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Borgini M, Wieteska Ł, Hinck CS, Krzysiak T, Hinck AP, Wipf P. Synthesis of 13C-methyl-labeled amino acids and their incorporation into proteins in mammalian cells. Org Biomol Chem 2023; 21:9216-9229. [PMID: 37964666 PMCID: PMC10825848 DOI: 10.1039/d3ob01320k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/06/2023] [Indexed: 11/16/2023]
Abstract
Isotopic labeling of methyl-substituted proteinogenic amino acids with 13C has transformed applications of solution-based NMR spectroscopy and allowed the study of much larger and more complex proteins than previously possible with 15N labeling. Procedures are well-established for producing methyl-labeled proteins expressed in bacteria, with efficient incorporation of 13C-methyl labeled metabolic precursors to enable the isotopic labeling of Ile, Val, and Leu methyl groups. Recently, similar methodology has been applied to enable 13C-methyl labeling of Ile, Val, and Leu in yeast, extending the approach to proteins that do not readily fold when produced in bacteria. Mammalian or insect cells are nonetheless preferable for production of many human proteins, yet 13C-methyl labeling using similar metabolic precursors is not feasible as these cells lack the requisite biosynthetic machinery. Herein, we report versatile and high-yielding synthetic routes to 13C methyl-labeled amino acids based on palladium-catalyzed C(sp3)-H functionalization. We demonstrate the efficient incorporation of two of the synthesized amino acids, 13C-γ2-Ile and 13C-γ1,γ2-Val, into human receptor extracellular domains with multiple disulfides using suspension-cultured HEK293 cells. Production costs are reasonable, even at moderate expression levels of 2-3 mg purified protein per liter of medium, and the method can be extended to label other methyl groups, such as 13C-δ1-Ile and 13C-δ1,δ2-Leu. In summary, we demonstrate the cost-effective production of methyl-labeled proteins in mammalian cells by incorporation of 13C methyl-labeled amino acids generated de novo by a versatile synthetic route.
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Affiliation(s)
- Matteo Borgini
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | - Łukasz Wieteska
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | - Cynthia S Hinck
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | - Troy Krzysiak
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | - Andrew P Hinck
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | - Peter Wipf
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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2
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Krempl C, Wurm JP, Beck Erlach M, Kremer W, Sprangers R. Insights into the Structure of Invisible Conformations of Large Methyl Group Labeled Molecular Machines from High Pressure NMR. J Mol Biol 2023; 435:167922. [PMID: 37330282 DOI: 10.1016/j.jmb.2022.167922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/08/2022] [Accepted: 12/11/2022] [Indexed: 06/19/2023]
Abstract
Most proteins are highly flexible and can adopt conformations that deviate from the energetically most favorable ground state. Structural information on these lowly populated, alternative conformations is often lacking, despite the functional importance of these states. Here, we study the pathway by which the Dcp1:Dcp2 mRNA decapping complex exchanges between an autoinhibited closed and an open conformation. We make use of methyl Carr-Purcell-Meiboom-Gill (CPMG) NMR relaxation dispersion (RD) experiments that report on the population of the sparsely populated open conformation as well as on the exchange rate between the two conformations. To obtain volumetric information on the open conformation as well as on the transition state structure we made use of RD measurements at elevated pressures. We found that the open Dcp1:Dcp2 conformation has a lower molecular volume than the closed conformation and that the transition state is close in volume to the closed state. In the presence of ATP the volume change upon opening of the complex increases and the volume of the transition state lies in-between the volumes of the closed and open state. These findings show that ATP has an effect on the volume changes that are associated with the opening-closing pathway of the complex. Our results highlight the strength of pressure dependent NMR methods to obtain insights into structural features of protein conformations that are not directly observable. As our work makes use of methyl groups as NMR probes we conclude that the applied methodology is also applicable to high molecular weight complexes.
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Affiliation(s)
- Christina Krempl
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Jan Philip Wurm
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Markus Beck Erlach
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Werner Kremer
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Remco Sprangers
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93053 Regensburg, Germany.
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3
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Ledwitch KV, Künze G, McKinney JR, Okwei E, Larochelle K, Pankewitz L, Ganguly S, Darling HL, Coin I, Meiler J. Sparse pseudocontact shift NMR data obtained from a non-canonical amino acid-linked lanthanide tag improves integral membrane protein structure prediction. J Biomol NMR 2023; 77:69-82. [PMID: 37016190 PMCID: PMC10443207 DOI: 10.1007/s10858-023-00412-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 03/20/2023] [Indexed: 06/19/2023]
Abstract
A single experimental method alone often fails to provide the resolution, accuracy, and coverage needed to model integral membrane proteins (IMPs). Integrating computation with experimental data is a powerful approach to supplement missing structural information with atomic detail. We combine RosettaNMR with experimentally-derived paramagnetic NMR restraints to guide membrane protein structure prediction. We demonstrate this approach using the disulfide bond formation protein B (DsbB), an α-helical IMP. Here, we attached a cyclen-based paramagnetic lanthanide tag to an engineered non-canonical amino acid (ncAA) using a copper-catalyzed azide-alkyne cycloaddition (CuAAC) click chemistry reaction. Using this tagging strategy, we collected 203 backbone HN pseudocontact shifts (PCSs) for three different labeling sites and used these as input to guide de novo membrane protein structure prediction protocols in Rosetta. We find that this sparse PCS dataset combined with 44 long-range NOEs as restraints in our calculations improves structure prediction of DsbB by enhancements in model accuracy, sampling, and scoring. The inclusion of this PCS dataset improved the Cα-RMSD transmembrane segment values of the best-scoring and best-RMSD models from 9.57 Å and 3.06 Å (no NMR data) to 5.73 Å and 2.18 Å, respectively.
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Affiliation(s)
- Kaitlyn V Ledwitch
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37240, USA.
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA.
