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Shekhar S, Meena R, Lal J, Yadav M, Kant R, Reddy DN. Stabilizing Bifurcated Hydrogen Bond in 8-Aminoquinoline Appended Peptides. Chem Asian J 2024:e202400248. [PMID: 38701035 DOI: 10.1002/asia.202400248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 04/21/2024] [Accepted: 05/03/2024] [Indexed: 05/05/2024]
Abstract
The hydrogen bonding interaction between an amide N-H and the amide N of the preceding residue is prevalent in proline-containing proteins and peptides. However, the N-H⋅⋅⋅N hydrogen bonding interaction is rare in non-prolyl natural peptides due to restricted dihedral angles. Herein, we stabilize this type of interaction in 8-aminoquinoline appended non-prolyl peptides through bifurcated N⋅⋅⋅H⋅⋅⋅N hydrogen bond. The 8-aminoquinoline-incorporated model peptides 2 a-i were designed, synthesized, and the crystal structures of 2 a-c and 2 i were solved. Analysis of crystal data reveals that the amide N-H of aminoquinoline is involved in bifurcated hydrogen bonding interaction with the nitrogen of the preceding amino acid residue and the nitrogen in quinoline. Analysis of crystal packing, Hirshfeld surface and fingerprint plots confirms that the intermolecular O⋅⋅⋅H contacts significantly contribute to stabilizing bifurcated N⋅⋅⋅H⋅⋅⋅N hydrogen bonding interaction. Furthermore, NMR experiments and CD spectroscopy were conducted to examine the preferred conformation in solution, and the data corroborate with the crystal structure conformation.
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Affiliation(s)
- Shashank Shekhar
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, 226031, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), 201002, Ghaziabad, India
| | - Rachana Meena
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, 226031, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), 201002, Ghaziabad, India
| | - Jhajan Lal
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, 226031, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), 201002, Ghaziabad, India
| | - Mukul Yadav
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, 226031, Lucknow, India
| | - Ruchir Kant
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, 226031, Lucknow, India
| | - Damodara N Reddy
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, 226031, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), 201002, Ghaziabad, India
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2
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Talukdar PD, Chatterji U. Transcriptional co-activators: emerging roles in signaling pathways and potential therapeutic targets for diseases. Signal Transduct Target Ther 2023; 8:427. [PMID: 37953273 PMCID: PMC10641101 DOI: 10.1038/s41392-023-01651-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/27/2023] [Accepted: 09/10/2023] [Indexed: 11/14/2023] Open
Abstract
Specific cell states in metazoans are established by the symphony of gene expression programs that necessitate intricate synergic interactions between transcription factors and the co-activators. Deregulation of these regulatory molecules is associated with cell state transitions, which in turn is accountable for diverse maladies, including developmental disorders, metabolic disorders, and most significantly, cancer. A decade back most transcription factors, the key enablers of disease development, were historically viewed as 'undruggable'; however, in the intervening years, a wealth of literature validated that they can be targeted indirectly through transcriptional co-activators, their confederates in various physiological and molecular processes. These co-activators, along with transcription factors, have the ability to initiate and modulate transcription of diverse genes necessary for normal physiological functions, whereby, deregulation of such interactions may foster tissue-specific disease phenotype. Hence, it is essential to analyze how these co-activators modulate specific multilateral processes in coordination with other factors. The proposed review attempts to elaborate an in-depth account of the transcription co-activators, their involvement in transcription regulation, and context-specific contributions to pathophysiological conditions. This review also addresses an issue that has not been dealt with in a comprehensive manner and hopes to direct attention towards future research that will encompass patient-friendly therapeutic strategies, where drugs targeting co-activators will have enhanced benefits and reduced side effects. Additional insights into currently available therapeutic interventions and the associated constraints will eventually reveal multitudes of advanced therapeutic targets aiming for disease amelioration and good patient prognosis.
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Affiliation(s)
- Priyanka Dey Talukdar
- Cancer Research Laboratory, Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, West Bengal, India
| | - Urmi Chatterji
- Cancer Research Laboratory, Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, West Bengal, India.
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3
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Hwang D, Wrigley LM, Lee M, Sobolewski AL, Domcke W, Schlenker CW. Local Hydrogen Bonding Determines Branching Pathways in Intermolecular Heptazine Photochemistry. J Phys Chem B 2023. [PMID: 37471476 DOI: 10.1021/acs.jpcb.3c01397] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
Heptazine is the molecular core of the widely studied photocatalyst carbon nitride. By analyzing the excited-state intermolecular proton-coupled electron-transfer (PCET) reaction between a heptazine derivative and a hydrogen-atom donor substrate, we are able to spectroscopically identify the resultant heptazinyl reactive radical species on a picosecond time scale. We provide detailed spectroscopic characterization of the tri-anisole heptazine:4-methoxyphenol hydrogen-bonded intermolecular complex (TAHz:MeOPhOH), using femtosecond transient absorption spectroscopy and global analysis, to reveal distinct product absorption signatures at ∼520, 1250, and 1600 nm. We assign these product peaks to the hydrogenated TAHz radical (TAHzH•) based on control experiments utilizing 1,4-dimethoxybenzene (DMB), which initiates electron transfer without concomitant proton transfer, i.e., no excited-state PCET. Additional control experiments with radical quenchers, protonation agents, and UV-vis-NIR spectroelectrochemistry also corroborate our product peak assignments. These spectral assignments allowed us to monitor the influence of the local hydrogen-bonding environment on the resulting evolution of photochemical products from excited-state PCET of heptazines. We observe that the preassociation of heptazine with the substrate in solution is extremely sensitive to the hydrogen-bond-accepting character of the solvent. This sensitivity directly influences which product signatures we detect with time-resolved spectroscopy. The spectral signature of the TAHzH• radical assigned in this work will facilitate future in-depth analysis of heptazine and carbon nitride photochemistry. Our results may also be utilized for designing improved PCET-based photochemical systems that will require precise control over local molecular environments. Examples include applications such as preparative synthesis involving organic photoredox catalysis, on-site solar water purification, as well as photocatalytic water splitting and artificial photosynthesis.
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Affiliation(s)
- Doyk Hwang
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Liam M Wrigley
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Micah Lee
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | | | - Wolfgang Domcke
- Department of Chemistry, Technical University of Munich, D-85747 Garching, Germany
| | - Cody W Schlenker
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, Washington 98195-1652, United States
- Clean Energy Institute, University of Washington, Seattle, Washington 98195-1653, United States
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4
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Roy A, Niharika, Chakraborty S, Mishra J, Singh SP, Patra SK. Mechanistic aspects of reversible methylation modifications of arginine and lysine of nuclear histones and their roles in human colon cancer. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 197:261-302. [PMID: 37019596 DOI: 10.1016/bs.pmbts.2023.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Developmental proceedings and maintenance of cellular homeostasis are regulated by the precise orchestration of a series of epigenetic events that eventually control gene expression. DNA methylation and post-translational modifications (PTMs) of histones are well-characterized epigenetic events responsible for fine-tuning gene expression. PTMs of histones bear molecular logic of gene expression at chromosomal territory and have become a fascinating field of epigenetics. Nowadays, reversible methylation on histone arginine and lysine is gaining increasing attention as a significant PTM related to reorganizing local nucleosomal structure, chromatin dynamics, and transcriptional regulation. It is now well-accepted and reported that histone marks play crucial roles in colon cancer initiation and progression by encouraging abnormal epigenomic reprogramming. It is becoming increasingly clear that multiple PTM marks at the N-terminal tails of the core histones cross-talk with one another to intricately regulate DNA-templated biological processes such as replication, transcription, recombination, and damage repair in several malignancies, including colon cancer. These functional cross-talks provide an additional layer of message, which spatiotemporally fine-tunes the overall gene expression regulation. Nowadays, it is evident that several PTMs instigate colon cancer development. How colon cancer-specific PTM patterns or codes are generated and how they affect downstream molecular events are uncovered to some extent. Future studies would address more about epigenetic communication, and the relationship between histone modification marks to define cellular functions in depth. This chapter will comprehensively highlight the importance of histone arginine and lysine-based methylation modifications and their functional cross-talk with other histone marks from the perspective of colon cancer development.
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Lian T, Wang X, Li S, Jiang H, Zhang C, Wang H, Jiang L. Comparative Transcriptome Analysis Reveals Mechanisms of Folate Accumulation in Maize Grains. Int J Mol Sci 2022; 23:ijms23031708. [PMID: 35163628 PMCID: PMC8836222 DOI: 10.3390/ijms23031708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 02/05/2023] Open
Abstract
Previously, the complexity of folate accumulation in the early stages of maize kernel development has been reported, but the mechanisms of folate accumulation are unclear. Two maize inbred lines, DAN3130 and JI63, with different patterns of folate accumulation and different total folate contents in mature kernels were used to investigate the transcriptional regulation of folate metabolism during late stages of kernel formation by comparative transcriptome analysis. The folate accumulation during DAP 24 to mature kernels could be controlled by circumjacent pathways of folate biosynthesis, such as pyruvate metabolism, glutamate metabolism, and serine/glycine metabolism. In addition, the folate variation between these two inbred lines was related to those genes among folate metabolism, such as genes in the pteridine branch, para-aminobenzoate branch, serine/tetrahydrofolate (THF)/5-methyltetrahydrofolate cycle, and the conversion of THF monoglutamate to THF polyglutamate. The findings provided insight into folate accumulation mechanisms during maize kernel formation to promote folate biofortification.
