1
|
Nagae T, Takeda M, Noji T, Saito K, Aoyama H, Miyanoiri Y, Ito Y, Kainosho M, Hirose Y, Ishikita H, Mishima M. Direct evidence for a deprotonated lysine serving as a H-bond "acceptor" in a photoreceptor protein. Proc Natl Acad Sci U S A 2024; 121:e2404472121. [PMID: 39190358 PMCID: PMC11388336 DOI: 10.1073/pnas.2404472121] [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: 03/22/2024] [Accepted: 07/11/2024] [Indexed: 08/28/2024] Open
Abstract
Deprotonation or suppression of the pKa of the amino group of a lysine sidechain is a widely recognized phenomenon whereby the sidechain amino group transiently can act as a nucleophile at the active site of enzymatic reactions. However, a deprotonated lysine and its molecular interactions have not been directly experimentally detected. Here, we demonstrate a deprotonated lysine stably serving as an "acceptor" in a H-bond between the photosensor protein RcaE and its chromophore. Signal splitting and trans-H-bond J coupling observed by NMR spectroscopy provide direct evidence that Lys261 is deprotonated and serves as a H-bond acceptor for the chromophore NH group. Quantum mechanical/molecular mechanical calculations also indicate that this H-bond exists stably. Interestingly, the sidechain amino group of the lysine can act as both donor and acceptor. The remarkable shift in the H-bond characteristics arises from a decrease in solvation, triggered by photoisomerization. Our results provide insights into the dual role of this lysine. This mechanism has broad implications for other biological reactions in which lysine plays a role.
Collapse
Affiliation(s)
- Takayuki Nagae
- Department of Molecular Biophysics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Mitsuhiro Takeda
- Department of Molecular Biophysics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Tomoyasu Noji
- Research Center for Advanced Science and Technology, The University of Tokyo, Meguro-ku, Tokyo 153-8904, Japan
- Department of Applied Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo 118-8656, Japan
| | - Keisuke Saito
- Research Center for Advanced Science and Technology, The University of Tokyo, Meguro-ku, Tokyo 153-8904, Japan
- Department of Applied Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo 118-8656, Japan
| | - Hiroshi Aoyama
- Department of Molecular Biophysics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Yohei Miyanoiri
- Research Center for State-of-the-Art Functional Protein Analysis, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yutaka Ito
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Hachioji 192-0397, Japan
| | - Masatsune Kainosho
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Hachioji 192-0397, Japan
| | - Yuu Hirose
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Aichi 441-8580, Japan
| | - Hiroshi Ishikita
- Research Center for Advanced Science and Technology, The University of Tokyo, Meguro-ku, Tokyo 153-8904, Japan
- Department of Applied Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo 118-8656, Japan
| | - Masaki Mishima
- Department of Molecular Biophysics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| |
Collapse
|
2
|
Alexandrescu AT, Dregni AJ. The Temperature Dependence of Hydrogen Bonds Is More Uniform in Stable Proteins: An Analysis of NMR h3J NC' Couplings in Four Different Protein Structures. Molecules 2024; 29:2950. [PMID: 38998901 PMCID: PMC11243222 DOI: 10.3390/molecules29132950] [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: 05/18/2024] [Revised: 06/11/2024] [Accepted: 06/18/2024] [Indexed: 07/14/2024] Open
Abstract
Long-range HNCO NMR spectra for proteins show crosspeaks due to 1JNC', 2JNC', 3JNCγ, and h3JNC' couplings. The h3JNC' couplings are transmitted through hydrogen bonds and their sizes are correlated to hydrogen bond lengths. We collected long-range HNCO data at a series of temperatures for four protein structures. P22i and CUS-3i are six-stranded beta-barrel I-domains from phages P22 and CUS-3 that share less than 40% sequence identity. The cis and trans states of the C-terminal domain from pore-forming toxin hemolysin ΙΙ (HlyIIC) arise from the isomerization of a single G404-P405 peptide bond. For P22i and CUS-3i, hydrogen bonds detected by NMR agree with those observed in the corresponding domains from cryoEM structures of the two phages. Hydrogen bond lengths derived from the h3JNC' couplings, however, are poorly conserved between the distantly related CUS-3i and P22i domains and show differences even between the closely related cis and trans state structures of HlyIIC. This is consistent with hydrogen bond lengths being determined by local differences in structure rather than the overall folding topology. With increasing temperature, hydrogen bonds typically show an apparent increase in length that has been attributed to protein thermal expansion. Some hydrogen bonds are invariant with temperature, however, while others show apparent decreases in length, suggesting they become stabilized with increasing temperature. Considering the data for the three proteins in this study and previously published data for ubiquitin and GB3, lowered protein folding stability and cooperativity corresponds with a larger range of temperature responses for hydrogen bonds. This suggests a partial uncoupling of hydrogen bond energetics from global unfolding cooperativity as protein stability decreases.
Collapse
Affiliation(s)
- Andrei T. Alexandrescu
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Aurelio J. Dregni
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| |
Collapse
|
3
|
Bhai L, Thomas JK, Conroy DW, Xu Y, Al-Hashimi HM, Jaroniec CP. Hydrogen bonding in duplex DNA probed by DNP enhanced solid-state NMR N-H bond length measurements. Front Mol Biosci 2023; 10:1286172. [PMID: 38111464 PMCID: PMC10726973 DOI: 10.3389/fmolb.2023.1286172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/09/2023] [Indexed: 12/20/2023] Open
Abstract
Numerous biological processes and mechanisms depend on details of base pairing and hydrogen bonding in DNA. Hydrogen bonds are challenging to quantify by X-ray crystallography and cryo-EM due to difficulty of visualizing hydrogen atom locations but can be probed with site specificity by NMR spectroscopy in solution and the solid state with the latter particularly suited to large, slowly tumbling DNA complexes. Recently, we showed that low-temperature dynamic nuclear polarization (DNP) enhanced solid-state NMR is a valuable tool for distinguishing Hoogsteen base pairs (bps) from canonical Watson-Crick bps in various DNA systems under native-like conditions. Here, using a model 12-mer DNA duplex containing two central adenine-thymine (A-T) bps in either Watson-Crick or Hoogsteen confirmation, we demonstrate DNP solid-state NMR measurements of thymine N3-H3 bond lengths, which are sensitive to details of N-H···N hydrogen bonding and permit hydrogen bonds for the two bp conformers to be systematically compared within the same DNA sequence context. For this DNA duplex, effectively identical TN3-H3 bond lengths of 1.055 ± 0.011 Å and 1.060 ± 0.011 Å were found for Watson-Crick A-T and Hoogsteen A (syn)-T base pairs, respectively, relative to a reference amide bond length of 1.015 ± 0.010 Å determined for N-acetyl-valine under comparable experimental conditions. Considering that prior quantum chemical calculations which account for zero-point motions predict a somewhat longer effective peptide N-H bond length of 1.041 Å, in agreement with solution and solid-state NMR studies of peptides and proteins at ambient temperature, to facilitate direct comparisons with these earlier studies TN3-H3 bond lengths for the DNA samples can be readily scaled appropriately to yield 1.083 Å and 1.087 Å for Watson-Crick A-T and Hoogsteen A (syn)-T bps, respectively, relative to the 1.041 Å reference peptide N-H bond length. Remarkably, in the context of the model DNA duplex, these results indicate that there are no significant differences in N-H···N A-T hydrogen bonds between Watson-Crick and Hoogsteen bp conformers. More generally, high precision measurements of N-H bond lengths by low-temperature DNP solid-state NMR based methods are expected to facilitate detailed comparative analysis of hydrogen bonding for a range of DNA complexes and base pairing environments.
Collapse
Affiliation(s)
- Lakshmi Bhai
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States
| | - Justin K. Thomas
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States
| | - Daniel W. Conroy
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States
| | - Yu Xu
- Department of Chemistry, Duke University, Durham, NC, United States
| | - Hashim M. Al-Hashimi
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, United States
| | - Christopher P. Jaroniec
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States
| |
Collapse
|
4
|
Wang J, Horwitz MA, Dürr AB, Ibba F, Pupo G, Gao Y, Ricci P, Christensen KE, Pathak TP, Claridge TDW, Lloyd-Jones GC, Paton RS, Gouverneur V. Asymmetric Azidation under Hydrogen Bonding Phase-Transfer Catalysis: A Combined Experimental and Computational Study. J Am Chem Soc 2022; 144:4572-4584. [PMID: 35230845 PMCID: PMC8931729 DOI: 10.1021/jacs.1c13434] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
![]()
Asymmetric catalytic
azidation has increased in importance to access
enantioenriched nitrogen containing molecules, but methods that employ
inexpensive sodium azide remain scarce. This encouraged us to undertake
a detailed study on the application of hydrogen bonding phase-transfer
catalysis (HB-PTC) to enantioselective azidation with sodium azide.
So far, this phase-transfer manifold has been applied exclusively
to insoluble metal alkali fluorides for carbon–fluorine bond
formation. Herein, we disclose the asymmetric ring opening of meso aziridinium electrophiles derived from β-chloroamines
with sodium azide in the presence of a chiral bisurea catalyst. The
structure of novel hydrogen bonded azide complexes was analyzed computationally,
in the solid state by X-ray diffraction, and in solution phase by 1H and 14N/15N NMR spectroscopy. With N-isopropylated BINAM-derived bisurea, end-on binding of
azide in a tripodal fashion to all three NH bonds is energetically
favorable, an arrangement reminiscent of the corresponding dynamically
more rigid trifurcated hydrogen-bonded fluoride complex. Computational
analysis informs that the most stable transition state leading to
the major enantiomer displays attack from the hydrogen-bonded end
of the azide anion. All three H-bonds are retained in the transition
state; however, as seen in asymmetric HB-PTC fluorination, the H-bond
between the nucleophile and the monodentate urea lengthens most noticeably
along the reaction coordinate. Kinetic studies corroborate with the
turnover rate limiting event resulting in a chiral ion pair containing
an aziridinium cation and a catalyst-bound azide anion, along with
catalyst inhibition incurred by accumulation of NaCl. This study demonstrates
that HB-PTC can serve as an activation mode for inorganic salts other
than metal alkali fluorides for applications in asymmetric synthesis.