- Department of Chemistry, Center for Structural Biology, MRBIII 5154E, Vanderbilt University, Nashville, TN, 37212, USA.
| | - Georg Künze
- Institute of Drug Discovery, Faculty of Medicine, University of Leipzig, 04103, Leipzig, Germany
| | - Jacob R McKinney
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37240, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
| | - Elleansar Okwei
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37240, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
| | - Katherine Larochelle
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37240, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
| | - Lisa Pankewitz
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37240, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
| | - Soumya Ganguly
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37240, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
| | - Heather L Darling
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37240, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
| | - Irene Coin
- Institute of Biochemistry, Faculty of Life Science, University of Leipzig, 04103, Leipzig, Germany
| | - Jens Meiler
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37240, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
- Institute of Drug Discovery, Faculty of Medicine, University of Leipzig, 04103, Leipzig, Germany
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Gyrdymova YV, Samoylenko DE, Rodygin KS. [ 13 C+D] Double Labeling with Calcium Carbide: Incorporation of Two Labels in One Step. Chem Asian J 2023; 18:e202201063. [PMID: 36530060 DOI: 10.1002/asia.202201063] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
D-labeling is a valuable tool in advanced synthetic chemistry and pharmacy. However, D-incorporation significantly complicates the identification of products. In fact, D labels are invisible in 1 H-NMR spectra and cause undesirable splitting in 13 C-NMR spectra which decreases the detectable limits. At the same time, 2 H-NMR spectra are not effective for precise identification due to low sensitivity and the absence of correlations with 1 H atoms. Here, 13 C-label was considered as an accompanying label for D-label in [13 C+D] unit for identification of D-containing sites and to track D-labels. [13 C+D]-doubly labeled vinyl derivatives and triazoles were synthesized using 13 C-labeled calcium carbide as a source of 13 C-label and deuterium oxide as a source of D-label. The reaction occurred in one-step manner accompanied with in situ doubly labeled acetylene formation. Non-labeled, mono-labeled and doubly labeled substrates were isolated in 25-80% yields.
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Affiliation(s)
- Yulia V Gyrdymova
- Institute of Chemistry, Saint Petersburg State University, Universitetskiy pr. 26, Saint Petersburg, 198504, Russia
| | - Dmitriy E Samoylenko
- Institute of Chemistry, Saint Petersburg State University, Universitetskiy pr. 26, Saint Petersburg, 198504, Russia
| | - Konstantin S Rodygin
- Institute of Chemistry, Saint Petersburg State University, Universitetskiy pr. 26, Saint Petersburg, 198504, Russia
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Tibble RW, Gross JD. A call to order: Examining structured domains in biomolecular condensates. J Magn Reson 2023; 346:107318. [PMID: 36657879 PMCID: PMC10878105 DOI: 10.1016/j.jmr.2022.107318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 09/20/2022] [Accepted: 10/13/2022] [Indexed: 06/17/2023]
Abstract
Diverse cellular processes have been observed or predicted to occur in biomolecular condensates, which are comprised of proteins and nucleic acids that undergo liquid-liquid phase separation (LLPS). Protein-driven LLPS often involves weak, multivalent interactions between intrinsically disordered regions (IDRs). Due to their inherent lack of defined tertiary structures, NMR has been a powerful resource for studying the behavior and interactions of IDRs in condensates. While IDRs in proteins are necessary for phase separation, core proteins enriched in condensates often contain structured domains that are essential for their function and contribute to phase separation. How phase separation can affect the structure and conformational dynamics of structured domains is critical for understanding how biochemical reactions can be effectively regulated in cellular condensates. In this perspective, we discuss the consequences phase separation can have on structured domains and outline NMR observables we believe are useful for assessing protein structure and dynamics in condensates.
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Affiliation(s)
- Ryan W Tibble
- Program in Chemistry and Chemical Biology, University of California, San Francisco, United States; Department of Pharmaceutical Chemistry, University of California, San Francisco, United States
| | - John D Gross
- Program in Chemistry and Chemical Biology, University of California, San Francisco, United States; Department of Pharmaceutical Chemistry, University of California, San Francisco, United States.
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6
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Nedielkov R, Möller HM. Detecting and Characterizing Interactions of Metabolites with Proteins by Saturation Transfer Difference Nuclear Magnetic Resonance (STD NMR) Spectroscopy. Methods Mol Biol 2023; 2554:123-139. [PMID: 36178624 DOI: 10.1007/978-1-0716-2624-5_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Saturation transfer difference (STD) nuclear magnetic resonance (NMR) spectroscopy is an established technique for detecting and characterizing the binding of small molecules, such as metabolites, to biological macromolecules like proteins and nucleic acids. STD NMR allows detection of binding in complex mixtures of potential ligands, which is often used for library screening in the pharmaceutical industry but may also be beneficial for binding studies with metabolite mixtures. The nature of the ligand is normally restricted to small molecules in terms of NMR spectroscopy, and the size of the macromolecule on the other side should be larger than 10-15 kDa. This technique is especially applicable to detecting binders of intermediate to low affinity with the dissociation constant (KD) above 1 μM. In this chapter, we focus on recent developments and the applications of STD NMR to studying interactions of natural products and metabolites, in particular. The reader is also referred to excellent reviews of the field and the literature cited therein. This chapter also provides a detailed experimental protocol for performing the STD NMR measurement based on the example of the subunit A of the Na+-transporting NADH/ubiquinone oxidoreductase (Na+-NQR) from V. cholerae interacting with its natural quinone substrate and inhibitors.
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Affiliation(s)
- Ruslan Nedielkov
- University of Potsdam, Institute for Chemistry, Potsdam, Germany.
| | - Heiko M Möller
- University of Potsdam, Institute for Chemistry, Potsdam, Germany
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Opdensteinen P, Sperl LE, Mohamadi M, Kündgen‐Redding N, Hagn F, Buyel JF. The transient expression of recombinant proteins in plant cell packs facilitates stable isotope labelling for NMR spectroscopy. Plant Biotechnol J 2022; 20:1928-1939. [PMID: 35702941 PMCID: PMC9491462 DOI: 10.1111/pbi.13873] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 04/05/2022] [Accepted: 06/03/2022] [Indexed: 06/15/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy can be used to determine the structure, dynamics and interactions of proteins. However, protein NMR requires stable isotope labelling for signal detection. The cells used for the production of recombinant proteins must therefore be grown in medium containing isotopically labelled substrates. Stable isotope labelling is well established in Escherichia coli, but bacteria are only suitable for the production of simple proteins without post-translational modifications. More complex proteins require eukaryotic production hosts, but their growth can be impaired by labelled media, thus reducing product yields and increasing costs. To address this limitation, we used media supplemented with isotope-labelled substrates to cultivate the tobacco-derived cell line BY-2, which was then cast into plant cell packs (PCPs) for the transient expression of a labelled version of the model protein GB1. Mass spectrometry confirmed the feasibility of isotope labelling with 15 N and 2 H using this approach. The resulting NMR spectrum featured a signal dispersion comparable to recombinant GB1 produced in E. coli. PCPs therefore offer a rapid and cost-efficient alternative for the production of isotope-labelled proteins for NMR analysis, especially suitable for complex proteins that cannot be produced in microbial systems.