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Affiliation(s)
- Tong Lian
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (T.L.); (S.L.); (C.Z.)
- Plant Genetics, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium
- Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya 572000, China
| | - Xuxia Wang
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (X.W.); (H.J.)
| | - Sha Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (T.L.); (S.L.); (C.Z.)
| | - Haiyang Jiang
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (X.W.); (H.J.)
| | - Chunyi Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (T.L.); (S.L.); (C.Z.)
- Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya 572000, China
| | - Huan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (T.L.); (S.L.); (C.Z.)
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (X.W.); (H.J.)
- National Agricultural Science and Technology Center, Chengdu 610213, China
- Correspondence: (H.W.); (L.J.)
| | - Ling Jiang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (T.L.); (S.L.); (C.Z.)
- Correspondence: (H.W.); (L.J.)
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6
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Chen JR, Ke TX, Frey PA, Ke SC. Electron Spin Echo Envelope Modulation Spectroscopy Reveals How Adenosylcobalamin-Dependent Lysine 5,6-Aminomutase Positions the Radical Pair Intermediates and Modulates Their Stabilities for Efficient Catalysis. ACS Catal 2021. [DOI: 10.1021/acscatal.1c03182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jun-Ru Chen
- Physics Department, National Dong Hwa University, Hualien 974301, Taiwan
| | - Ting-Xi Ke
- Physics Department, National Dong Hwa University, Hualien 974301, Taiwan
| | - Perry A. Frey
- Department of Biochemistry, University of Wisconsin−Madison, Madison, Wisconsin 53726, United States
| | - Shyue-Chu Ke
- Physics Department, National Dong Hwa University, Hualien 974301, Taiwan
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7
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Lim D, Wen X, Seebeck FP. Selenoimidazolium Salts as Supramolecular Reagents for Protein Alkylation. Chembiochem 2020; 21:3515-3520. [DOI: 10.1002/cbic.202000557] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Indexed: 12/15/2022]
Affiliation(s)
- David Lim
- Department of Chemistry University of Basel Mattenstrasse 24a Basel 4002 Switzerland
| | - Xiaojin Wen
- Department of Chemistry University of Basel Mattenstrasse 24a Basel 4002 Switzerland
| | - Florian P. Seebeck
- Department of Chemistry University of Basel Mattenstrasse 24a Basel 4002 Switzerland
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8
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Mordhorst S, Andexer JN. Round, round we go - strategies for enzymatic cofactor regeneration. Nat Prod Rep 2020; 37:1316-1333. [PMID: 32582886 DOI: 10.1039/d0np00004c] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Covering: up to the beginning of 2020Enzymes depending on cofactors are essential in many biosynthetic pathways of natural products. They are often involved in key steps: catalytic conversions that are difficult to achieve purely with synthetic organic chemistry. Hence, cofactor-dependent enzymes have great potential for biocatalysis, on the condition that a corresponding cofactor regeneration system is available. For some cofactors, these regeneration systems require multiple steps; such complex enzyme cascades/multi-enzyme systems are (still) challenging for in vitro biocatalysis. Further, artificial cofactor analogues have been synthesised that are more stable, show an altered reaction range, or act as inhibitors. The development of bio-orthogonal systems that can be used for the production of modified natural products in vivo is an ongoing challenge. In light of the recent progress in this field, this review aims to provide an overview of general strategies involving enzyme cofactors, cofactor analogues, and regeneration systems; highlighting the current possibilities for application of enzymes using some of the most common cofactors.
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Affiliation(s)
- Silja Mordhorst
- Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
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9
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Khumaeni A, Budi WS, Wardaya AY, Niki H, Kurihara K, Kagawa K. Emission Characteristics of Hydrogen and Carbon in Various Ambient Gases using Pulsed-CO2 Laser-Induced Breakdown Spectroscopy. CURR ANAL CHEM 2020. [DOI: 10.2174/1573411014666181115121139] [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:
Hydrogen (H) and Carbon (C) are major elements that occur in various materials,
including organic matter. The identification and analysis of C and H are necessary for several
fields. LIBS is an excellent method for such analysis because it is rapid, and can be conducted remotely.
The technique has been employed for the analysis of H in zircaloy metals. However, few
studies on the emission characteristics of H and C in various gases have been undertaken because of
the difficulty of identifying H and C using standard LIBS techniques. In this work, the emission
characteristics of H and C were studied using pulsed CO2 LIBS. H and C elements were obtained
from ethanol vapor. Various gas environments were employed, including Nitrogen (N2), Argon (Ar),
and Helium (He) gases, in order to study the stability of the laser-induced plasma, the plasma lifetime,
and the excitation mechanisms of H and C.
Methods:
The LIBS system used in this work consisted of a pulsed TEA CO2 laser (Shibuya SQ
2000), pulse generator, and optical multichannel analyzer. In this work, the laser with a wavelength
of 10.6 µm, pulse duration of 200 ns, and pulse energy of 3 J, was used as the irradiation source. The
laser energy used was 1.5 J. The laser was irradiated, and focused, using a 200 mm zinc selenide
(ZnSe) lens, onto a metal surface in order to initiate and induce a luminous plasma. The sample used
in this study was ethanol vapor, obtained from ethanol (99.5%, Merck). For this purpose, 10 mL ethanol
was poured into a glass beaker, and this was placed into a closed chamber that could be evacuated
by ambient gases including N2, Ar, and He gases.
Results:
Identification of H emission line has been successfully carried out using this present technique
demonstrated in various gases including N2, Ar, and He. From the results, it was observed that
in N2 gas, the Hα I 656.3 nm emission line was clearly expressed, with a wide, full-width halfmaximum,
and quite a low emission intensity.
Conclusion:
The emission characteristics of H and C in laser-induced plasma, produced in various
ambient gases, including N2, Ar, and He, were studied. The emission spectra of Hα and Hβ were expressed
clearly, with high intensity and low background emission, in He, while they were broad and
had high background emissions in N2 and Ar. Based on the time-resolved emissions, the Hα emission
had a longer lifetime in Ar and He. It was assumed that the metastable atoms of Arand He were predominant
in the excitation process of H and C. The characteristics of the H and C emissions in various
gases are important in selecting a suitable ambient gas for the study of light atomic emission in
the medical field, which mostly deals with organic materials containing H, C, and oxygen.
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Affiliation(s)
- Ali Khumaeni
- Department of Physics, Diponegoro University, Tembalang, Semarang 50275, Indonesia
| | - Wahyu S. Budi
- Department of Physics, Diponegoro University, Tembalang, Semarang 50275, Indonesia
| | - Asep Y. Wardaya
- Department of Physics, Diponegoro University, Tembalang, Semarang 50275, Indonesia
| | - Hideaki Niki
- Graduate School of Nuclear Power and Engineering, University of Fukui, Fukui 910-8507, Japan
| | - Kazuyoshi Kurihara
- Department of Physics, University of Fukui, Fukui 910-8507, Japan; 4Fukui Science Academy, Fukui, Japan
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Zhu K, Du D, Yang R, Tao H, Zhang H. Identification and Assessments of Novel and Potent Small-Molecule Inhibitors of EED-EZH2 Interaction of Polycomb Repressive Complex 2 by Computational Methods and Biological Evaluations. Chem Pharm Bull (Tokyo) 2019; 68:58-63. [PMID: 31685780 DOI: 10.1248/cpb.c19-00550] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Polycomb repressive complex 2 (PRC2) is an attractive drug target for anti-cancer treatment. Among the three core subunits (EZH2, EED and SUZ12) of PRC2, EZH2 is the catalytic subunit that methylates histone H3 lysine 27 (H3K27), while EED is the regulatory subunit. Besides the small-molecule inhibitors of EZH2, those targeting the protein-protein interaction (PPI) between EZH2 and EED have also been reported. Here, for the first time, we have identified the key residues that contributed most to the EED-EZH2 binding affinity by molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) calculations based on the 200 ns molecular dynamics simulation. Moreover, we report the identification of two novel and potent small-molecule inhibitors (35 and 49) of EZH2-EED interaction (bottom interaction surface) by virtual screening and biological evaluations. Binding modes of the two identified molecules with EED were probed by molecular docking. Additionally, 35 and 49 displayed cellular antiproliferative activity against diffuse large B-cell lymphoma (DLBCL) cancer cell line Toledo whose cell growth was driven by aberrant PRC2 activity. Our findings have provided structural insights for the design of novel EZH2-EED interaction inhibitors to regulate the activity of PRC2 complex.