Collapse
Affiliation(s)
- Jimmy Wang
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Matthew A Horwitz
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Alexander B Dürr
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Francesco Ibba
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Gabriele Pupo
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Yuan Gao
- School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, U.K
| | - Paolo Ricci
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Kirsten E Christensen
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Tejas P Pathak
- Novartis Institutes for Biomedical Research, 22 Windsor Street, Cambridge, Massachusetts 02139, United States
| | - Timothy D W Claridge
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Guy C Lloyd-Jones
- School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, U.K
| | - Robert S Paton
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80528, United States
| | - Véronique Gouverneur
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| |
Collapse
|
5
|
Aguion PI, Marchanka A. Strategies for RNA Resonance Assignment by 13C/ 15N- and 1H-Detected Solid-State NMR Spectroscopy. Front Mol Biosci 2021; 8:743181. [PMID: 34746232 PMCID: PMC8563574 DOI: 10.3389/fmolb.2021.743181] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 09/03/2021] [Indexed: 12/27/2022] Open
Abstract
Magic angle spinning (MAS) solid-state NMR (ssNMR) is an established tool that can be applied to non-soluble or non-crystalline biomolecules of any size or complexity. The ssNMR method advances rapidly due to technical improvements and the development of advanced isotope labeling schemes. While ssNMR has shown significant progress in structural studies of proteins, the number of RNA studies remains limited due to ssNMR methodology that is still underdeveloped. Resonance assignment is the most critical and limiting step in the structure determination protocol that defines the feasibility of NMR studies. In this review, we summarize the recent progress in RNA resonance assignment methods and approaches for secondary structure determination by ssNMR. We critically discuss advantages and limitations of conventional 13C- and 15N-detected experiments and novel 1H-detected methods, identify optimal regimes for RNA studies by ssNMR, and provide our view on future ssNMR studies of RNA in large RNP complexes.
Collapse
Affiliation(s)
| | - Alexander Marchanka
- Institute for Organic Chemistry and Centre of Biomolecular Drug Research (BMWZ), Leibniz University Hannover, Hanover, Germany
| |
Collapse
|
6
|
Tiwari S, Arya N, Mishra SK, Suryaprakash N. Competing HB acceptors: an extensive NMR investigations corroborated by single crystal XRD and DFT calculations. RSC Adv 2021; 11:15195-15202. [PMID: 35424030 PMCID: PMC8698242 DOI: 10.1039/d1ra02538d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 04/11/2021] [Indexed: 11/21/2022] Open
Abstract
A series of N-benzoylanthranilamide derivatives have been synthesized with the substitution of competitive HB acceptors and investigated by NMR spectroscopy and single crystal XRD. The interesting rivalry for HB acceptance between [double bond splayed left]C[double bond, length as m-dash]O and X (F or OMe) is observed in the investigated molecules which leads to an unusual increase in the electron density at the site of one of the NH protons, reflecting in the high field resonance in the 1H NMR spectrum. The NMR experimental findings and single crystal XRD are further reinforced by the DFT studies.
Collapse
Affiliation(s)
- Surbhi Tiwari
- NMR Research Centre and Solid State and Structural Chemistry Unit, Indian Institute of Science Bangalore 560012 India +91 80 23601550 +91 80 23607344 +91 80 22933300 +91 98 45124802
| | - Neeru Arya
- NMR Research Centre and Solid State and Structural Chemistry Unit, Indian Institute of Science Bangalore 560012 India +91 80 23601550 +91 80 23607344 +91 80 22933300 +91 98 45124802
| | - Sandeep Kumar Mishra
- Department of Physics and NMR Research Centre, Indian Institute of Science Education and Research Pune 411008 India
| | - N Suryaprakash
- NMR Research Centre and Solid State and Structural Chemistry Unit, Indian Institute of Science Bangalore 560012 India +91 80 23601550 +91 80 23607344 +91 80 22933300 +91 98 45124802
| |
Collapse
|
7
|
Linclau B, Ardá A, Reichardt NC, Sollogoub M, Unione L, Vincent SP, Jiménez-Barbero J. Fluorinated carbohydrates as chemical probes for molecular recognition studies. Current status and perspectives. Chem Soc Rev 2021; 49:3863-3888. [PMID: 32520059 DOI: 10.1039/c9cs00099b] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
This review provides an extensive summary of the effects of carbohydrate fluorination with regard to changes in physical, chemical and biological properties with respect to regular saccharides. The specific structural, conformational, stability, reactivity and interaction features of fluorinated sugars are described, as well as their applications as probes and in chemical biology.
Collapse
Affiliation(s)
- Bruno Linclau
- School of Chemistry, University of Southampton, Highfield, Southampton SO171BJ, UK
| | - Ana Ardá
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160 Derio, Spain.
| | | | - Matthieu Sollogoub
- Sorbonne Université, CNRS, Institut Parisien de Chimie Moléculaire, UMR 8232, 4 place Jussieu, 75005 Paris, France
| | - Luca Unione
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Science, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
| | - Stéphane P Vincent
- Department of Chemistry, Laboratory of Bio-organic Chemistry, University of Namur (UNamur), B-5000 Namur, Belgium
| | - Jesús Jiménez-Barbero
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160 Derio, Spain. and Ikerbasque, Basque Foundation for Science, Maria Diaz de Haro 3, 48013 Bilbao, Spain and Department of Organic Chemistry II, Faculty of Science and Technology, UPV/EHU, 48940 Leioa, Spain
| |
Collapse
|
8
|
Liu Y, He Y, Yang Y, Liu Y. Theoretical study on the detailed excited state triple proton transfer mechanism of cyclic 6-Azaindole trimer. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2020.138137] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
9
|
Advanced approaches for elucidating structures of large RNAs using NMR spectroscopy and complementary methods. Methods 2020; 183:93-107. [DOI: 10.1016/j.ymeth.2020.01.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 11/11/2019] [Accepted: 01/16/2020] [Indexed: 11/23/2022] Open
|
10
|
Bacanu GR, Rantaharju J, Hoffman G, Walkey MC, Bloodworth S, Concistrè M, Whitby RJ, Levitt MH. An Internuclear J-Coupling of 3He Induced by Molecular Confinement. J Am Chem Soc 2020; 142:16926-16929. [PMID: 32945165 DOI: 10.1021/jacs.0c08586] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The solution-state 13C NMR spectrum of the endofullerene 3He@C60 displays a doublet structure due to a J-coupling of magnitude 77.5 ± 0.2 mHz at 340 K between the 3He nucleus and a 13C nucleus of the enclosing carbon surface. The J-coupling increases in magnitude with increasing temperature. Quantum chemistry calculations successfully predict the approximate magnitude of the coupling. This observation shows that the mutual proximity of molecular or atomic species is sufficient to induce a finite scalar nuclear spin-spin coupling, providing that translational motion is restricted by confinement. The phenomenon may have applications to the study of surface interactions and to mechanically bound species.
Collapse
Affiliation(s)
| | - Jyrki Rantaharju
- Department of Chemistry, University of Southampton, Southampton, SO17 1BJ, U.K
| | - Gabriela Hoffman
- Department of Chemistry, University of Southampton, Southampton, SO17 1BJ, U.K
| | - Mark C Walkey
- Department of Chemistry, University of Southampton, Southampton, SO17 1BJ, U.K
| | - Sally Bloodworth
- Department of Chemistry, University of Southampton, Southampton, SO17 1BJ, U.K
| | - Maria Concistrè
- Department of Chemistry, University of Southampton, Southampton, SO17 1BJ, U.K
| | - Richard J Whitby
- Department of Chemistry, University of Southampton, Southampton, SO17 1BJ, U.K
| | - Malcolm H Levitt
- Department of Chemistry, University of Southampton, Southampton, SO17 1BJ, U.K
| |
Collapse
|
11
|
Tan C, Chen Y, Peng X, Chen Z, Cai S, Cross TA, Fu R. Revealing weak histidine 15N homonuclear scalar couplings using Solid-State Magic-Angle-Spinning NMR spectroscopy. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2020; 316:106757. [PMID: 32535401 PMCID: PMC7426724 DOI: 10.1016/j.jmr.2020.106757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 05/12/2020] [Accepted: 05/27/2020] [Indexed: 05/05/2023]
Abstract
The tautomeric structure and chemistry of the histidine imidazole ring play active roles in many structurally and functionally important proteins and polypeptides. While in NMR spectroscopy histidine chemical shifts (e.g. 15N, 13C, and 1H) have been commonly used to characterize the tautomeric structure, hydrogen bonding, and torsion angles, homonuclear 15N scalar couplings in histidine have rarely been reported. Here, we propose double spin-echo sequences to compare the observed signals with and without a 90° pulse between the two spin-echo periods, such that their signal ratio as a function of the echo time solely depends on homonuclear scalar couplings, allowing for measuring weak homonuclear scalar couplings without influence from transverse dephasing effects, thus capable of revealing hydrogen-bond mediated 15N-15N J-couplings that can provide direct and definitive evidence for the formation of N…H…N hydrogen-bonding associated with the imidazole ring. We used two 13C,15N labeled histidine samples recrystallized from solutions at pH 6.3 and pH 11.0 to demonstrate the feasibility of this method and reveal the existence of a weak two-bond scalar coupling between the Nδ1 and Nε2 sites in the histidine imidazole ring in three tautomeric states and the presence of a hydrogen-bond mediated scalar coupling between the Nδ1 site in the imidazole ring and the backbone Nα site in the histidine neutral τ and π states. Our results demonstrate that weak 15N homonuclear scalar couplings can be measured even when their values are less than their corresponding intrinsic natural linewidths, thus providing direct and definitive evidence for the formation of N…H…N hydrogen bonding that is associated with the histidine imidazole ring.