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Affiliation(s)
- Patrick Opdensteinen
- Fraunhofer Institute for Molecular Biology and Applied Ecology IMEAachenGermany
- Institute for Molecular BiotechnologyRWTH Aachen UniversityAachenGermany
| | - Laura E. Sperl
- Bavarian NMR Center (BNMRZ) at the Department of ChemistryTechnical University of MunichGarchingGermany
- Institute of Structural BiologyHelmholtz Zentrum MünchenNeuherbergGermany
| | - Mariam Mohamadi
- Bavarian NMR Center (BNMRZ) at the Department of ChemistryTechnical University of MunichGarchingGermany
- Institute of Structural BiologyHelmholtz Zentrum MünchenNeuherbergGermany
| | | | - Franz Hagn
- Bavarian NMR Center (BNMRZ) at the Department of ChemistryTechnical University of MunichGarchingGermany
- Institute of Structural BiologyHelmholtz Zentrum MünchenNeuherbergGermany
| | - Johannes Felix Buyel
- Fraunhofer Institute for Molecular Biology and Applied Ecology IMEAachenGermany
- Institute for Molecular BiotechnologyRWTH Aachen UniversityAachenGermany
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8
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Clore GM. NMR spectroscopy, excited states and relevance to problems in cell biology - transient pre-nucleation tetramerization of huntingtin and insights into Huntington's disease. J Cell Sci 2022; 135:jcs258695. [PMID: 35703323 PMCID: PMC9270955 DOI: 10.1242/jcs.258695] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Solution nuclear magnetic resonance (NMR) spectroscopy is a powerful technique for analyzing three-dimensional structure and dynamics of macromolecules at atomic resolution. Recent advances have exploited the unique properties of NMR in exchanging systems to detect, characterize and visualize excited sparsely populated states of biological macromolecules and their complexes, which are only transient. These states are invisible to conventional biophysical techniques, and play a key role in many processes, including molecular recognition, protein folding, enzyme catalysis, assembly and fibril formation. All the NMR techniques make use of exchange between sparsely populated NMR-invisible and highly populated NMR-visible states to transfer a magnetization property from the invisible state to the visible one where it can be easily detected and quantified. There are three classes of NMR experiments that rely on differences in distance, chemical shift or transverse relaxation (molecular mass) between the NMR-visible and -invisible species. Here, I illustrate the application of these methods to unravel the complex mechanism of sub-millisecond pre-nucleation oligomerization of the N-terminal region of huntingtin, encoded by exon-1 of the huntingtin gene, where CAG expansion leads to Huntington's disease, a fatal autosomal-dominant neurodegenerative condition. I also discuss how inhibition of tetramerization blocks the much slower (by many orders of magnitude) process of fibril formation.
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Affiliation(s)
- G. Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
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9
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Fucci IJ, Byrd RA. nightshift: A Python program for plotting simulated NMR spectra from assigned chemical shifts from the Biological Magnetic Resonance Data Bank. Protein Sci 2022; 31:63-74. [PMID: 34516045 PMCID: PMC8740831 DOI: 10.1002/pro.4181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/08/2021] [Accepted: 09/10/2021] [Indexed: 01/03/2023]
Abstract
Nuclear magnetic resonance (NMR) provides site specific information on local environments through chemical shifts. NMR is widely used in the study of proteins, ranging from determination of three-dimensional (3D) structures to characterizing dynamics and binding of small molecules and other proteins or ligands. Assigned chemical shift data for the atoms within proteins is a treasure trove of information that can facilitate a broad range of biochemical and biophysical studies. The Biological Magnetic Resonance Data Bank (BMRB) is a publicly accessible database that contains a large number of assigned chemical shifts; however, translating this wealth of knowledge into a practical application is not straightforward. Herein we present nightshift: a Python command line utility and library for plotting simulated two-dimensional (2D) and 3D NMR spectra from assigned chemical shifts in the BMRB. This tool allows users to simulate routinely collected amide and methyl fingerprint spectra, backbone triple-resonance assignment spectra, and user-defined custom correlations, including ones that do not necessarily correspond to published experiments. This tool enables experienced NMR spectroscopists, those learning the craft, and interested scientists seeking to utilize NMR the ability to preview or examine a wide range of spectra for proteins whose assignments are deposited in the BMRB, irrespective of whether those experiments have been executed or reported. The tool applies equally to folded and intrinsically disordered proteins, limited only by the existence of a BMRB deposition. The features of nightshift are described along with applications that illustrate the ease with which complicated correlation spectra and binding events can be simulated.
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Affiliation(s)
- Ian J. Fucci
- Center for Structural Biology, Center for Cancer Research, National Cancer InstituteFrederickMarylandUSA
| | - R. Andrew Byrd
- Center for Structural Biology, Center for Cancer Research, National Cancer InstituteFrederickMarylandUSA
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10
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Abstract
Proton detection developed in the last 20 years as the method of choice to study biomolecules in the solid state. In perdeuterated proteins, proton dipolar interactions are strongly attenuated, which allows yielding of high-resolution proton spectra. Perdeuteration and backsubstitution of exchangeable protons is essential if samples are rotated with MAS rotation frequencies below 60 kHz. Protonated samples can be investigated directly without spin dilution using proton detection methods in case the MAS frequency exceeds 110 kHz. This review summarizes labeling strategies and the spectroscopic methods to perform experiments that yield assignments, quantitative information on structure, and dynamics using perdeuterated samples. Techniques for solvent suppression, H/D exchange, and deuterium spectroscopy are discussed. Finally, experimental and theoretical results that allow estimation of the sensitivity of proton detected experiments as a function of the MAS frequency and the external B0 field in a perdeuterated environment are compiled.
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Affiliation(s)
- Bernd Reif
- Bayerisches NMR Zentrum (BNMRZ) at the Department of Chemistry, Technische Universität München (TUM), Lichtenbergstr. 4, 85747 Garching, Germany.,Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Institute of Structural Biology (STB), Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
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11
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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12
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Lin B, Hung I, Gan Z, Chien PH, Spencer HL, Smith SP, Wu G. 17 O NMR Studies of Yeast Ubiquitin in Aqueous Solution and in the Solid State. Chembiochem 2020; 22:826-829. [PMID: 33058374 DOI: 10.1002/cbic.202000659] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/14/2020] [Indexed: 12/18/2022]
Abstract
We report a general method for amino acid-type specific 17 O-labeling of recombinant proteins in Escherichia coli. In particular, we have prepared several [1-13 C,17 O]-labeled yeast ubiquitin (Ub) samples including Ub-[1-13 C,17 O]Gly, Ub-[1-13 C,17 O]Tyr, and Ub-[1-13 C,17 O]Phe using the auxotrophic E. coli strain DL39 GlyA λDE3 (aspC- tyrB- ilvE- glyA- λDE3). We have also produced Ub-[η-17 O]Tyr, in which the phenolic group of Tyr59 is 17 O-labeled. We show for the first time that 17 O NMR signals from protein terminal residues and side chains can be readily detected in aqueous solution. We also reported solid-state 17 O NMR spectra for Ub-[1-13 C,17 O]Tyr and Ub-[1-13 C,17 O]Phe obtained at an ultrahigh magnetic field, 35.2 T (1.5 GHz for 1 H). This work represents a significant advance in the field of 17 O NMR studies of proteins.