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Affiliation(s)
- Kongkai Zhu
- School of Biological Science and Technology, University of Jinan
| | - Daohai Du
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences
| | - Rui Yang
- School of Biological Science and Technology, University of Jinan
| | - Hongrui Tao
- School of Biological Science and Technology, University of Jinan
| | - Hua Zhang
- School of Biological Science and Technology, University of Jinan
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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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12
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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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13
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Wang Y, Hu W, Yuan Y. Protein Arginine Methyltransferase 5 (PRMT5) as an Anticancer Target and Its Inhibitor Discovery. J Med Chem 2018; 61:9429-9441. [PMID: 29870258 DOI: 10.1021/acs.jmedchem.8b00598] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
PRMT5 is a major enzyme responsible for symmetric dimethylation of arginine residues on both histone and non-histone proteins, regulating many biological pathways in mammalian cells. PRMT5 has been suggested as a therapeutic target in a variety of diseases including infectious disease, heart disease, and cancer. Many PRMT5 inhibitors have been discovered in the past 5 years, and one entered clinical trial in 2015 for the treatment of solid tumor and mantle cell lymphoma (MCL). The aim of this review is to summarize the current understanding of the roles of PRMT5 in cancer and the discovery of PRMT5 enzymatic inhibitors. By reviewing the structure-activity relationship (SAR) of known inhibitors of PRMT5, we hope to provide guidance for future drug designs and inhibitor optimization. Opportunities and limitations of PRMT5 inhibitors for the treatment of cancer are also discussed.
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Affiliation(s)
- Yuanxiang Wang
- School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou 510006 , China
| | - Wenhao Hu
- School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou 510006 , China
| | - Yanqiu Yuan
- School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou 510006 , China
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14
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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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15
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Orabi EA, Lamoureux G. Cation-π Interactions between Quaternary Ammonium Ions and Amino Acid Aromatic Groups in Aqueous Solution. J Phys Chem B 2018; 122:2251-2260. [PMID: 29397727 DOI: 10.1021/acs.jpcb.7b11983] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cation-π interactions play important roles in the stabilization of protein structures and protein-ligand complexes. They contribute to the binding of quaternary ammonium ligands (mainly RNH3+ and RN(CH3)3+) to various protein receptors and are likely involved in the blockage of potassium channels by tetramethylammonium (TMA+) and tetraethylammonium (TEA+). Polarizable molecular models are calibrated for NH4+, TMA+, and TEA+ interacting with benzene, toluene, 4-methylphenol, and 3-methylindole (representing aromatic amino acid side chains) based on the ab initio MP2(full)/6-311++G(d,p) properties of the complexes. Whereas the gas-phase affinity of the ions with a given aromatic follows the trend NH4+ > TMA+ > TEA+, molecular dynamics simulations using the polarizable models show a reverse trend in water, likely due to a contribution from the hydrophobic effect. This reversed trend follows the solubility of aromatic hydrocarbons in quaternary ammonium salt solutions, which suggests a role for cation-π interactions in the salting-in of aromatic compounds in solution. Simulations in water show that the complexes possess binding free energies ranging from -1.3 to -3.3 kcal/mol (compared to gas-phase binding energies between -8.5 and -25.0 kcal/mol). Interestingly, whereas the most stable complexes involve TEA+ (the largest ion), the most stable solvent-separated complexes involve TMA+ (the intermediate-size ion).
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Affiliation(s)
- Esam A Orabi
- Department of Chemistry and Biochemistry and Centre for Research in Molecular Modeling (CERMM), Concordia University , 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada
| | - Guillaume Lamoureux
- Department of Chemistry and Biochemistry and Centre for Research in Molecular Modeling (CERMM), Concordia University , 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada
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16
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Solis-Calero C, Zanatta G, Pessoa CDÓ, Carvalho HF, Freire VN. Explaining urokinase type plasminogen activator inhibition by amino-5-hydroxybenzimidazole and two naphthamidine-based compounds through quantum biochemistry. Phys Chem Chem Phys 2018; 20:22818-22830. [DOI: 10.1039/c8cp04315a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Urokinase plasminogen activator (uPA) is a biomarker and therapeutic target for several cancer types whose inhibition has been shown to slow tumor growth and metastasis.
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Affiliation(s)
- Christian Solis-Calero
- Department of Structural and Functional Biology
- State University of Campinas
- 13083-863 Campinas
- Brazil
| | - Geancarlo Zanatta
- Department of Physics
- Federal University of Ceará
- 60455-760 Fortaleza
- Brazil
| | - Claudia do Ó Pessoa
- Department of Physiology and Pharmacology
- Federal University of Ceará
- 60430-270 Fortaleza
- Brazil
| | - Hernandes F. Carvalho
- Department of Structural and Functional Biology
- State University of Campinas
- 13083-863 Campinas
- Brazil
| | - Valder N. Freire
- Department of Physics
- Federal University of Ceará
- 60455-760 Fortaleza
- Brazil
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17
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Ranasinghe C, Guo Q, Sapienza PJ, Lee AL, Quinn DM, Cheatum CM, Kohen A. Protein Mass Effects on Formate Dehydrogenase. J Am Chem Soc 2017; 139:17405-17413. [PMID: 29083897 PMCID: PMC5800309 DOI: 10.1021/jacs.7b08359] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Isotopically labeled enzymes (denoted as "heavy" or "Born-Oppenheimer" enzymes) have been used to test the role of protein dynamics in catalysis. The original idea was that the protein's higher mass would reduce the frequency of its normal-modes without altering its electrostatics. Heavy enzymes have been used to test if the vibrations in the native enzyme are coupled to the chemistry it catalyzes, and different studies have resulted in ambiguous findings. Here the temperature-dependence of intrinsic kinetic isotope effects of the enzyme formate dehydrogenase is used to examine the distribution of H-donor to H-acceptor distance as a function of the protein's mass. The protein dynamics are altered in the heavy enzyme to diminish motions that determine the transition state sampling in the native enzyme, in accordance with a Born-Oppenheimer-like effect on bond activation. Findings of this work suggest components related to fast frequencies that can be explained by Born-Oppenheimer enzyme hypothesis (vibrational) and also slower time scale events that are non-Born-Oppenheimer in nature (electrostatic), based on evaluations of protein mass dependence of donor-acceptor distance and forward commitment to catalysis along with steady state and single turnover measurements. Together, the findings suggest that the mass modulation affected both local, fast, protein vibrations associated with the catalyzed chemistry and the protein's macromolecular electrostatics at slower time scales; that is, both Born-Oppenheimer and non-Born-Oppenheimer effects are observed. Comparison to previous studies leads to the conclusion that isotopic labeling of the protein may have different effects on different systems, however, making heavy enzyme studies a very exciting technique for exploring the dynamics link to catalysis in proteins.
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Affiliation(s)
- Chethya Ranasinghe
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1727, USA
| | - Qi Guo
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1727, USA
| | - Paul J. Sapienza
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Andrew L. Lee
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Daniel M. Quinn
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1727, USA
| | | | - Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1727, USA
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18
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Lafreniere MA, Desrochers GF, Mekbib K, Pezacki JP. An affinity-based probe for methyltransferase enzymes based on sinefungin. CAN J CHEM 2017. [DOI: 10.1139/cjc-2017-0168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Epigenetics control numerous cellular processes such as gene transcription, signal transduction, and protein stabilization. An understanding of epigenetic mechanisms can lead to the development of therapeutic agents for various diseases. Herein, we report the design and synthesis of a sinefungin affinity-probe (BpyneSF) that targets methyltranferase enzymes and proteins involved in recognition of methylation. This probe contains a bioorthogonal alkyne residue for conjugation using the copper-catalyzed azide–alkyne cycloaddition and a photoactivatable crosslinker group for covalent attachment of the probe to its proteomic targets. We investigate the efficiency and selectivity of the probe to inhibit and label methyltransferase enzymes, and we demonstrate, through in-gel fluorescence, on-bead digestion, and tandem mass spectrometry, that BpyneSF can label methyltransferase SETD2 and reader proteins in vitro. These results establish the utility of BpyneSF as a tool for affinity-based protein profiling in complex biological environments.
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Affiliation(s)
- Matthew A. Lafreniere
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie Street, Ottawa, ON K1N 6N5, Canada
| | - Geneviève F. Desrochers
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie Street, Ottawa, ON K1N 6N5, Canada
| | - Kedous Mekbib
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie Street, Ottawa, ON K1N 6N5, Canada
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie Street, Ottawa, ON K1N 6N5, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
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19
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Shi Y, Wang XX, Zhuang YW, Jiang Y, Melcher K, Xu HE. Structure of the PRC2 complex and application to drug discovery. Acta Pharmacol Sin 2017; 38:963-976. [PMID: 28414199 PMCID: PMC5519257 DOI: 10.1038/aps.2017.7] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 01/10/2017] [Indexed: 02/07/2023] Open
Abstract
The polycomb repressive complexes 2 (PRC2) complex catalyzes tri-methylation of histone H3 lysine 27 (H3K27), a repressive chromatin marker associated with gene silencing. Overexpression and mutations of PRC2 are found in a wide variety of cancers, making the catalytic activity of PRC2 an important target of cancer therapy. This review highlights recent structural breakthroughs of the human PRC2 complex bound to the H3K27 peptide and a small molecule inhibitor, which provide critically needed insight into PRC2-targeted drug discovery.
