith CH, Schapira M, Vedadi M. PR Domain-containing Protein 7 (PRDM7) Is a Histone 3 Lysine 4 Trimethyltransferase. J Biol Chem 2016; 291:13509-19. [PMID: 27129774 PMCID: PMC4919437 DOI: 10.1074/jbc.m116.721472] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Indexed: 12/22/2022] Open
Abstract
PR domain-containing protein 7 (PRDM7) is a primate-specific histone methyltransferase that is the result of a recent gene duplication of PRDM9. The two proteins are highly homologous, especially in the catalytic PR/SET domain, where they differ by only three amino acid residues. Here we report that PRDM7 is an efficient methyltransferase that selectively catalyzes the trimethylation of H3 lysine 4 (H3K4) both in vitro and in cells. Through selective mutagenesis we have dissected the functional roles of each of the three divergent residues between the PR domains of PRDM7 and PRDM9. These studies indicate that after a single serine to tyrosine mutation at residue 357 (S357Y), PRDM7 regains the substrate specificities and catalytic activities similar to its evolutionary predecessor, including the ability to efficiently methylate H3K36.
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Affiliation(s)
- Levi L Blazer
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7
| | - Evelyne Lima-Fernandes
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7
| | - Elisa Gibson
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7
| | - Mohammad S Eram
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7
| | - Peter Loppnau
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7
| | - Cheryl H Arrowsmith
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, the Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 2M9, and
| | - Matthieu Schapira
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, the Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Masoud Vedadi
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, the Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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