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Affiliation(s)
- Binyang Lin
- Department of Chemistry, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Ivan Hung
- Center for Interdisciplinary Magnetic Resonance, National High Magnetic Field Laboratory, Tallahassee, FL 32310, USA
| | - Zhehong Gan
- Center for Interdisciplinary Magnetic Resonance, National High Magnetic Field Laboratory, Tallahassee, FL 32310, USA
| | - Po-Hsiu Chien
- Center for Interdisciplinary Magnetic Resonance, National High Magnetic Field Laboratory, Tallahassee, FL 32310, USA
| | - Holly L Spencer
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Steven P Smith
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Gang Wu
- Department of Chemistry, Queen's University, Kingston, ON K7L 3N6, Canada
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13
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Bayer P, Matena A, Beuck C. NMR Spectroscopy of supramolecular chemistry on protein surfaces. Beilstein J Org Chem 2020; 16:2505-2522. [PMID: 33093929 PMCID: PMC7554676 DOI: 10.3762/bjoc.16.203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 09/18/2020] [Indexed: 01/17/2023] Open
Abstract
As one of the few analytical methods that offer atomic resolution, NMR spectroscopy is a valuable tool to study the interaction of proteins with their interaction partners, both biomolecules and synthetic ligands. In recent years, the focus in chemistry has kept expanding from targeting small binding pockets in proteins to recognizing patches on protein surfaces, mostly via supramolecular chemistry, with the goal to modulate protein–protein interactions. Here we present NMR methods that have been applied to characterize these molecular interactions and discuss the challenges of this endeavor.
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Affiliation(s)
- Peter Bayer
- Structural and Medicinal Biochemistry, University of Duisburg-Essen, Universitätsstr. 1-5, 45141 Essen, Germany
| | - Anja Matena
- Structural and Medicinal Biochemistry, University of Duisburg-Essen, Universitätsstr. 1-5, 45141 Essen, Germany
| | - Christine Beuck
- Structural and Medicinal Biochemistry, University of Duisburg-Essen, Universitätsstr. 1-5, 45141 Essen, Germany
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14
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Srivastava A, Tiwari SP, Miyashita O, Tama F. Integrative/Hybrid Modeling Approaches for Studying Biomolecules. J Mol Biol 2020; 432:2846-2860. [DOI: 10.1016/j.jmb.2020.01.039] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/20/2020] [Accepted: 01/24/2020] [Indexed: 12/12/2022]
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15
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Zhang M. Recent developments of methyl-labeling strategies in Pichia pastoris for NMR spectroscopy. Protein Expr Purif 2020; 166:105521. [DOI: 10.1016/j.pep.2019.105521] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 10/16/2019] [Accepted: 10/18/2019] [Indexed: 11/26/2022]
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16
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Chen MD, Fucci IJ, Sinha K, Rule GS. dGMP Binding to Thymidylate Kinase from Plasmodium falciparum Shows Half-Site Binding and Induces Protein Dynamics at the Dimer Interface. Biochemistry 2020; 59:694-703. [PMID: 31934749 DOI: 10.1021/acs.biochem.9b00898] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Plasmodium falciparum thymidylate kinase (PfTMK) is an essential enzyme for the growth of the organism because of its critical role in the de novo synthesis of deoxythymidine 5'-diphosphate (TDP), a precursor for TTP that is required for DNA replication and repair. The kinetics, thermodynamic parameters, and substrate binding properties of PfTMK for TMP, dGMP, ADP, and ATP were measured and characterized by steady-state kinetics and a combination of isothermal titration calorimetry, tryptophan fluorescence titration, and NMR. Mutational studies were performed to investigate residues that contribute to the unique ability of PfTMK to also utilize dGMP as a substrate. Isothermal titration calorimetry experiments revealed that dGMP binding exhibits a unique half-site binding mechanism. The occlusion of the empty site in the dGMP complex is supported by molecular mechanics calculations. Relaxation dispersion experiments show that the dGMP and enzyme complex is more dynamic at the dimer interface than the TMP complex on the μs-ms time scale. The unique properties of dGMP binding need to be considered in the design of guanosine-based PfTMK-specific inhibitors.
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Affiliation(s)
- Mengshen David Chen
- Department of Biological Sciences , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States
| | - Ian J Fucci
- Department of Biological Sciences , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States
| | - Kaustubh Sinha
- Department of Biological Sciences , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States
| | - Gordon S Rule
- Department of Biological Sciences , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States
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17
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Whitaker AM, Naik MT, Mosser RE, Reinhart GD. Propagation of the Allosteric Signal in Phosphofructokinase from Bacillus stearothermophilus Examined by Methyl-Transverse Relaxation-Optimized Spectroscopy Nuclear Magnetic Resonance. Biochemistry 2019; 58:5294-5304. [PMID: 31478644 PMCID: PMC9924234 DOI: 10.1021/acs.biochem.9b00229] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Phosphofructokinase from Bacillus stearothermophilus (BsPFK) is a 136 kDa homotetromeric enzyme. Binding of the substrate, fructose 6-phosphate (Fru-6-P), is allosterically regulated by the K-type inhibitor phosphoenolpyruvate (PEP). The allosteric coupling between the substrate and inhibitor is quantified by a standard coupling free energy that defines an equilibrium with the Fru-6-P-bound and PEP-bound complexes on one side and the apo form and ternary complex on the other. Methyl-transverse relaxation-optimized spectroscopy (Me-TROSY) nuclear magnetic resonance was employed to gain structural information about BsPFK in all four states of ligation relevant to the allosteric coupling. BsPFK was uniformly labeled with 15N and 2H and specifically labeled with δ-[13CH3]-isoleucine utilizing an isotopically labeled α-keto acid isoleucine precursor. Me-TROSY experiments were conducted on all four ligation states, and all 30 isoleucines, which are well dispersed throughout each subunit of the enzyme, are well-resolved in chemical shift correlation maps of 13C and 1H. Assignments for 17 isoleucines were determined through three-dimensional HMQC-NOESY experiments with [U-15N,2H];Ileδ1-[13CH3]-BsPFK and complementary HNCA and HNCOCA experiments with [U-2H,15N,13C]-BsPFK. The assignments allowed for the mapping of resonances representing isoleucine residues to a previously determined X-ray crystallography structure. This analysis, performed for all four states of ligation, has allowed specific regions of the enzyme influenced by the binding of allosteric ligands and those involved in the propagation of the allosteric effect to be identified and distinguished from one another.