Collapse
Affiliation(s)
- Chunhua Tan
- National High Magnet Field Lab, 1800 East Paul Dirac Drive, Tallahassee, FL 32310, USA; Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen, Fujian 361005, China
| | - Yuquan Chen
- CAS Key Laboratory of Microscale Magnetic Resonance and Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
| | - Xinhua Peng
- CAS Key Laboratory of Microscale Magnetic Resonance and Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
| | - Zhong Chen
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen, Fujian 361005, China
| | - Shuhui Cai
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen, Fujian 361005, China
| | - Timothy A Cross
- National High Magnet Field Lab, 1800 East Paul Dirac Drive, Tallahassee, FL 32310, USA; Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Riqiang Fu
- National High Magnet Field Lab, 1800 East Paul Dirac Drive, Tallahassee, FL 32310, USA.
| |
Collapse
|
12
|
Vícha J, Švec P, Růžičková Z, Samsonov MA, Bártová K, Růžička A, Straka M, Dračínský M. Experimental and Theoretical Evidence of Spin‐Orbit Heavy Atom on the Light Atom
1
H NMR Chemical Shifts Induced through H⋅⋅⋅I
−
Hydrogen Bond. Chemistry 2020; 26:8698-8702. [DOI: 10.1002/chem.202001532] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Indexed: 01/11/2023]
Affiliation(s)
- Jan Vícha
- Institute of Organic Chemistry and Biochemistry, AS CR Flemingovo nám. 2 Prague 16610 Czech Republic
- Centre of Polymer SystemsTomas Bata University in Zlín Tomáše Bati 5678 Zlín 760 01 Czech Republic
| | - Petr Švec
- Department of General and Inorganic ChemistryUniversity of Pardubice Studentská 573 Pardubice 53210 Czech Republic
| | - Zdeňka Růžičková
- Department of General and Inorganic ChemistryUniversity of Pardubice Studentská 573 Pardubice 53210 Czech Republic
| | - Maksim A. Samsonov
- Department of General and Inorganic ChemistryUniversity of Pardubice Studentská 573 Pardubice 53210 Czech Republic
| | - Kateřina Bártová
- Institute of Organic Chemistry and Biochemistry, AS CR Flemingovo nám. 2 Prague 16610 Czech Republic
| | - Aleš Růžička
- Department of General and Inorganic ChemistryUniversity of Pardubice Studentská 573 Pardubice 53210 Czech Republic
| | - Michal Straka
- Institute of Organic Chemistry and Biochemistry, AS CR Flemingovo nám. 2 Prague 16610 Czech Republic
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry, AS CR Flemingovo nám. 2 Prague 16610 Czech Republic
| |
Collapse
|
13
|
von der Heiden D, Vanderkooy A, Erdélyi M. Halogen bonding in solution: NMR spectroscopic approaches. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2019.213147] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
14
|
Liu Y, Yang Y, Jia X, Ma Q, He Y, Zhai H, Zhang Y, Liu Y. Theoretical study of the excited state intramolecular double proton transfer and spectral behaviors of 7-hydroxyquinoline-8-carboxylic acid. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.112552] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
15
|
Yu B, Pletka CC, Iwahara J. NMR Observation of Intermolecular Hydrogen Bonds between Protein Tyrosine Side-Chain OH and DNA Phosphate Groups. J Phys Chem B 2020; 124:1065-1070. [PMID: 31958014 PMCID: PMC7021563 DOI: 10.1021/acs.jpcb.9b10987] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Hydrogen bonds between protein side-chain hydroxyl (OH) and phosphate groups are one of the most common types of intermolecular hydrogen bonds in protein-DNA/RNA complexes. Using NMR spectroscopy, we identified and characterized the hydrogen bonds between tyrosine side-chain OH and DNA phosphate groups in a protein-DNA complex. These OH groups exhibited relatively slow hydrogen-exchange rates and sizable scalar couplings between hydroxyl 1H and DNA phosphate 31P nuclei across the hydrogen bonds. Information about intermolecular hydrogen bonds facilitates investigations of the DNA/RNA recognition by the protein.
Collapse
Affiliation(s)
- Binhan Yu
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, USA
| | - Channing C. Pletka
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, USA
| | - Junji Iwahara
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, USA
| |
Collapse
|
16
|
Movellan K, Wegstroth M, Overkamp K, Leonov A, Becker S, Andreas LB. Imidazole-Imidazole Hydrogen Bonding in the pH-Sensing Histidine Side Chains of Influenza A M2. J Am Chem Soc 2020; 142:2704-2708. [PMID: 31970979 PMCID: PMC7307898 DOI: 10.1021/jacs.9b10984] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Indexed: 12/28/2022]
Abstract
The arrangement of histidine side chains in influenza A M2 tetramer determines their pKa values, which define pH-controlled proton conduction critical to the virus lifecycle. Both water-associated and hydrogen-bonded imidazole-imidazolium histidine quaternary structures have been proposed, based on crystal structures and NMR chemical shifts, respectively. Here we show, using the conduction domain construct of M2 in lipid bilayers, that the imidazole rings are hydrogen bonded even at a pH of 7.8 in the neutral charge state. An intermolecular 8.9 ± 0.3 Hz 2hJNN hydrogen bond is observed between H37 Nε and Nδ recorded in a fully protonated sample with 100 kHz magic-angle spinning. This interaction could not be detected in the drug-bound sample.
Collapse
Affiliation(s)
- Kumar
Tekwani Movellan
- Department of NMR Based Structural
Biology, Max Planck Institute for Biophysical
Chemistry, Am Fassberg 11, Göttingen 37077, Germany
| | - Melanie Wegstroth
- Department of NMR Based Structural
Biology, Max Planck Institute for Biophysical
Chemistry, Am Fassberg 11, Göttingen 37077, Germany
| | - Kerstin Overkamp
- Department of NMR Based Structural
Biology, Max Planck Institute for Biophysical
Chemistry, Am Fassberg 11, Göttingen 37077, Germany
| | - Andrei Leonov
- Department of NMR Based Structural
Biology, Max Planck Institute for Biophysical
Chemistry, Am Fassberg 11, Göttingen 37077, Germany
| | - Stefan Becker
- Department of NMR Based Structural
Biology, Max Planck Institute for Biophysical
Chemistry, Am Fassberg 11, Göttingen 37077, Germany
| | - Loren B. Andreas
- Department of NMR Based Structural
Biology, Max Planck Institute for Biophysical
Chemistry, Am Fassberg 11, Göttingen 37077, Germany
| |
Collapse
|
17
|
Fu R, Miao Y, Qin H, Cross TA. Observation of the Imidazole-Imidazolium Hydrogen Bonds Responsible for Selective Proton Conductance in the Influenza A M2 Channel. J Am Chem Soc 2020; 142:2115-2119. [PMID: 31970982 DOI: 10.1021/jacs.9b09985] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The integral membrane M2 protein is a 97-residue membrane protein that assembles as a tetramer to conduct protons at a slow rate (102-103/s) when activated by low pH. The proton conductance mechanism has been extensively debated in the literature, but it is accepted that the proton conductance is facilitated by hydrogen bonds involving the His37 residues. However, the hydrogen bonding partnership remains unresolved. Here, we report on the measurement of 15N-15N J-couplings of 15N His37-labeled full length M2 (M2FL) protein from Influenza A virus embedded in synthetic liquid crystalline lipid bilayers using two-dimensional J-resolved NMR spectroscopy. We experimentally observed the hydrogen-bond mediated J-couplings between Nδ1 and Nε2 of adjacent His37 imidazole rings, providing direct evidence for the existence of various imidazolium-imidazole hydrogen-bonding geometries in the histidine tetrad at low pH, thus validating the proton conduction mechanism in the M2FL protein by which the proton is transferred through the breaking and reforming of the hydrogen bonds between pairs of His37 residues.
Collapse
Affiliation(s)
- Riqiang Fu
- National High Magnet Field Lab , 1800 East Paul Dirac Drive , Tallahassee , Florida 32310 , United States
| | - Yimin Miao
- Department of Chemistry and Biochemistry , Florida State University , Tallahassee , Florida 32306 , United States
| | - Huajun Qin
- Department of Chemistry and Biochemistry , Florida State University , Tallahassee , Florida 32306 , United States
| | - Timothy A Cross
- National High Magnet Field Lab , 1800 East Paul Dirac Drive , Tallahassee , Florida 32310 , United States.,Department of Chemistry and Biochemistry , Florida State University , Tallahassee , Florida 32306 , United States
| |
Collapse
|
18
|
On the calculation of magnetic properties of nucleic acids in liquid water with the sequential QM/MM method. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111611] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
|
19
|
Li Y, Zhong W, Koay AZ, Ng HQ, Nah Q, Wong YH, Hill J, Lescar J, Dedon PC, Kang C. Backbone resonance assignment for the full length tRNA-(N 1G37) methyltransferase of Pseudomonas aeruginosa. BIOMOLECULAR NMR ASSIGNMENTS 2019; 13:327-332. [PMID: 31175551 DOI: 10.1007/s12104-019-09900-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 05/31/2019] [Indexed: 06/09/2023]
Abstract
Bacterial tRNA (guanine37-N1)-methyltransferase (TrmD) plays important roles in translation, making it an important target for the development of new antibacterial compounds. TrmD comprises two domains with the N-terminal domain binding to the S-adenosyl-L-methionine (SAM) cofactor and the C-terminal domain critical for tRNA binding. Bacterial TrmD is functional as a dimer. Here we report the backbone NMR resonance assignments for the full length TrmD protein of Pseudomonas aeruginosa. Most resonances were assigned and the secondary structure for each amino acid was determined according to the assigned backbone resonances. The availability of the assignment will be valuable for exploring molecular interactions of TrmD with ligands, inhibitors and tRNA.
Collapse
Affiliation(s)
- Yan Li
- Experimental Drug Development Centre, 10 Biopolis Road, #05-01, Singapore, 138670, Singapore
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, 430030, Hubei, People's Republic of China
| | - Wenhe Zhong
- Infectious Disease and Antimicrobial Resistance Interdisciplinary Research Groups, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore, 138602, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, 636921, Singapore
| | - Ann Zhufang Koay
- Experimental Drug Development Centre, 10 Biopolis Road, #05-01, Singapore, 138670, Singapore
| | - Hui Qi Ng
- Experimental Drug Development Centre, 10 Biopolis Road, #05-01, Singapore, 138670, Singapore
| | - Qianhui Nah
- Infectious Disease and Antimicrobial Resistance Interdisciplinary Research Groups, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore, 138602, Singapore
| | - Yee Hwa Wong
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, 636921, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Jeffrey Hill
- Experimental Drug Development Centre, 10 Biopolis Road, #05-01, Singapore, 138670, Singapore
| | - Julien Lescar
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, 636921, Singapore.
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
| | - Peter C Dedon
- Infectious Disease and Antimicrobial Resistance Interdisciplinary Research Groups, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore, 138602, Singapore.
