1
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Öster C, Lange S, Hendriks K, Lange A. Detecting Bound Ions in Ion Channels by Solid-State NMR Experiments on 15N-Labelled Ammonium Ions. Methods Mol Biol 2024; 2796:23-34. [PMID: 38856893 DOI: 10.1007/978-1-0716-3818-7_2] [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] [Indexed: 06/11/2024]
Abstract
Solid-state NMR allows for the study of membrane proteins under physiological conditions. Here we describe a method for detection of bound ions in the selectivity filter of ion channels using solid-state NMR. This method employs standard 1H-detected solid-state NMR setup and experiment types, which is enabled by using 15N-labelled ammonium ions to mimic potassium ions.
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Affiliation(s)
- Carl Öster
- Research Unit Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany.
| | - Sascha Lange
- Research Unit Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Kitty Hendriks
- Research Unit Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Adam Lange
- Research Unit Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany.
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany.
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2
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Walker T, Sun HM, Gunnels T, Wysocki V, Laganowsky A, Rye H, Russell D. Dissecting the Thermodynamics of ATP Binding to GroEL One Nucleotide at a Time. ACS CENTRAL SCIENCE 2023; 9:466-475. [PMID: 36968544 PMCID: PMC10037461 DOI: 10.1021/acscentsci.2c01065] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Indexed: 06/18/2023]
Abstract
Variable-temperature electrospray ionization (vT-ESI) native mass spectrometry (nMS) is used to determine the thermodynamics for stepwise binding of up to 14 ATP molecules to the 801 kDa GroEL tetradecamer chaperonin complex. Detailed analysis reveals strong enthalpy-entropy compensation (EEC) for the ATP binding events leading to formation of GroEL-ATP7 and GroEL-ATP14 complexes. The observed variations in EEC and stepwise free energy changes of specific ATP binding are consistent with the well-established nested cooperativity model describing GroEL-ATP interactions, viz., intraring positive cooperativity and inter-ring negative cooperativity (Dyachenko A.; Proc. Natl. Acad. Sci. U.S.A.2013, 110, 7235-7239). Entropy-driven ATP binding is to be expected for ligand-induced conformational changes of the GroEL tetradecamer, though the magnitude of the entropy change suggests that reorganization of GroEL-hydrating water molecules and/or expulsion of water from the GroEL cavity may also play key roles. The capability for determining complete thermodynamic signatures (ΔG, ΔH, and -TΔS) for individual ligand binding reactions for the large, nearly megadalton GroEL complex expands our fundamental view of chaperonin functional chemistry. Moreover, this work and related studies of protein-ligand interactions illustrate important new capabilities of vT-ESI-nMS for thermodynamic studies of protein interactions with ligands and other molecules such as proteins and drugs.
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Affiliation(s)
- Thomas Walker
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - He Mirabel Sun
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Tiffany Gunnels
- Department
of Biochemistry & Biophysics, Texas
A&M University, College
Station, Texas 77843, United States
| | - Vicki Wysocki
- Department
of Chemistry and Biochemistry, The Ohio
State University, Columbus, Ohio 43210, United States
| | - Arthur Laganowsky
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Hays Rye
- Department
of Biochemistry & Biophysics, Texas
A&M University, College
Station, Texas 77843, United States
| | - David Russell
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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3
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Torres Cabán C, Yang M, Lai C, Yang L, Subach FV, Smith BO, Piatkevich KD, Boyden ES. Tuning the Sensitivity of Genetically Encoded Fluorescent Potassium Indicators through Structure-Guided and Genome Mining Strategies. ACS Sens 2022; 7:1336-1346. [PMID: 35427452 PMCID: PMC9150168 DOI: 10.1021/acssensors.1c02201] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 03/09/2022] [Indexed: 12/31/2022]
Abstract
Genetically encoded potassium indicators lack optimal binding affinity for monitoring intracellular dynamics in mammalian cells. Through structure-guided design and genome mining of potassium binding proteins, we developed green fluorescent potassium indicators with a broad range of binding affinities. KRaION1 (K+ ratiometric indicator for optical imaging based on mNeonGreen 1), based on the insertion of a potassium binding protein, Kbp, from E. coli (Ec-Kbp) into the fluorescent protein mNeonGreen, exhibits an isotonically measured Kd of 69 ± 10 mM (mean ± standard deviation used throughout). We identified Ec-Kbp's binding site using NMR spectroscopy to detect protein-thallium scalar couplings and refined the structure of Ec-Kbp in its potassium-bound state. Guided by this structure, we modified KRaION1, yielding KRaION1/D9N and KRaION2, which exhibit isotonically measured Kd's of 138 ± 21 and 96 ± 9 mM. We identified four Ec-Kbp homologues as potassium binding proteins, which yielded indicators with isotonically measured binding affinities in the 39-112 mM range. KRaIONs functioned in HeLa cells, but the Kd values differed from the isotonically measured case. We found that, by tuning the experimental conditions, Kd values could be obtained that were consistent in vitro and in vivo. We thus recommend characterizing potassium indicator Kd in the physiological context of interest before application.
