1
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Nouri S, Boudet J, Dreher-Teo H, Allain FHT, Glockshuber R, Salmon L, Giese C. Elongated Bacterial Pili as a Versatile Alignment Medium for NMR Spectroscopy. Angew Chem Int Ed Engl 2023; 62:e202305120. [PMID: 37248171 DOI: 10.1002/anie.202305120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 05/31/2023]
Abstract
In NMR spectroscopy, residual dipolar couplings (RDCs) have emerged as one of the most exquisite probes of biological structure and dynamics. The measurement of RDCs relies on the partial alignment of the molecule of interest, for example by using a liquid crystal as a solvent. Here, we establish bacterial type 1 pili as an alternative liquid-crystalline alignment medium for the measurement of RDCs. To achieve alignment at pilus concentrations that allow for efficient NMR sample preparation, we elongated wild-type pili by recombinant overproduction of the main structural pilus subunit. Building on the extraordinary stability of type 1 pili against spontaneous dissociation and unfolding, we show that the medium is compatible with challenging experimental conditions such as high temperature, the presence of detergents, organic solvents or very acidic pH, setting it apart from most established alignment media. Using human ubiquitin, HIV-1 TAR RNA and camphor as spectroscopic probes, we demonstrate the applicability of the medium for the determination of RDCs of proteins, nucleic acids and small molecules. Our results show that type 1 pili represent a very useful alternative to existing alignment media and may readily assist the characterization of molecular structure and dynamics by NMR.
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Affiliation(s)
- Sirine Nouri
- Centre de RMN à Très Hauts Champs, CNRS, ENSL, UCBL, Université de Lyon, 5 rue de la Doua, 69100, Villeurbanne, France
| | - Julien Boudet
- Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland
| | - Hiang Dreher-Teo
- Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland
| | - Frédéric H-T Allain
- Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland
- Institute of Biochemistry, ETH Zurich, Otto-Stern-Weg 3, 8093, Zürich, Switzerland
| | - Rudi Glockshuber
- Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland
| | - Loïc Salmon
- Centre de RMN à Très Hauts Champs, CNRS, ENSL, UCBL, Université de Lyon, 5 rue de la Doua, 69100, Villeurbanne, France
- Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland
| | - Christoph Giese
- Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland
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2
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Sun B, Kekenes-Huskey PM. Myofilament-associated proteins with intrinsic disorder (MAPIDs) and their resolution by computational modeling. Q Rev Biophys 2023; 56:e2. [PMID: 36628457 PMCID: PMC11070111 DOI: 10.1017/s003358352300001x] [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: 01/12/2023]
Abstract
The cardiac sarcomere is a cellular structure in the heart that enables muscle cells to contract. Dozens of proteins belong to the cardiac sarcomere, which work in tandem to generate force and adapt to demands on cardiac output. Intriguingly, the majority of these proteins have significant intrinsic disorder that contributes to their functions, yet the biophysics of these intrinsically disordered regions (IDRs) have been characterized in limited detail. In this review, we first enumerate these myofilament-associated proteins with intrinsic disorder (MAPIDs) and recent biophysical studies to characterize their IDRs. We secondly summarize the biophysics governing IDR properties and the state-of-the-art in computational tools toward MAPID identification and characterization of their conformation ensembles. We conclude with an overview of future computational approaches toward broadening the understanding of intrinsic disorder in the cardiac sarcomere.
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Affiliation(s)
- Bin Sun
- Research Center for Pharmacoinformatics (The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin 150081, China
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3
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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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4
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Sensing Magnetic Field and Intermolecular Interactions in Diamagnetic Solution Using Residual Dipolar Couplings of Zephycandidine. Int J Mol Sci 2022; 23:ijms232315118. [PMID: 36499439 PMCID: PMC9737189 DOI: 10.3390/ijms232315118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 12/05/2022] Open
Abstract
An unusual residual dipolar coupling of methylene protons was recorded in NMR spectra because aromatic zephycandidine has preferential orientation at the external magnetic field. The observed splitting contains contribution from the dipole-dipole D-coupling and the anisotropic component of J-coupling. Absolute values of the anisotropy of magnetic susceptibility |Δχax| are larger for protic solvents because of the hydrogen-bonding compared to aprotic solvents for which polar and dispersion forces are more important. The energy barrier for the reorientation due to hydrogen-bonding is 1.22 kJ/mol in methanol-d4, 0.85 kJ/mol in ethanol-d6 and 0.87 kJ/mol in acetic acid-d6. In dimethyl sulfoxide-d6, 1.08 kJ/mol corresponds to the interaction of solvent lone pair electrons with π-electrons of zephycandidine. This energy barrier decreases for acetone-d6 which has smaller electric dipole moment. In acetonitrile-d3, there is no energy barrier which suggests solvent ordering around the solute due to the solvent-solvent interactions. The largest absolute values of the magnetic anisotropy are observed for aromatic benezene-d6 and tolune-d8 which have their own preferential orientation and enhance the order in the solution. The magnetic anisotropy of "isolated" zephycandidine, not hindered by intermolecular interaction could be estimated from the correlation between Δχax and cohesion energy density.
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Krishnarjuna B, Ravula T, Faison EM, Tonelli M, Zhang Q, Ramamoorthy A. Polymer-Nanodiscs as a Novel Alignment Medium for High-Resolution NMR-Based Structural Studies of Nucleic Acids. Biomolecules 2022; 12:1628. [PMID: 36358983 PMCID: PMC9687133 DOI: 10.3390/biom12111628] [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] [Received: 09/29/2022] [Revised: 10/28/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022] Open
Abstract
Residual dipolar couplings (RDCs) are increasingly used for high-throughput NMR-based structural studies and to provide long-range angular constraints to validate and refine structures of various molecules determined by X-ray crystallography and NMR spectroscopy. RDCs of a given molecule can be measured in an anisotropic environment that aligns in an external magnetic field. Here, we demonstrate the first application of polymer-based nanodiscs for the measurement of RDCs from nucleic acids. Polymer-based nanodiscs prepared using negatively charged SMA-EA polymer and zwitterionic DMPC lipids were characterized by size-exclusion chromatography, 1H NMR, dynamic light-scattering, and 2H NMR. The magnetically aligned polymer-nanodiscs were used as an alignment medium to measure RDCs from a 13C/15N-labeled fluoride riboswitch aptamer using 2D ARTSY-HSQC NMR experiments. The results showed that the alignment of nanodiscs is stable for nucleic acids and nanodisc-induced RDCs fit well with the previously determined solution structure of the riboswitch. These results demonstrate that SMA-EA-based lipid-nanodiscs can be used as a stable alignment medium for high-resolution structural and dynamical studies of nucleic acids, and they can also be applicable to study various other biomolecules and small molecules in general.
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Affiliation(s)
- Bankala Krishnarjuna
- Biophysics Program, Department of Chemistry, Biomedical Engineering, and Macromolecular Science and Engineering, Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Thirupathi Ravula
- Biophysics Program, Department of Chemistry, Biomedical Engineering, and Macromolecular Science and Engineering, Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109, USA
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Edgar M. Faison
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Qi Zhang
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ayyalusamy Ramamoorthy
- Biophysics Program, Department of Chemistry, Biomedical Engineering, and Macromolecular Science and Engineering, Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109, USA
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6
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Lenard AJ, Mulder FAA, Madl T. Solvent paramagnetic relaxation enhancement as a versatile method for studying structure and dynamics of biomolecular systems. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 132-133:113-139. [PMID: 36496256 DOI: 10.1016/j.pnmrs.2022.09.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 06/17/2023]
Abstract
Solvent paramagnetic relaxation enhancement (sPRE) is a versatile nuclear magnetic resonance (NMR)-based method that allows characterization of the structure and dynamics of biomolecular systems through providing quantitative experimental information on solvent accessibility of NMR-active nuclei. Addition of soluble paramagnetic probes to the solution of a biomolecule leads to paramagnetic relaxation enhancement in a concentration-dependent manner. Here we review recent progress in the sPRE-based characterization of structural and dynamic properties of biomolecules and their complexes, and aim to deliver a comprehensive illustration of a growing number of applications of the method to various biological systems. We discuss the physical principles of sPRE measurements and provide an overview of available co-solute paramagnetic probes. We then explore how sPRE, in combination with complementary biophysical techniques, can further advance biomolecular structure determination, identification of interaction surfaces within protein complexes, and probing of conformational changes and low-population transient states, as well as deliver insights into weak, nonspecific, and transient interactions between proteins and co-solutes. In addition, we present examples of how the incorporation of solvent paramagnetic probes can improve the sensitivity of NMR experiments and discuss the prospects of applying sPRE to NMR metabolomics, drug discovery, and the study of intrinsically disordered proteins.
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Affiliation(s)
- Aneta J Lenard
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Ageing, Molecular Biology and Biochemistry, Research Unit Integrative Structural Biology, Medical University of Graz, 8010 Graz, Austria.
| | - Frans A A Mulder
- Interdisciplinary Nanoscience Center and Department of Chemistry, University of Aarhus, DK-8000 Aarhus, Denmark; Institute of Biochemistry, Johannes Kepler Universität Linz, 4040 Linz, Austria.
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Ageing, Molecular Biology and Biochemistry, Research Unit Integrative Structural Biology, Medical University of Graz, 8010 Graz, Austria; BioTechMed-Graz, 8010 Graz, Austria.
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7
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Tolkatchev D, Gregorio CC, Kostyukova AS. The role of leiomodin in actin dynamics: a new road or a secret gate. FEBS J 2022; 289:6119-6131. [PMID: 34273242 PMCID: PMC8761783 DOI: 10.1111/febs.16128] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/10/2021] [Accepted: 07/16/2021] [Indexed: 12/29/2022]
Abstract
Leiomodin is an important emerging regulator of thin filaments. As novel molecular, cellular, animal model, and human data accumulate, the mechanisms of its action become clearer. Structural studies played a significant part in understanding the functional significance of leiomodin's interacting partners and functional domains. In this review, we present the current state of knowledge on the structural and cellular properties of leiomodin which has led to two proposed mechanisms of its function. Although it is known that leiomodin is essential for life, numerous domains within leiomodin remain unstudied and as such, we outline future directions for investigations that we predict will provide evidence that leiomodin is a multifunctional protein.