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - CongBao Kang
- Experimental Drug Development Centre, 10 Biopolis Road, #05-01, Singapore, 138670, Singapore.
| |
Collapse
|
20
|
Emwas AH, Roy R, McKay RT, Tenori L, Saccenti E, Gowda GAN, Raftery D, Alahmari F, Jaremko L, Jaremko M, Wishart DS. NMR Spectroscopy for Metabolomics Research. Metabolites 2019; 9:E123. [PMID: 31252628 PMCID: PMC6680826 DOI: 10.3390/metabo9070123] [Citation(s) in RCA: 519] [Impact Index Per Article: 103.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 06/14/2019] [Accepted: 06/18/2019] [Indexed: 12/14/2022] Open
Abstract
Over the past two decades, nuclear magnetic resonance (NMR) has emerged as one of the three principal analytical techniques used in metabolomics (the other two being gas chromatography coupled to mass spectrometry (GC-MS) and liquid chromatography coupled with single-stage mass spectrometry (LC-MS)). The relative ease of sample preparation, the ability to quantify metabolite levels, the high level of experimental reproducibility, and the inherently nondestructive nature of NMR spectroscopy have made it the preferred platform for long-term or large-scale clinical metabolomic studies. These advantages, however, are often outweighed by the fact that most other analytical techniques, including both LC-MS and GC-MS, are inherently more sensitive than NMR, with lower limits of detection typically being 10 to 100 times better. This review is intended to introduce readers to the field of NMR-based metabolomics and to highlight both the advantages and disadvantages of NMR spectroscopy for metabolomic studies. It will also explore some of the unique strengths of NMR-based metabolomics, particularly with regard to isotope selection/detection, mixture deconvolution via 2D spectroscopy, automation, and the ability to noninvasively analyze native tissue specimens. Finally, this review will highlight a number of emerging NMR techniques and technologies that are being used to strengthen its utility and overcome its inherent limitations in metabolomic applications.
Collapse
Affiliation(s)
- Abdul-Hamid Emwas
- Core Labs, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Raja Roy
- Centre of Biomedical Research, Formerly, Centre of Biomedical Magnetic Resonance, Sanjay Gandhi Post-Graduate Institute of Medical Sciences Campus, Uttar Pradesh 226014, India
| | - Ryan T McKay
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2W2, Canada
| | - Leonardo Tenori
- Department of Experimental and Clinical Medicine, University of Florence, Largo Brambilla 3, 50134 Florence, Italy
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - G A Nagana Gowda
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican St., Seattle, WA 98109, USA
| | - Daniel Raftery
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican St., Seattle, WA 98109, USA
- Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue, Seattle, WA 98109, USA
| | - Fatimah Alahmari
- Department of NanoMedicine Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman bin Faisal University, Dammam 31441, Saudi Arabia
| | - Lukasz Jaremko
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Mariusz Jaremko
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - David S Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E8, Canada
| |
Collapse
|
21
|
Zhang H, Keane SC. Advances that facilitate the study of large RNA structure and dynamics by nuclear magnetic resonance spectroscopy. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1541. [PMID: 31025514 PMCID: PMC7169810 DOI: 10.1002/wrna.1541] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 01/18/2019] [Accepted: 04/02/2019] [Indexed: 12/22/2022]
Abstract
The characterization of functional yet nonprotein coding (nc) RNAs has expanded the role of RNA in the cell from a passive player in the central dogma of molecular biology to an active regulator of gene expression. The misregulation of ncRNA function has been linked with a variety of diseases and disorders ranging from cancers to neurodegeneration. However, a detailed molecular understanding of how ncRNAs function has been limited; due, in part, to the difficulties associated with obtaining high-resolution structures of large RNAs. Tertiary structure determination of RNA as a whole is hampered by various technical challenges, all of which are exacerbated as the size of the RNA increases. Namely, RNAs tend to be highly flexible and dynamic molecules, which are difficult to crystallize. Biomolecular nuclear magnetic resonance (NMR) spectroscopy offers a viable alternative to determining the structure of large RNA molecules that do not readily crystallize, but is itself hindered by some technical limitations. Recently, a series of advancements have allowed the biomolecular NMR field to overcome, at least in part, some of these limitations. These advances include improvements in sample preparation strategies as well as methodological improvements. Together, these innovations pave the way for the study of ever larger RNA molecules that have important biological function. This article is categorized under: RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.
Collapse
Affiliation(s)
- Huaqun Zhang
- Biophysics Program, University of Michigan, Ann Arbor, Michigan
| | - Sarah C Keane
- Biophysics Program, University of Michigan, Ann Arbor, Michigan.,Department of Chemistry, University of Michigan, Ann Arbor, Michigan
| |
Collapse
|
22
|
Li Y, Zhong W, Koay AZ, Ng HQ, Koh-Stenta X, Nah Q, Lim SH, Larsson A, Lescar J, Hill J, Dedon PC, Kang C. Backbone resonance assignment for the N-terminal region of bacterial tRNA-(N 1G37) methyltransferase. BIOMOLECULAR NMR ASSIGNMENTS 2019; 13:49-53. [PMID: 30298375 DOI: 10.1007/s12104-018-9849-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 09/15/2018] [Indexed: 06/08/2023]
Abstract
Bacterial tRNA (guanine37-N1)-methyltransferase (TrmD) is an important antibacterial target due to its essential role in translation. TrmD has two domains connected with a flexible linker. The N-terminal domain (NTD) of TrmD contains the S-adenosyl-L-methionine (SAM) cofactor binding site and the C-terminal domain is critical for tRNA binding. Here we report the backbone NMR resonance assignments for NTD of Pseudomonas aeruginosa TrmD. Its secondary structure was determined based on the assigned resonances. Relaxation analysis revealed that NTD existed as dimers in solution. NTD also exhibited thermal stability in solution. Its interactions with SAM and other compounds suggest it can be used for evaluating SAM competitive inhibitors by NMR.
Collapse
Affiliation(s)
- Yan Li
- Experimental Therapeutics Centre, 31 Biopolis Way, #03-01 Nanos, Singapore, 138669, Singapore
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei, 430030, People's Republic of China
| | - Wenhe Zhong
- Infectious Disease and Antimicrobial Resistance Interdisciplinary Research Groups, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore, 138602, Singapore
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore, 138602, Singapore
| | - Ann Zhufang Koay
- Experimental Therapeutics Centre, 31 Biopolis Way, #03-01 Nanos, Singapore, 138669, Singapore
| | - Hui Qi Ng
- Experimental Therapeutics Centre, 31 Biopolis Way, #03-01 Nanos, Singapore, 138669, Singapore
| | - Xiaoying Koh-Stenta
- Experimental Therapeutics Centre, 31 Biopolis Way, #03-01 Nanos, Singapore, 138669, Singapore
| | - Qianhui Nah
- Infectious Disease and Antimicrobial Resistance Interdisciplinary Research Groups, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore, 138602, Singapore
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore, 138602, Singapore
| | - Siau Hoi Lim
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
- Experimental Biotherapeutics Centre, 30 Biopolis Street, #08-01 Matrix, Singapore, 138671, Singapore
| | - Andreas Larsson
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Julien Lescar
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, 636921, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Jeffrey Hill
- Experimental Therapeutics Centre, 31 Biopolis Way, #03-01 Nanos, Singapore, 138669, Singapore.
| | - Peter C Dedon
- Infectious Disease and Antimicrobial Resistance Interdisciplinary Research Groups, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore, 138602, Singapore.
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore, 138602, Singapore.
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - CongBao Kang
- Experimental Therapeutics Centre, 31 Biopolis Way, #03-01 Nanos, Singapore, 138669, Singapore.
| |
Collapse
|
23
|
Structural and ligand-binding analysis of the YAP-binding domain of transcription factor TEAD4. Biochem J 2018; 475:2043-2055. [DOI: 10.1042/bcj20180225] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 05/07/2018] [Accepted: 05/10/2018] [Indexed: 12/18/2022]
Abstract
The oncoprotein YAP (Yes-associated protein) requires the TEAD family of transcription factors for the up-regulation of genes important for cell proliferation. Disrupting YAP–TEAD interaction is an attractive strategy for cancer therapy. Targeting TEADs using small molecules that either bind to the YAP-binding pocket or the palmitate-binding pocket is proposed to disrupt the YAP–TEAD interaction. There is a need for methodologies to facilitate robust and reliable identification of compounds that occupy either YAP-binding pocket or palmitate-binding pocket. Here, using NMR spectroscopy, we validated compounds that bind to these pockets and also identify the residues in mouse TEAD4 (mTEAD4) that interact with these compounds. Flufenamic acid (FA) was used as a positive control for validation of palmitate-binding pocket-occupying compounds by NMR. Furthermore, we identify a hit from a fragment screen and show that it occupies a site close to YAP-binding pocket on the TEAD surface. Our results also indicate that purified mTEAD4 can catalyze autopalmitoylation. NMR studies on mTEAD4 revealed that exchanges exist in TEAD as NMR signal broadening was observed for residues close to the palmitoylation site. Mutating the palmitoylated cysteine (C360S mutant) abolished palmitoylation, while no significant changes in the NMR spectrum were observed for the mutant which still binds to YAP. We also show that FA inhibits TEAD autopalmitoylation. Our studies highlight the utility of NMR spectroscopy in identifying small molecules that bind to TEAD pockets and reinforce the notion that both palmitate-binding pocket and YAP-binding pocket are targetable.
Collapse
|
24
|
Structural Insights into the Inhibition of Zika Virus NS2B-NS3 Protease by a Small-Molecule Inhibitor. Structure 2018. [DOI: 10.1016/j.str.2018.02.005] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
|
25
|
Duchardt-Ferner E, Wöhnert J. NMR experiments for the rapid identification of P=O···H-X type hydrogen bonds in nucleic acids. JOURNAL OF BIOMOLECULAR NMR 2017; 69:101-110. [PMID: 29032519 DOI: 10.1007/s10858-017-0140-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 10/05/2017] [Indexed: 05/24/2023]
Abstract
Hydrogen bonds involving the backbone phosphate groups occur with high frequency in functional RNA molecules. They are often found in well-characterized tertiary structural motifs presenting powerful probes for the rapid identification of these motifs for structure elucidation purposes. We have shown recently that stable hydrogen bonds to the phosphate backbone can in principle be detected by relatively simple NMR-experiments, providing the identity of both the donor hydrogen and the acceptor phosphorous within the same experiment (Duchardt-Ferner et al., Angew Chem Int Ed Engl 50:7927-7930, 2011). However, for imino and hydroxyl hydrogen bond donor groups rapidly exchanging with the solvent as well as amino groups broadened by conformational exchange experimental sensitivity is severely hampered by extensive line broadening. Here, we present improved methods for the rapid identification of hydrogen bonds to phosphate groups in nucleic acids by NMR. The introduction of the SOFAST technique into 1H,31P-correlation experiments as well as a BEST-HNP experiment exploiting 3hJN,P rather than 2hJH,P coupling constants enables the rapid and sensitive identification of these hydrogen bonds in RNA. The experiments are applicable for larger RNAs (up to ~ 100-nt), for donor groups influenced by conformational exchange processes such as amino groups and for hydrogen bonds with rather labile hydrogens such as 2'-OH groups as well as for moderate sample concentrations. Interestingly, the size of the through-hydrogen bond scalar coupling constants depends not only on the type of the donor group but also on the structural context. The largest coupling constants were measured for hydrogen bonds involving the imino groups of protonated cytosine nucleotides as donors.