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Affiliation(s)
- Cristina
C. Torres Cabán
- McGovern
Institute for Brain Research, MIT, Cambridge, Massachusetts 02139, United States
- Department
of Biological Engineering, MIT, Cambridge, Massachusetts 02139, United States
- Department
of Media Arts & Sciences, MIT, Cambridge, Massachusetts 02139, United States
| | - Minghan Yang
- School
of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
- Westlake
Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
- Institute
of Basic Medical Sciences, Westlake Institute
for Advanced Study, Hangzhou, Zhejiang 310024, China
- College
of Physics, Jilin University, Changchun, Jilin 130012, China
| | - Cuixin Lai
- School
of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
- Westlake
Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
- Institute
of Basic Medical Sciences, Westlake Institute
for Advanced Study, Hangzhou, Zhejiang 310024, China
| | - Lina Yang
- School
of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
- Westlake
Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
- Institute
of Basic Medical Sciences, Westlake Institute
for Advanced Study, Hangzhou, Zhejiang 310024, China
| | - Fedor V. Subach
- Complex
of NBICS Technologies, National Research
Center “Kurchatov Institute”, Moscow 123182, Russia
| | - Brian O. Smith
- Institute
of Molecular, Cell & Systems Biology, College of Medical Veterinary
& Life Sciences, University of Glasgow, Glasgow G128QQ, United Kingdom
| | - Kiryl D. Piatkevich
- School
of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
- Westlake
Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
- Institute
of Basic Medical Sciences, Westlake Institute
for Advanced Study, Hangzhou, Zhejiang 310024, China
| | - Edward S. Boyden
- McGovern
Institute for Brain Research, MIT, Cambridge, Massachusetts 02139, United States
- Department
of Biological Engineering, MIT, Cambridge, Massachusetts 02139, United States
- Department
of Media Arts & Sciences, MIT, Cambridge, Massachusetts 02139, United States
- Koch
Institute for Integrative Cancer Research, MIT, Cambridge, Massachusetts 02139, United States
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, United States
- Department
of Brain and Cognitive Sciences, MIT, Cambridge, Massachusetts 02139, United States
- K.
Lisa Yang Center for Bionics, MIT, Cambridge, Massachusetts 02139, United States
- Center
for Neurobiological Engineering, MIT, Cambridge, Massachusetts 02139, United States
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4
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Öster C, Tekwani Movellan K, Goold B, Hendriks K, Lange S, Becker S, de Groot BL, Kopec W, Andreas LB, Lange A. Direct Detection of Bound Ammonium Ions in the Selectivity Filter of Ion Channels by Solid-State NMR. J Am Chem Soc 2022; 144:4147-4157. [PMID: 35200002 PMCID: PMC8915258 DOI: 10.1021/jacs.1c13247] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The flow of ions across cell membranes facilitated by ion channels is an important function for all living cells. Despite the huge amount of structural data provided by crystallography, elucidating the exact interactions between the selectivity filter atoms and bound ions is challenging. Here, we detect bound 15N-labeled ammonium ions as a mimic for potassium ions in ion channels using solid-state NMR under near-native conditions. The non-selective ion channel NaK showed two ammonium peaks corresponding to its two ion binding sites, while its potassium-selective mutant NaK2K that has a signature potassium-selective selectivity filter with four ion binding sites gave rise to four ammonium peaks. Ions bound in specific ion binding sites were identified based on magnetization transfer between the ions and carbon atoms in the selectivity filters. Magnetization transfer between bound ions and water molecules revealed that only one out of four ions in the selectivity filter of NaK2K is in close contact with water, which is in agreement with the direct knock-on ion conduction mechanism where ions are conducted through the channel by means of direct interactions without water molecules in between. Interestingly, the potassium-selective ion channels investigated here (NaK2K and, additionally, KcsA-Kv1.3) showed remarkably different chemical shifts for their bound ions, despite having identical amino acid sequences and crystal structures of their selectivity filters. Molecular dynamics simulations show similar ion binding and conduction behavior between ammonium and potassium ions and identify the origin of the differences between the investigated potassium channels.
