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Astani EK, Iravani H, Sardari S. Theoretical investigation of the effects of diverse hydrogen-bonding characteristics on the 17O chemical shielding and electric field gradient tensors within the active sites of MraY AA bound to nucleoside antibiotics capuramycin, carbacaprazamycin, 3'-Hydroxymureidomycin A, and muraymycin D2. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2024; 133:101960. [PMID: 39208660 DOI: 10.1016/j.ssnmr.2024.101960] [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: 05/10/2024] [Revised: 07/31/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024]
Abstract
This study builds upon our prior researches and seeks to investigate and clarify the influences of various characteristics of hydrogen bonds (H-bonds) and charge transfer (CT) interactions, which were detected within the inhibitor binding pockets (labeled as the QM models I-IV) of MraYAA-capuramycin, MraYAA-carbacaprazamycin, MraYAA-3'-hydroxymureidomycin A, and MraYAA-muraymycin D2 complexes by QTAIM and NBO analyses from DFT QM/MM MD calculations, on the 17O chemical shielding (CS) and electric field gradient (EFG) tensors of carboxylate (Oδ), carbonyl (C═O), and hydroxyl (O-H) oxygens in these models. The 17O CS and EFG tensors of these three types of oxygens in QM models I-IV were calculated at the M06-2X/6-31G** level by including the solvent effects using the polarizable continuum model. From the computed 17O CS and EFG tensors in these models, it was found that the nuclear shielding, σiso, for carboxylate or carbonyl oxygen increases (shielding effect) as the H-bond length decreases and the percentage p-character of nOδ/nC═O lone pair partner in the CT interaction enhances. In contrast, the σiso (17O-H) decreases (deshielding effect) with a reduction in the H-bond length as well as with an enhancement in percentage s-character of the nOH lone pair/σ*O-H antibond. By reducing the H-bond length or by increasing p-character of the nOδ/nC═O lone pair, the 17Oδ/17O═C quadrupole coupling constant smoothly decreases, while the 17Oδ/17O═C asymmetry parameter smoothly increases. Moreover, these calculated parameters are in a good agreement with the experimental values. The information garnered here is valuable particularly for further understanding of empirical correlations between 17O NMR spectroscopic and H-bonding characteristics in the protein-ligand complexes.
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Affiliation(s)
- Elahe K Astani
- Drug Design and Bioinformatics Unit, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, 13169-43551, Iran; Department of Chemistry, Faculty of Science, Tarbiat Modares University, Tehran, 14115-175, Iran.
| | - Hossein Iravani
- Department of Chemistry, Faculty of Science, Tarbiat Modares University, Tehran, 14115-175, Iran
| | - Soroush Sardari
- Drug Design and Bioinformatics Unit, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, 13169-43551, Iran
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Feng RR, Wang M, Zhang W, Gai F. Unnatural Amino Acids for Biological Spectroscopy and Microscopy. Chem Rev 2024; 124:6501-6542. [PMID: 38722769 DOI: 10.1021/acs.chemrev.3c00944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
Due to advances in methods for site-specific incorporation of unnatural amino acids (UAAs) into proteins, a large number of UAAs with tailored chemical and/or physical properties have been developed and used in a wide array of biological applications. In particular, UAAs with specific spectroscopic characteristics can be used as external reporters to produce additional signals, hence increasing the information content obtainable in protein spectroscopic and/or imaging measurements. In this Review, we summarize the progress in the past two decades in the development of such UAAs and their applications in biological spectroscopy and microscopy, with a focus on UAAs that can be used as site-specific vibrational, fluorescence, electron paramagnetic resonance (EPR), or nuclear magnetic resonance (NMR) probes. Wherever applicable, we also discuss future directions.