Collapse
Affiliation(s)
- Elke Duchardt-Ferner
- Institute for Molecular Biosciences, Goethe-University, Frankfurt/M., Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University, Frankfurt/M., Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Jens Wöhnert
- Institute for Molecular Biosciences, Goethe-University, Frankfurt/M., Max-von-Laue-Str. 9, 60438, Frankfurt, Germany.
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University, Frankfurt/M., Max-von-Laue-Str. 9, 60438, Frankfurt, Germany.
| |
Collapse
|
26
|
Li Y, Ng HQ, Ngo A, Liu S, Tan YW, Kwek PZ, Hung AW, Joy J, Hill J, Keller TH, Kang C. Backbone resonance assignments for the SET domain of human methyltransferase NSD3 in complex with its cofactor. BIOMOLECULAR NMR ASSIGNMENTS 2017; 11:225-229. [PMID: 28808922 DOI: 10.1007/s12104-017-9753-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 08/05/2017] [Indexed: 06/07/2023]
Abstract
NSD3 is a histone H3 methyltransferase that plays an important role in chromatin biology. A construct containing the methyltransferase domain encompassing residues Q1049-K1299 of human NSD3 was obtained and biochemical activity was demonstrated using histone as a substrate. Here we report the backbone HN, N, Cα, C', and side chain Cβ assignments of the construct in complex with S-adenosyl-L-methionine (SAM). Based on these assignments, secondary structures of NSD3/SAM complex in solution were determined.
Collapse
Affiliation(s)
- Yan Li
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way Nanos, #03-01, Singapore, 138669, Singapore
| | - Hui Qi Ng
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way Nanos, #03-01, Singapore, 138669, Singapore
| | - Anna Ngo
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way Nanos, #03-01, Singapore, 138669, Singapore
| | - Shuang Liu
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way Nanos, #03-01, Singapore, 138669, Singapore
| | - Yih Wan Tan
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way Nanos, #03-01, Singapore, 138669, Singapore
| | - Perlyn Zekui Kwek
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way Nanos, #03-01, Singapore, 138669, Singapore
| | - Alvin W Hung
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way Nanos, #03-01, Singapore, 138669, Singapore
| | - Joma Joy
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way Nanos, #03-01, Singapore, 138669, Singapore
| | - Jeffrey Hill
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way Nanos, #03-01, Singapore, 138669, Singapore
| | - Thomas H Keller
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way Nanos, #03-01, Singapore, 138669, Singapore
| | - CongBao Kang
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way Nanos, #03-01, Singapore, 138669, Singapore.
| |
Collapse
|
27
|
Bártová K, Čechová L, Procházková E, Socha O, Janeba Z, Dračínský M. Influence of Intramolecular Charge Transfer and Nuclear Quantum Effects on Intramolecular Hydrogen Bonds in Azopyrimidines. J Org Chem 2017; 82:10350-10359. [PMID: 28829606 DOI: 10.1021/acs.joc.7b01810] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Intramolecular hydrogen bonds (IMHBs) in 5-azopyrimidines are investigated by NMR spectroscopy and DFT computations that involve nuclear quantum effects. A series of substituted 5-phenylazopyrimidines with one or two hydrogen bond donors able to form IMHBs with the azo group is prepared by azo coupling. The barrier of interconversion between two rotamers of the compounds with two possible IMHBs is determined by variable temperature NMR spectroscopy and it is demonstrated that the barrier is significantly affected by intramolecular charge transfer. Through-hydrogen-bond scalar coupling is investigated in 15N labeled compounds and the stability of the IMHBs is correlated with experimental NMR parameters and rationalized by path integral molecular dynamics simulations that involve nuclear quantum effects. Detailed information on the hydrogen bond geometry upon hydrogen-to-deuterium isotope exchange is obtained from a comparison of experimental and calculated NMR data.
Collapse
Affiliation(s)
- Kateřina Bártová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo nam. 2, 166 10 Prague, Czech Republic.,Faculty of Science, Charles University , 116 36 Prague, Czech Republic
| | - Lucie Čechová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo nam. 2, 166 10 Prague, Czech Republic.,Department of Chemistry of Natural Compounds, University of Chemistry and Technology Prague , Technická 5, 166 28 Prague, Czech Republic
| | - Eliška Procházková
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo nam. 2, 166 10 Prague, Czech Republic
| | - Ondřej Socha
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo nam. 2, 166 10 Prague, Czech Republic
| | - Zlatko Janeba
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo nam. 2, 166 10 Prague, Czech Republic
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo nam. 2, 166 10 Prague, Czech Republic
| |
Collapse
|
28
|
Li Y, Zhang Z, Phoo WW, Loh YR, Wang W, Liu S, Chen MW, Hung AW, Keller TH, Luo D, Kang C. Structural Dynamics of Zika Virus NS2B-NS3 Protease Binding to Dipeptide Inhibitors. Structure 2017; 25:1242-1250.e3. [DOI: 10.1016/j.str.2017.06.006] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 03/13/2017] [Accepted: 06/08/2017] [Indexed: 01/13/2023]
|
29
|
Mishra SK, Suryaprakash N. Intramolecular Hydrogen Bonding Involving Organic Fluorine: NMR Investigations Corroborated by DFT-Based Theoretical Calculations. Molecules 2017; 22:E423. [PMID: 28272370 PMCID: PMC6155419 DOI: 10.3390/molecules22030423] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 03/02/2017] [Indexed: 01/24/2023] Open
Abstract
The combined utility of many one and two dimensional NMR methodologies and DFT-based theoretical calculations have been exploited to detect the intramolecular hydrogen bond (HB) in number of different organic fluorine-containing derivatives of molecules, viz. benzanilides, hydrazides, imides, benzamides, and diphenyloxamides. The existence of two and three centered hydrogen bonds has been convincingly established in the investigated molecules. The NMR spectral parameters, viz., coupling mediated through hydrogen bond, one-bond NH scalar couplings, physical parameter dependent variation of chemical shifts of NH protons have paved the way for understanding the presence of hydrogen bond involving organic fluorine in all the investigated molecules. The experimental NMR findings are further corroborated by DFT-based theoretical calculations including NCI, QTAIM, MD simulations and NBO analysis. The monitoring of H/D exchange with NMR spectroscopy established the effect of intramolecular HB and the influence of electronegativity of various substituents on the chemical kinetics in the number of organic building blocks. The utility of DQ-SQ technique in determining the information about HB in various fluorine substituted molecules has been convincingly established.
Collapse
Affiliation(s)
- Sandeep Kumar Mishra
- NMR Research Centre, Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India.
| | - N Suryaprakash
- NMR Research Centre, Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India.
| |
Collapse
|
30
|
Cho HY, Kim S, Jeon YH. Fragment-based methods for the discovery of inhibitors modulating lysyl-tRNA synthetase and laminin receptor interaction. Methods 2017; 113:56-63. [PMID: 27789335 DOI: 10.1016/j.ymeth.2016.10.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Revised: 10/14/2016] [Accepted: 10/20/2016] [Indexed: 10/20/2022] Open
Abstract
Lysyl-tRNA synthetase (KRS) is an enzyme that conjugates lysine to its cognate tRNAs in the process of protein synthesis. In addition to its catalytic function, KRS binds to the 67-kDa laminin receptor (LR) on the cell membrane and facilitates cell migration and metastasis. Modulation of this interaction by small-molecule inhibitors can be exploited to suppress cancer metastasis. In this study, we present fragment-based methods for the identification of inhibitors and monitoring protein-protein interactions between KRS and LR. First, we identified the amino acid residues, located on the KRS anticodon-binding domain, which interact with the C-terminal extension of the LR. One-dimensional (1D) relaxation-edited nuclear magnetic resonance spectroscopy (NMR) and competition experiments were designed and optimized to screen the fragment library. For screening using two-dimensional (2D) NMR, we identified the indicative signals in the KRS anticodon-binding domain and selected inhibitors that bind to KRS and compete with LR at the KRS-LR binding interface. These methods may offer an efficient approach for the discovery of anti-metastatic drugs.
Collapse
Affiliation(s)
- Hye Young Cho
- College of Pharmacy, Korea University, Sejong 30019, Republic of Korea
| | - Sunghoon Kim
- Medicinal Bioconvergence Research Center, Seoul National University, Seoul 08826, Republic of Korea; Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea.
| | - Young Ho Jeon
- College of Pharmacy, Korea University, Sejong 30019, Republic of Korea.
| |
Collapse
|
31
|
Fukal J, Páv O, Buděšínský M, Šebera J, Sychrovský V. The benchmark of 31P NMR parameters in phosphate: a case study on structurally constrained and flexible phosphate. Phys Chem Chem Phys 2017; 19:31830-31841. [DOI: 10.1039/c7cp06969c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A benchmark for structural interpretation of the 31P NMR shift and the 2JP,C spin–spin coupling in the phosphate group was obtained by means of theoretical calculations and measurements in diethylphosphate and 5,5-dimethyl-2-hydroxy-1,3,2-dioxaphosphinane 2-oxide.
Collapse
Affiliation(s)
- Jiří Fukal
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Praha 6
- Czech Republic
| | - Ondřej Páv
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Praha 6
- Czech Republic
| | - Miloš Buděšínský
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Praha 6
- Czech Republic
| | - Jakub Šebera
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Praha 6
- Czech Republic
| | - Vladimír Sychrovský
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Praha 6
- Czech Republic
- Department of Electrotechnology
| |
Collapse
|
32
|
Zhang Q, Lv H, Wang L, Chen M, Li F, Liang C, Yu Y, Jiang F, Lu A, Zhang G. Recent Methods for Purification and Structure Determination of Oligonucleotides. Int J Mol Sci 2016; 17:E2134. [PMID: 27999357 PMCID: PMC5187934 DOI: 10.3390/ijms17122134] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 12/13/2016] [Accepted: 12/14/2016] [Indexed: 12/14/2022] Open
Abstract
Aptamers are single-stranded DNA or RNA oligonucleotides that can interact with target molecules through specific three-dimensional structures. The excellent features, such as high specificity and affinity for target proteins, small size, chemical stability, low immunogenicity, facile chemical synthesis, versatility in structural design and engineering, and accessible for site-specific modifications with functional moieties, make aptamers attractive molecules in the fields of clinical diagnostics and biopharmaceutical therapeutics. However, difficulties in purification and structural identification of aptamers remain a major impediment to their broad clinical application. In this mini-review, we present the recently attractive developments regarding the purification and identification of aptamers. We also discuss the advantages, limitations, and prospects for the major methods applied in purifying and identifying aptamers, which could facilitate the application of aptamers.