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Affiliation(s)
- Carl Öster
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Kumar Tekwani Movellan
- Department of NMR-Based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Benjamin Goold
- Faculty of Engineering and Physical Sciences, University of Southampton, University Road, SO17 1BJ Southampton, U.K.,Computational Biomolecular Dynamics Group, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Kitty Hendriks
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Sascha Lange
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Stefan Becker
- Department of NMR-Based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Bert L de Groot
- Computational Biomolecular Dynamics Group, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Wojciech Kopec
- Computational Biomolecular Dynamics Group, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Loren B Andreas
- Department of NMR-Based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Adam Lange
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany.,Institut für Biologie, Humboldt-Universität zu Berlin, Invalidenstr. 42, 10115 Berlin, Germany
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5
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Shukla VK, Siemons L, Gervasio FL, Hansen DF. Aromatic side-chain flips orchestrate the conformational sampling of functional loops in human histone deacetylase 8. Chem Sci 2021; 12:9318-9327. [PMID: 34349901 PMCID: PMC8278956 DOI: 10.1039/d1sc01929e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 05/27/2021] [Indexed: 12/12/2022] Open
Abstract
Human histone deacetylase 8 (HDAC8) is a key hydrolase in gene regulation and an important drug-target. High-resolution structures of HDAC8 in complex with substrates or inhibitors are available, which have provided insights into the bound state of HDAC8 and its function. Here, using long all-atom unbiased molecular dynamics simulations and Markov state modelling, we show a strong correlation between the conformation of aromatic side chains near the active site and opening and closing of the surrounding functional loops of HDAC8. We also investigated two mutants known to allosterically downregulate the enzymatic activity of HDAC8. Based on experimental data, we hypothesise that I19S-HDAC8 is unable to release the product, whereas both product release and substrate binding are impaired in the S39E-HDAC8 mutant. The presented results deliver detailed insights into the functional dynamics of HDAC8 and provide a mechanism for the substantial downregulation caused by allosteric mutations, including a disease causing one.
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Affiliation(s)
- Vaibhav Kumar Shukla
- Department of Structural and Molecular Biology, Division of Biosciences, University College London London WC1E 6BT UK
| | - Lucas Siemons
- Department of Structural and Molecular Biology, Division of Biosciences, University College London London WC1E 6BT UK
| | - Francesco L Gervasio
- Department of Chemistry, University College London London WC1E 6BT UK
- Pharmaceutical Sciences, University of Geneva Geneva CH-1211 Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva Geneva CH-1211 Switzerland
| | - D Flemming Hansen
- Department of Structural and Molecular Biology, Division of Biosciences, University College London London WC1E 6BT UK
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6
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Waters JK, Mawhinney TP, Emerich DW. Nitrogen Assimilation and Transport by Ex Planta Nitrogen-Fixing Bradyrhizobium diazoefficiens Bacteroids Is Modulated by Oxygen, Bacteroid Density and l-Malate. Int J Mol Sci 2020; 21:E7542. [PMID: 33066093 PMCID: PMC7589128 DOI: 10.3390/ijms21207542] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 10/09/2020] [Accepted: 10/12/2020] [Indexed: 12/23/2022] Open
Abstract
Symbiotic nitrogen fixation requires the transfer of fixed organic nitrogen compounds from the symbiotic bacteria to a host plant, yet the chemical nature of the compounds is in question. Bradyrhizobium diazoefficiens bacteroids were isolated anaerobically from soybean nodules and assayed at varying densities, varying partial pressures of oxygen, and varying levels of l-malate. Ammonium was released at low bacteroid densities and high partial pressures of oxygen, but was apparently taken up at high bacteroid densities and low partial pressures of oxygen in the presence of l-malate; these later conditions were optimal for amino acid excretion. The ratio of partial pressure of oxygen/bacteroid density of apparent ammonium uptake and of alanine excretion displayed an inverse relationship. Ammonium uptake, alanine and branch chain amino acid release were all dependent on the concentration of l-malate displaying similar K0.5 values of 0.5 mM demonstrating concerted regulation. The hyperbolic kinetics of ammonium uptake and amino acid excretion suggests transport via a membrane carrier and also suggested that transport was rate limiting. Glutamate uptake displayed exponential kinetics implying transport via a channel. The chemical nature of the compounds released were dependent upon bacteroid density, partial pressure of oxygen and concentration of l-malate demonstrating an integrated metabolism.