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Affiliation(s)
- Dmitri Tolkatchev
- Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA 99164, USA
| | - Carol C. Gregorio
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program, The University of Arizona, Tucson, AZ 85724, USA
| | - Alla S. Kostyukova
- Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA 99164, USA
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8
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Gao Q, Cleves AE, Wang X, Liu Y, Bowen S, Williamson RT, Jain AN, Sherer E, Reibarkh M. Solution cis-Proline Conformation of IPCs Inhibitor Aureobasidin A Elucidated via NMR-Based Conformational Analysis. JOURNAL OF NATURAL PRODUCTS 2022; 85:1449-1458. [PMID: 35622967 DOI: 10.1021/acs.jnatprod.1c01071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Aureobasidin A (abA) is a natural depsipeptide that inhibits inositol phosphorylceramide (IPC) synthases with significant broad-spectrum antifungal activity. abA is known to have two distinct conformations in solution corresponding to trans- and cis-proline (Pro) amide bond rotamers. While the trans-Pro conformation has been studied extensively, cis-Pro conformers have remained elusive. Conformational properties of cyclic peptides are known to strongly affect both potency and cell permeability, making a comprehensive characterization of abA conformation highly desirable. Here, we report a high-resolution 3D structure of the cis-Pro conformer of aureobasidin A elucidated for the first time using a recently developed NMR-driven computational approach. This approach utilizes ForceGen's advanced conformational sampling of cyclic peptides augmented by sparse distance and torsion angle constraints derived from NMR data. The obtained 3D conformational structure of cis-Pro abA has been validated using anisotropic residual dipolar coupling measurements. Support for the biological relevance of both the cis-Pro and trans-Pro abA configurations was obtained through molecular similarity experiments, which showed a significant 3D similarity between NMR-restrained abA conformational ensembles and another IPC synthase inhibitor, pleofungin A. Such ligand-based comparisons can further our understanding of the important steric and electrostatic characteristics of abA and can be utilized in the design of future therapeutics.
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Affiliation(s)
- Qi Gao
- Analytical Research and Development, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Ann E Cleves
- Applied Science, BioPharmics LLC, Santa Rosa, California 95404, United States
| | - Xiao Wang
- Analytical Research and Development, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Yizhou Liu
- Analytical Research and Development, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Sean Bowen
- Analytical Research and Development, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Robert Thomas Williamson
- Analytical Research and Development, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Ajay N Jain
- Applied Science, BioPharmics LLC, Santa Rosa, California 95404, United States
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94143, United States
| | - Edward Sherer
- Analytical Research and Development, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Mikhail Reibarkh
- Analytical Research and Development, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
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9
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Knoll K, Herold D, Hirschmann M, Thiele CM. A supramolecular and liquid crystalline water-based alignment medium based on azobenzene-substituted 1,3,5-benzenetricarboxamides. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2022; 60:563-571. [PMID: 35266585 DOI: 10.1002/mrc.5266] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/04/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
A supramolecular, lyotropic liquid crystalline alignment medium based on an azobenzene-containing 1,3,5-benzenetricarboxamide (BTA) building block is described and investigated. As we demonstrate, this water-based system is suitable for the investigation of various water-soluble analytes and allows for a scaling of alignment strength through variation of temperature. Additionally, alignment is shown to reversibly collapse above a certain temperature, yielding an isotropic solution. This collapse allows for isotropic reference measurements, which are typically needed in addition to those in an anisotropic environment, to be performed using the same sample just by varying the temperature. The medium described thus provides easy access to anisotropic NMR observables and simplifies structure elucidation techniques based thereon.
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Affiliation(s)
- Kevin Knoll
- Clemens-Schöpf-Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Dominik Herold
- Clemens-Schöpf-Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Max Hirschmann
- Clemens-Schöpf-Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
- Department of Fibre and Polymer Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Christina M Thiele
- Clemens-Schöpf-Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
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10
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Ahlawat S, Mote KR, Lakomek NA, Agarwal V. Solid-State NMR: Methods for Biological Solids. Chem Rev 2022; 122:9643-9737. [PMID: 35238547 DOI: 10.1021/acs.chemrev.1c00852] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In the last two decades, solid-state nuclear magnetic resonance (ssNMR) spectroscopy has transformed from a spectroscopic technique investigating small molecules and industrial polymers to a potent tool decrypting structure and underlying dynamics of complex biological systems, such as membrane proteins, fibrils, and assemblies, in near-physiological environments and temperatures. This transformation can be ascribed to improvements in hardware design, sample preparation, pulsed methods, isotope labeling strategies, resolution, and sensitivity. The fundamental engagement between nuclear spins and radio-frequency pulses in the presence of a strong static magnetic field is identical between solution and ssNMR, but the experimental procedures vastly differ because of the absence of molecular tumbling in solids. This review discusses routinely employed state-of-the-art static and MAS pulsed NMR methods relevant for biological samples with rotational correlation times exceeding 100's of nanoseconds. Recent developments in signal filtering approaches, proton methodologies, and multiple acquisition techniques to boost sensitivity and speed up data acquisition at fast MAS are also discussed. Several examples of protein structures (globular, membrane, fibrils, and assemblies) solved with ssNMR spectroscopy have been considered. We also discuss integrated approaches to structurally characterize challenging biological systems and some newly emanating subdisciplines in ssNMR spectroscopy.
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Affiliation(s)
- Sahil Ahlawat
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Kaustubh R Mote
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Nils-Alexander Lakomek
- University of Düsseldorf, Institute for Physical Biology, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Vipin Agarwal
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
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11
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Knoll K, Kostner T, Lorenz C, Thiele C. Investigations into Supramolecular Lyotropic Liquid Crystals based on 1,3,5‐Benzenetricarboxaramides by NMR‐spectroscopy. European J Org Chem 2022. [DOI: 10.1002/ejoc.202101490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Kevin Knoll
- Technische Universität Darmstadt: Technische Universitat Darmstadt Chemistry GERMANY
| | - Tobias Kostner
- Technische Universität Darmstadt: Technische Universitat Darmstadt Chemistry GERMANY
| | - Christian Lorenz
- Technische Universität Darmstadt: Technische Universitat Darmstadt Chemistry GERMANY
| | - Christina Thiele
- Technische Universität Darmstadt: Technische Universitat Darmstadt Chemistry Alarich Weiss Strasse 16 64287 Darmstadt GERMANY
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12
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Aroulanda C, Lesot P. Molecular enantiodiscrimination by NMR spectroscopy in chiral oriented systems: Concept, tools, and applications. Chirality 2021; 34:182-244. [PMID: 34936130 DOI: 10.1002/chir.23386] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/20/2021] [Accepted: 10/15/2021] [Indexed: 11/06/2022]
Abstract
The study of enantiodiscriminations in relation to various facets of enantiomorphism (chirality/prochirality) and/or molecular symmetry is an exciting area of modern organic chemistry and an ongoing challenge for nuclear magnetic resonance (NMR) spectroscopists who have developed many useful analytical approaches to solve stereochemical problems. Among them, the anisotropic NMR using chiral aligning solvents has provided a set of new and original tools by making accessible all intramolecular, order-dependent NMR interactions (anisotropic interactions), such as residual chemical shift anisotropy (RCSA), residual dipolar coupling (RDC), and residual quadrupolar coupling (RQC) for spin I > 1/2, while preserving high spectral resolution. The force of NMR in enantiopure, oriented solvents lies on its ability to orient differently in average on the NMR timescale enantiomers of chiral molecules and enantiotopic elements of prochiral ones, leading distinct NMR spectra or signals to be detected. In this compendium mainly written for all chemists playing with (pro)chirality, we overview various key aspects of NMR in weakly aligning chiral solvents as the lyotropic liquid crystals (LLCs), in particular those developed in France to study (pro)chiral compounds in relation with chemists needs: study of enantiopurity of mixture, stereochemistry, natural isotopic fractionation, as well as molecular conformation and configuration. Key representative examples covering the diversity of enantiomorphism concept, and the main and most recent applications illustrating the analytical potential of this NMR in polypeptide-based chiral liquid crystals (CLCs) are examined. The latest analytical strategy developed to determine in-solution conformational distribution of flexibles solutes using NMR in polypeptide-based aligned solvents is also proposed.
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Affiliation(s)
- Christie Aroulanda
- RMN en Milieu Orienté, ICMMO, UMR CNRS 8182, Université Paris-Saclay, Orsay cedex, France
| | - Philippe Lesot
- RMN en Milieu Orienté, ICMMO, UMR CNRS 8182, Université Paris-Saclay, Orsay cedex, France
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13
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Robertson AJ, Courtney JM, Shen Y, Ying J, Bax A. Concordance of X-ray and AlphaFold2 Models of SARS-CoV-2 Main Protease with Residual Dipolar Couplings Measured in Solution. J Am Chem Soc 2021; 143:19306-19310. [PMID: 34757725 PMCID: PMC8592127 DOI: 10.1021/jacs.1c10588] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
![]()
The
68-kDa homodimeric 3C-like protease of SARS-CoV-2, Mpro (3CLpro/Nsp5), is a promising antiviral drug target. We evaluate
the concordance of models generated by the newly introduced AlphaFold2
structure prediction program with residual dipolar couplings (RDCs)
measured in solution for 15N–1HN and 13C′–1HN atom
pairs. The latter were measured using a new, highly precise TROSY-AntiTROSY
Encoded RDC (TATER) experiment. Three sets of AlphaFold2 models were
evaluated: (1) MproAF, generated using the standard
AlphaFold2 input structural database; (2) MproAFD, where the AlphaFold2 implementation was modified to exclude all
candidate template X-ray structures deposited after Jan 1, 2020; and
(3) MproAFS, which excluded all structures homologous
to coronaviral Mpro. Close agreement between all three
sets of AlphaFold models and experimental RDC data is found for most
of the protein. For residues in well-defined secondary structure,
the agreement decreases somewhat upon Amber relaxation. For these
regions, MproAF agreement exceeds that of most
high-resolution X-ray structures. Residues from domain 2 that comprise
elements of both the active site and the homo-dimerization interface
fit less well across all structures. These results indicate novel
opportunities for combining experimentation with molecular dynamics
simulations, where solution RDCs provide highly precise input for
QM/MM simulations of substrate binding/reaction trajectories.