Collapse
MESH Headings
- Aptamers, Nucleotide/chemistry
- Chromatography, High Pressure Liquid/methods
- Chromatography, Ion Exchange/methods
- Chromatography, Reverse-Phase/methods
- Crystallography, X-Ray/methods
- DNA, Single-Stranded/chemistry
- DNA, Single-Stranded/ultrastructure
- Electrophoresis, Gel, Two-Dimensional/methods
- Nuclear Magnetic Resonance, Biomolecular/methods
Collapse
Affiliation(s)
- Qiulong Zhang
- Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong, China.
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU (Haimen) Institute of Science and Technology, Haimen 226100, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China.
| | - Huanhuan Lv
- Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong, China.
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU (Haimen) Institute of Science and Technology, Haimen 226100, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China.
| | - Lili Wang
- Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong, China.
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU (Haimen) Institute of Science and Technology, Haimen 226100, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China.
| | - Man Chen
- Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong, China.
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU (Haimen) Institute of Science and Technology, Haimen 226100, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China.
| | - Fangfei Li
- Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong, China.
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU (Haimen) Institute of Science and Technology, Haimen 226100, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China.
| | - Chao Liang
- Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong, China.
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU (Haimen) Institute of Science and Technology, Haimen 226100, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China.
| | - Yuanyuan Yu
- Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong, China.
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU (Haimen) Institute of Science and Technology, Haimen 226100, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China.
| | - Feng Jiang
- Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong, China.
- The State Key Laboratory Base of Novel Functional Materials and Preparation Science, Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, China.
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU (Haimen) Institute of Science and Technology, Haimen 226100, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China.
| | - Aiping Lu
- Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong, China.
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU (Haimen) Institute of Science and Technology, Haimen 226100, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China.
| | - Ge Zhang
- Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong, China.
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU (Haimen) Institute of Science and Technology, Haimen 226100, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China.
| |
Collapse
|
33
|
Zhang Z, Li Y, Loh YR, Phoo WW, Hung AW, Kang C, Luo D. Crystal structure of unlinked NS2B-NS3 protease from Zika virus. Science 2016; 354:1597-1600. [PMID: 27940580 DOI: 10.1126/science.aai9309] [Citation(s) in RCA: 147] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 11/22/2016] [Indexed: 12/19/2022]
Abstract
Zika virus (ZIKV) has rapidly emerged as a global public health concern. Viral NS2B-NS3 protease processes viral polyprotein and is essential for the virus replication, making it an attractive antiviral drug target. We report crystal structures at 1.58-angstrom resolution of the unlinked NS2B-NS3 protease from ZIKV as free enzyme and bound to a peptide reversely oriented at the active site. The unlinked NS2B-NS3 protease adopts a closed conformation in which NS2B engages NS3 to form an empty substrate-binding site. A second protease in the same crystal binds to the residues K14K15G16E17 from the neighboring NS3 in reverse orientation, resisting proteolysis. These features of ZIKV NS2B-NS3 protease may accelerate the discovery of structure-based antiviral drugs against ZIKV and related pathogenic flaviviruses.
Collapse
Affiliation(s)
- Zhenzhen Zhang
- Lee Kong Chian School of Medicine, Nanyang Technological University, Experimental Medicine Building 03-07, 59 Nanyang Drive, Singapore 636921.,NTU Institute of Structural Biology, Nanyang Technological University, Experimental Medicine Building 06-01, 59 Nanyang Drive, Singapore 636921
| | - Yan Li
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669
| | - Ying Ru Loh
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669
| | - Wint Wint Phoo
- Lee Kong Chian School of Medicine, Nanyang Technological University, Experimental Medicine Building 03-07, 59 Nanyang Drive, Singapore 636921.,NTU Institute of Structural Biology, Nanyang Technological University, Experimental Medicine Building 06-01, 59 Nanyang Drive, Singapore 636921.,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Alvin W Hung
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669
| | - CongBao Kang
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669.
| | - Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, Experimental Medicine Building 03-07, 59 Nanyang Drive, Singapore 636921. .,NTU Institute of Structural Biology, Nanyang Technological University, Experimental Medicine Building 06-01, 59 Nanyang Drive, Singapore 636921
| |
Collapse
|
34
|
Takeuchi K, Arthanari H, Wagner G. Perspective: revisiting the field dependence of TROSY sensitivity. JOURNAL OF BIOMOLECULAR NMR 2016; 66:221-225. [PMID: 27866370 PMCID: PMC5218892 DOI: 10.1007/s10858-016-0075-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 11/01/2016] [Indexed: 05/03/2023]
Abstract
The discovery of the TROSY effect (Pervushin et al. in Proc Natl Acad Sci USA 94:12366-12371, 1997) for reducing transverse relaxation and line sharpening through selecting pathways in which dipole-dipole and CSA Hamiltonians partially cancel each other had a tremendous impact on solution NMR studies of macromolecules. Together with the methyl TROSY (Tugarinov and Kay in J Biomol NMR 28:165-172, 2004) it enabled structural and functional studies of significantly larger systems. The optimal field strengths for TROSY have been estimated to be on spectrometers operating around 900 MHz (21.14 T) for the 1HN TROSY (Pervushin et al. in Proc Natl Acad Sci USA 94:12366-12371, 1997) while the aromatic 13C (13Caro) TROSY is posited to be optimal at around 600 MHz (14.09 T) (Pervushin et al. in J Am Chem Soc 120:6394-6400, 1998b; Pervushin in Q Rev Biophys 33:161-197, 2000). The initial rational was based on the consideration of where the quadratic B0 field dependences of the TROSY relaxation rates reach a minimum. For sensitivity consideration, however, it is interesting to estimate which field strengths yield the tallest peaks. Recent studies of 15N-detected TROSYs suggested that maximal peak heights are expected at 1.15 GHz (27.01 T) although the slowest relaxation rates or longest transverse relaxation times T2 are indeed expected around 900 MHz (21.14 T) (Takeuchi in J Biomol NMR 63:323-331, 2015; Takeuchi et al. in J Biomol NMR 64:143-151, 2016). This was based on the fact that the heights of Lorentzian lines are proportional to B o3/2 * T2 (Bo). Thus, multiplying the parabolic T2(Bo) dependence with the increasing function of B o3/2 shifts the maxima of peak-height field dependence from the T2 maximum at 900 MHz to higher fields. Moreover, besides shifting the peak height maximum for 15N TROSY, this analysis yields estimates for optimal peak heights for 1HN detected TROSY to 1.5 GHz, and to 900 MHz for 13C-detected 13CaroTROSY as is detailed below. To our knowledge, this aspect of field dependence of TROSY sensitivity has not been in the attention of the NMR community but may affect perspectives of NMR at ultra-high fields.
Collapse
Affiliation(s)
- Koh Takeuchi
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo, 135-0064, Japan
- PRESTO, Japan Science and Technology Agency, Tokyo, 135-0064, Japan
| | - Haribabu Arthanari
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.
| |
Collapse
|
35
|
Phoo WW, Li Y, Zhang Z, Lee MY, Loh YR, Tan YB, Ng EY, Lescar J, Kang C, Luo D. Structure of the NS2B-NS3 protease from Zika virus after self-cleavage. Nat Commun 2016; 7:13410. [PMID: 27845325 PMCID: PMC5116066 DOI: 10.1038/ncomms13410] [Citation(s) in RCA: 163] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 09/30/2016] [Indexed: 12/22/2022] Open
Abstract
The recent outbreak of Zika virus (ZIKV) infections in the Americas represents a serious threat to the global public health. The viral protease that processes viral polyproteins during infection appears as an attractive drug target. Here we report a crystal structure at 1.84 Å resolution of ZIKV non-structural protein NS2B-NS3 protease with the last four amino acids of the NS2B cofactor bound at the NS3 active site. This structure represents a post-proteolysis state of the enzyme during viral polyprotein processing and provides insights into peptide substrate recognition by the protease. Nuclear magnetic resonance (NMR) studies and protease activity assays unravel the protein dynamics upon binding the protease inhibitor BPTI in solution and confirm this finding. The structural and functional insights of the ZIKV protease presented here should advance our current understanding of flavivirus replication and accelerate structure-based antiviral drug discovery against ZIKV. The proteases of flaviviruses are promising targets for development of specific antiviral drugs. Here, the authors report a high resolution crystal structure of the NS2B-NS3 protease of Zika virus that provides insight into substrate and inhibitor binding.
Collapse
Affiliation(s)
- Wint Wint Phoo
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore.,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 636921, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Yan Li
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis way, Nanos, #03-01, Singapore 138669, Singapore
| | - Zhenzhen Zhang
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Michelle Yueqi Lee
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis way, Nanos, #03-01, Singapore 138669, Singapore
| | - Ying Ru Loh
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis way, Nanos, #03-01, Singapore 138669, Singapore
| | - Yaw Bia Tan
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Elizabeth Yihui Ng
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis way, Nanos, #03-01, Singapore 138669, Singapore
| | - Julien Lescar
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 636921, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore
| | - CongBao Kang
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis way, Nanos, #03-01, Singapore 138669, Singapore
| | - Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore.,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 636921, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore
| |
Collapse
|
36
|
Chattopadhyay A, Esadze A, Roy S, Iwahara J. NMR Scalar Couplings across Intermolecular Hydrogen Bonds between Zinc-Finger Histidine Side Chains and DNA Phosphate Groups. J Phys Chem B 2016; 120:10679-10685. [PMID: 27685459 PMCID: PMC5386832 DOI: 10.1021/acs.jpcb.6b08137] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
NMR scalar couplings across hydrogen bonds represent direct evidence for the partial covalent nature of hydrogen bonds and provide structural and dynamic information on hydrogen bonding. In this article, we report heteronuclear 15N-31P and 1H-31P scalar couplings across the intermolecular hydrogen bonds between protein histidine (His) imidazole and DNA phosphate groups. These hydrogen-bond scalar couplings were observed for the Egr-1 zinc-finger-DNA complex. Although His side-chain NH protons are typically undetectable in heteronuclear 1H-15N correlation spectra due to rapid hydrogen exchange, this complex exhibited two His side-chain NH signals around 1H 14.3 ppm and 15N 178 ppm at 35 °C. Through various heteronuclear multidimensional NMR experiments, these signals were assigned to two zinc-coordinating His side chains in contact with DNA phosphate groups. The data show that the Nδ1 atoms of these His side chains are protonated and exhibit the 1H-15N cross-peaks. Using heteronuclear 1H, 15N, and 31P NMR experiments, we observed the hydrogen-bond scalar couplings between the His 15Nδ1/1Hδ1 and DNA phosphate 31P nuclei. These results demonstrate the direct involvement of the zinc-coordinating His side chains in the recognition of DNA by the Cys2His2-class zinc fingers in solution.