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Affiliation(s)
| | | | - David W. Emerich
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA; (J.K.W.); (T.P.M.)
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7
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Werbeck ND, Shukla VK, Kunze MBA, Yalinca H, Pritchard RB, Siemons L, Mondal S, Greenwood SOR, Kirkpatrick J, Marson CM, Hansen DF. A distal regulatory region of a class I human histone deacetylase. Nat Commun 2020; 11:3841. [PMID: 32737323 PMCID: PMC7395746 DOI: 10.1038/s41467-020-17610-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 07/09/2020] [Indexed: 01/05/2023] Open
Abstract
Histone deacetylases (HDACs) are key enzymes in epigenetics and important drug targets in cancer biology. Whilst it has been established that HDACs regulate many cellular processes, far less is known about the regulation of these enzymes themselves. Here, we show that HDAC8 is allosterically regulated by shifts in populations between exchanging states. An inactive state is identified, which is stabilised by a range of mutations and resembles a sparsely-populated state in equilibrium with active HDAC8. Computational models show that the inactive and active states differ by small changes in a regulatory region that extends up to 28 Å from the active site. The regulatory allosteric region identified here in HDAC8 corresponds to regions in other class I HDACs known to bind regulators, thus suggesting a general mechanism. The presented results pave the way for the development of allosteric HDAC inhibitors and regulators to improve the therapy for several disease states.
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Affiliation(s)
- Nicolas D Werbeck
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, UK
- Nuvisan ICB GmbH, Innovation Campus Berlin, Müllerstraße 178, 13353, Berlin, Germany
| | - Vaibhav Kumar Shukla
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - Micha B A Kunze
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - Havva Yalinca
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - Ruth B Pritchard
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - Lucas Siemons
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - Somnath Mondal
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - Simon O R Greenwood
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, UK
- Department of Chemistry, University College London, London, WC1E 6BT, UK
| | - John Kirkpatrick
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - Charles M Marson
- Department of Chemistry, University College London, London, WC1E 6BT, UK
| | - D Flemming Hansen
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, UK.
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8
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Rosenberg MM, Yao T, Patton GC, Redfield AG, Roberts MF, Hedstrom L. Enzyme-Substrate-Cofactor Dynamical Networks Revealed by High-Resolution Field Cycling Relaxometry. Biochemistry 2020; 59:2359-2370. [PMID: 32479091 PMCID: PMC8364753 DOI: 10.1021/acs.biochem.0c00212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The remarkable power and specificity of enzyme catalysis rely on the dynamic alignment of the enzyme, substrates, and cofactors, yet the role of dynamics has usually been approached from the perspective of the protein. We have been using an underappreciated NMR technique, subtesla high-resolution field cycling 31P NMR relaxometry, to investigate the dynamics of the enzyme-bound substrates and cofactor on guanosine-5'-monophosphate reductase (GMPR). GMPR forms two dead end, yet catalytically competent, complexes that mimic distinct steps in the catalytic cycle: E·IMP·NADP+ undergoes a partial hydride transfer reaction, while E·GMP·NADP+ undergoes a partial deamination reaction. A different cofactor conformation is required for each partial reaction. Here we report the effects of mutations designed to perturb cofactor conformation and ammonia binding with the goal of identifying the structural features that contribute to the distinct dynamic signatures of the hydride transfer and deamination complexes. These experiments suggest that Asp129 is a central cog in a dynamic network required for both hydride transfer and deamination. In contrast, Lys77 modulates the conformation and mobility of substrates and cofactors in a reaction-specific manner. Thr105 and Tyr318 are part of a deamination-specific dynamic network that includes the 2'-OH of GMP. These residues have comparatively little effect on the dynamic properties of the hydride transfer complex. These results further illustrate the potential of high-resolution field cycling NMR relaxometry for the investigation of ligand dynamics. In addition, exchange experiments indicate that NH3/NH4+ has a high affinity for the deamination complex but a low affinity for the hydride transfer complex, suggesting that the movement of ammonia may gate the cofactor conformational change. Collectively, these experiments reinforce the view that the enzyme, substrates, and cofactor are linked in intricate, reaction-specific, dynamic networks and demonstrate that distal portions of the substrates and cofactors are critical features in these networks.