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Affiliation(s)
- Ran-Ran Feng
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Manxi Wang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wenkai Zhang
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875, China
| | - Feng Gai
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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Matsuzaki K, Hayashi S, Nakanishi W. Origin of 17O NMR chemical shifts based on molecular orbital theory: paramagnetic terms of the pre-α, α and β effects from orbital-to-orbital transitions, along with the effects from vinyl, carbonyl and carboxyl groups. RSC Adv 2024; 14:14340-14356. [PMID: 38690112 PMCID: PMC11060305 DOI: 10.1039/d4ra00843j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 04/24/2024] [Indexed: 05/02/2024] Open
Abstract
17O NMR chemical shifts (δ(O)) were analysed based on the molecular orbital (MO) theory, using the diamagnetic, paramagnetic and total absolute magnetic shielding tensors (σd(O), σp(O) and σt(O), respectively). O2- was selected as the standard for the analysis. An excellent relationship was observed between σd(O) and the charges on O for O6+, O4+, O2+, O0 and O2-. The data from H2O, HO+, HO- and H3O+ were on the correlation line. However, such relationship was not observed for the oxygen species, other than above. The pre-α, α and β effects were evaluated bases on σt(O), where the pre-α effect arises from the protonation to a lone pair orbital on O2-, for an example. The 30-40 ppm and 20-40 ppm (downfield shifts) were predicted for the pre-α and β effects, respectively, whereas the values for the α effect was very small in magnitude, where the effect from the hydrogen bond formation should be considered. Similarly, the carbonyl effect in H2C[double bond, length as m-dash]O and the carboxyl effects in H(HO)C[double bond, length as m-dash]O were evaluated from MeOH, together with H2C[double bond, length as m-dash]CHOH from CH3CH2OH. Very large downfield shifts of 752, 425 and 207 ppm were predicted for H2C[double bond, length as m-dash]O*, H(HO)C[double bond, length as m-dash]O* and H(HO*)C[double bond, length as m-dash]O, respectively, together with the 81 ppm downfield shift for H2C[double bond, length as m-dash]CHO*H. The origin of the effect were visualized based on the occupied-to-unoccupied orbital transitions. As a result, the origin of the 17O NMR chemical shifts (δ(17O)) can be more easily imaged and understand through the image of the effects. The results would help to understand the role of O in the specific position of a compound in question and the mechanisms to arise the shift values also for the experimental scientists. The aim of this study is to establish the plain rules founded in theory for δ(17O), containing the origin, which has been achieved through the treatments.
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Affiliation(s)
- Keigo Matsuzaki
- Faculty of Systems Engineering, Wakayama University 930 Sakaedani Wakayama 640-8510 Japan
| | - Satoko Hayashi
- Faculty of Systems Engineering, Wakayama University 930 Sakaedani Wakayama 640-8510 Japan
| | - Waro Nakanishi
- Faculty of Systems Engineering, Wakayama University 930 Sakaedani Wakayama 640-8510 Japan
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Fu R, Ramamoorthy A. 17O Solid-State NMR Spectroscopy of Lipid Membranes. J Phys Chem B 2024; 128:3527-3537. [PMID: 38568422 DOI: 10.1021/acs.jpcb.4c01016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Despite the limitations posed by poor sensitivity, studies have reported the unique advantages of 17O based NMR spectroscopy to study systems existing in liquid, solid, or semisolid states. 17O NMR studies have exploited the remarkable sensitivity of quadrupole coupling and chemical shift anisotropy tensors to the local environment in the characterization of a variety of intra- and intermolecular interactions and motion. Recent studies have considerably expanded the use of 17O NMR to study dynamic intermolecular interactions associated with some of the challenging biological systems under magic angle spinning (MAS) and aligned conditions. The very fast relaxing nature of 17O has been well utilized in cellular and in vivo MRS (magnetic resonance spectroscopy) and MRI (magnetic resonance imaging) applications. The main focus of this Review is to highlight the new developments in the biological solids with a detailed discussion for a few selected examples including membrane proteins and nanodiscs. In addition to the unique benefits and limitations, the remaining challenges to overcome, and the impacts of higher magnetic fields and sensitivity enhancement techniques are discussed.
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Affiliation(s)
- Riqiang Fu
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
| | - Ayyalusamy Ramamoorthy
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
- Department of Chemical and Biomedical Engineering, Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32310, United States
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Krivdin LB. 17 O nuclear magnetic resonance: Recent advances and applications. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2023; 61:507-529. [PMID: 37449419 DOI: 10.1002/mrc.5378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/25/2023] [Accepted: 06/26/2023] [Indexed: 07/18/2023]
Abstract
The present review is focused on the most recent achievements in the application of liquid phase 17 O nuclear magnetic resonance (NMR) to inorganic, organic, and biochemical molecules focusing on their structure, conformations, and (bio)chemical behavior. The review is composed of four basic parts, namely, (1) simple molecules; (2) water and hydrogen bonding; (3) metal oxides, clusters, and complexes; and (4) biological molecules. Experimental 17 O NMR chemical shifts are thoroughly tabulated. They span a range of as much as almost 650 ppm (from -35.6 to +610.0 ppm) for inorganic and organic molecules, whereas this range is much wider for biological species being of about 1350 ppm (from -12 to +1332 ppm), and in the case of hemoproteins and heme-model compounds, isotropic chemical shifts of up to 2500 ppm were observed. The general prospects and caveats in the modern development of the liquid phase 17 O NMR in chemistry and biochemistry are critically discussed and briefly outlined in view of their future applications.
