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Winston DS, Boehr DD. Allosteric and dynamic control of RNA-dependent RNA polymerase function and fidelity. Enzymes 2021; 49:149-193. [PMID: 34696831 DOI: 10.1016/bs.enz.2021.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
All RNA viruses encode an RNA-dependent RNA polymerase (RdRp) responsible for genome replication. It is now recognized that enzymes in general, and RdRps specifically, are dynamic macromolecular machines such that their moving parts, including active site loops, play direct functional roles. While X-ray crystallography has provided deep insight into structural elements important for RdRp function, this methodology generally provides only static snapshots, and so is limited in its ability to report on dynamic fluctuations away from the lowest energy conformation. Nuclear magnetic resonance (NMR), molecular dynamics (MD) simulations and other biophysical techniques have brought new insight into RdRp function by their ability to characterize the trajectories, kinetics and thermodynamics of conformational motions. In particular, these methodologies have identified coordinated motions among conserved structural motifs necessary for nucleotide selection and incorporation. Disruption of these motions through amino acid substitutions or inhibitor binding impairs RdRp function. Understanding and re-engineering these motions thus provides exciting new avenues for anti-viral strategies. This chapter outlines the basics of these methodologies, summarizes the dynamic motions observed in different RdRps important for nucleotide selection and incorporation, and illustrates how this information can be leveraged towards rational vaccine strain development and anti-viral drug design.
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Affiliation(s)
- Dennis S Winston
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
| | - David D Boehr
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States.
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Rusakova IL, Rusakov YY. Quantum chemical calculations of 77 Se and 125 Te nuclear magnetic resonance spectral parameters and their structural applications. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:359-407. [PMID: 33095923 DOI: 10.1002/mrc.5111] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/01/2020] [Accepted: 10/07/2020] [Indexed: 06/11/2023]
Abstract
An accurate quantum chemical (QC) modeling of 77 Se and 125 Te nuclear magnetic resonance (NMR) spectra is deeply involved in the NMR structural assignment for selenium and tellurium compounds that are of utmost importance both in organic and inorganic chemistry nowadays due to their huge application potential in many fields, like biology, medicine, and metallurgy. The main interest of this review is focused on the progress in QC computations of 77 Se and 125 Te NMR chemical shifts and indirect spin-spin coupling constants involving these nuclei. Different computational methodologies that have been used to simulate the NMR spectra of selenium and tellurium compounds since the middle of the 1990s are discussed with a strong emphasis on their accuracy. A special accent is placed on the calculations resorting to the relativistic methodologies, because taking into account the relativistic effects appreciably influences the precision of NMR calculations of selenium and, especially, tellurium compounds. Stereochemical applications of quantum chemical calculations of 77 Se and 125 Te NMR parameters are discussed so as to exemplify the importance of integrated approach of experimental and computational NMR techniques.
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Affiliation(s)
- Irina L Rusakova
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russian Federation
| | - Yuriy Yu Rusakov
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russian Federation
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Cancelieri NM, Ferreira TR, Vieira IJC, Braz-Filho R, Piló-Veloso D, Alcântara AFDC. Correlations among experimental and theoretical NMR data to determine the absolute stereochemistry of darcyribeirine, a pentacyclic indole alkaloid isolated from Rauvolfia grandiflora. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2015.05.038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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4
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Rusakova IL, Krivdin LB, Rusakov YY, Trofimov AB. Algebraic-diagrammatic construction polarization propagator approach to indirect nuclear spin–spin coupling constants. J Chem Phys 2012; 137:044119. [DOI: 10.1063/1.4737181] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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5
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Gerothanassis IP. Oxygen-17 NMR spectroscopy: basic principles and applications (part I). PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2010; 56:95-197. [PMID: 20633350 DOI: 10.1016/j.pnmrs.2009.09.002] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Accepted: 09/24/2009] [Indexed: 05/29/2023]
Affiliation(s)
- Ioannis P Gerothanassis
- Section of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, Ioannina GR-451 10, Greece.
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Rusakov YY, Krivdin LB, Sauer SPA, Levanova EP, Levkovskaya GG. Structural trends of 77Se-1H spin-spin coupling constants and conformational behavior of 2-substituted selenophenes. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2010; 48:44-52. [PMID: 19877126 DOI: 10.1002/mrc.2537] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Experimental measurements and second-order polarization propagator approach (SOPPA) calculations of (77)Se-(1)H spin-spin coupling constants together with theoretical energy-based conformational analysis in the series of 2-substituted selenophenes have been carried out. A new basis set optimized for the calculation of (77)Se-(1)H spin-spin coupling constants has been introduced by extending the aug-cc-pVTZ-J basis for selenium. Most of the spin-spin coupling constants under study, especially vicinal (77)Se-(1)H couplings, demonstrated a remarkable stereochemical behavior with respect to the internal rotation of the substituent in the 2-position of the selenophene ring, which is of major importance in the stereochemical studies of the related organoselenium compounds.