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Affiliation(s)
- Masha M. Rosenberg
- Department of Biology, Brandeis University, MS009, 415 South St., Waltham MA 02453-9110 USA
| | - Tianjiong Yao
- Department of Biology, Brandeis University, MS009, 415 South St., Waltham MA 02453-9110 USA
| | - Gregory C. Patton
- Department of Biology, Brandeis University, MS009, 415 South St., Waltham MA 02453-9110 USA
| | - Alfred G. Redfield
- Department of Biochemistry, Brandeis University, MS009, 415 South Street, Waltham, MA 02453-9110 USA
| | - Mary F. Roberts
- Department of Chemistry, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467-9110 USA
| | - Lizbeth Hedstrom
- Department of Biology, Brandeis University, MS009, 415 South St., Waltham MA 02453-9110 USA
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02453-3808 USA
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9
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Eichmann C, Frey L, Maslennikov I, Riek R. Probing Ion Binding in the Selectivity Filter of the KcsA Potassium Channel. J Am Chem Soc 2019; 141:7391-7398. [DOI: 10.1021/jacs.9b01092] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Cédric Eichmann
- Laboratory of Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Lukas Frey
- Laboratory of Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | | | - Roland Riek
- Laboratory of Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
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10
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Eisele A, Zaun H, Kuballa J, Elling L. In Vitro One-Pot Enzymatic Synthesis of Hyaluronic Acid from Sucrose and N
-Acetylglucosamine: Optimization of the Enzyme Module System and Nucleotide Sugar Regeneration. ChemCatChem 2018. [DOI: 10.1002/cctc.201800370] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Anna Eisele
- Laboratory for Biomaterials, Institute of Biotechnology and Helmholtz-Institute for Biomedical Engineering; RWTH Aachen University; Pauwelsstraße 20 52074 Aachen Germany
| | - Henning Zaun
- Research and Development Department; GALAB Laboratories GmbH; Am Schleusengraben 7 21029 Hamburg Germany
| | - Jürgen Kuballa
- Research and Development Department; GALAB Laboratories GmbH; Am Schleusengraben 7 21029 Hamburg Germany
| | - Lothar Elling
- Laboratory for Biomaterials, Institute of Biotechnology and Helmholtz-Institute for Biomedical Engineering; RWTH Aachen University; Pauwelsstraße 20 52074 Aachen Germany
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11
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Liu J, Wang M, Yi H, Liu M, Zhu D, Wu Y, Jia R, Sun K, Yang Q, Chen S, Zhao X, Chen X, Cheng A. ATPase activity of GroEL is dependent on GroES and it is response for environmental stress in Riemerella anatipestifer. Microb Pathog 2018; 121:51-58. [PMID: 29678739 DOI: 10.1016/j.micpath.2018.04.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 04/06/2018] [Accepted: 04/16/2018] [Indexed: 12/13/2022]
Abstract
Riemerella anatipestifer (Ra) is a serious gram-negative pathogen of birds and can cause considerable economic losses. The survival mechanisms of R. anatipestifer in the host and environment remain largely unknown. Previous results have demonstrated that GroEL is a molecular chaperone and an important component of the response to various stresses in most bacteria. This study focused on whether GroEL is implicated in this process in R. anatipestifer. The 1629 bp groEL is highly conserved among other gram-negative bacteria (levels of sequence similarity > 60%). A structural analysis and ATPase activity assay revealed that RaGroEL had weak ATPase activity and that the enzyme activity was temperature and ion dependent. GroES partially enhanced the GroEL ATPase activity in the same temperature range. In addition, we studied the mRNA expression of groEL under abiotic stresses caused by heat shock, pH, salt and hydrogen peroxide. These stresses increased the transcription of groEL to varying degrees. In R. anatipestifer, the ATPase activity of GroEL is dependent on GroES and temperature. The expression of groEL was strongly induced by heat, pH, hydrogen peroxide and salt stress. This study is the first to show that GroEL in R. anatipestifer might play a major role in response to environmental stress.