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Affiliation(s)
- Angus J Robertson
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - Joseph M Courtney
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - Yang Shen
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - Jinfa Ying
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - Ad Bax
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
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14
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Chiliveri SC, Robertson AJ, Shen Y, Torchia DA, Bax A. Advances in NMR Spectroscopy of Weakly Aligned Biomolecular Systems. Chem Rev 2021; 122:9307-9330. [PMID: 34766756 DOI: 10.1021/acs.chemrev.1c00730] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The measurement and application of residual dipolar couplings (RDCs) in solution NMR studies of biological macromolecules has become well established over the past quarter of a century. Numerous methods for generating the requisite anisotropic orientational molecular distribution have been demonstrated, each with its specific strengths and weaknesses. In parallel, an enormous number of pulse schemes have been introduced to measure the many different types of RDCs, ranging from the most widely measured backbone amide 15N-1H RDCs, to 1H-1H RDCs and couplings between low-γ nuclei. Applications of RDCs range from structure validation and refinement to the determination of relative domain orientations, the measurement of backbone and domain motions, and de novo structure determination. Nevertheless, it appears that the power of the RDC methodology remains underutilized. This review aims to highlight the practical aspects of sample preparation and RDC measurement while describing some of the most straightforward applications that take advantage of the exceptionally precise information contained in such data. Some emphasis will be placed on more recent developments that enable the accurate measurement of RDCs in larger systems, which is key to the ongoing shift in focus of biological NMR spectroscopy from structure determination toward gaining improved understanding of how molecular flexibility drives protein function.
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Affiliation(s)
- Sai Chaitanya Chiliveri
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Angus J Robertson
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Yang Shen
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Dennis A Torchia
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
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15
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Abstract
Membrane proteins (MPs) play essential roles in numerous cellular processes. Because around 70% of the currently marketed drugs target MPs, a detailed understanding of their structure, binding properties, and functional dynamics in a physiologically relevant environment is crucial for a more detailed understanding of this important protein class. We here summarize the benefits of using lipid nanodiscs for NMR structural investigations and provide a detailed overview of the currently used lipid nanodisc systems as well as their applications in solution-state NMR. Despite the increasing use of other structural methods for the structure determination of MPs in lipid nanodiscs, solution NMR turns out to be a versatile tool to probe a wide range of MP features, ranging from the structure determination of small to medium-sized MPs to probing ligand and partner protein binding as well as functionally relevant dynamical signatures in a lipid nanodisc setting. We will expand on these topics by discussing recent NMR studies with lipid nanodiscs and work out a key workflow for optimizing the nanodisc incorporation of an MP for subsequent NMR investigations. With this, we hope to provide a comprehensive background to enable an informed assessment of the applicability of lipid nanodiscs for NMR studies of a particular MP of interest.
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Affiliation(s)
- Umut Günsel
- Bavarian NMR Center (BNMRZ) at the Department of Chemistry, Technical University of Munich, Ernst-Otto-Fischer-Strasse 2, 85748 Garching, Germany
| | - Franz Hagn
- Bavarian NMR Center (BNMRZ) at the Department of Chemistry, Technical University of Munich, Ernst-Otto-Fischer-Strasse 2, 85748 Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
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16
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Cucuzza S, Güntert P, Plückthun A, Zerbe O. An automated iterative approach for protein structure refinement using pseudocontact shifts. JOURNAL OF BIOMOLECULAR NMR 2021; 75:319-334. [PMID: 34338940 PMCID: PMC8473369 DOI: 10.1007/s10858-021-00376-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 07/19/2021] [Indexed: 05/02/2023]
Abstract
NMR structure calculation using NOE-derived distance restraints requires a considerable number of assignments of both backbone and sidechains resonances, often difficult or impossible to get for large or complex proteins. Pseudocontact shifts (PCSs) also play a well-established role in NMR protein structure calculation, usually to augment existing structural, mostly NOE-derived, information. Existing refinement protocols using PCSs usually either require a sizeable number of sidechain assignments or are complemented by other experimental restraints. Here, we present an automated iterative procedure to perform backbone protein structure refinements requiring only a limited amount of backbone amide PCSs. Already known structural features from a starting homology model, in this case modules of repeat proteins, are framed into a scaffold that is subsequently refined by experimental PCSs. The method produces reliable indicators that can be monitored to judge about the performance. We applied it to a system in which sidechain assignments are hardly possible, designed Armadillo repeat proteins (dArmRPs), and we calculated the solution NMR structure of YM4A, a dArmRP containing four sequence-identical internal modules, obtaining high convergence to a single structure. We suggest that this approach is particularly useful when approximate folds are known from other techniques, such as X-ray crystallography, while avoiding inherent artefacts due to, for instance, crystal packing.
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Affiliation(s)
- Stefano Cucuzza
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Peter Güntert
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt am Main, Germany
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
- Department of Chemistry, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, 192-0397, Tokyo, Japan
| | - Andreas Plückthun
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Oliver Zerbe
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland.
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17
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Gaalswyk K, Liu Z, Vogel HJ, MacCallum JL. An Integrative Approach to Determine 3D Protein Structures Using Sparse Paramagnetic NMR Data and Physical Modeling. Front Mol Biosci 2021; 8:676268. [PMID: 34476238 PMCID: PMC8407082 DOI: 10.3389/fmolb.2021.676268] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 07/29/2021] [Indexed: 11/13/2022] Open
Abstract
Paramagnetic nuclear magnetic resonance (NMR) methods have emerged as powerful tools for structure determination of large, sparsely protonated proteins. However traditional applications face several challenges, including a need for large datasets to offset the sparsity of restraints, the difficulty in accounting for the conformational heterogeneity of the spin-label, and noisy experimental data. Here we propose an integrative approach to structure determination combining sparse paramagnetic NMR with physical modelling to infer approximate protein structural ensembles. We use calmodulin in complex with the smooth muscle myosin light chain kinase peptide as a model system. Despite acquiring data from samples labeled only at the backbone amide positions, we are able to produce an ensemble with an average RMSD of ∼2.8 Å from a reference X-ray crystal structure. Our approach requires only backbone chemical shifts and measurements of the paramagnetic relaxation enhancement and residual dipolar couplings that can be obtained from sparsely labeled samples.
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Affiliation(s)
- Kari Gaalswyk
- Department of Chemistry, University of Calgary, Calgary, AB, Canada
| | - Zhihong Liu
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Hans J. Vogel
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
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18
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Fowler NJ, Sljoka A, Williamson MP. The accuracy of NMR protein structures in the Protein Data Bank. Structure 2021; 29:1430-1439.e2. [PMID: 34331857 DOI: 10.1016/j.str.2021.07.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/18/2021] [Accepted: 07/14/2021] [Indexed: 11/18/2022]
Abstract
The program ANSURR measures the accuracy of NMR structures by comparing rigidity obtained from experimental backbone chemical shifts and from structures. We report on ANSURR analysis of 7,000 PDB NMR ensembles within the Protein Data Bank, which can be found at ansurr.com. The accuracy of NMR structures progressively improved up until 2005, but since then, it has plateaued. Most structures have accurate secondary structure, but are generally too floppy, particularly in loops. Thus, there is a need for more experimental restraints in loops. Currently, the best predictors of accuracy are Ramachandran distribution and the number of NOE restraints per residue. The precision of structures within the ensemble correlates well with accuracy, as does the number of hydrogen bond restraints per residue. Structure accuracy is improved when other components (such as additional polypeptide chains or ligands) are included.
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Affiliation(s)
- Nicholas J Fowler
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Adnan Sljoka
- RIKEN Center for Advanced Intelligence Project, RIKEN, 1-4-1 Nihombashi, Chuo-ku, Tokyo 103-0027 Japan; Department of Chemistry, University of Toronto, UTM, 3359 Mississauga Road North, Mississauga, ON L5L 1C6, Canada.
| | - Mike P Williamson
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK.
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19
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Ravula T, Dai X, Ramamoorthy A. Solid-State NMR Study to Probe the Effects of Divalent Metal Ions (Ca 2+ and Mg 2+) on the Magnetic Alignment of Polymer-Based Lipid Nanodiscs. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:7780-7788. [PMID: 34129342 PMCID: PMC8587631 DOI: 10.1021/acs.langmuir.1c01018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Divalent cations, especially Ca2+ and Mg2+, play a vital role in the function of biomolecules and making them important to be constituents in samples for in vitro biophysical and biochemical characterizations. Although lipid nanodiscs are becoming valuable tools for structural biology studies on membrane proteins and for drug delivery, most types of nanodiscs used in these studies are unstable in the presence of divalent metal ions. To avoid the interaction of divalent metal ions with the belt of the nanodiscs, synthetic polymers have been designed and demonstrated to form stable lipid nanodiscs under such unstable conditions. Such polymer-based nanodiscs have been shown to provide an ideal platform for structural studies using both solid-state and solution NMR spectroscopies because of the near-native cell-membrane environment they provide and the unique magnetic-alignment behavior of large-size nanodiscs. In this study, we report an investigation probing the effects of Ca2+ and Mg2+ ions on the formation of polymer-based lipid nanodiscs and the magnetic-alignment properties using a synthetic polymer, styrene maleimide quaternary ammonium (SMA-QA), and 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) lipids. Phosphorus-31 NMR experiments were used to evaluate the stability of the magnetic-alignment behavior of the nanodiscs for varying concentrations of Ca2+ or Mg2+ at different temperatures. It is remarkable that the interaction of divalent cations with lipid headgroups promotes the stacking up of nanodiscs that results in the enhanced magnetic alignment of nanodiscs. Interestingly, the reported results show that both the temperature and the concentration of divalent metal ions can be optimized to achieve the optimal alignment of nanodiscs in the presence of an applied magnetic field. We expect the reported results to be useful in the design of nanodisc-based nanoparticles for various applications in addition to atomic-resolution structural and dynamics studies using NMR and other biophysical techniques.