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Affiliation(s)
| | | | | | - Gregory D. Reinhart
- Corresponding Author Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843-2128. . Phone: (979) 862-2263
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18
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Affiliation(s)
- Jordan H. Chill
- Department of ChemistryBar Ilan University Ramat Gan 52900 Israel
| | - Arwa Qasim
- Department of ChemistryBar Ilan University Ramat Gan 52900 Israel
| | - Inbal Sher
- Department of ChemistryBar Ilan University Ramat Gan 52900 Israel
| | - Renana Gross
- Department of ChemistryBar Ilan University Ramat Gan 52900 Israel
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19
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Puthenveetil R, Vinogradova O. Solution NMR: A powerful tool for structural and functional studies of membrane proteins in reconstituted environments. J Biol Chem 2019; 294:15914-15931. [PMID: 31551353 DOI: 10.1074/jbc.rev119.009178] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
A third of the genes in prokaryotic and eukaryotic genomes encode membrane proteins that are either essential for signal transduction and solute transport or function as scaffold structures. Unlike many of their soluble counterparts, the overall structural and functional organization of membrane proteins is sparingly understood. Recent advances in X-ray crystallography, cryo-EM, and nuclear magnetic resonance (NMR) are closing this gap by enabling an in-depth view of these ever-elusive proteins at atomic resolution. Despite substantial technological advancements, however, the overall proportion of membrane protein entries in the Protein Data Bank (PDB) remains <4%. This paucity is mainly attributed to difficulties associated with their expression and purification, propensity to form large multisubunit complexes, and challenges pertinent to identification of an ideal detergent, lipid, or detergent/lipid mixture that closely mimic their native environment. NMR is a powerful technique to obtain atomic-resolution and dynamic details of a protein in solution. This is accomplished through an assortment of isotopic labeling schemes designed to acquire multiple spectra that facilitate deduction of the final protein structure. In this review, we discuss current approaches and technological developments in the determination of membrane protein structures by solution NMR and highlight recent structural and mechanistic insights gained with this technique. We also discuss strategies for overcoming size limitations in NMR applications, and we explore a plethora of membrane mimetics available for the structural and mechanistic understanding of these essential cellular proteins.
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Affiliation(s)
- Robbins Puthenveetil
- Department of Molecular and Cell Biology, college of liberal arts and sciences, University of Connecticut at Storrs, Storrs, Connecticut 06269
| | - Olga Vinogradova
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut at Storrs, Storrs, Connecticut 06269
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20
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Weiditch SA, Seraphim TV, Houry WA, Kanelis V. Strategies for purification of the bacteriophage HK97 small and large terminase subunits that yield pure and homogeneous samples that are functional. Protein Expr Purif 2019; 160:45-55. [DOI: 10.1016/j.pep.2019.03.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 03/30/2019] [Accepted: 03/30/2019] [Indexed: 02/06/2023]
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21
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Qasim A, Sher I, Hirschhorn O, Shaked H, Qasem Z, Ruthstein S, Chill JH. Investigation of a KcsA Cytoplasmic pH Gate in Lipoprotein Nanodiscs. Chembiochem 2019; 20:813-821. [PMID: 30565824 DOI: 10.1002/cbic.201800627] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Indexed: 12/14/2022]
Abstract
The bacterial potassium channel KcsA is gated by pH, opening for conduction under acidic conditions. Molecular determinants responsible for this effect have been identified at the extracellular selectivity filter, at the membrane-cytoplasm interface (TM2 gate), and in the cytoplasmic C-terminal domain (CTD), an amphiphilic four-helix bundle mediated by hydrophobic and electrostatic interactions. Here we have employed NMR and EPR to provide a structural view of the pH-induced open-to-closed CTD transition. KcsA was embedded in lipoprotein nanodiscs (LPNs), selectively methyl-protonated at Leu/Val residues to allow observation of both states by NMR, and spin-labeled for the purposes of EPR studies. We observed a pHinduced structural change between an associated structured CTD at neutral pH and a dissociated flexible CTD at acidic pH, with a transition in the 5.0-5.5 range, consistent with a stabilization of the CTD by channel architecture. A double mutant constitutively open at the TM2 gate exhibited reduced stability of associated CTD, as indicated by weaker spin-spin interactions, a shift to higher transition pH values, and a tenfold reduction in the population of the associated "closed" channels. We extended these findings for isolated CTD-derived peptides to full-length KcsA and have established a contribution of the CTD to KcsA pH-controlled gating, which exhibits a strong correlation with the state of the proximal TM2 gate.
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Affiliation(s)
- Arwa Qasim
- Department of Chemistry, Bar Ilan University, Ramat Gan, 52900, Israel
| | - Inbal Sher
- Department of Chemistry, Bar Ilan University, Ramat Gan, 52900, Israel
| | - Orel Hirschhorn
- Department of Chemistry, Bar Ilan University, Ramat Gan, 52900, Israel
| | - Hadassa Shaked
- Department of Chemistry, Bar Ilan University, Ramat Gan, 52900, Israel
| | - Zena Qasem
- Department of Chemistry, Bar Ilan University, Ramat Gan, 52900, Israel
| | - Sharon Ruthstein
- Department of Chemistry, Bar Ilan University, Ramat Gan, 52900, Israel
| | - Jordan H Chill
- Department of Chemistry, Bar Ilan University, Ramat Gan, 52900, Israel
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22
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Lacabanne D, Fogeron ML, Wiegand T, Cadalbert R, Meier BH, Böckmann A. Protein sample preparation for solid-state NMR investigations. Prog Nucl Magn Reson Spectrosc 2019; 110:20-33. [PMID: 30803692 DOI: 10.1016/j.pnmrs.2019.01.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/11/2019] [Accepted: 01/12/2019] [Indexed: 06/09/2023]
Abstract
Preparation of a protein sample for solid-state NMR is in many aspects similar to solution-state NMR approaches, mainly with respect to the need for stable isotope labeling. But the possibility of using solid-state NMR to investigate membrane proteins in (native) lipids adds the important requirement of adapted membrane-reconstitution schemes. Also, dynamic nuclear polarization and paramagnetic NMR in solids need specific schemes using metal ions and radicals. Sample sedimentation has enabled structural investigations of objects inaccessible to other structural techniques, but rotor filling using sedimentation has become increasingly complex with smaller and smaller rotors, as needed for higher and higher magic-angle spinning (MAS) frequencies. Furthermore, solid-state NMR can investigate very large proteins and their complexes without the concomitant increase in line widths, motivating the use of selective labeling and unlabeling strategies, as well as segmental labeling, to decongest spectra. The possibility of investigating sub-milligram amounts of protein today using advanced fast MAS techniques enables alternative protein synthesis schemes such as cell-free expression. Here we review these specific aspects of solid-state NMR sample preparation.