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Affiliation(s)
- Jibin Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, 611130, Sichuan Province, PR China; Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan Province, 611130, PR China
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, 611130, Sichuan Province, PR China; Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan Province, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan Province, 611130, PR China
| | - Haibo Yi
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, 611130, Sichuan Province, PR China; Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan Province, 611130, PR China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, 611130, Sichuan Province, PR China; Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan Province, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan Province, 611130, PR China
| | - Dekang Zhu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, 611130, Sichuan Province, PR China; Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan Province, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan Province, 611130, PR China
| | - Ying Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, 611130, Sichuan Province, PR China; Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan Province, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan Province, 611130, PR China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, 611130, Sichuan Province, PR China; Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan Province, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan Province, 611130, PR China
| | - Kunfeng Sun
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, 611130, Sichuan Province, PR China; Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan Province, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan Province, 611130, PR China
| | - Qiao Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, 611130, Sichuan Province, PR China; Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan Province, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan Province, 611130, PR China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, 611130, Sichuan Province, PR China; Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan Province, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan Province, 611130, PR China
| | - Xinxin Zhao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, 611130, Sichuan Province, PR China; Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan Province, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan Province, 611130, PR China
| | - Xiaoyue Chen
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan Province, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan Province, 611130, PR China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, 611130, Sichuan Province, PR China; Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan Province, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan Province, 611130, PR China.
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12
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Lu W, Zhang R, Jiang H, Zhang H, Luo C. Computer-Aided Drug Design in Epigenetics. Front Chem 2018; 6:57. [PMID: 29594101 PMCID: PMC5857607 DOI: 10.3389/fchem.2018.00057] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 02/23/2018] [Indexed: 12/31/2022] Open
Abstract
Epigenetic dysfunction has been widely implicated in several diseases especially cancers thus highlights the therapeutic potential for chemical interventions in this field. With rapid development of computational methodologies and high-performance computational resources, computer-aided drug design has emerged as a promising strategy to speed up epigenetic drug discovery. Herein, we make a brief overview of major computational methods reported in the literature including druggability prediction, virtual screening, homology modeling, scaffold hopping, pharmacophore modeling, molecular dynamics simulations, quantum chemistry calculation, and 3D quantitative structure activity relationship that have been successfully applied in the design and discovery of epi-drugs and epi-probes. Finally, we discuss about major limitations of current virtual drug design strategies in epigenetics drug discovery and future directions in this field.
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Affiliation(s)
- Wenchao Lu
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Department of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Rukang Zhang
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Department of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Hao Jiang
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Department of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Huimin Zhang
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Cheng Luo
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Department of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
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13
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Sixto-López Y, Bello M, Correa-Basurto J. Insights into structural features of HDAC1 and its selectivity inhibition elucidated by Molecular dynamic simulation and Molecular Docking. J Biomol Struct Dyn 2018; 37:584-610. [PMID: 29447615 DOI: 10.1080/07391102.2018.1441072] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Histone deacetylases (HDACs) are a family of proteins whose main function is the removal of acetyl groups from lysine residues located on histone and non-histone substrates, which regulates gene transcription and other activities in cells. HDAC1 dysfunction has been implicated in cancer development and progression; thus, its inhibition has emerged as a new therapeutic strategy. Two additional metal binding sites (Site 1 and Site 2) in HDACs have been described that are primarily occupied by potassium ions, suggesting a possible structural role that affects HDAC activity. In this work, we explored the structural role of potassium ions in Site 1 and Site 2 and how they affect the interactions of compounds with high affinities for HDAC1 (AC1OCG0B, Chlamydocin, Dacinostat and Quisinostat) and SAHA (a pan-inhibitor) using molecular docking and molecular dynamics (MD) simulations in concert with a Molecular-Mechanics-Generalized-Born-Surface-Area (MMGBSA) approach. Four models were generated: one with a potassium ion (K+) in both sites (HDAC1k), a second with K+ only at site 1 (HDAC1ks1), a third with K+ only at site 2 (HDAC1ks2) and a fourth with no K+ (HDAC1wk). We found that the presence or absence of K+ not only impacted the structural flexibility of HDAC1, but also its molecular recognition, consistent with experimental findings. These results could therefore be useful for further structure-based drug design studies addressing new HDAC1 inhibitors.