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Affiliation(s)
- Yi Shi
- Key Laboratory of Receptor Research, VARI-SIMM Center, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xiao-xi Wang
- Key Laboratory of Receptor Research, VARI-SIMM Center, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - You-wen Zhuang
- Key Laboratory of Receptor Research, VARI-SIMM Center, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yi Jiang
- Key Laboratory of Receptor Research, VARI-SIMM Center, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Karsten Melcher
- Laboratory of Structural Sciences, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - H Eric Xu
- Key Laboratory of Receptor Research, VARI-SIMM Center, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- Laboratory of Structural Sciences, Van Andel Research Institute, Grand Rapids, MI 49503, USA
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20
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Sadler JC, Chung CWH, Mosley JE, Burley GA, Humphreys LD. Structural and Functional Basis of C-Methylation of Coumarin Scaffolds by NovO. ACS Chem Biol 2017; 12:374-379. [PMID: 28068060 DOI: 10.1021/acschembio.6b01053] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
C-methylation of aromatic small molecules by C-methyltransferases (C-MTs) is an important biological transformation that involves C-C bond formation using S-adenosyl-l-methionine (SAM) as the methyl donor. Here, two advances in the mechanistic understanding of C-methylation of the 8-position of coumarin substrates catalyzed by the C-MT NovO from Streptomyces spheroides are described. First, a crystal structure of NovO reveals the Arg116-Asn117 and His120-Arg121 motifs are essential for coumarin substrate binding. Second, the active-site His120 is responsible for deprotonation of the phenolic 7-hydroxyl group on the coumarin substrate, activating the rate-determining methyl transfer step from SAM. This work expands our mechanistic knowledge of C-MTs, which could be used in the downstream development of engineered biocatalysts for small molecule C-alkylations.
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Affiliation(s)
- Joanna C. Sadler
- GlaxoSmithKline Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2NY, United Kingdom
- WestCHEM,
Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, Scotland, United Kingdom
| | - Chun-wa H. Chung
- GlaxoSmithKline Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2NY, United Kingdom
| | - Julie E. Mosley
- GlaxoSmithKline Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2NY, United Kingdom
| | - Glenn A. Burley
- WestCHEM,
Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, Scotland, United Kingdom
| | - Luke D. Humphreys
- GlaxoSmithKline Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2NY, United Kingdom
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21
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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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22
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Lu C, Zhang Q, Chen X. New method for synthesis of EZH2 methyltransferase inhibitor GSK126. SYNTHETIC COMMUN 2016. [DOI: 10.1080/00397911.2016.1193875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Chen Lu
- School of Pharmaceutical Engineering and Life Sciences, Changzhou University, Changzhou, Jiangsu, China
| | - Qiang Zhang
- School of Pharmaceutical Engineering and Life Sciences, Changzhou University, Changzhou, Jiangsu, China
| | - Xin Chen
- School of Pharmaceutical Engineering and Life Sciences, Changzhou University, Changzhou, Jiangsu, China
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23
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Ma S, Martin-Laffon J, Mininno M, Gigarel O, Brugière S, Bastien O, Tardif M, Ravanel S, Alban C. Molecular Evolution of the Substrate Specificity of Chloroplastic Aldolases/Rubisco Lysine Methyltransferases in Plants. MOLECULAR PLANT 2016; 9:569-81. [PMID: 26785049 DOI: 10.1016/j.molp.2016.01.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 12/07/2015] [Accepted: 01/11/2016] [Indexed: 05/09/2023]
Abstract
Rubisco and fructose-1,6-bisphosphate aldolases (FBAs) are involved in CO2 fixation in chloroplasts. Both enzymes are trimethylated at a specific lysine residue by the chloroplastic protein methyltransferase LSMT. Genes coding LSMT are present in all plant genomes but the methylation status of the substrates varies in a species-specific manner. For example, chloroplastic FBAs are naturally trimethylated in both Pisum sativum and Arabidopsis thaliana, whereas the Rubisco large subunit is trimethylated only in the former species. The in vivo methylation status of aldolases and Rubisco matches the catalytic properties of AtLSMT and PsLSMT, which are able to trimethylate FBAs or FBAs and Rubisco, respectively. Here, we created chimera and site-directed mutants of monofunctional AtLSMT and bifunctional PsLSMT to identify the molecular determinants responsible for substrate specificity. Our results indicate that the His-Ala/Pro-Trp triad located in the central part of LSMT enzymes is the key motif to confer the capacity to trimethylate Rubisco. Two of the critical residues are located on a surface loop outside the methyltransferase catalytic site. We observed a strict correlation between the presence of the triad motif and the in vivo methylation status of Rubisco. The distribution of the motif into a phylogenetic tree further suggests that the ancestral function of LSMT was FBA trimethylation. In a recent event during higher plant evolution, this function evolved in ancestors of Fabaceae, Cucurbitaceae, and Rosaceae to include Rubisco as an additional substrate to the archetypal enzyme. Our study provides insight into mechanisms by which SET-domain protein methyltransferases evolve new substrate specificity.
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Affiliation(s)
- Sheng Ma
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire & Végétale, 38041 Grenoble, France; CNRS, UMR5168, 38054 Grenoble, France; CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, 38054 Grenoble, France; INRA, USC1359, 38054 Grenoble, France
| | - Jacqueline Martin-Laffon
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire & Végétale, 38041 Grenoble, France; CNRS, UMR5168, 38054 Grenoble, France; CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, 38054 Grenoble, France; INRA, USC1359, 38054 Grenoble, France
| | - Morgane Mininno
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire & Végétale, 38041 Grenoble, France; CNRS, UMR5168, 38054 Grenoble, France; CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, 38054 Grenoble, France; INRA, USC1359, 38054 Grenoble, France
| | - Océane Gigarel
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire & Végétale, 38041 Grenoble, France; CNRS, UMR5168, 38054 Grenoble, France; CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, 38054 Grenoble, France; INRA, USC1359, 38054 Grenoble, France
| | - Sabine Brugière
- Université Grenoble Alpes, 38041 Grenoble, France; CEA, iRTSV, Biologie à Grande Echelle, 38054 Grenoble, France; INSERM, U1038, 38054 Grenoble, France
| | - Olivier Bastien
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire & Végétale, 38041 Grenoble, France; CNRS, UMR5168, 38054 Grenoble, France; CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, 38054 Grenoble, France; INRA, USC1359, 38054 Grenoble, France
| | - Marianne Tardif
- Université Grenoble Alpes, 38041 Grenoble, France; CEA, iRTSV, Biologie à Grande Echelle, 38054 Grenoble, France; INSERM, U1038, 38054 Grenoble, France
| | - Stéphane Ravanel
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire & Végétale, 38041 Grenoble, France; CNRS, UMR5168, 38054 Grenoble, France; CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, 38054 Grenoble, France; INRA, USC1359, 38054 Grenoble, France
| | - Claude Alban
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire & Végétale, 38041 Grenoble, France; CNRS, UMR5168, 38054 Grenoble, France; CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, 38054 Grenoble, France; INRA, USC1359, 38054 Grenoble, France.
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24
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Boriack-Sjodin PA, Swinger KK. Protein Methyltransferases: A Distinct, Diverse, and Dynamic Family of Enzymes. Biochemistry 2015; 55:1557-69. [PMID: 26652298 DOI: 10.1021/acs.biochem.5b01129] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Methyltransferase proteins make up a superfamily of enzymes that add one or more methyl groups to substrates that include protein, DNA, RNA, and small molecules. The subset of proteins that act upon arginine and lysine side chains are characterized as epigenetic targets because of their activity on histone molecules and their ability to affect transcriptional regulation. However, it is now clear that these enzymes target other protein substrates, as well, greatly expanding their potential impact on normal and disease biology. Protein methyltransferases are well-characterized structurally. In addition to revealing the overall architecture of the subfamilies of enzymes, structures of complexes with substrates and ligands have permitted detailed analysis of biochemical mechanism, substrate recognition, and design of potent and selective inhibitors. This review focuses on how knowledge gained from structural studies has impacted the understanding of this large class of epigenetic enzymes.
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Affiliation(s)
- P Ann Boriack-Sjodin
- Epizyme, Inc. , 400 Technology Square, Cambridge, Massachusetts 02139, United States
| | - Kerren K Swinger
- Epizyme, Inc. , 400 Technology Square, Cambridge, Massachusetts 02139, United States
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25
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Zhang G, Richardson SL, Mao Y, Huang R. Design, synthesis, and kinetic analysis of potent protein N-terminal methyltransferase 1 inhibitors. Org Biomol Chem 2015; 13:4149-54. [PMID: 25712161 PMCID: PMC4857722 DOI: 10.1039/c5ob00120j] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The protein N-terminal methyltransferase 1 (NTMT1) methylates the α-N-terminal amines of proteins. NTMT1 is upregulated in a variety of cancers and knockdown of NTMT1 results in cell mitotic defects. Therefore, NTMT1 inhibitors could be potential anticancer therapeutics. This study describes the design and synthesis of the first inhibitor targeting NTMT1. A novel bisubstrate analogue (NAM-TZ-SPKRIA) was shown to be a potent inhibitor (Ki = 0.20 μM) for NTMT1 and was selective versus protein lysine methyltransferase G9a and arginine methyltransferase 1. NAM-TZ-SPKRIA was found to exhibit a competitive inhibition pattern for both substrates, and mass spectrometry experiments revealed that the inhibitor substantially suppressed the methylation progression. Our results demonstrate the feasibility of using a triazole group to link an S-adenosyl-L-methionine analog with a peptide substrate to construct bisubstrate analogues as NTMT1 potent and selective inhibitors. This study lays a foundation to further discover small molecule NTMT1 inhibitors to interrogate its biological functions, and suggests a general strategy for the development of selective protein methyltransferase inhibitors.