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Affiliation(s)
- Denis Lacabanne
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, 69367 Lyon, France; Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Marie-Laure Fogeron
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, 69367 Lyon, France
| | - Thomas Wiegand
- Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | | | - Beat H Meier
- Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland.
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, 69367 Lyon, France.
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23
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Coote PW, Robson SA, Dubey A, Boeszoermenyi A, Zhao M, Wagner G, Arthanari H. Optimal control theory enables homonuclear decoupling without Bloch-Siegert shifts in NMR spectroscopy. Nat Commun 2018; 9:3014. [PMID: 30069002 PMCID: PMC6070575 DOI: 10.1038/s41467-018-05400-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 06/29/2018] [Indexed: 12/05/2022] Open
Abstract
The Bloch-Siegert shift is a phenomenon in NMR spectroscopy and atomic physics in which the observed resonance frequency is changed by the presence of an off-resonance applied field. In NMR, it occurs especially in the context of homonuclear decoupling. Here we develop a practical method for homonuclear decoupling that avoids inducing Bloch-Siegert shifts. This approach enables accurate observation of the resonance frequencies of decoupled nuclear spins. We apply this method to increase the resolution of the HNCA experiment. We also observe a doubling in sensitivity for a 30 kDa protein. We demonstrate the use of band-selective Cβ decoupling to produce amino acid-specific line shapes, which are valuable for assigning resonances to the protein sequence. Finally, we assign the backbone of a 30 kDa protein, Human Carbonic Anhydrase II, using only HNCA experiments acquired with band-selective decoupling schemes, and instrument time of one week.
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Affiliation(s)
- Paul W Coote
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA
| | - Scott A Robson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA
| | - Abhinav Dubey
- Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA
| | - Andras Boeszoermenyi
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA
- Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA
| | - Mengxia Zhao
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA
| | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA.
- Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA.
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24
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Nichols PJ, Born A, Henen MA, Strotz D, Celestine CN, Güntert P, Vögeli B. Extending the Applicability of Exact Nuclear Overhauser Enhancements to Large Proteins and RNA. Chembiochem 2018; 19:1695-1701. [PMID: 29883016 DOI: 10.1002/cbic.201800237] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Indexed: 01/24/2023]
Abstract
Distance-dependent nuclear Overhauser enhancements (NOEs) are one of the most popular and important experimental restraints for calculating NMR structures. Despite this, they are mostly employed as semiquantitative upper distance bounds, and this discards the wealth of information that is encoded in the cross-relaxation rate constant. Information that is lost includes exact distances between protons and dynamics that occur on the sub-millisecond timescale. Our recently introduced exact measurement of the NOE (eNOE) requires little additional experimental effort relative to other NMR observables. So far, we have used eNOEs to calculate multistate ensembles of proteins up to approximately 150 residues. Here, we briefly revisit eNOE methodology and present two new directions for the use of eNOEs: applications to large proteins and RNA.
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Affiliation(s)
- Parker J Nichols
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, CO, 80045, USA
| | - Alexandra Born
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, CO, 80045, USA
| | - Morkos A Henen
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, CO, 80045, USA
- Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
| | - Dean Strotz
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Chi N Celestine
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, 75123, Uppsala, Sweden
| | - Peter Güntert
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
- Institute of Biophysical Chemistry, Goethe Universität Frankfurt, Max-von-Laue-Strasse 9, 60438, Frankfurt am Main, Germany
- Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami-ohsawa, Hachioji, Tokyo, 192-0397, Japan
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, CO, 80045, USA
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25
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Abstract
Plasmodium falciparum thymidylate kinase (PfTMK) is a critical enzyme in the de novo biosynthesis pathway of pyrimidine nucleotides. N-(5'-Deoxy-α-thymidin-5'-yl)- N'-[4-(2-chlorobenzyloxy)phenyl]urea was developed as an inhibitor of PfTMK and has been reported as an effective inhibitor of P. falciparum growth with an EC50 of 28 nM [Cui, H., et al. (2012) J. Med. Chem. 55, 10948-10957]. Using this compound as a scaffold, a number of derivatives were developed and, along with the original compound, were characterized in terms of their enzyme inhibition ( Ki) and binding affinity ( KD). Furthermore, the binding site of the synthesized compounds was investigated by a combination of mutagenesis and docking simulations. Although the reported compound is indicated to be highly effective in its inhibition of parasite growth, we observed significantly lower binding affinity and weaker inhibition of PfTMK than expected from the reported EC50. This suggests that significant structural optimization will be required for the use of this scaffold as an effective PfTMK inhibitor and that the inhibition of parasite growth is due to an off-target effect.
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Affiliation(s)
- Mengshen David Chen
- Department of Biological Sciences , Carnegie Mellon University , 4400 Fifth Avenue , Pittsburgh , Pennsylvania 15213 , United States
| | - Kaustubh Sinha
- Department of Biological Sciences , Carnegie Mellon University , 4400 Fifth Avenue , Pittsburgh , Pennsylvania 15213 , United States
| | - Gordon S Rule
- Department of Biological Sciences , Carnegie Mellon University , 4400 Fifth Avenue , Pittsburgh , Pennsylvania 15213 , United States
| | - Danith H Ly
- Department of Chemistry , Carnegie Mellon University , 4400 Fifth Avenue , Pittsburgh , Pennsylvania 15213 , United States
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26
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Casiraghi M, Damian M, Lescop E, Banères JL, Catoire LJ. Illuminating the Energy Landscape of GPCRs: The Key Contribution of Solution-State NMR Associated with Escherichia coli as an Expression Host. Biochemistry 2018; 57:2297-2307. [PMID: 29607648 DOI: 10.1021/acs.biochem.8b00035] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Conformational dynamics of GPCRs are central to their function but are difficult to explore at the atomic scale. Solution-state NMR has provided the major contribution in that area of study during the past decade, despite nonoptimized labeling schemes due to the use of insect cells and, to a lesser extent, yeast as the main expression hosts. Indeed, the most efficient isotope-labeling scheme ever to address energy landscape issues for large proteins or protein complexes relies on the use of 13CH3 probes immersed in a perdeuterated dipolar environment, which is essentially out of reach of eukaryotic expression systems. In contrast, although its contribution has been underestimated because of technical issues, Escherichia coli is by far the best-adapted host for such labeling. As it is now tightly controlled, we show in this review that bacterial expression can provide an NMR spectral resolution never achieved in the GPCR field.