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Affiliation(s)
- Yury Yu Rusakov
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033 Irkutsk, Russia
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Solvent effects on 13C and 1H NMR shielding of cyclic ketones: An experimental and theoretical study. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.theochem.2006.12.057] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Investigations of the 1J(13C1H) spin–spin coupling and 13C magnetic shielding of gaseous benzene-13C. J Mol Struct 2005. [DOI: 10.1016/j.molstruc.2004.10.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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The NMR indirect nuclear spin–spin coupling constants for some small rigid hydrocarbons: molecular equilibrium values and vibrational corrections. Chem Phys 2004. [DOI: 10.1016/j.chemphys.2003.08.018] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Ruden TA, Lutnæs OB, Helgaker T, Ruud K. Vibrational corrections to indirect nuclear spin–spin coupling constants calculated by density-functional theory. J Chem Phys 2003. [DOI: 10.1063/1.1569846] [Citation(s) in RCA: 142] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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13
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Solvent Effects on Nuclear Magnetic Resonance 2J(C,Hf) and 1J(C,Hf) Spin–Spin Coupling Constants in Acetaldehyde. Int J Mol Sci 2003. [DOI: 10.3390/i4030093] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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14
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Solvent Effects on the Indirect Spin–Spin Coupling Constants of Benzene: The DFT-PCM Approach. Int J Mol Sci 2003. [DOI: 10.3390/i4030119] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Schaefer T, Bernard GM, Hruska FE. An estimate of the spin–spin coupling constant, 1J(1H,13C), in gaseous benzene. CAN J CHEM 1996. [DOI: 10.1139/v96-169] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
An excellent linear correlation (r = 0.9999) exists between the spin–spin coupling constants 1J(1H,13C), in benzene dissolved in four solvents (R. Laatikainen et al. J. Am. Chem. Soc. 117, 11006 (1995)) and Ando's solvation dielectric function, ε/(ε – 1). The solvents are cyclohexane, carbon disulfide, pyridine, and acetone. 1J(1H,13C)for gaseous benzene is predicted to be 156.99(2) Hz at 300 K. Key words: spin–spin coupling constants, 1J(1H,13C) for benzene in the vapor phase; spin–spin coupling constants, solvent dielectric constant dependence of 1J(1H,13C) in benzene; benzene, estimate of 1J(1H,13C) in the vapor; nuclear magnetic resonance, estimate of 1J(1H,13C) in gaseous benzene.
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Gerothanassis IP, Demetropoulos IN, Vakka C. Hydration ofcis andtrans N-methylformamide as revealed by the use of17O-NMR, molecular mechanics, and ab initio calculations. Biopolymers 1995. [DOI: 10.1002/bip.360360405] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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18
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Ehlend A, Hausen HD, Kaim W, Lichtblau A, Schwarz W. Insertion von CO2, COS and CS2 in die NSi-Bindung des extrem elektronenreichen 1,4-Bis(trimethylsilyl) -1,4-dihydropyrazins und Bildung eines neuen poly(N,S-) heterocyclischen Systems durch mehrfache Cycloaddition. J Organomet Chem 1995. [DOI: 10.1016/0022-328x(95)05673-d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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19
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Tvaroska I, Taravel FR. Carbon-proton coupling constants in the conformational analysis of sugar molecules. Adv Carbohydr Chem Biochem 1995; 51:15-61. [PMID: 7484362 DOI: 10.1016/s0065-2318(08)60191-2] [Citation(s) in RCA: 101] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- I Tvaroska
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic
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Takayama T, Ando I. Conformation and dynamics of a polysiloxane containing rigid groups in the solid state as studied by variable-temperature high-resolution 29Si NMR. J Mol Struct 1992. [DOI: 10.1016/0022-2860(92)80211-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Tvaroska I, Taravel FR. One-bond carbon-proton coupling constants: angular dependence in alpha-linked oligosaccharides. Carbohydr Res 1991; 221:83-94. [PMID: 1667856 DOI: 10.1016/0008-6215(91)80050-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
An investigation is presented of the angular dependence of 1JC,H in model compounds related to alpha-linked oligosaccharides. Values calculated by FPT formulation in the semi-empirical INDO method for models of (1----1)-, (1----2)-, (1----3)-, and (1----4)-linked disaccharides were compared, and the effect of the orientation of HO-2 was elucidated. The angular dependence of 1JC,H on the glycosidic dihedral angles phi H and psi H was characterised in the form 1JC,H = A cos 2 phi + B cos phi + C sin 2 phi + D sin phi + E. The 1JC,H values, measured by DEPT methods for C-1-H-1 and C-X'-H-X' in various rigid carbohydrates, were used to adjust the calculated angular dependences and to determine solvent effects. Based on the abundance of the conformers for maltose and isomaltose, the thermodynamically averaged 1JC,H values have been calculated. The results obtained (less than 1JC-1,H-1 greater than 169.9, less than 1JC-4',H-4' greater than 147.7 Hz for methyl beta-maltoside and less than 1JC-1,H-1 greater than 169.8 Hz for methyl beta-isomaltoside) agree with the experimental values of 172.4, 147.7, and 170.3 Hz, respectively.