Collapse
Affiliation(s)
- Abhijnan Chattopadhyay
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, USA
| | - Alexandre Esadze
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, USA
| | - Sourav Roy
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, USA
| | - Junji Iwahara
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, USA
| |
Collapse
|
37
|
Li Y, Wong YL, Ng FM, Liu B, Wong YX, Poh ZY, Liu S, Then SW, Lee MY, Ng HQ, Huang Q, Hung AW, Cherian J, Hill J, Keller TH, Kang C. Escherichia coli Topoisomerase IV E Subunit and an Inhibitor Binding Mode Revealed by NMR Spectroscopy. J Biol Chem 2016; 291:17743-53. [PMID: 27365392 PMCID: PMC5016168 DOI: 10.1074/jbc.m116.737429] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 06/29/2016] [Indexed: 11/06/2022] Open
Abstract
Bacterial topoisomerases are attractive antibacterial drug targets because of their importance in bacterial growth and low homology with other human topoisomerases. Structure-based drug design has been a proven approach of efficiently developing new antibiotics against these targets. Past studies have focused on developing lead compounds against the ATP binding pockets of both DNA gyrase and topoisomerase IV. A detailed understanding of the interactions between ligand and target in a solution state will provide valuable information for further developing drugs against topoisomerase IV targets. Here we describe a detailed characterization of a known potent inhibitor containing a 9H-pyrimido[4,5-b]indole scaffold against the N-terminal domain of the topoisomerase IV E subunit from Escherichia coli (eParE). Using a series of biophysical and biochemical experiments, it has been demonstrated that this inhibitor forms a tight complex with eParE. NMR studies revealed the exact protein residues responsible for inhibitor binding. Through comparative studies of two inhibitors of markedly varied potencies, it is hypothesized that gaining molecular interactions with residues in the α4 and residues close to the loop of β1-α2 and residues in the loop of β3-β4 might improve the inhibitor potency.
Collapse
Affiliation(s)
- Yan Li
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Ying Lei Wong
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Fui Mee Ng
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Boping Liu
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Yun Xuan Wong
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Zhi Ying Poh
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Shuang Liu
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Siew Wen Then
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Michelle Yueqi Lee
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Hui Qi Ng
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Qiwei Huang
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Alvin W Hung
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Joseph Cherian
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Jeffrey Hill
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - Thomas H Keller
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| | - CongBao Kang
- From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669
| |
Collapse
|
38
|
Biophysical Studies of Bacterial Topoisomerases Substantiate Their Binding Modes to an Inhibitor. Biophys J 2016; 109:1969-77. [PMID: 26536273 DOI: 10.1016/j.bpj.2015.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 09/25/2015] [Accepted: 10/01/2015] [Indexed: 12/18/2022] Open
Abstract
Bacterial DNA topoisomerases are essential for bacterial growth and are attractive, important targets for developing antibacterial drugs. Consequently, different potent inhibitors that target bacterial topoisomerases have been developed. However, the development of potent broad-spectrum inhibitors against both Gram-positive (G(+)) and Gram-negative (G(-)) bacteria has proven challenging. In this study, we carried out biophysical studies to better understand the molecular interactions between a potent bis-pyridylurea inhibitor and the active domains of the E-subunits of topoisomerase IV (ParE) from a G(+) strain (Streptococcus pneumoniae (sParE)) and a G(-) strain (Pseudomonas aeruginosa (pParE)). NMR results demonstrated that the inhibitor forms a tight complex with ParEs and the resulting complexes adopt structural conformations similar to those observed for free ParEs in solution. Further chemical-shift perturbation experiments and NOE analyses indicated that there are four regions in ParE that are important for inhibitor binding, namely, α2, the loop between β2 and α3, and the β2 and β6 strands. Surface plasmon resonance showed that this inhibitor binds to sParE with a higher KD than pParE. Point mutations in α2 of ParE, such as A52S (sParE), affected its binding affinity with the inhibitor. Taken together, these results provide a better understanding of the development of broad-spectrum antibacterial agents.
Collapse
|
39
|
Tormena CF. Conformational analysis of small molecules: NMR and quantum mechanics calculations. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2016; 96:73-88. [PMID: 27573182 DOI: 10.1016/j.pnmrs.2016.04.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 04/14/2016] [Accepted: 04/14/2016] [Indexed: 06/06/2023]
Abstract
This review deals with conformational analysis in small organic molecules, and describes the stereoelectronic interactions responsible for conformational stability. Conformational analysis is usually performed using NMR spectroscopy through measurement of coupling constants at room or low temperature in different solvents to determine the populations of conformers in solution. Quantum mechanical calculations are used to address the interactions responsible for conformer stability. The conformational analysis of a large number of small molecules is described, using coupling constant measurements in different solvents and at low temperature, as well as recent applications of through-space and through-hydrogen bond coupling constants JFH as tools for the conformational analysis of fluorinated molecules. Besides NMR parameters, stereoelectronic interactions such as conjugative, hyperconjugative, steric and intramolecular hydrogen bond interactions involved in conformational preferences are discussed.
Collapse
Affiliation(s)
- Cláudio F Tormena
- Institute of Chemistry, University of Campinas, PO Box 6154, 13083-970 Campinas, Sao Paulo, Brazil.
| |
Collapse
|
40
|
Nelissen FHT, Tessari M, Wijmenga SS, Heus HA. Stable isotope labeling methods for DNA. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2016; 96:89-108. [PMID: 27573183 DOI: 10.1016/j.pnmrs.2016.06.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 06/02/2016] [Accepted: 06/02/2016] [Indexed: 06/06/2023]
Abstract
NMR is a powerful method for studying proteins and nucleic acids in solution. The study of nucleic acids by NMR is far more challenging than for proteins, which is mainly due to the limited number of building blocks and unfavorable spectral properties. For NMR studies of DNA molecules, (site specific) isotope enrichment is required to facilitate specific NMR experiments and applications. Here, we provide a comprehensive review of isotope-labeling strategies for obtaining stable isotope labeled DNA as well as specifically stable isotope labeled building blocks required for enzymatic DNA synthesis.
Collapse
Affiliation(s)
- Frank H T Nelissen
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands.
| | - Marco Tessari
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands.
| | - Sybren S Wijmenga
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands.
| | - Hans A Heus
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands.
| |
Collapse
|
41
|
Li Y, Wong YL, Lee MY, Ng HQ, Kang C. Backbone assignment of the N-terminal 24-kDa fragment of Escherichia coli topoisomerase IV ParE subunit. BIOMOLECULAR NMR ASSIGNMENTS 2016; 10:135-138. [PMID: 26482923 DOI: 10.1007/s12104-015-9652-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 10/16/2015] [Indexed: 06/05/2023]
Abstract
Bacterial DNA topoisomerases are important drug targets due to their importance in DNA replication and low homology to human topoisomerases. The N-terminal 24 kDa region of E. coli topoisomerase IV E subunit (eParE) contains the ATP binding pocket. Structure-based drug discovery has been proven to be an efficient way to develop potent ATP competitive inhibitors against ParEs. NMR spectroscopy is a powerful tool to understand protein and inhibitor interactions in solution. In this study, we report the backbone assignment for the N-terminal domain of E. coli ParE. The secondary structural information and the assignment will aid in structure-based antibacterial agents development targeting eParE.
Collapse
Affiliation(s)
- Yan Li
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way Nanos, #03-01, Singapore, 138669, Singapore
| | - Ying Lei Wong
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way Nanos, #03-01, Singapore, 138669, Singapore
| | - Michelle Yueqi Lee
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way Nanos, #03-01, Singapore, 138669, Singapore
| | - Hui Qi Ng
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way Nanos, #03-01, Singapore, 138669, Singapore
| | - CongBao Kang
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way Nanos, #03-01, Singapore, 138669, Singapore.
| |
Collapse
|
42
|
Fan TWM, Lane AN. Applications of NMR spectroscopy to systems biochemistry. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2016; 92-93:18-53. [PMID: 26952191 PMCID: PMC4850081 DOI: 10.1016/j.pnmrs.2016.01.005] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 01/26/2016] [Accepted: 01/28/2016] [Indexed: 05/05/2023]
Abstract
The past decades of advancements in NMR have made it a very powerful tool for metabolic research. Despite its limitations in sensitivity relative to mass spectrometric techniques, NMR has a number of unparalleled advantages for metabolic studies, most notably the rigor and versatility in structure elucidation, isotope-filtered selection of molecules, and analysis of positional isotopomer distributions in complex mixtures afforded by multinuclear and multidimensional experiments. In addition, NMR has the capacity for spatially selective in vivo imaging and dynamical analysis of metabolism in tissues of living organisms. In conjunction with the use of stable isotope tracers, NMR is a method of choice for exploring the dynamics and compartmentation of metabolic pathways and networks, for which our current understanding is grossly insufficient. In this review, we describe how various direct and isotope-edited 1D and 2D NMR methods can be employed to profile metabolites and their isotopomer distributions by stable isotope-resolved metabolomic (SIRM) analysis. We also highlight the importance of sample preparation methods including rapid cryoquenching, efficient extraction, and chemoselective derivatization to facilitate robust and reproducible NMR-based metabolomic analysis. We further illustrate how NMR has been applied in vitro, ex vivo, or in vivo in various stable isotope tracer-based metabolic studies, to gain systematic and novel metabolic insights in different biological systems, including human subjects. The pathway and network knowledge generated from NMR- and MS-based tracing of isotopically enriched substrates will be invaluable for directing functional analysis of other 'omics data to achieve understanding of regulation of biochemical systems, as demonstrated in a case study. Future developments in NMR technologies and reagents to enhance both detection sensitivity and resolution should further empower NMR in systems biochemical research.