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Affiliation(s)
- Gang Zhang
- Department of Medicinal Chemistry, and the Institute of Structural Biology & Drug Discovery, Virginia Commonwealth University, Richmond, VA, USA.
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26
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Kim J, Xiao H, Koh J, Wang Y, Bonanno JB, Thomas K, Babbitt PC, Brown S, Lee YS, Almo SC. Determinants of the CmoB carboxymethyl transferase utilized for selective tRNA wobble modification. Nucleic Acids Res 2015; 43:4602-13. [PMID: 25855808 PMCID: PMC4482062 DOI: 10.1093/nar/gkv206] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 02/27/2015] [Indexed: 12/31/2022] Open
Abstract
Enzyme-mediated modifications at the wobble position of tRNAs are essential for the translation of the genetic code. We report the genetic, biochemical and structural characterization of CmoB, the enzyme that recognizes the unique metabolite carboxy-S-adenosine-L-methionine (Cx-SAM) and catalyzes a carboxymethyl transfer reaction resulting in formation of 5-oxyacetyluridine at the wobble position of tRNAs. CmoB is distinctive in that it is the only known member of the SAM-dependent methyltransferase (SDMT) superfamily that utilizes a naturally occurring SAM analog as the alkyl donor to fulfill a biologically meaningful function. Biochemical and genetic studies define the in vitro and in vivo selectivity for Cx-SAM as alkyl donor over the vastly more abundant SAM. Complementary high-resolution structures of the apo- and Cx-SAM bound CmoB reveal the determinants responsible for this remarkable discrimination. Together, these studies provide mechanistic insight into the enzymatic and non-enzymatic feature of this alkyl transfer reaction which affords the broadened specificity required for tRNAs to recognize multiple synonymous codons.
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Affiliation(s)
- Jungwook Kim
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Hui Xiao
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Junseock Koh
- Laboratory of Cell Biology and Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Yikai Wang
- Chemical Biology Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Jeffrey B Bonanno
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Keisha Thomas
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Patricia C Babbitt
- Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, San Francisco, CA 94158, USA
| | - Shoshana Brown
- Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, San Francisco, CA 94158, USA
| | - Young-Sam Lee
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Steven C Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA Department of Physiology & Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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27
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Horowitz S, Adhikari U, Dirk LMA, Del Rizzo PA, Mehl RA, Houtz RL, Al-Hashimi HM, Scheiner S, Trievel RC. Manipulating unconventional CH-based hydrogen bonding in a methyltransferase via noncanonical amino acid mutagenesis. ACS Chem Biol 2014; 9:1692-7. [PMID: 24914947 DOI: 10.1021/cb5001185] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Recent studies have demonstrated that the active sites of S-adenosylmethionine (AdoMet)-dependent methyltransferases form strong carbon-oxygen (CH···O) hydrogen bonds with the substrate's sulfonium group that are important in AdoMet binding and catalysis. To probe these interactions, we substituted the noncanonical amino acid p-aminophenylalanine (pAF) for the active site tyrosine in the lysine methyltransferase SET7/9, which forms multiple CH···O hydrogen bonds to AdoMet and is invariant in SET domain enzymes. Using quantum chemistry calculations to predict the mutation's effects, coupled with biochemical and structural studies, we observed that pAF forms a strong CH···N hydrogen bond to AdoMet that is offset by an energetically unfavorable amine group rotamer within the SET7/9 active site that hinders AdoMet binding and activity. Together, these results illustrate that the invariant tyrosine in SET domain methyltransferases functions as an essential hydrogen bonding hub and cannot be readily substituted by residues bearing other hydrogen bond acceptors.
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Affiliation(s)
- Scott Horowitz
- Howard Hughes Medical Institute, Ann Arbor, Michigan 48109, United States
| | - Upendra Adhikari
- Department
of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Lynnette M. A. Dirk
- Department
of Horticulture, University of Kentucky, Lexington, Kentucky 40546, United States
| | | | - Ryan A. Mehl
- Department
of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Robert L. Houtz
- Department
of Horticulture, University of Kentucky, Lexington, Kentucky 40546, United States
| | | | - Steve Scheiner
- Department
of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
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Lanouette S, Mongeon V, Figeys D, Couture JF. The functional diversity of protein lysine methylation. Mol Syst Biol 2014; 10:724. [PMID: 24714364 PMCID: PMC4023394 DOI: 10.1002/msb.134974] [Citation(s) in RCA: 177] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Large‐scale characterization of post‐translational modifications (PTMs), such as phosphorylation, acetylation and ubiquitination, has highlighted their importance in the regulation of a myriad of signaling events. While high‐throughput technologies have tremendously helped cataloguing the proteins modified by these PTMs, the identification of lysine‐methylated proteins, a PTM involving the transfer of one, two or three methyl groups to the ε‐amine of a lysine side chain, has lagged behind. While the initial findings were focused on the methylation of histone proteins, several studies have recently identified novel non‐histone lysine‐methylated proteins. This review provides a compilation of all lysine methylation sites reported to date. We also present key examples showing the impact of lysine methylation and discuss the circuitries wired by this important PTM.
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Affiliation(s)
- Sylvain Lanouette
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
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29
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EZH2: biology, disease, and structure-based drug discovery. Acta Pharmacol Sin 2014; 35:161-74. [PMID: 24362326 PMCID: PMC3914023 DOI: 10.1038/aps.2013.161] [Citation(s) in RCA: 153] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 09/28/2013] [Indexed: 12/27/2022] Open
Abstract
EZH2 is the catalytic subunit of the polycomb repressive complex 2 (PRC2), which is a highly conserved histone methyltransferase that methylates lysine 27 of histone 3. Overexpression of EZH2 has been found in a wide range of cancers, including those of the prostate and breast. In this review, we address the current understanding of the oncogenic role of EZH2, including its PRC2-dependent transcriptional repression and PRC2-independent gene activation. We also discuss the connections between EZH2 and other silencing enzymes, such as DNA methyltransferase and histone deacetylase. We comprehensively address the architecture of the PRC2 complex and the crucial roles of each subunit. Finally, we summarize new progress in developing EZH2 inhibitors, which could be a new epigenetic therapy for cancers.
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30
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Targeting protein arginine N-methyltransferases with peptide-based inhibitors: opportunities and challenges. Future Med Chem 2013; 5:2199-206. [DOI: 10.4155/fmc.13.184] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Recently peptide-based inhibitors have been used to selectively inhibit a family of epigenetic enzymes called protein arginine N-methyltransferases (PRMTs), which has been implicated in different physiological processes and human diseases, such as heart disease and cancer. The diverse efforts to tease out subtle structural differences among PRMT enzymes in order to generate selective inhibitors as well as existing challenges in the field will be examined. The acquisition of PRMT substrate sequence preferences and structural information obtained from small-molecule inhibitors have helped in developing different peptide-based inhibitors that show great promise not only as inhibitors, but also as molecular probes to characterize PRMTs.
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31
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Horowitz S, Dirk LMA, Yesselman JD, Nimtz JS, Adhikari U, Mehl RA, Scheiner S, Houtz RL, Al-Hashimi HM, Trievel RC. Conservation and functional importance of carbon-oxygen hydrogen bonding in AdoMet-dependent methyltransferases. J Am Chem Soc 2013; 135:15536-48. [PMID: 24093804 DOI: 10.1021/ja407140k] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
S-adenosylmethionine (AdoMet)-based methylation is integral to metabolism and signaling. AdoMet-dependent methyltransferases belong to multiple distinct classes and share a catalytic mechanism that arose through convergent evolution; however, fundamental determinants underlying this shared methyl transfer mechanism remain undefined. A survey of high-resolution crystal structures reveals that unconventional carbon-oxygen (CH···O) hydrogen bonds coordinate the AdoMet methyl group in different methyltransferases irrespective of their class, active site structure, or cofactor binding conformation. Corroborating these observations, quantum chemistry calculations demonstrate that these charged interactions formed by the AdoMet sulfonium cation are stronger than typical CH···O hydrogen bonds. Biochemical and structural studies using a model lysine methyltransferase and an active site mutant that abolishes CH···O hydrogen bonding to AdoMet illustrate that these interactions are important for high-affinity AdoMet binding and transition-state stabilization. Further, crystallographic and NMR dynamics experiments of the wild-type enzyme demonstrate that the CH···O hydrogen bonds constrain the motion of the AdoMet methyl group, potentially facilitating its alignment during catalysis. Collectively, the experimental findings with the model methyltransferase and structural survey imply that methyl CH···O hydrogen bonding represents a convergent evolutionary feature of AdoMet-dependent methyltransferases, mediating a universal mechanism for methyl transfer.