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Affiliation(s)
- Thirupathi Ravula
- Biophysics Program and Department of Chemistry, Biomedical Engineering, and Macromolecular Science and Engineering, The University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Xiaofeng Dai
- Biophysics Program and Department of Chemistry, Biomedical Engineering, and Macromolecular Science and Engineering, The University of Michigan, Ann Arbor, MI 48109-1055, USA
- Xiaofeng Dai was a visiting student from the College of Chemistry, Nankai University, Tianjin 300071, China
| | - Ayyalusamy Ramamoorthy
- Biophysics Program and Department of Chemistry, Biomedical Engineering, and Macromolecular Science and Engineering, The University of Michigan, Ann Arbor, MI 48109-1055, USA
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20
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Rogals MJ, Yang JY, Williams RV, Moremen KW, Amster IJ, Prestegard JH. Sparse isotope labeling for nuclear magnetic resonance (NMR) of glycoproteins using 13C-glucose. Glycobiology 2021; 31:425-435. [PMID: 32902634 PMCID: PMC8091466 DOI: 10.1093/glycob/cwaa071] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 07/22/2020] [Accepted: 07/24/2020] [Indexed: 01/02/2023] Open
Abstract
Preparation of samples for nuclear magnetic resonance (NMR) characterization of larger proteins requires enrichment with less abundant, NMR-active, isotopes such as 13C and 15N. This is routine for proteins that can be expressed in bacterial culture where low-cost isotopically enriched metabolic substrates can be used. However, it can be expensive for glycosylated proteins expressed in mammalian culture where more costly isotopically enriched amino acids are usually used. We describe a simple, relatively inexpensive procedure in which standard commercial media is supplemented with 13C-enriched glucose to achieve labeling of all glycans plus all alanines of the N-terminal domain of the highly glycosylated protein, CEACAM1. We demonstrate an ability to detect partially occupied N-glycan sites, sites less susceptible to processing by an endoglycosidase, and some unexpected truncation of the amino acid sequence. The labeling of both the protein (through alanines) and the glycans in a single culture requiring no additional technical expertise past standard mammalian expression requirements is anticipated to have several applications, including structural and functional screening of the many glycosylated proteins important to human health.
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Affiliation(s)
- Monique J Rogals
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd., Athens, GA 30602, USA
| | - Jeong-Yeh Yang
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd., Athens, GA 30602, USA
| | - Robert V Williams
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd., Athens, GA 30602, USA
- Department of Chemistry
| | - Kelley W Moremen
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd., Athens, GA 30602, USA
- Department of Biochemistry and Molecular Biology
| | | | - James H Prestegard
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd., Athens, GA 30602, USA
- Department of Chemistry
- Department of Biochemistry and Molecular Biology
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21
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REDCRAFT: A computational platform using residual dipolar coupling NMR data for determining structures of perdeuterated proteins in solution. PLoS Comput Biol 2021; 17:e1008060. [PMID: 33524015 PMCID: PMC7877757 DOI: 10.1371/journal.pcbi.1008060] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 02/11/2021] [Accepted: 01/05/2021] [Indexed: 01/10/2023] Open
Abstract
Nuclear Magnetic Resonance (NMR) spectroscopy is one of the three primary experimental means of characterizing macromolecular structures, including protein structures. Structure determination by solution NMR spectroscopy has traditionally relied heavily on distance restraints derived from nuclear Overhauser effect (NOE) measurements. While structure determination of proteins from NOE-based restraints is well understood and broadly used, structure determination from Residual Dipolar Couplings (RDCs) is relatively less well developed. Here, we describe the new features of the protein structure modeling program REDCRAFT and focus on the new Adaptive Decimation (AD) feature. The AD plays a critical role in improving the robustness of REDCRAFT to missing or noisy data, while allowing structure determination of larger proteins from less data. In this report we demonstrate the successful application of REDCRAFT in structure determination of proteins ranging in size from 50 to 145 residues using experimentally collected data, and of larger proteins (145 to 573 residues) using simulated RDC data. In both cases, REDCRAFT uses only RDC data that can be collected from perdeuterated proteins. Finally, we compare the accuracy of structure determination from RDCs alone with traditional NOE-based methods for the structurally novel PF.2048.1 protein. The RDC-based structure of PF.2048.1 exhibited 1.0 Å BB-RMSD with respect to a high-quality NOE-based structure. Although optimal strategies would include using RDC data together with chemical shift, NOE, and other NMR data, these studies provide proof-of-principle for robust structure determination of largely-perdeuterated proteins from RDC data alone using REDCRAFT. Residual Dipolar Couplings have the potential to improve the accuracy and reduce the time needed to characterize protein structures. In addition, RDC data have been demonstrated to concurrently elucidate structure of proteins, provide assignment of resonances, and characterize the internal dynamics of proteins. Given all the advantages associated with the study of proteins from RDC data, based on the statistics provided by the Protein Databank (PDB), surprisingly only 124 proteins (out of nearly 150,000 proteins) have utilized RDCs as part of their structure determination. Even a smaller subset of these proteins (approximately 7) have utilized RDCs as the primary source of data for structure determination. One key factor in the use of RDCs is the challenging computational and analytical aspects of this source of data. In this report, we demonstrate the success of the REDCRAFT software package in structure determination of proteins using RDC data that can be collected from small and large proteins in a routine fashion. REDCRAFT accomplishes the challenging task of structure determination from RDCs by introducing a unique search and optimization technique that is both robust and computationally tractable. Structure determination from routinely collectable RDC data using REDCRAFT can complement existing methods to provide faster and more accurate studies of larger and more complex protein structures by NMR spectroscopy in solution state.
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22
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Baroni F, Gallo M, Pazzagli L, Luti S, Baccelli I, Spisni A, Pertinhez TA. A mechanistic model may explain the dissimilar biological efficiency of the fungal elicitors cerato-platanin and cerato-populin. Biochim Biophys Acta Gen Subj 2021; 1865:129843. [PMID: 33444726 DOI: 10.1016/j.bbagen.2021.129843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 12/17/2020] [Accepted: 01/08/2021] [Indexed: 11/19/2022]
Abstract
Among their various functions, the members of the cerato-platanin family can stimulate plants' defense responses and induce resistance against microbial pathogens. Recent results suggest that conserved loops, also involved in chitin binding, might be a structural motif central for their eliciting activity. Here, we focus on cerato-platanin and its orthologous cerato-populin, searching for a rationale of their diverse efficiency to elicit plants' defense and to interact with oligosaccharides. A 3D model of cerato-populin has been generated by homology modeling using the NMR-derived cerato-platanin structure as template, and it has been validated by fitting with residual dipolar couplings. Loops β1-β2 and β2-β3 have been indicated as important for some CPPs members to express their biological function. When compared to cerato-platanin, in cerato-populin they present two mutations and an insertion that significantly modify their electrostatic surface. NMR relaxation experiments point to a reduced conformational plasticity of cerato-populin loops with respect to the ones of cerato-platanin. The different electrostatic surface of the loops combined with a distinct network of intra-molecular interactions are expected to be factors that, by leading to a diverse spatial organization and dissimilar collective motions, can regulate the eliciting efficacy of the two proteins and their affinity for oligosaccharides.
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Affiliation(s)
- Fabio Baroni
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Mariana Gallo
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Luigia Pazzagli
- Department of Biomedical Experimental and Clinical Sciences, University of Florence, Firenze, Italy
| | - Simone Luti
- Department of Biomedical Experimental and Clinical Sciences, University of Florence, Firenze, Italy
| | - Ivan Baccelli
- Institute for Sustainable Plant Protection, National Research Council of Italy, Sesto Fiorentino (Florence), Italy
| | - Alberto Spisni
- Department of Medicine and Surgery, University of Parma, Parma, Italy.
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23
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Pochapsky TC. A dynamic understanding of cytochrome P450 structure and function through solution NMR. Curr Opin Biotechnol 2020; 69:35-42. [PMID: 33360373 DOI: 10.1016/j.copbio.2020.11.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/17/2020] [Indexed: 12/12/2022]
Abstract
Many economically important biosyntheses incorporate regiospecific and stereospecific oxidations at unactivated carbons. Such oxidations are commonly catalyzed by cytochrome P450 monooxygenases, heme-containing enzymes that activate molecular oxygen while selectively binding and orienting the substrate for reaction. Despite the plethora of P450-catalyzed reactions, the P450 fold is highly conserved, and static structures are often insufficient for characterizing conformational states that contribute to specificity. High-resolution solution nuclear magnetic resonance (NMR) offers insights into dynamic processes and conformational changes that are required of a P450 in order to attain the combination of specificity and efficiency required for these reactions.
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Affiliation(s)
- Thomas C Pochapsky
- Departments of Chemistry, Biochemistry and The Rosenstiel Institute for Basic Medical Research, Brandeis University, 415 South St., Waltham, MA 02454, USA.
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24
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Giassa IC, Vavrinská A, Zelinka J, Šebera J, Sychrovský V, Boelens R, Fiala R, Trantírek L. HERMES - A Software Tool for the Prediction and Analysis of Magnetic-Field-Induced Residual Dipolar Couplings in Nucleic Acids. Chempluschem 2020; 85:2177-2185. [PMID: 32986260 DOI: 10.1002/cplu.202000505] [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: 06/30/2020] [Revised: 08/31/2020] [Indexed: 11/06/2022]
Abstract
Field-Induced Residual Dipolar Couplings (fiRDC) are a valuable source of long-range information on structure of nucleic acids (NA) in solution. A web application (HERMES) was developed for structure-based prediction and analysis of the (fiRDCs) in NA. fiRDC prediction is based on input 3D model structure(s) of NA and a built-in library of nucleobase-specific magnetic susceptibility tensors and reference geometries. HERMES allows three basic applications: (i) the prediction of fiRDCs for a given structural model of NAs, (ii) the validation of experimental or modeled NA structures using experimentally derived fiRDCs, and (iii) assessment of the oligomeric state of the NA fragment and/or the identification of a molecular NA model that is consistent with experimentally derived fiRDC data. Additionally, the program's built-in routine for rigid body modeling allows the evaluation of relative orientation of domains within NA that is in agreement with experimental fiRDCs.