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Affiliation(s)
- Marina Casiraghi
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires , UMR 7099, CNRS/Université Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique (FRC 550) , 13 rue Pierre et Marie Curie , 75005 Paris , France
| | - Marjorie Damian
- Institut des Biomolécules Max Mousseron (IBMM), UMR5247 CNRS, Université Montpellier, ENSCM , 15 av. Charles Flahault , 34093 Montpellier , France
| | - Ewen Lescop
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay , 1 av. de la Terrasse , 91198 Gif-sur-Yvette , France
| | - Jean-Louis Banères
- Institut des Biomolécules Max Mousseron (IBMM), UMR5247 CNRS, Université Montpellier, ENSCM , 15 av. Charles Flahault , 34093 Montpellier , France
| | - Laurent J Catoire
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires , UMR 7099, CNRS/Université Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique (FRC 550) , 13 rue Pierre et Marie Curie , 75005 Paris , France
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27
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Danmaliki GI, Liu PB, Hwang PM. Stereoselective Deuteration in Aspartate, Asparagine, Lysine, and Methionine Amino Acid Residues Using Fumarate as a Carbon Source for Escherichia coli in D2O. Biochemistry 2017; 56:6015-6029. [DOI: 10.1021/acs.biochem.7b00991] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gaddafi I. Danmaliki
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta Canada T6G 2H7
| | - Philip B. Liu
- Department
of Medicine, University of Alberta, Edmonton, Alberta Canada T6G 2R3
| | - Peter M. Hwang
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta Canada T6G 2H7
- Department
of Medicine, University of Alberta, Edmonton, Alberta Canada T6G 2R3
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28
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Schörghuber J, Geist L, Bisaccia M, Weber F, Konrat R, Lichtenecker RJ. Anthranilic acid, the new player in the ensemble of aromatic residue labeling precursor compounds. J Biomol NMR 2017; 69:13-22. [PMID: 28861670 PMCID: PMC5626795 DOI: 10.1007/s10858-017-0129-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 08/28/2017] [Indexed: 06/07/2023]
Abstract
The application of metabolic precursors for selective stable isotope labeling of aromatic residues in cell-based protein overexpression has already resulted in numerous NMR probes to study the structural and dynamic characteristics of proteins. With anthranilic acid, we present the structurally simplest precursor for exclusive tryptophan side chain labeling. A synthetic route to 13C, 2H isotopologues allows the installation of isolated 13C-1H spin systems in the indole ring of tryptophan, representing a versatile tool to investigate side chain motion using relaxation-based experiments without the loss of magnetization due to strong 1JCC and weaker 2JCH scalar couplings, as well as dipolar interactions with remote hydrogens. In this article, we want to introduce this novel precursor in the context of hitherto existing techniques of in vivo aromatic residue labeling.
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Affiliation(s)
- Julia Schörghuber
- Institute of Organic Chemistry, University of Vienna, Währingerstr. 38, 1090, Vienna, Austria
| | - Leonhard Geist
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Dr-Bohr-Gasse 9, 1030, Vienna, Austria
| | - Marilena Bisaccia
- Institute of Organic Chemistry, University of Vienna, Währingerstr. 38, 1090, Vienna, Austria
| | - Frederik Weber
- Institute of Organic Chemistry, University of Vienna, Währingerstr. 38, 1090, Vienna, Austria
| | - Robert Konrat
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Dr-Bohr-Gasse 9, 1030, Vienna, Austria
| | - Roman J Lichtenecker
- Institute of Organic Chemistry, University of Vienna, Währingerstr. 38, 1090, Vienna, Austria.
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29
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Sim DW, Lu Z, Won HS, Lee SN, Seo MD, Lee BJ, Kim JH. Application of Solution NMR to Structural Studies on α-Helical Integral Membrane Proteins. Molecules 2017; 22:molecules22081347. [PMID: 28809779 PMCID: PMC6152068 DOI: 10.3390/molecules22081347] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 08/10/2017] [Accepted: 08/12/2017] [Indexed: 02/05/2023] Open
Abstract
A large portion of proteins in living organisms are membrane proteins which play critical roles in the biology of the cell, from maintenance of the biological membrane integrity to communication of cells with their surroundings. To understand their mechanism of action, structural information is essential. Nevertheless, structure determination of transmembrane proteins is still a challenging area, even though recently the number of deposited structures of membrane proteins in the PDB has rapidly increased thanks to the efforts using X-ray crystallography, electron microscopy, and solid and solution nuclear magnetic resonance (NMR) technology. Among these technologies, solution NMR is a powerful tool for studying protein-protein, protein-ligand interactions and protein dynamics at a wide range of time scales as well as structure determination of membrane proteins. This review provides general and useful guideline for membrane protein sample preparation and the choice of membrane-mimetic media, which are the key step for successful structural analysis. Furthermore, this review provides an opportunity to look at recent applications of solution NMR to structural studies on α-helical membrane proteins through some success stories.
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Affiliation(s)
- Dae-Won Sim
- Department of Biotechnology, College of Biomedical and Health Science, Konkuk University, Chungbuk 27478, Korea.
| | - Zhenwei Lu
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37204, USA.
| | - Hyung-Sik Won
- Department of Biotechnology, College of Biomedical and Health Science, Konkuk University, Chungbuk 27478, Korea.
| | - Seu-Na Lee
- Department of Biotechnology, College of Biomedical and Health Science, Konkuk University, Chungbuk 27478, Korea.
| | - Min-Duk Seo
- Department of Molecular Science and Technology & College of Pharmacy, Ajou University, Suwon 16499, Korea.
| | - Bong-Jin Lee
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanak-gu, Seoul 151-742, Korea.
| | - Ji-Hun Kim
- College of Pharmacy, Chungbuk National University, Cheongju 28160, Chungbuk, Korea.
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30
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Affiliation(s)
- Kaustubh Sinha
- Department of Biological
Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Gordon S. Rule
- Department of Biological
Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
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31
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Abstract
Recent breakthroughs in isotope-labeling and pulse sequence techniques have enabled the NMR characterization of large protein systems with molecular masses of hundreds of kilodaltons. NMR studies of a great variety of large proteins have provided unique insights into the binding, dynamic, and allosteric mechanisms. Here we present a brief summary of these developments by highlighting few cases that exemplify the uniqueness of NMR in providing atomic resolution information into key dynamic processes and structures of protein complexes with high degree of flexibility.
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Affiliation(s)
- Yajun Jiang
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455, United States; Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, United States
| | - Charalampos G Kalodimos
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455, United States; Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, United States.