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Affiliation(s)
- Scott Horowitz
- Howard Hughes Medical Institute , Ann Arbor, Michigan 48109, United States
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32
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Defining efficient enzyme-cofactor pairs for bioorthogonal profiling of protein methylation. Proc Natl Acad Sci U S A 2013; 110:16778-83. [PMID: 24082136 DOI: 10.1073/pnas.1216365110] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Protein methyltransferase (PMT)-mediated posttranslational modification of histone and nonhistone substrates modulates stability, localization, and interacting partners of target proteins in diverse cellular contexts. These events play critical roles in normal biological processes and are frequently deregulated in human diseases. In the course of identifying substrates of individual PMTs, bioorthogonal profiling of protein methylation (BPPM) has demonstrated its merits. In this approach, specific PMTs are engineered to process S-adenosyl-L-methionine (SAM) analogs as cofactor surrogates and label their substrates with distinct chemical modifications for target elucidation. Despite the proof-of-concept advancement of BPPM, few efforts have been made to explore its generality. With two cancer-relevant PMTs, EuHMT1 (GLP1/KMT1D) and EuHMT2 (G9a/KMT1C), as models, we defined the key structural features of engineered PMTs and matched SAM analogs that can render the orthogonal enzyme-cofactor pairs for efficient catalysis. Here we have demonstrated that the presence of sulfonium-β-sp(2) carbon and flexible, medium-sized sulfonium-δ-substituents are crucial for SAM analogs as BPPM reagents. The bulky cofactors can be accommodated by tailoring the conserved Y1211/Y1154 residues and nearby hydrophobic cavities of EuHMT1/2. Profiling proteome-wide substrates with BPPM allowed identification of >500 targets of EuHMT1/2 with representative targets validated using native EuHMT1/2 and SAM. This finding indicates that EuHMT1/2 may regulate many cellular events previously unrecognized to be modulated by methylation. The present work, therefore, paves the way to a broader application of the BPPM technology to profile methylomes of diverse PMTs and elucidate their downstream functions.
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33
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Adhikari U, Scheiner S. Magnitude and Mechanism of Charge Enhancement of CH··O Hydrogen Bonds. J Phys Chem A 2013; 117:10551-62. [DOI: 10.1021/jp4081788] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Upendra Adhikari
- Department
of Chemistry and
Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
| | - Steve Scheiner
- Department
of Chemistry and
Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
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34
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Small molecule epigenetic inhibitors targeted to histone lysine methyltransferases and demethylases. Q Rev Biophys 2013; 46:349-73. [PMID: 23991894 DOI: 10.1017/s0033583513000085] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Altered chromatin structures and dynamics are responsible for a range of human malignancies, among which the status of histone lysine methylation remains of paramount importance. Histone lysine methylation is maintained by the relative activities of sequence-specific methyltransferase (KMT) writers and demethylase (KDM) erasers, with aberrant enzymatic activities or expression profiles closely correlated with multiple human diseases. Hence, targeting these epigenetic enzymes should provide a promising avenue for pharmacological intervention of aberrantly marked sites within the epigenome. Here we present an up-to-date critical evaluation on the development and optimization of potent small molecule inhibitors targeted to histone KMTs and KDMs, with the emphasis on contributions of structural biology to development of epigenetic drugs for therapeutic intervention. We anticipate that ongoing advances in the development of epigenetic inhibitors should lead to novel drugs that site-specifically target KMTs and KDMs, key enzymes responsible for maintenance of the lysine methylation landscape in the epigenome.
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35
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Mujtaba S, Winer BY, Jaganathan A, Patel J, Sgobba M, Schuch R, Gupta YK, Haider S, Wang R, Fischetti VA. Anthrax SET protein: a potential virulence determinant that epigenetically represses NF-κB activation in infected macrophages. J Biol Chem 2013; 288:23458-72. [PMID: 23720780 DOI: 10.1074/jbc.m113.467696] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Toxins play a major role in the pathogenesis of Bacillus anthracis by subverting the host defenses. However, besides toxins, B. anthracis expresses effector proteins, whose role in pathogenesis are yet to be investigated. Here we present that suppressor-of-variegation, enhancer-of-zeste, trithorax protein from B. anthracis (BaSET) methylates human histone H1, resulting in repression of NF-κB functions. Notably, BaSET is secreted and undergoes nuclear translocation to enhance H1 methylation in B. anthracis-infected macrophages. Compared with wild type Sterne, delayed growth kinetics and altered septum formation were observed in the BaSET knock-out (BaΔSET) bacilli. Uncontrolled BaSET expression during complementation of the BaSET gene in BaΔSET partially restored growth during stationary phase but resulted in substantially shorter bacilli throughout the growth cycle. Importantly, in contrast to Sterne, the BaΔSET B. anthracis is avirulent in a lethal murine bacteremia model of infection. Collectively, BaSET is required for repression of host transcription as well as proper B. anthracis growth, making it a potentially unique virulence determinant.
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Affiliation(s)
- Shiraz Mujtaba
- Department of Structural and Chemical, Mount Sinai School of Medicine, New York, New York 10029, USA.
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36
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Niwa H, Handa N, Tomabechi Y, Honda K, Toyama M, Ohsawa N, Shirouzu M, Kagechika H, Hirano T, Umehara T, Yokoyama S. Structures of histone methyltransferase SET7/9 in complexes with adenosylmethionine derivatives. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:595-602. [DOI: 10.1107/s0907444912052092] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Accepted: 12/31/2012] [Indexed: 11/10/2022]
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37
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Abstract
Carbon-oxygen (CH···O) hydrogen bonding represents an unusual category of molecular interactions first documented in biological structures over 4 decades ago. Although CH···O hydrogen bonding has remained generally underappreciated in the biochemical literature, studies over the last 15 years have begun to yield direct evidence of these interactions in biological systems. In this minireview, we provide a historical context of biological CH···O hydrogen bonding and summarize some major advancements from experimental studies over the past several years that have elucidated the importance, prevalence, and functions of these interactions. In particular, we examine the impact of CH···O bonds on protein and nucleic acid structure, molecular recognition, and enzyme catalysis and conclude by exploring overarching themes and unresolved questions regarding unconventional interactions in biomolecular structure.
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38
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Gao ZP, Chen GX, Yang ZN. Regulatory role of Arabidopsis pTAC14 in chloroplast development and plastid gene expression. PLANT SIGNALING & BEHAVIOR 2012; 7:1354-6. [PMID: 22902688 PMCID: PMC3493425 DOI: 10.4161/psb.21618] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Transcriptionally active chromosome (TAC) is a fraction of protein/DNA complexes with RNA polymerase activity in the plastid. The function of most TAC proteins is not well known. We isolated a mutant gene encoding a plastid TAC component, pTAC14, and performed functional analysis of plastid gene expression and chloroplast development in Arabidopsis. We found that knockout of pTAC14 led to the blockage of thylakoid formation in the initial process of chloroplast development. Furthermore, the transcript levels of plastid-encoded polymerase (PEP)-dependent genes were downregulated in ptac14, suggesting that PEP activity was decreased in the mutant. On the basis of these results, we briefly review the available evidence and highlight the interaction between pTAC14 and pTAC12 that could help us understand the regulatory role of pTAC14 in chloroplast development and plastid gene expression.
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Affiliation(s)
- Zhi-Ping Gao
- College of Life Sciences; Nanjing Normal University; Jiangsu, China
- School of Life Sciences; The Chinese University of HongKong; Shatin, Hong Kong, China
- College of Life and Environmental Sciences; Shanghai Normal University; Shanghai, China
| | - Guo-Xiang Chen
- College of Life Sciences; Nanjing Normal University; Jiangsu, China
- Correspondence to: Guo-Xiang Chen, and Zhong-Nan Yang,
| | - Zhong-Nan Yang
- College of Life and Environmental Sciences; Shanghai Normal University; Shanghai, China
- Correspondence to: Guo-Xiang Chen, and Zhong-Nan Yang,
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39
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Abstract
Epigenetic regulation of gene expression is a dynamic and reversible process that establishes normal cellular phenotypes but also contributes to human diseases. At the molecular level, epigenetic regulation involves hierarchical covalent modification of DNA and the proteins that package DNA, such as histones. Here, we review the key protein families that mediate epigenetic signalling through the acetylation and methylation of histones, including histone deacetylases, protein methyltransferases, lysine demethylases, bromodomain-containing proteins and proteins that bind to methylated histones. These protein families are emerging as druggable classes of enzymes and druggable classes of protein-protein interaction domains. In this article, we discuss the known links with disease, basic molecular mechanisms of action and recent progress in the pharmacological modulation of each class of proteins.