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Affiliation(s)
| | - Andrea Vavrinská
- Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, 3584 CH, The Netherlands
| | - Jiří Zelinka
- Department of Mathematics and Statistics, Faculty of Science, Masaryk University, Brno, 611 37, Czech Republic
| | - Jakub Šebera
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, 166 10, Czech Republic
| | - Vladimír Sychrovský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, 166 10, Czech Republic
| | - Rolf Boelens
- Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, 3584 CH, The Netherlands
| | - Radovan Fiala
- Central European Institute of Technology, Masaryk University, Brno
| | - Lukáš Trantírek
- Central European Institute of Technology, Masaryk University, Brno
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25
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Tolkatchev D, Smith GE, Schultz LE, Colpan M, Helms GL, Cort JR, Gregorio CC, Kostyukova AS. Leiomodin creates a leaky cap at the pointed end of actin-thin filaments. PLoS Biol 2020; 18:e3000848. [PMID: 32898131 PMCID: PMC7500696 DOI: 10.1371/journal.pbio.3000848] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 09/18/2020] [Accepted: 08/17/2020] [Indexed: 01/26/2023] Open
Abstract
Improper lengths of actin-thin filaments are associated with altered contractile activity and lethal myopathies. Leiomodin, a member of the tropomodulin family of proteins, is critical in thin filament assembly and maintenance; however, its role is under dispute. Using nuclear magnetic resonance data and molecular dynamics simulations, we generated the first atomic structural model of the binding interface between the tropomyosin-binding site of cardiac leiomodin and the N-terminus of striated muscle tropomyosin. Our structural data indicate that the leiomodin/tropomyosin complex only forms at the pointed end of thin filaments, where the tropomyosin N-terminus is not blocked by an adjacent tropomyosin protomer. This discovery provides evidence supporting the debated mechanism where leiomodin and tropomodulin regulate thin filament lengths by competing for thin filament binding. Data from experiments performed in cardiomyocytes provide additional support for the competition model; specifically, expression of a leiomodin mutant that is unable to interact with tropomyosin fails to displace tropomodulin at thin filament pointed ends and fails to elongate thin filaments. Together with previous structural and biochemical data, we now propose a molecular mechanism of actin polymerization at the pointed end in the presence of bound leiomodin. In the proposed model, the N-terminal actin-binding site of leiomodin can act as a "swinging gate" allowing limited actin polymerization, thus making leiomodin a leaky pointed-end cap. Results presented in this work answer long-standing questions about the role of leiomodin in thin filament length regulation and maintenance.
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Affiliation(s)
- Dmitri Tolkatchev
- Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, Washington, United States of America
| | - Garry E. Smith
- Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, Washington, United States of America
| | - Lauren E. Schultz
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program, The University of Arizona, Tucson, Arizona, United States of America
| | - Mert Colpan
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program, The University of Arizona, Tucson, Arizona, United States of America
| | - Gregory L. Helms
- The Center for NMR Spectroscopy, Washington State University, Pullman, Washington, United States of America
| | - John R. Cort
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, United States of America
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, United States of America
| | - Carol C. Gregorio
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program, The University of Arizona, Tucson, Arizona, United States of America
| | - Alla S. Kostyukova
- Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, Washington, United States of America
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26
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Ravula T, Sahoo BR, Dai X, Ramamoorthy A. Natural-abundance 17O NMR spectroscopy of magnetically aligned lipid nanodiscs. Chem Commun (Camb) 2020; 56:9998-10001. [PMID: 32724998 PMCID: PMC7484029 DOI: 10.1039/d0cc04011h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Natural-abundance 17O NMR experiments are used to investigate the hydrated water in magnetically aligned synthetic polymer based lipid-nanodiscs. Residual quadrupole couplings (RQCs) measured from the observed five 17O (central and satellite) transitions, and molecular dynamics simulations, are used to probe the ordering of water molecules across the lipid bilayer.
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Affiliation(s)
- Thirupathi Ravula
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA.
| | - Bikash R Sahoo
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA.
| | - Xiaofeng Dai
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA.
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA.
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27
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Hamada H, Yanagi M, Shimoda K, Uchida N. Water-Soluble Glycosylated Resveratrol for Measuring Residual Dipolar Coupling in NMR. Nat Prod Commun 2020. [DOI: 10.1177/1934578x20947232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Residual dipolar coupling (RDC) is a newly emerging technique for obtaining more precise conformational features of molecules in nuclear magnetic resonance (NMR), which can be observed when the molecules are oriented in NMR sample solutions. Unlike the case of solubilization of resveratrol (Res) in aqueous media by surfactants, multiglycosylated resveratrol (GlyRes) was dispersed in aqueous media forming nanoparticles with an extremely small size. In the presence of an NMR alignment medium of bacteriophage, GlyRes molecules were efficiently oriented in the strong magnetic field allowing for observations of RDCs in NMR. Structural refinement using the observed RDC values enabled differentiation of trans and cis forms of Res.
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Affiliation(s)
- Hiroki Hamada
- Department of Life Science, Faculty of Science, Okayama University of Science, Kita-ku, Japan
| | - Masayoshi Yanagi
- Department of Life Science, Faculty of Science, Okayama University of Science, Kita-ku, Japan
| | - Kei Shimoda
- Department of Biomedical Chemistry, Faculty of Medicine, Oita University, Hasama-machi, Japan
| | - Noriyuki Uchida
- RIKEN Center for Emergent Matter Science, Wako, Saitama, Japan
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28
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Softley CA, Bostock MJ, Popowicz GM, Sattler M. Paramagnetic NMR in drug discovery. JOURNAL OF BIOMOLECULAR NMR 2020; 74:287-309. [PMID: 32524233 PMCID: PMC7311382 DOI: 10.1007/s10858-020-00322-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 05/26/2020] [Indexed: 05/05/2023]
Abstract
The presence of an unpaired electron in paramagnetic molecules generates significant effects in NMR spectra, which can be exploited to provide restraints complementary to those used in standard structure-calculation protocols. NMR already occupies a central position in drug discovery for its use in fragment screening, structural biology and validation of ligand-target interactions. Paramagnetic restraints provide unique opportunities, for example, for more sensitive screening to identify weaker-binding fragments. A key application of paramagnetic NMR in drug discovery, however, is to provide new structural restraints in cases where crystallography proves intractable. This is particularly important at early stages in drug-discovery programs where crystal structures of weakly-binding fragments are difficult to obtain and crystallization artefacts are probable, but structural information about ligand poses is crucial to guide medicinal chemistry. Numerous applications show the value of paramagnetic restraints to filter computational docking poses and to generate interaction models. Paramagnetic relaxation enhancements (PREs) generate a distance-dependent effect, while pseudo-contact shift (PCS) restraints provide both distance and angular information. Here, we review strategies for introducing paramagnetic centers and discuss examples that illustrate the utility of paramagnetic restraints in drug discovery. Combined with standard approaches, such as chemical shift perturbation and NOE-derived distance information, paramagnetic NMR promises a valuable source of information for many challenging drug-discovery programs.
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Affiliation(s)
- Charlotte A Softley
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Lichtenbergstraße 4, 85747, Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Mark J Bostock
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Lichtenbergstraße 4, 85747, Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Grzegorz M Popowicz
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Lichtenbergstraße 4, 85747, Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Michael Sattler
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Lichtenbergstraße 4, 85747, Garching, Germany.
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany.
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29
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Danmaliki GI, Hwang PM. Solution NMR spectroscopy of membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183356. [PMID: 32416193 DOI: 10.1016/j.bbamem.2020.183356] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 05/08/2020] [Accepted: 05/10/2020] [Indexed: 02/06/2023]
Abstract
Integral membrane proteins (IMPs) perform unique and indispensable functions in the cell, making them attractive targets for fundamental research and drug discovery. Developments in protein production, isotope labeling, sample preparation, and pulse sequences have extended the utility of solution NMR spectroscopy for studying IMPs with multiple transmembrane segments. Here we review some recent applications of solution NMR for studying structure, dynamics, and interactions of polytopic IMPs, emphasizing strategies used to overcome common technical challenges.
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Affiliation(s)
- Gaddafi I Danmaliki
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Peter M Hwang
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada; Department of Medicine, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.
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30
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Shine A, Shenoy J, Jayan P, Jiji AC, Vijayan V. Residual Dipolar‐Coupling‐Based Conformational Comparison of Noncovalent Ubiquitin Homodimer with Covalently Linked Diubiquitin. Chemphyschem 2020; 21:888-894. [DOI: 10.1002/cphc.201901100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 01/06/2020] [Indexed: 11/08/2022]
Affiliation(s)
- A. Shine
- School of Chemistry IISER Thiruvananthapuram Maruthamala PO Vithura Kerala India
| | - J. Shenoy
- School of Chemistry IISER Thiruvananthapuram Maruthamala PO Vithura Kerala India
| | - Parvathy Jayan
- School of Chemistry IISER Thiruvananthapuram Maruthamala PO Vithura Kerala India
| | - A. C. Jiji
- School of Chemistry IISER Thiruvananthapuram Maruthamala PO Vithura Kerala India
| | - Vinesh Vijayan
- School of Chemistry IISER Thiruvananthapuram Maruthamala PO Vithura Kerala India
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31
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Liu H, Chen P, Li XL, Sun H, Lei X. Practical aspects of oligopeptide AAKLVFF as an alignment medium for the measurements of residual dipolar coupling of organic molecules. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:404-410. [PMID: 32239576 DOI: 10.1002/mrc.4825] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 12/03/2018] [Accepted: 12/26/2018] [Indexed: 06/11/2023]
Abstract
Practical aspects of the oligopeptide AAKLVFF as an alignment medium are discussed, including large-scale synthesis of the oligopeptide, detailed description of preparation of the alignment medium, and acquisition of the RDCs. The resulting orienting medium is stable and highly homogeneous with tunable alignment strength in methanol.
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Affiliation(s)
- Han Liu
- School of Pharmaceutical Sciences, South Central University for Nationalities, Wuhan, China
| | - Pian Chen
- School of Pharmaceutical Sciences, South Central University for Nationalities, Wuhan, China
| | - Xiao-Lu Li
- Department of Structural Biology, Leibniz-Institut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Han Sun
- Department of Structural Biology, Leibniz-Institut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Xinxiang Lei
- School of Pharmaceutical Sciences, South Central University for Nationalities, Wuhan, China
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32
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Ibáñez de Opakua A, Klama F, Ndukwe IE, Martin GE, Williamson RT, Zweckstetter M. Determination of Complex Small-Molecule Structures Using Molecular Alignment Simulation. Angew Chem Int Ed Engl 2020; 59:6172-6176. [PMID: 31971323 PMCID: PMC7187346 DOI: 10.1002/anie.202000311] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 01/23/2020] [Indexed: 11/12/2022]
Abstract
Correct structural assignment of small molecules and natural products is critical for drug discovery and organic chemistry. Anisotropy-based NMR spectroscopy is a powerful tool for the structural assignment of organic molecules, but it relies on the utilization of a medium that disrupts the isotropic motion of molecules in organic solvents. Here, we establish a quantitative correlation between the atomic structure of the alignment medium, the molecular structure of the small molecule, and molecule-specific anisotropic NMR parameters. The quantitative correlation uses an accurate three-dimensional molecular alignment model that predicts residual dipolar couplings of small molecules aligned by poly(γ-benzyl-l-glutamate). The technique facilitates reliable determination of the correct stereoisomer and enables unequivocal, rapid determination of complex molecular structures from extremely sparse NMR data.