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Affiliation(s)
- Yudibeth Sixto-López
- a Laboratorio de Modelado Molecular, Bioinformática y Diseño de fármacos, Sección de Estudios de Posgrado e Investigación , Escuela Superior de Medicina, Instituto Politécnico Nacional , Mexico City 11340 , Mexico
| | - Martiniano Bello
- a Laboratorio de Modelado Molecular, Bioinformática y Diseño de fármacos, Sección de Estudios de Posgrado e Investigación , Escuela Superior de Medicina, Instituto Politécnico Nacional , Mexico City 11340 , Mexico
| | - José Correa-Basurto
- a Laboratorio de Modelado Molecular, Bioinformática y Diseño de fármacos, Sección de Estudios de Posgrado e Investigación , Escuela Superior de Medicina, Instituto Politécnico Nacional , Mexico City 11340 , Mexico
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Hansen DF. Measurement of 15N longitudinal relaxation rates in 15NH 4+ spin systems to characterise rotational correlation times and chemical exchange. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2017; 279:91-98. [PMID: 28511856 PMCID: PMC5441844 DOI: 10.1016/j.jmr.2017.01.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 01/16/2017] [Accepted: 01/20/2017] [Indexed: 06/07/2023]
Abstract
Many chemical and biological processes rely on the movement of monovalent cations and an understanding of such processes can therefore only be achieved by characterising the dynamics of the involved ions. It has recently been shown that 15N-ammonium can be used as a proxy for potassium to probe potassium binding in bio-molecules such as DNA quadruplexes and enzymes. Moreover, equations have been derived to describe the time-evolution of 15N-based spin density operator elements of 15NH4+ spin systems. Herein NMR pulse sequences are derived to select specific spin density matrix elements of the 15NH4+ spin system and to measure their longitudinal relaxation in order to characterise the rotational correlation time of the 15NH4+ ion as well as report on chemical exchange events of the 15NH4+ ion. Applications to 15NH4+ in acidic aqueous solutions are used to cross-validate the developed pulse sequence while measurements of spin-relaxation rates of 15NH4+ bound to a 41kDa domain of the bacterial Hsp70 homologue DnaK are presented to show the general applicability of the derived pulse sequence. The rotational correlation time obtained for 15N-ammonium bound to DnaK is similar to the correlation time that describes the rotation about the threefold axis of a methyl group. The methodology presented here provides, together with the previous theoretical framework, an important step towards characterising the motional properties of cations in macromolecular systems.
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Affiliation(s)
- D Flemming Hansen
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom.
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15
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Vašák M, Schnabl J. Sodium and Potassium Ions in Proteins and Enzyme Catalysis. Met Ions Life Sci 2016; 16:259-90. [DOI: 10.1007/978-3-319-21756-7_8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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16
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Abstract
SAHA (vorinostat, Merck) is a famous clinical drug for zinc-containing histone deacetylase (HDAC) targets against cancer and several other human disorders, whose inhibition mechanism (namely the protonation mechanism) upon binding to HDAC has been debated for more than ten years. It is very challenging to verify experimentally and is still controversial theoretically. The popular "Class-dependent" (namely "Tyr-dependent") hypothesis is that the deprotonation of SAHA is mostly regulated by the conserved Tyr308 in class I HDAC while it is replaced by the His843 in class IIa HDAC. Herein, by elaborate QM(DFT)/MM MD simulations, we exclude the prevalent "Class-dependent" mechanism and advance a novel "Metal-dependent" mechanism, where the remote second metal site (K(+) in most HDAC and Ca(2+) in HDAC2) determines the protonation of SAHA. This proof-of-principle "Metal-dependent" mechanism opens up a new avenue to utilize the second metal site for isoform-selective inhibitor design.
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Affiliation(s)
- Jingwei Zhou
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P. R. China.