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Affiliation(s)
- I Tvaroska
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Czechoslovakia
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22
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Configuration and conformation of polysilanes in the solid state as studied by variable-temperature 29Si CP/MAS NMR part II. Copoly (Dimethylsilyl diphenylsilane). J Mol Struct 1991. [DOI: 10.1016/0022-2860(91)87028-g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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23
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Takayama T, Ando I. Conformation of polysilanes in the solid state as studied by variable-temperature 29Si CP/MAS NMR. J Mol Struct 1990. [DOI: 10.1016/0022-2860(90)85039-l] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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24
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Sakurai M, Hoshi H, Inoue Y, Chûjô R. Medium Effects on the Molecular Electronic Structure. III. Quantum-Chemical Analysis of Solvent-Induced13C NMR Chemical Shift Changes of Some Polyene Compounds. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 1990. [DOI: 10.1246/bcsj.63.1335] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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25
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Takayama T, Ando S, Ando I. Conformation of cyclic polysilane in the solid state as studied by variable-temperature 29Si CP/ MAS NMR. J Mol Struct 1990. [DOI: 10.1016/0022-2860(90)80114-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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26
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Ebraheem KAK, Shargi SN, Kadum SA. INDO-SCPT calculations of the solvent dependence of some carbon-proton spin-spin coupling constants. MONATSHEFTE FUR CHEMIE 1989. [DOI: 10.1007/bf00808763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Laatikainen R. Dipolar coupling and solvent dependence of 1H, 1H spin-spin coupling in naphthalene. analysis of spectra containing overlapping lines. ACTA ACUST UNITED AC 1988. [DOI: 10.1016/0022-2364(88)90162-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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29
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Hoshi H, Sakurai M, Inoue Y, Chûjô R. Medium effects on the molecular electronic structure. I. The formulation of a theory for the estimation of a molecular electronic structure surrounded by an anisotropic medium. J Chem Phys 1987. [DOI: 10.1063/1.453343] [Citation(s) in RCA: 159] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Geometry of ?-cyclodextrin inclusion complex with m-nitrophenol deduced from quantum chemical analysis of carbon-13 chemical shifts. ACTA ACUST UNITED AC 1987. [DOI: 10.1007/bf00656402] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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31
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Yamanobe T, Ando I, Webb G. The effects of intermolecular interactions on 13C NMR chemical shifts. I. Methyl alcohol. J Mol Liq 1986. [DOI: 10.1016/0167-7322(86)80037-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Yamanobe T, Ando I, Saito H, Tabeta R, Shoji A, Ozaki T. Carbon-13 NMR Chemical Shift and Electronic Structure of Solid Polypeptides as Studied by Tight-binding MO Theory. Polyglycine and Poly(L-alanine). BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 1985. [DOI: 10.1246/bcsj.58.23] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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34
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Brémond M, Martin GJ, Webb GA, Reynolds DJ. Electronic delocalization in NC and NN bonds. ACTA ACUST UNITED AC 1984. [DOI: 10.1002/mrc.1270221009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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35
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Geometry of ?-cyclodextrin inclusion-complexes with some substituted benzenes deduced from C-13 NMR chemical shifts. ACTA ACUST UNITED AC 1984. [DOI: 10.1007/bf00662222] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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36
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Kozerski L, Kamienska-Trela K, Kania L, Von Philipsborn W. 15N-NMR study of activated enamines. Structural dependence of ? (15N) andnJ(N,H) in primary, secondary and tertiary enamino-ketones, esters and amides. Helv Chim Acta 1983. [DOI: 10.1002/hlca.19830660722] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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37
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Lamphun BN, Webb GA, Witanowski M. Some INDO/SSOS calculations of the effects of hydrogen bonding on the nitrogen shielding of some heterocycles. ACTA ACUST UNITED AC 1983. [DOI: 10.1002/omr.1270210810] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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38
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Shargi S, Webb G, Ando I, Watanabe S. Calculations of solvent effects on 1J(NC) values. ACTA ACUST UNITED AC 1983. [DOI: 10.1016/0166-1280(83)80077-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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39
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Kozerski L. Solvent-induced isotope effects in NMR spectroscopy. A study of hydrogen bonding between the carbonyl group in chalcone and trifluoracetic acid (TFA-d or TFA) in chloroform solution. ACTA ACUST UNITED AC 1982. [DOI: 10.1002/mrc.1270200317] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Kozerski L, von Philipsborn W. 15N chemical shifts as a conformational probe in enaminones A variable temperature study at natural isotope abundance. ACTA ACUST UNITED AC 1981. [DOI: 10.1002/mrc.1270170418] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Witanowski M, Stefaniak L, Lamphun BN, Webb GA. Solvent effects on the nitrogen screening of some nitroalkanes. ACTA ACUST UNITED AC 1981. [DOI: 10.1002/mrc.1270160115] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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