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Affiliation(s)
- Alain Ibáñez de Opakua
- Structural Biology in DementiaGerman Center for Neurodegenerative Diseases (DZNE)Von-Siebold-Strasse 3a37075GöttingenGermany
| | - Frederik Klama
- Department for NMR-based Structural BiologyMax Planck Institute for Biophysical ChemistryAm Fassberg 1137077GöttingenGermany
| | - Ikenna E. Ndukwe
- Analytical Research & Development (Rahway)Merck & Co. Inc.KenilworthNJUSA
- Complex Carbohydrate Research CenterUniversity of GeorgiaAthensGA30602USA
| | - Gary E. Martin
- Analytical Research & Development (Rahway)Merck & Co. Inc.KenilworthNJUSA
- Department of Chemistry and BiochemistrySeton Hall UniversitySouth OrangeNJ07079USA
| | - R. Thomas Williamson
- Analytical Research & Development (Rahway)Merck & Co. Inc.KenilworthNJUSA
- Department of Chemistry & BiochemistryUniversity of North Carolina WilmingtonWilmingtonNC28409USA
| | - Markus Zweckstetter
- Structural Biology in DementiaGerman Center for Neurodegenerative Diseases (DZNE)Von-Siebold-Strasse 3a37075GöttingenGermany
- Department for NMR-based Structural BiologyMax Planck Institute for Biophysical ChemistryAm Fassberg 1137077GöttingenGermany
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33
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Lee HS, Lim YB. Slow-Motion Self-Assembly: Access to Intermediates with Heterochiral Peptides to Gain Control over Alignment Media Development. ACS NANO 2020; 14:3344-3352. [PMID: 32058708 DOI: 10.1021/acsnano.9b09070] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Understanding the intermediates or transition states in organic reactions has made it possible to develop theories and to synthesize important compounds. In contrast to organic reaction intermediates and even protein folding intermediates, the intermediates of peptide/protein self-assembly are not very well understood. Here we report that the self-assembly kinetics of linear heterochiral peptides are significantly slower than those of the corresponding homochiral peptides, which enables direct microscopic observation of assembly intermediates. By designing racemic or asymmetric heterochiral peptides, we were able to discover unusual mixed helical (MP-helix) and overtwisted intermediates. The convergence of equilibrium morphology between the homochiral and heterochiral peptides enables us to reasonably deduce the unobservable intermediates of rapidly assembling homochiral peptides. By utilizing the discovered information about the assembly intermediates, we were able to develop a functional NMR alignment medium that enables the measurement of residual dipolar couplings (RDCs) in a time-dependent manner. Although much less studied than their cyclic counterparts, the linear form of heterochiral peptides provides a means of obtaining a more in-depth understanding of the self-assembly pathway and of developing sophisticated bottom-up materials.
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Affiliation(s)
- Hye-Soo Lee
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Yong-Beom Lim
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
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34
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Ibáñez de Opakua A, Klama F, Ndukwe IE, Martin GE, Williamson RT, Zweckstetter M. Bestimmung komplexer kleiner Molekülstrukturen mittels molekularer Ausrichtungssimulation. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202000311] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Alain Ibáñez de Opakua
- Translationale Strukturelle Biologie der DemenzDeutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) Von-Siebold-Str. 3a 37075 Göttingen Deutschland
| | - Frederik Klama
- Abteilung für NMR-basierte StrukturbiologieMax-Planck-Institut für Biophysikalische Chemie Am Fassberg 11 37077 Göttingen Deutschland
| | - Ikenna E. Ndukwe
- Analytical Research & Development (Rahway), Merck & Co. Inc. Kenilworth NJ USA
- Complex Carbohydrate Research CenterUniversity of Georgia Athens GA 30602 USA
| | - Gary E. Martin
- Analytical Research & Development (Rahway), Merck & Co. Inc. Kenilworth NJ USA
- Department of Chemistry and BiochemistrySeton Hall University South Orange NJ 07079 USA
| | - R. Thomas Williamson
- Analytical Research & Development (Rahway), Merck & Co. Inc. Kenilworth NJ USA
- Department of Chemistry & BiochemistryUniversity of North Carolina Wilmington Wilmington NC 28409 USA
| | - Markus Zweckstetter
- Translationale Strukturelle Biologie der DemenzDeutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) Von-Siebold-Str. 3a 37075 Göttingen Deutschland
- Abteilung für NMR-basierte StrukturbiologieMax-Planck-Institut für Biophysikalische Chemie Am Fassberg 11 37077 Göttingen Deutschland
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35
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Lesot P, Aroulanda C, Berdagué P, Meddour A, Merlet D, Farjon J, Giraud N, Lafon O. Multinuclear NMR in polypeptide liquid crystals: Three fertile decades of methodological developments and analytical challenges. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2020; 116:85-154. [PMID: 32130960 DOI: 10.1016/j.pnmrs.2019.10.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 10/24/2019] [Indexed: 06/10/2023]
Abstract
NMR spectroscopy of oriented samples makes accessible residual anisotropic intramolecular NMR interactions, such as chemical shift anisotropy (RCSA), dipolar coupling (RDC), and quadrupolar coupling (RQC), while preserving high spectral resolution. In addition, in a chiral aligned environment, enantiomers of chiral molecules or enantiopic elements of prochiral compounds adopt different average orientations on the NMR timescale, and hence produce distinct NMR spectra or signals. NMR spectroscopy in chiral aligned media is a powerful analytical tool, and notably provides unique information on (pro)chirality analysis, natural isotopic fractionation, stereochemistry, as well as molecular conformation and configuration. Significant progress has been made in this area over the three last decades, particularly using polypeptide-based chiral liquid crystals (CLCs) made of organic solutions of helically chiral polymers (as PBLG) in organic solvents. This review presents an overview of NMR in polymeric LCs. In particular, we describe the theoretical tools and the major NMR methods that have been developed and applied to study (pro)chiral molecules dissolved in such oriented solvents. We also discuss the representative applications illustrating the analytical potential of this original NMR tool. This overview article is dedicated to thirty years of original contributions to the development of NMR spectroscopy in polypeptide-based chiral liquid crystals.
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Affiliation(s)
- Philippe Lesot
- Université Paris Sud/Université Paris-Saclay, UMR CNRS 8182, Institut de Chimie Moléculaire et des Matériaux d'Orsay, ICMMO, Equipe RMN en Milieu Orienté, Bât. 410, 15 rue du Doyen Georges Poitou, F-91405 Orsay cedex, France; Centre National de la Recherche Scientifique (CNRS), France.
| | - Christie Aroulanda
- Université Paris Sud/Université Paris-Saclay, UMR CNRS 8182, Institut de Chimie Moléculaire et des Matériaux d'Orsay, ICMMO, Equipe RMN en Milieu Orienté, Bât. 410, 15 rue du Doyen Georges Poitou, F-91405 Orsay cedex, France
| | - Philippe Berdagué
- Université Paris Sud/Université Paris-Saclay, UMR CNRS 8182, Institut de Chimie Moléculaire et des Matériaux d'Orsay, ICMMO, Equipe RMN en Milieu Orienté, Bât. 410, 15 rue du Doyen Georges Poitou, F-91405 Orsay cedex, France
| | - Abdelkrim Meddour
- Université Paris Sud/Université Paris-Saclay, UMR CNRS 8182, Institut de Chimie Moléculaire et des Matériaux d'Orsay, ICMMO, Equipe RMN en Milieu Orienté, Bât. 410, 15 rue du Doyen Georges Poitou, F-91405 Orsay cedex, France
| | - Denis Merlet
- Université Paris Sud/Université Paris-Saclay, UMR CNRS 8182, Institut de Chimie Moléculaire et des Matériaux d'Orsay, ICMMO, Equipe RMN en Milieu Orienté, Bât. 410, 15 rue du Doyen Georges Poitou, F-91405 Orsay cedex, France
| | - Jonathan Farjon
- Centre National de la Recherche Scientifique (CNRS), France; Faculté des Sciences et Techniques de Nantes, UMR CNRS 6230, Chimie et Interdisciplinarité, Synthèse, Analyse, Modélisation, CEISAM, Equipe EBSI, BP 92208, 2 rue de la Houssinière, F-44322 Nantes cedex 3, France
| | - Nicolas Giraud
- Université Paris Descartes, Sorbonne Paris Cité, UMR CNRS 8601, Laboratory of Pharmacological and Toxicological Chemistry and Biochemistry, LPTCB, 45 rue des Saints Pères, F-75006 Paris, France
| | - Olivier Lafon
- Universite de Lille, CNRS, Centrale Lille, ENSCL, Univ. Artois, UMR CNRS 8181, Unité de Catalyse et Chimie du Solide, UCCS, F-59000 Lille, France; Institut Universitaire de France (IUF), France
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36
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Ma ZK, Han XY, Liu H, Ji JC, Qin SY, Li XD, Lei X. Lyotropic liquid crystal to measure residual dipolar couplings in dimethyl sulfoxide based on modified cellulose nanocrystals. NEW J CHEM 2020. [DOI: 10.1039/c9nj06031f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel lyotropic liquid crystal was developed for the measurement of RDCs of organic molecules with no background signals.
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Affiliation(s)
- Zong-Kai Ma
- Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education & Hubei Key Laboratory of Catalysis and Materials Science
- South-Central University for Nationalities
- Wuhan 430074
- P. R. China
| | - Xiao-Yang Han
- School of Pharmaceutical Sciences
- South-Central University for Nationalities
- Wuhan
- P. R. China
| | - Han Liu
- School of Pharmaceutical Sciences
- South-Central University for Nationalities
- Wuhan
- P. R. China
| | - Jia-Cheng Ji
- School of Pharmaceutical Sciences
- South-Central University for Nationalities
- Wuhan
- P. R. China
| | - Si-Yong Qin
- Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education & Hubei Key Laboratory of Catalysis and Materials Science
- South-Central University for Nationalities
- Wuhan 430074
- P. R. China
| | - Xiang-Dan Li
- Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education & Hubei Key Laboratory of Catalysis and Materials Science
- South-Central University for Nationalities
- Wuhan 430074
- P. R. China
| | - Xinxiang Lei
- School of Pharmaceutical Sciences
- South-Central University for Nationalities
- Wuhan
- P. R. China
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37
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Carlon A, Gigli L, Ravera E, Parigi G, Gronenborn AM, Luchinat C. Assessing Structural Preferences of Unstructured Protein Regions by NMR. Biophys J 2019; 117:1948-1953. [PMID: 31676138 PMCID: PMC7018990 DOI: 10.1016/j.bpj.2019.10.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 09/30/2019] [Accepted: 10/08/2019] [Indexed: 11/28/2022] Open
Abstract
Biomacromolecules, such as proteins, often exhibit significant motions intimately associated with their function. Intrinsically disordered proteins and proteins with intrinsically disordered regions, although extremely important for a plethora of cellular functions, are difficult to structurally characterize at the atomic level because the experimental parameters report on ensemble and time averages. Here, we demonstrate for the C-terminal domain of the human immunodeficiency virus type 1 capsid protein that NMR and, in particular, residual dipolar couplings (RDCs) measured for the folded portion of the protein can inform on the structural preferences of the unstructured portion using RDC-prediction tools and the maximum occurrence approach.