Collapse
Affiliation(s)
- Teresa W-M Fan
- Department of Toxicology and Cancer Biology, University of Kentucky, 789 S. Limestone St., Lexington, KY 40536, United States.
| | - Andrew N Lane
- Department of Toxicology and Cancer Biology, University of Kentucky, 789 S. Limestone St., Lexington, KY 40536, United States.
| |
Collapse
|
43
|
Kim WJ, Kim NK. Proper NMR methods for studying RNA thermometers. JOURNAL OF THE KOREAN MAGNETIC RESONANCE SOCIETY 2015. [DOI: 10.6564/jkmrs.2015.19.3.143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
44
|
Amarante TD, Weber G. Evaluating Hydrogen Bonds and Base Stacking of Single, Tandem and Terminal GU Mismatches in RNA with a Mesoscopic Model. J Chem Inf Model 2015; 56:101-9. [DOI: 10.1021/acs.jcim.5b00571] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tauanne D. Amarante
- Departamento de Física, Universidade Federal de Minas Gerais, 31270-901 Belo
Horizonte-MG, Brazil
| | - Gerald Weber
- Departamento de Física, Universidade Federal de Minas Gerais, 31270-901 Belo
Horizonte-MG, Brazil
| |
Collapse
|
45
|
Southern SA, Bryce DL. NMR Investigations of Noncovalent Carbon Tetrel Bonds. Computational Assessment and Initial Experimental Observation. J Phys Chem A 2015; 119:11891-9. [PMID: 26562616 DOI: 10.1021/acs.jpca.5b10848] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Group IV tetrel elements may act as tetrel bond donors, whereby a region of positive electrostatic potential (σ-hole) interacts with a Lewis base. The results of calculations of NMR parameters are reported for a series of model compounds exhibiting tetrel bonding from a methyl carbon to the oxygen or nitrogen atoms in various functional groups. The (13)C chemical shift (δiso) and the (1c)J((13)C,Y) coupling (Y = (17)O, (15)N) across the tetrel bond are recorded as a function of geometry. The sensitivity of the NMR parameters to the noncovalent interaction is demonstrated via an increase in δiso and in |(1c)J((13)C,Y)| as the tetrel bond shortens. Gauge-including projector-augmented wave density functional theory (DFT) calculations of δiso are reported for crystals that exhibit tetrel bonding in the solid state. Experimental δiso values for solid sarcosine and its tetrel-bonded salts corroborate the computational findings. This work offers new insights into tetrel bonding and facilitates the incorporation of tetrel bonds as restraints in NMR crystallographic structure refinement.
Collapse
Affiliation(s)
- Scott A Southern
- Department of Chemistry and Biomolecular Sciences & Centre for Catalysis Research and Innovation, University of Ottawa , 10 Marie Curie Private, Ottawa, Ontario K1N 6N5, Canada
| | - David L Bryce
- Department of Chemistry and Biomolecular Sciences & Centre for Catalysis Research and Innovation, University of Ottawa , 10 Marie Curie Private, Ottawa, Ontario K1N 6N5, Canada
| |
Collapse
|
46
|
Preimesberger M, Majumdar A, Rice SL, Que L, Lecomte JTJ. Helix-Capping Histidines: Diversity of N-H···N Hydrogen Bond Strength Revealed by (2h)JNN Scalar Couplings. Biochemistry 2015; 54:6896-908. [PMID: 26523621 PMCID: PMC4660981 DOI: 10.1021/acs.biochem.5b01002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 10/31/2015] [Indexed: 11/29/2022]
Abstract
In addition to its well-known roles as an electrophile and general acid, the side chain of histidine often serves as a hydrogen bond (H-bond) acceptor. These H-bonds provide a convenient pH-dependent switch for local structure and functional motifs. In hundreds of instances, a histidine caps the N-terminus of α- and 310-helices by forming a backbone NH···Nδ1 H-bond. To characterize the resilience and dynamics of the histidine cap, we measured the trans H-bond scalar coupling constant, (2h)JNN, in several forms of Group 1 truncated hemoglobins and cytochrome b5. The set of 19 measured (2h)JNN values were between 4.0 and 5.4 Hz, generally smaller than in nucleic acids (~6-10 Hz) and indicative of longer, weaker bonds in the studied proteins. A positive linear correlation between (2h)JNN and the difference in imidazole ring (15)N chemical shift (Δ(15)N = |δ(15)Nδ1 - δ(15)Nε2|) was found to be consistent with variable H-bond length and variable cap population related to the ionization of histidine in the capping and noncapping states. The relative ease of (2h)JNN detection suggests that this parameter can become part of the standard arsenal for describing histidines in helix caps and other key structural and catalytic elements involving NH···N H-bonds. The combined nucleic acid and protein data extend the utility of (2h)JNN as a sensitive marker of local structural, dynamic, and thermodynamic properties in biomolecules.
Collapse
Affiliation(s)
- Matthew
R. Preimesberger
- T.
C. Jenkins Department of Biophysics, Johns
Hopkins University, Baltimore, Maryland 21218, United States
| | - Ananya Majumdar
- Biomolecular
NMR Center, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Selena L. Rice
- T.
C. Jenkins Department of Biophysics, Johns
Hopkins University, Baltimore, Maryland 21218, United States
| | - Lauren Que
- T.
C. Jenkins Department of Biophysics, Johns
Hopkins University, Baltimore, Maryland 21218, United States
| | - Juliette T. J. Lecomte
- T.
C. Jenkins Department of Biophysics, Johns
Hopkins University, Baltimore, Maryland 21218, United States
| |
Collapse
|
47
|
Li Y, Wong YL, Ng FM, Liu B, Wong YX, Poh ZY, Then SW, Lee MY, Ng HQ, Hung AW, Cherian J, Hill J, Keller TH, Kang C. Characterization of the interaction between Escherichia coli topoisomerase IV E subunit and an ATP competitive inhibitor. Biochem Biophys Res Commun 2015; 467:961-6. [PMID: 26471301 DOI: 10.1016/j.bbrc.2015.10.036] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 10/07/2015] [Indexed: 10/22/2022]
Abstract
Bacterial topoisomerase IV (ParE) is essential for DNA replication and serves as an attractive target for antibacterial drug development. The X-ray structure of the N-terminal 24 kDa ParE, responsible for ATP binding has been solved. Due to the accessibility of structural information of ParE, many potent ParE inhibitors have been discovered. In this study, a pyridylurea lead molecule against ParE of Escherichia coli (eParE) was characterized with a series of biochemical and biophysical techniques. More importantly, solution NMR analysis of compound binding to eParE provides better understanding of the molecular interactions between the inhibitor and eParE.
Collapse
Affiliation(s)
- Yan Li
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, 138669, Singapore
| | - Ying Lei Wong
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, 138669, Singapore
| | - Fui Mee Ng
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, 138669, Singapore
| | - Boping Liu
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, 138669, Singapore
| | - Yun Xuan Wong
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, 138669, Singapore
| | - Zhi Ying Poh
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, 138669, Singapore
| | - Siew Wen Then
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, 138669, Singapore
| | - Michelle Yueqi Lee
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, 138669, Singapore
| | - Hui Qi Ng
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, 138669, Singapore
| | - Alvin W Hung
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, 138669, Singapore
| | - Joseph Cherian
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, 138669, Singapore
| | - Jeffrey Hill
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, 138669, Singapore
| | - Thomas H Keller
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, 138669, Singapore
| | - CongBao Kang
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, 138669, Singapore.
| |
Collapse
|
48
|
Li Y, Li Q, Wong YL, Liew LSY, Kang C. Membrane topology of NS2B of dengue virus revealed by NMR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:2244-52. [DOI: 10.1016/j.bbamem.2015.06.010] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 05/20/2015] [Accepted: 06/09/2015] [Indexed: 12/27/2022]
|
49
|
Iwahara J, Esadze A, Zandarashvili L. Physicochemical Properties of Ion Pairs of Biological Macromolecules. Biomolecules 2015; 5:2435-63. [PMID: 26437440 PMCID: PMC4693242 DOI: 10.3390/biom5042435] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 09/09/2015] [Accepted: 09/11/2015] [Indexed: 11/23/2022] Open
Abstract
Ion pairs (also known as salt bridges) of electrostatically interacting cationic and anionic moieties are important for proteins and nucleic acids to perform their function. Although numerous three-dimensional structures show ion pairs at functionally important sites of biological macromolecules and their complexes, the physicochemical properties of the ion pairs are not well understood. Crystal structures typically show a single state for each ion pair. However, recent studies have revealed the dynamic nature of the ion pairs of the biological macromolecules. Biomolecular ion pairs undergo dynamic transitions between distinct states in which the charged moieties are either in direct contact or separated by water. This dynamic behavior is reasonable in light of the fundamental concepts that were established for small ions over the last century. In this review, we introduce the physicochemical concepts relevant to the ion pairs and provide an overview of the recent advancement in biophysical research on the ion pairs of biological macromolecules.
Collapse
Affiliation(s)
- Junji Iwahara
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - Alexandre Esadze
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Levani Zandarashvili
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| |
Collapse
|
50
|
Neuner S, Santner T, Kreutz C, Micura R. The "Speedy" Synthesis of Atom-Specific (15)N Imino/Amido-Labeled RNA. Chemistry 2015; 21:11634-11643. [PMID: 26237536 PMCID: PMC4946632 DOI: 10.1002/chem.201501275] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Although numerous reports on the synthesis of atom-specific (15)N-labeled nucleosides exist, fast and facile access to the corresponding phosphoramidites for RNA solid-phase synthesis is still lacking. This situation represents a severe bottleneck for NMR spectroscopic investigations on functional RNAs. Here, we present optimized procedures to speed up the synthesis of (15)N(1) adenosine and (15)N(1) guanosine amidites, which are the much needed counterparts of the more straightforward-to-achieve (15)N(3) uridine and (15)N(3) cytidine amidites in order to tap full potential of (1)H/(15)N/(15)N-COSY experiments for directly monitoring individual Watson-Crick base pairs in RNA. Demonstrated for two preQ1 riboswitch systems, we exemplify a versatile concept for individual base-pair labeling in the analysis of conformationally flexible RNAs when competing structures and conformational dynamics are encountered.
Collapse
Affiliation(s)
- Sandro Neuner
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck (Austria)
| | - Tobias Santner
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck (Austria)
| | - Christoph Kreutz
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck (Austria)
| | - Ronald Micura
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck (Austria)
| |
Collapse
|