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40
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Yao J, Chu Y, An R, Guo H. Understanding Product Specificity of Protein Lysine Methyltransferases from QM/MM Molecular Dynamics and Free Energy Simulations: The Effects of Mutation on SET7/9 beyond the Tyr/Phe Switch. J Chem Inf Model 2012; 52:449-56. [DOI: 10.1021/ci200364m] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Jianzhuang Yao
- Department
of Biochemistry and Cellular and Molecular Biology and ‡National Institute for Mathematical
and Biological Synthesis, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Yuzhuo Chu
- Department
of Biochemistry and Cellular and Molecular Biology and ‡National Institute for Mathematical
and Biological Synthesis, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Ran An
- Department
of Biochemistry and Cellular and Molecular Biology and ‡National Institute for Mathematical
and Biological Synthesis, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Hong Guo
- Department
of Biochemistry and Cellular and Molecular Biology and ‡National Institute for Mathematical
and Biological Synthesis, University of Tennessee, Knoxville, Tennessee 37996, United States
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41
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Abstract
Methylation of DNA and histones in chromatin has been implicated in numerous biological processes. For many years, methylation has been recognized as static and stable modification, as compared with other covalent modifications of chromatin. Recently, however, several mechanisms have been demonstrated to be involved in demethylation of chromatin, suggesting that chromatin methylation is more dynamically regulated. One chemical reaction that mediates demethylation of both DNA and histones is hydroxylation, catalysed by Fe(II) and α-ketoglutarate (KG)-dependent hydroxylase/dioxygenase. Given that methylation of chromatin is an important epigenetic mark involved in fundamental biological processes such as cell fate determination, understanding how chromatin methylation is dynamically regulated has implications for human diseases and regenerative medicine.
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Affiliation(s)
- Yu-ichi Tsukada
- Division of Molecular Immunology, Research Center for Infectious Diseases, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan.
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42
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Gao ZP, Yu QB, Zhao TT, Ma Q, Chen GX, Yang ZN. A functional component of the transcriptionally active chromosome complex, Arabidopsis pTAC14, interacts with pTAC12/HEMERA and regulates plastid gene expression. PLANT PHYSIOLOGY 2011; 157:1733-45. [PMID: 22010110 PMCID: PMC3327189 DOI: 10.1104/pp.111.184762] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Accepted: 10/14/2011] [Indexed: 05/18/2023]
Abstract
The SET domain-containing protein, pTAC14, was previously identified as a component of the transcriptionally active chromosome (TAC) complexes. Here, we investigated the function of pTAC14 in the regulation of plastid-encoded bacterial-type RNA polymerase (PEP) activity and chloroplast development. The knockout of pTAC14 led to the blockage of thylakoid formation in Arabidopsis (Arabidopsis thaliana), and ptac14 was seedling lethal. Sequence and transcriptional analysis showed that pTAC14 encodes a specific protein in plants that is located in the chloroplast associated with the thylakoid and that its expression depends on light. In addition, the transcript levels of all investigated PEP-dependent genes were clearly reduced in the ptac14-1 mutants, while the accumulation of nucleus-encoded phage-type RNA polymerase-dependent transcripts was increased, indicating an important role of pTAC14 in maintaining PEP activity. pTAC14 was found to interact with pTAC12/HEMERA, another component of TACs that is involved in phytochrome signaling. The data suggest that pTAC14 is essential for proper chloroplast development, most likely by affecting PEP activity and regulating PEP-dependent plastid gene transcription in Arabidopsis together with pTAC12.
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43
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Akey DL, Li S, Konwerski JR, Confer LA, Bernard SM, Anzai Y, Kato F, Sherman DH, Smith JL. A new structural form in the SAM/metal-dependent o‑methyltransferase family: MycE from the mycinamicin biosynthetic pathway. J Mol Biol 2011; 413:438-50. [PMID: 21884704 PMCID: PMC3193595 DOI: 10.1016/j.jmb.2011.08.040] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Revised: 08/16/2011] [Accepted: 08/16/2011] [Indexed: 01/07/2023]
Abstract
O-linked methylation of sugar substituents is a common modification in the biosynthesis of many natural products and is catalyzed by multiple families of S-adenosyl-L-methionine (SAM or AdoMet)-dependent methyltransferases (MTs). Mycinamicins, potent antibiotics from Micromonospora griseorubida, can be methylated at two positions on a 6-deoxyallose substituent. The first methylation is catalyzed by MycE, a SAM- and metal-dependent MT. Crystal structures were determined for MycE bound to the product S-adenosyl-L-homocysteine (AdoHcy) and magnesium, both with and without the natural substrate mycinamicin VI. This represents the first structure of a natural product sugar MT in complex with its natural substrate. MycE is a tetramer of a two-domain polypeptide, comprising a C-terminal catalytic MT domain and an N-terminal auxiliary domain, which is important for quaternary assembly and for substrate binding. The symmetric MycE tetramer has a novel MT organization in which each of the four active sites is formed at the junction of three monomers within the tetramer. The active-site structure supports a mechanism in which a conserved histidine acts as a general base, and the metal ion helps to position the methyl acceptor and to stabilize a hydroxylate intermediate. A conserved tyrosine is suggested to support activity through interactions with the transferred methyl group from the SAM methyl donor. The structure of the free enzyme reveals a dramatic order-disorder transition in the active site relative to the S-adenosyl-L-homocysteine complexes, suggesting a mechanism for product/substrate exchange through concerted movement of five loops and the polypeptide C-terminus.
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Affiliation(s)
- David L. Akey
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
| | - Shengying Li
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
| | | | - Laura A. Confer
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109,Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Steffen M. Bernard
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109,Chemical Biology Doctoral Program, University of Michigan, Ann Arbor, MI 48109
| | - Yojiro Anzai
- Faculty of Pharmaceutical Sciences, Toho University 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Fumio Kato
- Faculty of Pharmaceutical Sciences, Toho University 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - David H. Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109,Departments of Medicinal Chemistry, Chemistry, Microbiology & Immunology, University of Michigan, Ann Arbor, MI 48109
| | - Janet L. Smith
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109,Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109,Correspondence: (734) 615-9564, Fax: (734) 763-6492
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Ulucan O, Keskin O, Erman B, Gursoy A. A comparative molecular dynamics study of methylation state specificity of JMJD2A. PLoS One 2011; 6:e24664. [PMID: 21931800 PMCID: PMC3172282 DOI: 10.1371/journal.pone.0024664] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Accepted: 08/16/2011] [Indexed: 11/19/2022] Open
Abstract
Histone modifications have great importance in epigenetic regulation. JMJD2A is a histone demethylase which is selective for di- and trimethyl forms of residues Lys9 and Lys36 of Histone 3 tail (H3K9 and H3K36). We present a molecular dynamics simulations of mono-, di- and trimethylated histone tails in complex with JMJD2A catalytic domain to gain insight into how JMJD2A discriminates between the methylation states of H3K9. The methyl groups are located at specific distances and orientations with respect to Fe(II) in methylammonium binding pocket. For the trimethyllysine the mechanism which provides the effectual orientation of methyl groups is the symmetry, whereas for the dimethyllysine case the determining factors are the interactions between methyllysine head and its environment and subsequently the restriction on angular motion. The occurrence frequency of methyl groups in a certain proximity of Fe(II) comes out as the explanation of the enzyme activity difference on di- and tri-methylated peptides. Energy analysis suggests that recognition is mostly driven by van der Waals and followed by Coulombic interactions in the enzyme-substrate interface. The number (mono, di or tri) and orientations of methyl groups and water molecules significantly affect the extent of van der Waals interaction strengths. Hydrogen bonding analysis suggests that the interaction between JMJD2A and its substrates mainly comes from main chain-side chain interactions. Binding free energy analysis points out Arg8 as an important residue forming an intra-substrate hydrogen bond with tri and dimethylated Lys9 of the H3 chain. Our study provides new insights into how JMJD2A discriminates between its substrates from both a structural and dynamical point of view.
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Affiliation(s)
- Ozlem Ulucan
- Center for Computational Biology and Bioinformatics and College of Engineering, Koc University, Istanbul, Turkey
| | - Ozlem Keskin
- Center for Computational Biology and Bioinformatics and College of Engineering, Koc University, Istanbul, Turkey
| | - Burak Erman
- Center for Computational Biology and Bioinformatics and College of Engineering, Koc University, Istanbul, Turkey
| | - Attila Gursoy
- Center for Computational Biology and Bioinformatics and College of Engineering, Koc University, Istanbul, Turkey
- * E-mail:
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45
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Horowitz S, Yesselman JD, Al-Hashimi HM, Trievel RC. Direct evidence for methyl group coordination by carbon-oxygen hydrogen bonds in the lysine methyltransferase SET7/9. J Biol Chem 2011; 286:18658-63. [PMID: 21454678 PMCID: PMC3099682 DOI: 10.1074/jbc.m111.232876] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Revised: 03/17/2011] [Indexed: 12/27/2022] Open
Abstract
SET domain lysine methyltransferases (KMTs) are S-adenosylmethionine (AdoMet)-dependent enzymes that catalyze the site-specific methylation of lysyl residues in histone and non-histone proteins. Based on crystallographic and cofactor binding studies, carbon-oxygen (CH · · · O) hydrogen bonds have been proposed to coordinate the methyl groups of AdoMet and methyllysine within the SET domain active site. However, the presence of these hydrogen bonds has only been inferred due to the uncertainty of hydrogen atom positions in x-ray crystal structures. To experimentally resolve the positions of the methyl hydrogen atoms, we used NMR (1)H chemical shift coupled with quantum mechanics calculations to examine the interactions of the AdoMet methyl group in the active site of the human KMT SET7/9. Our results indicated that at least two of the three hydrogens in the AdoMet methyl group engage in CH · · · O hydrogen bonding. These findings represent direct, quantitative evidence of CH · · · O hydrogen bond formation in the SET domain active site and suggest a role for these interactions in catalysis. Furthermore, thermodynamic analysis of AdoMet binding indicated that these interactions are important for cofactor binding across SET domain enzymes.