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Affiliation(s)
- Azzurra Carlon
- Magnetic Resonance Center, University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine, Sesto Fiorentino, Florence, Italy; Department of Chemistry "Ugo Schiff," University of Florence, Sesto Fiorentino, Florence, Italy
| | - Lucia Gigli
- Magnetic Resonance Center, University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine, Sesto Fiorentino, Florence, Italy; Department of Chemistry "Ugo Schiff," University of Florence, Sesto Fiorentino, Florence, Italy
| | - Enrico Ravera
- Magnetic Resonance Center, University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine, Sesto Fiorentino, Florence, Italy; Department of Chemistry "Ugo Schiff," University of Florence, Sesto Fiorentino, Florence, Italy
| | - Giacomo Parigi
- Magnetic Resonance Center, University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine, Sesto Fiorentino, Florence, Italy; Department of Chemistry "Ugo Schiff," University of Florence, Sesto Fiorentino, Florence, Italy
| | - Angela M Gronenborn
- Department of Structural Biology and Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh, School of Medicine, Pittsburgh, Pennsylvania.
| | - Claudio Luchinat
- Magnetic Resonance Center, University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine, Sesto Fiorentino, Florence, Italy; Department of Chemistry "Ugo Schiff," University of Florence, Sesto Fiorentino, Florence, Italy.
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38
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Ravula T, Ramamoorthy A. Magnetic Alignment of Polymer Macro-Nanodiscs Enables Residual-Dipolar-Coupling-Based High-Resolution Structural Studies by NMR Spectroscopy. Angew Chem Int Ed Engl 2019; 58:14925-14928. [PMID: 31310700 PMCID: PMC7161179 DOI: 10.1002/anie.201907655] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Indexed: 01/18/2023]
Abstract
Experimentally measured residual dipolar couplings (RDCs) are highly valuable for atomic-resolution structural and dynamic studies of molecular systems ranging from small molecules to large proteins by solution NMR spectroscopy. Here we demonstrate the first use of magnetic-alignment behavior of lyotropic liquid-crystalline polymer macro-nanodiscs (>20 nm in diameter) as a novel alignment medium for the measurement of RDCs using high-resolution NMR. The easy preparation of macro-nanodiscs, their high stability against pH changes and the presence of divalent metal ions, and their high homogeneity make them an efficient tool to investigate a wide range of molecular systems including natural products, proteins, and RNA.
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Affiliation(s)
- Thirupathi Ravula
- Department of Chemistry and Biophysics, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI, 48109-1055, USA
| | - Ayyalusamy Ramamoorthy
- Department of Chemistry and Biophysics, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI, 48109-1055, USA
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39
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Ravula T, Ramamoorthy A. Magnetic Alignment of Polymer Macro‐Nanodiscs Enables Residual‐Dipolar‐Coupling‐Based High‐Resolution Structural Studies by NMR Spectroscopy. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201907655] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Thirupathi Ravula
- Department of Chemistry and Biophysics Biomedical Engineering, Macromolecular Science and Engineering University of Michigan Ann Arbor MI 48109-1055 USA
| | - Ayyalusamy Ramamoorthy
- Department of Chemistry and Biophysics Biomedical Engineering, Macromolecular Science and Engineering University of Michigan Ann Arbor MI 48109-1055 USA
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40
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Bax A, Clore GM. Protein NMR: Boundless opportunities. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 306:187-191. [PMID: 31311710 PMCID: PMC6703950 DOI: 10.1016/j.jmr.2019.07.037] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 04/22/2019] [Accepted: 07/08/2019] [Indexed: 05/04/2023]
Abstract
Over the past approximately three decades, isotope-directed NMR spectroscopy has become a powerful method for determining 3D structures of biological macromolecules and their complexes in solution. From a structural perspective NMR provides an invaluable tool for studying systems that are not amenable to crystallization, including intrinsically disordered proteins and weak complexes. In contrast to both X-ray crystallography and cryo-electron microscopy which afford a largely static view of the systems under consideration, the great power of NMR lies in its ability to quantitatively probe exchange dynamics between interconverting states, and to reveal and characterize at atomic resolution the existence of transient states that may be populated at levels as low as 1%. Such "excited" states play a key role in macromolecular recognition, allostery, signal transduction and macromolecular assembly, including the initial events involved in aggregation and amyloid formation. Optimal application of NMR to such systems of fundamental biological interest requires a sound footing of the physical underpinnings of today's and tomorrow's sophisticated NMR experiments.
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Affiliation(s)
- Ad Bax
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, MD 20892-0520, USA.
| | - G Marius Clore
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, MD 20892-0520, USA.
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41
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Affiliation(s)
- Giulio Fittolani
- Department of Biomolecular SystemsMax Planck Institute of Colloids and Interfaces Potsdam Germany
| | - Peter H. Seeberger
- Department of Biomolecular SystemsMax Planck Institute of Colloids and Interfaces Potsdam Germany
- Institute of Chemistry and BiochemistryFreie Universität Berlin Berlin Germany
| | - Martina Delbianco
- Department of Biomolecular SystemsMax Planck Institute of Colloids and Interfaces Potsdam Germany
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Barnes CA, Shen Y, Ying J, Takagi Y, Torchia DA, Sellers JR, Bax A. Remarkable Rigidity of the Single α-Helical Domain of Myosin-VI As Revealed by NMR Spectroscopy. J Am Chem Soc 2019; 141:9004-9017. [PMID: 31117653 PMCID: PMC6556874 DOI: 10.1021/jacs.9b03116] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Indexed: 11/29/2022]
Abstract
Although the α-helix has long been recognized as an all-important element of secondary structure, it generally requires stabilization by tertiary interactions with other parts of a protein's structure. Highly charged single α-helical (SAH) domains, consisting of a high percentage (>75%) of Arg, Lys, and Glu residues, are exceptions to this rule but have been difficult to characterize structurally. Our study focuses on the 68-residue medial tail domain of myosin-VI, which is found to contain a highly ordered α-helical structure extending from Glu-6 to Lys-63. High hydrogen exchange protection factors (15-150), small (ca. 4 Hz) 3 JHNHα couplings, and a near-perfect fit to an ideal model α-helix for its residual dipolar couplings (RDCs), measured in a filamentous phage medium, support the high regularity of this helix. Remarkably, the hydrogen exchange rates are far more homogeneous than the protection factors derived from them, suggesting that for these transiently broken helices the intrinsic exchange rates derived from the amino acid sequence are not appropriate reference values. 15N relaxation data indicate a very high degree of rotational diffusion anisotropy ( D∥/ D⊥ ≈ 7.6), consistent with the hydrodynamic behavior predicted for such a long, nearly straight α-helix. Alignment of the helix by a paramagnetic lanthanide ion attached to its N-terminal region shows a decrease in alignment as the distance from the tagging site increases. This decrease yields a precise measure for the persistence length of 224 ± 10 Å at 20 °C, supporting the idea that the role of the SAH helix is to act as an extension of the myosin-VI lever arm.
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Abstract
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Enzyme function requires that enzyme structures be dynamic. Substrate
binding, product release, and transition state stabilization typically
involve different enzyme conformers. Furthermore, in multistep enzyme-catalyzed
reactions, more than one enzyme conformation may be important for
stabilizing different transition states. While X-ray crystallography
provides the most detailed structural information of any current methodology,
X-ray crystal structures of enzymes capture only those conformations
that fit into the crystal lattice, which may or may not be relevant
to function. Solution nuclear magnetic resonance (NMR) methods can
provide an alternative approach to characterizing enzymes under nonperturbing
and controllable conditions, allowing one to identify and localize
dynamic processes that are important to function. However, many enzymes
are too large for standard approaches to making sequential resonance
assignments, a critical first step in analyzing and interpreting the
wealth of information inherent in NMR spectra. This Account
describes our long-standing NMR-based research into
structural and dynamic aspects of function in the cytochrome P450
monooxygenase superfamily. These heme-containing enzymes typically
catalyze the oxidation of unactivated C–H and C=C bonds
in a multitude of substrates, often with complete regio- and stereospecificity.
Over 600 000 genes in GenBank have been assigned to P450s,
yet all known P450 structures exhibit a highly conserved and unique
fold. This combination of functional and structural conservation with
a vast substrate clientele, each substrate having multiple possible
sites for oxidation, makes the P450s a unique target for understanding
the role of enzyme structure and dynamics in determining a particular
substrate–product combination. P450s are large by solution
NMR standards, requiring us to develop specialized approaches for
making sequential resonance assignments and interpreting the spectral
changes that occur as a function of changing conditions (e.g., oxidation
and spin state changes, ligand, substrate or effector binding). Solution
conformations are characterized by the fitting of residual dipolar
couplings (RDCs) measured for sequence-specifically assigned amide
N–H correlations to alignment tensors optimized in the course
of restrained molecular dynamics (MD) simulations. The conformational
ensembles obtained by such RDC-restrained simulations, which we call
“soft annealing”, are then tested by site-directed mutation
and spectroscopic and activity assays for relevance. These efforts
have gained us insights into cryptic conformational changes associated
with substrate and redox partner binding that were not suspected from
crystal structures, but were shown by subsequent work to be relevant
to function. Furthermore, it appears that many of these changes can
be generalized to P450s besides those that we have characterized,
providing guidance for enzyme engineering efforts. While past research
was primarily directed at the more tractable prokaryotic P450s, our
current efforts are aimed at medically relevant human enzymes, including
CYP17A1, CYP2D6, and CYP3A4.