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Affiliation(s)
- Leonid B Krivdin
- A.E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
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Špačková J, Goldberga I, Yadav R, Cazals G, Lebrun A, Verdié P, Métro TX, Laurencin D. Fast and Cost-Efficient 17 O-Isotopic Labeling of Carboxylic Groups in Biomolecules: From Free Amino Acids to Peptide Chains. Chemistry 2023; 29:e202203014. [PMID: 36333272 DOI: 10.1002/chem.202203014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 11/04/2022] [Indexed: 11/08/2022]
Abstract
17 O NMR spectroscopy is a powerful technique, which can provide unique information regarding the structure and reactivity of biomolecules. However, the low natural abundance of 17 O (0.04 %) generally requires working with enriched samples, which are not easily accessible. Here, we present simple, fast and cost-efficient 17 O-enrichment strategies for amino acids and peptides by using mechanochemistry. First, five unprotected amino acids were enriched under ambient conditions, consuming only microliter amounts of costly labeled water, and producing pure molecules with enrichment levels up to ∼40 %, yields ∼60-85 %, and no loss of optical purity. Subsequently, 17 O-enriched Fmoc/tBu-protected amino acids were produced on a 1 g/day scale with high enrichment levels. Lastly, a site-selective 17 O-labeling of carboxylic functions in peptide side-chains was achieved for RGD and GRGDS peptides, with ∼28 % enrichment level. For all molecules, 17 O ssNMR spectra were recorded at 14.1 T in reasonable times, making this an important step forward for future NMR studies of biomolecules.
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Affiliation(s)
| | | | - Rishit Yadav
- ICGM, CNRS, UM, ENSCM, 34293, Montpellier, France
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McCalpin SD, Fu R, Ravula T, Wu G, Ramamoorthy A. Magnetically aligned nanodiscs enable direct measurement of 17O residual quadrupolar coupling for small molecules. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 346:107341. [PMID: 36473327 DOI: 10.1016/j.jmr.2022.107341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/17/2022] [Accepted: 11/18/2022] [Indexed: 06/17/2023]
Abstract
The use of 17O in NMR spectroscopy for structural studies has been limited due to its low natural abundance, low gyromagnetic ratio, and quadrupolar relaxation. Previous solution 17O work has primarily focused on studies of liquids where the 17O quadrupolar coupling is averaged to zero by isotropic molecular tumbling, and therefore has ignored the structural information contained in this parameter. Here, we use magnetically aligned polymer nanodiscs as an alignment medium to measure residual quadrupolar couplings (RQCs) for 17O-labelled benzoic acid in the aqueous phase. We show that increasing the magnetic field strength improves spectral sensitivity and resolution and that each satellite peak of the expected pentet pattern resolves clearly at 18.8 T. We observed no significant dependence of the RQC magnitudes on the magnetic field strength. However, changing the orientation of the alignment medium alters the RQC by a consistent factor, suggesting that 17O RQCs measured in this way can provide reliable orientational information for elucidations of molecular structures.
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Affiliation(s)
- Samuel D McCalpin
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Riqiang Fu
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA
| | - Thirupathi Ravula
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA; Biophysics, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Gang Wu
- Department of Chemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Ayyalusamy Ramamoorthy
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA; Biophysics, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI 48109, USA.
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Dynamic rotation featured translocations of human serum albumin with a conical glass nanopore. J Electroanal Chem (Lausanne) 2022. [DOI: 10.1016/j.jelechem.2022.116397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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9
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Liang L, Ji Y, Chen K, Gao P, Zhao Z, Hou G. Solid-State NMR Dipolar and Chemical Shift Anisotropy Recoupling Techniques for Structural and Dynamical Studies in Biological Systems. Chem Rev 2022; 122:9880-9942. [PMID: 35006680 DOI: 10.1021/acs.chemrev.1c00779] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
With the development of NMR methodology and technology during the past decades, solid-state NMR (ssNMR) has become a particularly important tool for investigating structure and dynamics at atomic scale in biological systems, where the recoupling techniques play pivotal roles in modern high-resolution MAS NMR. In this review, following a brief introduction on the basic theory of recoupling in ssNMR, we highlight the recent advances in dipolar and chemical shift anisotropy recoupling methods, as well as their applications in structural determination and dynamical characterization at multiple time scales (i.e., fast-, intermediate-, and slow-motion). The performances of these prevalent recoupling techniques are compared and discussed in multiple aspects, together with the representative applications in biomolecules. Given the recent emerging advances in NMR technology, new challenges for recoupling methodology development and potential opportunities for biological systems are also discussed.
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Affiliation(s)
- Lixin Liang
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Ji
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kuizhi Chen
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China
| | - Pan Gao
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China
| | - Zhenchao Zhao
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China
| | - Guangjin Hou
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China
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