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Affiliation(s)
- Scott Horowitz
- Chemistry, and Biophysics, University of Michigan, Ann Arbor, Michigan 48109
| | - Joseph D. Yesselman
- Chemistry, and Biophysics, University of Michigan, Ann Arbor, Michigan 48109
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46
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Chang Y, Horton JR, Bedford MT, Zhang X, Cheng X. Structural insights for MPP8 chromodomain interaction with histone H3 lysine 9: potential effect of phosphorylation on methyl-lysine binding. J Mol Biol 2011; 408:807-14. [PMID: 21419134 DOI: 10.1016/j.jmb.2011.03.018] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Revised: 03/04/2011] [Accepted: 03/09/2011] [Indexed: 12/24/2022]
Abstract
M-phase phosphoprotein 8 (MPP8) harbors an N-terminal chromodomain and a C-terminal ankyrin repeat domain. MPP8, via its chromodomain, binds histone H3 peptide tri- or di-methylated at lysine 9 (H3K9me3/H3K9me2) in submicromolar affinity. We determined the crystal structure of MPP8 chromodomain in complex with H3K9me3 peptide. MPP8 interacts with at least six histone H3 residues from glutamine 5 to serine 10, enabling its ability to distinguish lysine-9-containing peptide (QTARKS) from that of lysine 27 (KAARKS), both sharing the ARKS sequence. A partial hydrophobic cage with three aromatic residues (Phe59, Trp80 and Tyr83) and one aspartate (Asp87) encloses the methylated lysine 9. MPP8 has been reported to be phosphorylated in vivo, including the cage residue Tyr83 and the succeeding Thr84 and Ser85. Modeling a phosphate group onto the side-chain hydroxyl oxygen of Tyr83 suggests that the negatively charged phosphate group could enhance the binding of positively charged methyl-lysine or create a regulatory signal by allowing or inhibiting binding of other protein(s).
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Affiliation(s)
- Yanqi Chang
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
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47
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Krishnan S, Horowitz S, Trievel RC. Structure and function of histone H3 lysine 9 methyltransferases and demethylases. Chembiochem 2011; 12:254-63. [PMID: 21243713 DOI: 10.1002/cbic.201000545] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Indexed: 12/20/2022]
Abstract
Histone lysine methylation is a dynamic chromatin modification that plays key regulatory roles in gene expression and other genomic functions. Methylation of Lys9 in histone H3 (H3K9) is a prominent modification that has been implicated in diverse processes, including transcriptional silencing, heterochromatin formation, and DNA methylation. In this review, we summarize recent advances in understanding the structure and substrate specificity of the H3K9-specific methyltransferases G9A and GLP and explore current efforts to develop inhibitors of these enzymes. In addition, we discuss the structure and specificity of the recently discovered PHF8 family of histone demethylases that target H3K9 as well as other methylation sites in histones H3 and H4. Finally, we conclude by comparing the H3K9 binding modes displayed by these enzymes and examine the relevance of these studies to their biological functions and to structure-based inhibitor design.
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Affiliation(s)
- Swathi Krishnan
- University of Michigan Medical School, Department of Biological Chemistry, Ann Arbor, MI 48109, USA
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48
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Levy D, Kuo AJ, Chang Y, Schaefer U, Kitson C, Cheung P, Espejo A, Zee BM, Liu CL, Tangsombatvisit S, Tennen RI, Kuo AY, Tanjing S, Cheung R, Chua KF, Utz PJ, Shi X, Prinjha RK, Lee K, Garcia BA, Bedford MT, Tarakhovsky A, Cheng X, Gozani O. Lysine methylation of the NF-κB subunit RelA by SETD6 couples activity of the histone methyltransferase GLP at chromatin to tonic repression of NF-κB signaling. Nat Immunol 2011; 12:29-36. [PMID: 21131967 PMCID: PMC3074206 DOI: 10.1038/ni.1968] [Citation(s) in RCA: 204] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Accepted: 11/09/2010] [Indexed: 12/13/2022]
Abstract
Signaling via the methylation of lysine residues in proteins has been linked to diverse biological and disease processes, yet the catalytic activity and substrate specificity of many human protein lysine methyltransferases (PKMTs) are unknown. We screened over 40 candidate PKMTs and identified SETD6 as a methyltransferase that monomethylated chromatin-associated transcription factor NF-κB subunit RelA at Lys310 (RelAK310me1). SETD6-mediated methylation rendered RelA inert and attenuated RelA-driven transcriptional programs, including inflammatory responses in primary immune cells. RelAK310me1 was recognized by the ankryin repeat of the histone methyltransferase GLP, which under basal conditions promoted a repressed chromatin state at RelA target genes through GLP-mediated methylation of histone H3 Lys9 (H3K9). NF-κB-activation-linked phosphorylation of RelA at Ser311 by protein kinase C-ζ (PKC-ζ) blocked the binding of GLP to RelAK310me1 and relieved repression of the target gene. Our findings establish a previously uncharacterized mechanism by which chromatin signaling regulates inflammation programs.
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Affiliation(s)
- Dan Levy
- Department of Biology, Stanford University, Stanford, California, USA
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Del Rizzo PA, Couture JF, Dirk LMA, Strunk BS, Roiko MS, Brunzelle JS, Houtz RL, Trievel RC. SET7/9 catalytic mutants reveal the role of active site water molecules in lysine multiple methylation. J Biol Chem 2010; 285:31849-58. [PMID: 20675860 DOI: 10.1074/jbc.m110.114587] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
SET domain lysine methyltransferases (KMTs) methylate specific lysine residues in histone and non-histone substrates. These enzymes also display product specificity by catalyzing distinct degrees of methylation of the lysine ε-amino group. To elucidate the molecular mechanism underlying this specificity, we have characterized the Y245A and Y305F mutants of the human KMT SET7/9 (also known as KMT7) that alter its product specificity from a monomethyltransferase to a di- and a trimethyltransferase, respectively. Crystal structures of these mutants in complex with peptides bearing unmodified, mono-, di-, and trimethylated lysines illustrate the roles of active site water molecules in aligning the lysine ε-amino group for methyl transfer with S-adenosylmethionine. Displacement or dissociation of these solvent molecules enlarges the diameter of the active site, accommodating the increasing size of the methylated ε-amino group during successive methyl transfer reactions. Together, these results furnish new insights into the roles of active site water molecules in modulating lysine multiple methylation by SET domain KMTs and provide the first molecular snapshots of the mono-, di-, and trimethyl transfer reactions catalyzed by these enzymes.
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Affiliation(s)
- Paul A Del Rizzo
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
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50
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Zhang X, Bruice TC. Product specificity and mechanism of protein lysine methyltransferases: insights from the histone lysine methyltransferase SET8. Biochemistry 2010; 47:6671-7. [PMID: 18512960 DOI: 10.1021/bi800244s] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular dynamics simulations employing a molecular mechanics (MM) force field and hybrid quantum mechanics (QM) and MM (QM/MM) have been carried out to investigate the product specificity and mechanism of the histone H4 lysine 20 (H4-K20) methylation by human histone lysine methyltransferase SET8. At neutral pH, the target lysine is available to only the enzyme in the protonated state. The first step in the methylation reaction must be deprotonation of the lysine target which is followed by the (+)AdoMet methylation of the neutral lysine [Enz.Lys-CH(2)-NH(3)(+).(+)AdoMet --> H(+) + Enz.Lys-CH(2)-NH(2).(+)AdoMet -->--> Enz.Lys-CH(2)-N(Me)H(2)(+).AdoHcy]. The electrostatic interactions between two positive charges on (+)AdoMet and Lys20-NH(3)(+) decrease the pK(a) of Lys20-NH(3)(+). Upon formation of Enz.Lys-NH(3)(+).(+)AdoMet, a water channel by which the proton escapes to the outer solvent phase is formed. The formation of a water channel for the escape of a proton from Lys20-N(Me)H(2)(+) in Enz.Lys20-N(Me)H(2)(+).(+)AdoMet is not formed because the methyl substituent blocks the starting of the water channel. Thus, a second methylation does not take place. The dependence of the occurrence of methyl transfer on the formation of a water channel in SET8 is in accord with our previous reports on product specificity by histone lysine monomethyltransferase SET7/9, large subunit lysine dimethyltransferase (LSMT), and viral histone lysine trimethyltransferase (vSET). The average value of the experimental DeltaG(E)() for the six lysine methyl transfer reactions catalyzed by vSET, LSMT, and SET7/9 with p53 as a substrate is 22.1 +/- 1.0 kcal/mol, and the computed average (DeltaG(C)()) is 22.2 +/- 0.8 kcal/mol. In this study, the computed free energy barrier of the methyl transfer reaction [Lys20-NH(2) + (+)AdoMet --> Lys20-N(Me)H(2)(+) + AdoHcy] catalyzed by SET8 is 20.8 kcal/mol. This is in agreement with the value of 20.6 kcal/mol calculated from the experimental rate constant (0.43 +/- 0.02 min(-1)). Our bond-order computations establish that the H4-K20 monomethylation in SET8 is a concerted linear S(N)2 displacement reaction.
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Affiliation(s)
- Xiaodong Zhang
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
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