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NMR Resonance Assignment Methodology: Characterizing Large Sparsely Labeled Glycoproteins. J Mol Biol 2019; 431:2369-2382. [PMID: 31034888 DOI: 10.1016/j.jmb.2019.04.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 04/17/2019] [Accepted: 04/18/2019] [Indexed: 01/02/2023]
Abstract
Characterization of proteins using NMR methods begins with assignment of resonances to specific residues. This is usually accomplished using sequential connectivities between nuclear pairs in proteins uniformly labeled with NMR active isotopes. This becomes impractical for larger proteins, and especially for proteins that are best expressed in mammalian cells, including glycoproteins. Here an alternate protocol for the assignment of NMR resonances of sparsely labeled proteins, namely, the ones labeled with a single amino acid type, or a limited subset of types, isotopically enriched with 15N or 13C, is described. The protocol is based on comparison of data collected using extensions of simple two-dimensional NMR experiments (correlated chemical shifts, nuclear Overhauser effects, residual dipolar couplings) to predictions from molecular dynamics trajectories that begin with known protein structures. Optimal pairing of predicted and experimental values is facilitated by a software package that employs a genetic algorithm, ASSIGN_SLP_MD. The approach is applied to the 36-kDa luminal domain of the sialyltransferase, rST6Gal1, in which all phenylalanines are labeled with 15N, and the results are validated by elimination of resonances via single-point mutations of selected phenylalanines to tyrosines. Assignment allows the use of previously published paramagnetic relaxation enhancements to evaluate placement of a substrate analog in the active site of this protein. The protocol will open the way to structural characterization of the many glycosylated and other proteins that are best expressed in mammalian cells.
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Ciambellotti S, Turano P. Structural Biology of Iron‐Binding Proteins by NMR Spectroscopy. Eur J Inorg Chem 2019. [DOI: 10.1002/ejic.201801261] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Silvia Ciambellotti
- Resonance Magnetic Center (CERM) University of Florence via Luigi Sacconi 6 50019 Sesto Fiorentino Italy
- Department of Chemistry University of Florence via della Lastruccia 3 50019 Sesto Fiorentino, Italy
| | - Paola Turano
- Resonance Magnetic Center (CERM) University of Florence via Luigi Sacconi 6 50019 Sesto Fiorentino Italy
- Department of Chemistry University of Florence via della Lastruccia 3 50019 Sesto Fiorentino, Italy
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Knoll K, Leyendecker M, Thiele CM. l
‐Valine Derivatised 1,3,5‐Benzene‐Tricarboxamides as Building Blocks for a New Supramolecular Organogel‐Like Alignment Medium. European J Org Chem 2019. [DOI: 10.1002/ejoc.201801306] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Kevin Knoll
- Technische Universität Darmstadt Clemens‐Schöpf Institut für Organische Chemie und Biochemie Alarich‐Weiss‐Str. 4 64287 Darmstadt Germany
| | - Martin Leyendecker
- Technische Universität Darmstadt Clemens‐Schöpf Institut für Organische Chemie und Biochemie Alarich‐Weiss‐Str. 4 64287 Darmstadt Germany
| | - Christina M. Thiele
- Technische Universität Darmstadt Clemens‐Schöpf Institut für Organische Chemie und Biochemie Alarich‐Weiss‐Str. 4 64287 Darmstadt Germany
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47
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Lin Y, Zeng Q, Lin L, Chen Z, Barker PB. High-resolution methods for the measurement of scalar coupling constants. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018; 109:135-159. [PMID: 30527134 DOI: 10.1016/j.pnmrs.2018.08.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 08/14/2018] [Accepted: 08/14/2018] [Indexed: 06/09/2023]
Abstract
Scalar couplings provide important information regarding molecular structure and dynamics. The measurement of scalar coupling constants constitutes a topic of interest and significance in NMR spectroscopy. However, the measurement of J values is often not straightforward because of complex signal splitting patterns and signal overlap. Many methods have been proposed for the measurement of scalar coupling constants, both for homonuclear and heteronuclear cases. Different approaches to the measurement of scalar coupling constants are reviewed here with several applications presented. The accurate measurement of scalar coupling constants can greatly facilitate molecular structure elucidation and the study of molecule dynamics.
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Affiliation(s)
- Yanqin Lin
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China.
| | - Qing Zeng
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China
| | - Liangjie Lin
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China
| | - Zhong Chen
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China
| | - Peter B Barker
- Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; F. M. Kirby Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, MD 21205, USA
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Rigling C, Kisunzu JK, Duschmalé J, Häussinger D, Wiesner M, Ebert MO, Wennemers H. Conformational Properties of a Peptidic Catalyst: Insights from NMR Spectroscopic Studies. J Am Chem Soc 2018; 140:10829-10838. [PMID: 30106584 DOI: 10.1021/jacs.8b05459] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Peptides have become valuable as catalysts for a variety of different reactions, but little is known about the conformational properties of peptidic catalysts. We investigated the conformation of the peptide H-dPro-Pro-Glu-NH2, a highly reactive and stereoselective catalyst for conjugate addition reactions, and the corresponding enamine intermediate in solution by NMR spectroscopy and computational methods. The combination of nuclear Overhauser effects (NOEs), residual dipolar couplings (RDCs), J-couplings, and temperature coefficients revealed that the tripeptide adopts a single predominant conformation in its ground state. The structure is a type I β-turn, which gains stabilization from three hydrogen bonds that are cooperatively formed between all functional groups (secondary amine, carboxylic acid, amides) within the tripeptide. In contrast, the conformation of the enamine intermediate is significantly more flexible. The conformational ensemble of the enamine is still dominated by the β-turn, but the backbone and the side chain of the glutamic acid residue are more dynamic. The key to the switch between rigidity and flexibility of the peptidic catalyst is the CO2H group in the side chain of the glutamic acid residue, which acts as a lid that can open and close. As a result, the peptidic catalyst is able to adapt to the structural requirements of the intermediates and transition states of the catalytic cycle. These insights might explain the robustness and high reactivity of the peptidic catalyst, which exceeds that of other secondary amine-based organocatalysts. The data suggest that a balance between rigidity and flexibility, which is reminiscent of the dynamic nature of enzymes, is beneficial for peptidic catalysts and other synthetic catalysts.
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Affiliation(s)
- Carla Rigling
- Laboratorium für Organische Chemie , ETH Zürich , D-CHAB, Vladimir-Prelog-Weg 3 , 8093 Zürich , Switzerland
| | - Jessica K Kisunzu
- Laboratorium für Organische Chemie , ETH Zürich , D-CHAB, Vladimir-Prelog-Weg 3 , 8093 Zürich , Switzerland
| | - Jörg Duschmalé
- Laboratorium für Organische Chemie , ETH Zürich , D-CHAB, Vladimir-Prelog-Weg 3 , 8093 Zürich , Switzerland.,Department of Chemistry , University of Basel , St. Johanns-Ring 19 , 4056 Basel , Switzerland
| | - Daniel Häussinger
- Department of Chemistry , University of Basel , St. Johanns-Ring 19 , 4056 Basel , Switzerland
| | - Markus Wiesner
- Department of Chemistry , University of Basel , St. Johanns-Ring 19 , 4056 Basel , Switzerland
| | - Marc-Olivier Ebert
- Laboratorium für Organische Chemie , ETH Zürich , D-CHAB, Vladimir-Prelog-Weg 3 , 8093 Zürich , Switzerland
| | - Helma Wennemers
- Laboratorium für Organische Chemie , ETH Zürich , D-CHAB, Vladimir-Prelog-Weg 3 , 8093 Zürich , Switzerland
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49
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Larsen EK, Olivieri C, Walker C, V S M, Gao J, Bernlohr DA, Tonelli M, Markley JL, Veglia G. Probing Protein-Protein Interactions Using Asymmetric Labeling and Carbonyl-Carbon Selective Heteronuclear NMR Spectroscopy. Molecules 2018; 23:E1937. [PMID: 30081441 PMCID: PMC6205158 DOI: 10.3390/molecules23081937] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 07/23/2018] [Accepted: 07/25/2018] [Indexed: 11/23/2022] Open
Abstract
Protein-protein interactions (PPIs) regulate a plethora of cellular processes and NMR spectroscopy has been a leading technique for characterizing them at the atomic resolution. Technically, however, PPIs characterization has been challenging due to multiple samples required to characterize the hot spots at the protein interface. In this paper, we review our recently developed methods that greatly simplify PPI studies, which minimize the number of samples required to fully characterize residues involved in the protein-protein binding interface. This original strategy combines asymmetric labeling of two binding partners and the carbonyl-carbon label selective (CCLS) pulse sequence element implemented into the heteronuclear single quantum correlation (¹H-15N HSQC) spectra. The CCLS scheme removes signals of the J-coupled 15N⁻13C resonances and records simultaneously two individual amide fingerprints for each binding partner. We show the application to the measurements of chemical shift correlations, residual dipolar couplings (RDCs), and paramagnetic relaxation enhancements (PRE). These experiments open an avenue for further modifications of existing experiments facilitating the NMR analysis of PPIs.
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Affiliation(s)
- Erik K Larsen
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Cristina Olivieri
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Caitlin Walker
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Manu V S
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Jiali Gao
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
| | - David A Bernlohr
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, Madison, WI 53706, USA.
| | - John L Markley
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Gianluigi Veglia
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
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50
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Determination of the conformational states of strychnine in solution using NMR residual dipolar couplings in a tensor-free approach. Methods 2018; 148:4-8. [PMID: 30036639 DOI: 10.1016/j.ymeth.2018.07.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 07/10/2018] [Accepted: 07/17/2018] [Indexed: 12/14/2022] Open
Abstract
Small molecules with rotatable bonds can occupy different conformational states in solution as a consequence of their thermal fluctuations. The accurate determination of the structures of such states, as well as of their statistical weights, has been challenging because of the technical difficulties in extracting information from experimental measurements, which are normally averaged over the conformational space available. Here, to achieve this objective, we present an approach based on a recently proposed tensor-free method for incorporating NMR residual dipolar couplings as structural restraints in replica-averaged molecular dynamics simulations. This approach enables the information provided by the experimental data to be used in the spirit of the maximum entropy principle to determine the structural ensembles of small molecules. Furthermore, in order to enhance the sampling of the conformational space we incorporated the metadynamics method in the simulations. We illustrate the method in the case of strychnine, determining the three major conformational states of this small molecule and their associated occupation probabilities.
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