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17
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Lamb AL, Kappock TJ, Silvaggi NR. You are lost without a map: Navigating the sea of protein structures. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1854:258-68. [PMID: 25554228 DOI: 10.1016/j.bbapap.2014.12.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 12/22/2014] [Indexed: 11/26/2022]
Abstract
X-ray crystal structures propel biochemistry research like no other experimental method, since they answer many questions directly and inspire new hypotheses. Unfortunately, many users of crystallographic models mistake them for actual experimental data. Crystallographic models are interpretations, several steps removed from the experimental measurements, making it difficult for nonspecialists to assess the quality of the underlying data. Crystallographers mainly rely on "global" measures of data and model quality to build models. Robust validation procedures based on global measures now largely ensure that structures in the Protein Data Bank (PDB) are largely correct. However, global measures do not allow users of crystallographic models to judge the reliability of "local" features in a region of interest. Refinement of a model to fit into an electron density map requires interpretation of the data to produce a single "best" overall model. This process requires inclusion of most probable conformations in areas of poor density. Users who misunderstand this can be misled, especially in regions of the structure that are mobile, including active sites, surface residues, and especially ligands. This article aims to equip users of macromolecular models with tools to critically assess local model quality. Structure users should always check the agreement of the electron density map and the derived model in all areas of interest, even if the global statistics are good. We provide illustrated examples of interpreted electron density as a guide for those unaccustomed to viewing electron density.
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Affiliation(s)
- Audrey L Lamb
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, United States.
| | - T Joseph Kappock
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, United States
| | - Nicholas R Silvaggi
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, United States.
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Zhou J, Xie H, Liu Z, Luo HB, Wu R. Structure–Function Analysis of the Conserved Tyrosine and Diverse π-Stacking among Class I Histone Deacetylases: A QM (DFT)/MM MD Study. J Chem Inf Model 2014; 54:3162-71. [DOI: 10.1021/ci500513n] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Jingwei Zhou
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006 Guangdong, P.R. China
| | - Hujun Xie
- School
of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310035 Zhejiang, P.R. China
| | - Zhihong Liu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006 Guangdong, P.R. China
| | - Hai-Bin Luo
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006 Guangdong, P.R. China
| | - Ruibo Wu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006 Guangdong, P.R. China
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Werbeck ND, Hansen DF. Heteronuclear transverse and longitudinal relaxation in AX4 spin systems: application to (15)N relaxations in (15)NH4(+). JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 246:136-148. [PMID: 25128779 PMCID: PMC4283223 DOI: 10.1016/j.jmr.2014.06.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 06/06/2014] [Accepted: 06/09/2014] [Indexed: 06/03/2023]
Abstract
The equations that describe the time-evolution of transverse and longitudinal (15)N magnetisations in tetrahedral ammonium ions, (15)NH4(+), are derived from the Bloch-Wangsness-Redfield density operator relaxation theory. It is assumed that the relaxation of the spin-states is dominated by (1) the intra-molecular (15)N-(1)H and (1)H-(1)H dipole-dipole interactions and (2) interactions of the ammonium protons with remote spins, which also include the contribution to the relaxations that arise from the exchange of the ammonium protons with the bulk solvent. The dipole-dipole cross-correlated relaxation mechanisms between each of the (15)N-(1)H and (1)H-(1)H interactions are explicitly taken into account in the derivations. An application to (15)N-ammonium bound to a 41kDa domain of the protein DnaK is presented, where a comparison between experiments and simulations show that the ammonium ion rotates rapidly within its binding site with a local correlation time shorter than approximately 1ns. The theoretical framework provided here forms the basis for further investigations of dynamics of AX4 spin systems, with ammonium ions in solution and bound to proteins of particular interest.
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Affiliation(s)
- Nicolas D Werbeck
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - D Flemming Hansen
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom.
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Abstract
Histone deacetylases (HDACs) have found intense interest as drug targets for a variety of diseases, but there is disagreement about basic aspects of the inhibition and mechanism of HDACs. QM/MM calculations of HDAC8 including a large QM region provide a model that is consistent with the available crystal structures and structure-activity relationships of different HDAC inhibitors. The calculations support a spontaneous proton transfer from a hydroxamic acid to an active site histidine upon binding to the zinc. The role of the H142/D176 catalytic dyad as the general base of the reaction is elucidated. The reasons for the disagreements between previous proposals are discussed. The results provide detailed insights into the unique mechanism of HDACs, including the role of the two catalytic dyads and function of the potassium near the active site. They also have important implications for the design of novel inhibitors for a number of HDACs such as the class IIa HDACs.
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Affiliation(s)
- Kai Chen
- Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School , Shenzhen 518055, China
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