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32
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Gao Q, Chalmers GR, Moremen KW, Prestegard JH. NMR assignments of sparsely labeled proteins using a genetic algorithm. J Biomol NMR 2017; 67:283-294. [PMID: 28289927 PMCID: PMC5434516 DOI: 10.1007/s10858-017-0101-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 02/22/2017] [Indexed: 05/16/2023]
Abstract
Sparse isotopic labeling of proteins for NMR studies using single types of amino acid (15N or 13C enriched) has several advantages. Resolution is enhanced by reducing numbers of resonances for large proteins, and isotopic labeling becomes economically feasible for glycoproteins that must be expressed in mammalian cells. However, without access to the traditional triple resonance strategies that require uniform isotopic labeling, NMR assignment of crosspeaks in heteronuclear single quantum coherence (HSQC) spectra is challenging. We present an alternative strategy which combines readily accessible NMR data with known protein domain structures. Based on the structures, chemical shifts are predicted, NOE cross-peak lists are generated, and residual dipolar couplings (RDCs) are calculated for each labeled site. Simulated data are then compared to measured values for a trial set of assignments and scored. A genetic algorithm uses the scores to search for an optimal pairing of HSQC crosspeaks with labeled sites. While none of the individual data types can give a definitive assignment for a particular site, their combination can in most cases. Four test proteins previously assigned using triple resonance methods and a sparsely labeled glycosylated protein, Robo1, previously assigned by manual analysis, are used to validate the method and develop a criterion for identifying sites assigned with high confidence.
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Affiliation(s)
- Qi Gao
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Gordon R Chalmers
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
- Department of Computer Science and Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Kelley W Moremen
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - James H Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA.
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Abstract
Segmental isotopic labeling of samples for NMR studies is attractive for large complex biomacromolecular systems, especially for studies of function-related protein-ligand interactions and protein dynamics (Goto and Kay, Curr Opin Struct Biol 10:585-592, 2000; Rosa et al., Molecules (Basel, Switzerland) 18:440, 2013; Hiroaki, Expert Opin Drug Discovery 8:523-536, 2013). Advantages of segmental isotopic labeling include selective examination of specific segment(s) within a protein by NMR, significantly reducing the spectral complexity for large proteins, and allowing for the application of a variety of solution-based NMR strategies. By utilizing intein techniques (Wood and Camarero, J Biol Chem 289:14512-14519, 2014; Paulus, Annu Rev Biochem 69:447-496, 2000), two related approaches can generally be used in the segmental isotopic labeling of proteins: expressed protein ligation (Muir, Annu Rev Biochem 72:249-289, 2003) and protein trans-splicing (Shah et al., J Am Chem Soc 134:11338-11341, 2012). Here, we describe general implementation and latest improvements of expressed protein ligation method for the production of segmental isotopic labeled NMR samples.
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Affiliation(s)
- Dongsheng Liu
- iHuman Institute, ShanghaiTech University, 99 Haike Road, Pudong, Shanghai, 201203, China
| | - David Cowburn
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461, USA.
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Mote KR, Agarwal V, Madhu PK. Five decades of homonuclear dipolar decoupling in solid-state NMR: Status and outlook. Prog Nucl Magn Reson Spectrosc 2016; 97:1-39. [PMID: 27888838 DOI: 10.1016/j.pnmrs.2016.08.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 07/11/2016] [Accepted: 08/02/2016] [Indexed: 06/06/2023]
Abstract
It has been slightly more than fifty years since the first homonuclear spin decoupling scheme, Lee-Goldburg decoupling, was proposed for removing homonuclear dipolar interactions in solid-state nuclear magnetic resonance. A family of such schemes has made observation of high-resolution NMR spectra of abundant spins possible in various applications in solid state. This review outlines the strategies used in this field and the future prospects of homonuclear spin decoupling in solid-state NMR.
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Affiliation(s)
- Kaustubh R Mote
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, 21 Brundavan Colony, Narsingi, Hyderabad 500 075, India
| | - Vipin Agarwal
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, 21 Brundavan Colony, Narsingi, Hyderabad 500 075, India
| | - P K Madhu
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, 21 Brundavan Colony, Narsingi, Hyderabad 500 075, India; Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400 005, India
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Abstract
AbstractIncreasing evidence suggests that most proteins occur and function in complexes rather than as isolated entities when embedded in cellular membranes. Nuclear magnetic resonance (NMR) provides increasing possibilities to study structure, dynamics and assembly of such systems. In our review, we discuss recent methodological progress to study membrane–protein complexes (MPCs) by NMR, starting with expression, isotope-labeling and reconstitution protocols. We review approaches to deal with spectral complexity and limited spectral spectroscopic sensitivity that are usually encountered in NMR-based studies of MPCs. We highlight NMR applications in various classes of MPCs, including G-protein-coupled receptors, ion channels and retinal proteins and extend our discussion to protein–protein complexes that span entire cellular compartments or orchestrate processes such as protein transport across or within membranes. These examples demonstrate the growing potential of NMR-based studies of MPCs to provide critical insight into the energetics of protein–ligand and protein–protein interactions that underlie essential biological functions in cellular membranes.
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Jeyaharan D, Aston P, Garcia-Perez A, Schouten J, Davis P, Dixon AM. Soluble expression, purification and functional characterisation of carboxypeptidase G2 and its individual domains. Protein Expr Purif 2016; 127:44-52. [PMID: 27374188 DOI: 10.1016/j.pep.2016.06.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 06/27/2016] [Accepted: 06/29/2016] [Indexed: 11/24/2022]
Abstract
Due to its applications in the treatment of cancer and autoimmune diseases, the 42 kDa zinc-dependent metalloenzyme carboxypeptidase G2 (CPG2) is of great therapeutic interest. An X-ray crystal structure of unliganded CPG2 reported in 1997 revealed the domain architecture and informed early rational drug design efforts, however further efforts at co-crystallization of CPG2 with ligands, substrates or inhibitors have not been reported. Thus key features of CPG2 such as the location of the active site, the presence of additional ligand-binding sites, stability, oligomeric state, and the molecular basis of activity remain largely unknown, with the current working understanding of CPG2 activity based primarily on computational modelling. To facilitate renewed efforts in CPG2 structural biology, we report the first high-yield (250 mg L(-1)) recombinant expression (and purification) of soluble and active CPG2 using the Escherichia coli expression system. We used this protocol to produce full-length enzyme, as well as protein fragments corresponding to the individual catalytic and dimerization domains, and the activity and stability of each construct was characterised. We adapted our protocol to allow for uniform incorporation of NMR labels ((13)C, (15)N and (2)H) and present preliminary solution-state NMR spectra of high quality. Taken together, our results offer a route for production and solution-state characterization that supports renewed effort in CPG2 structural biology as well as design of significantly truncated CPG2 proteins, which retain activity while yielding (potentially) improved immunogenicity.
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Affiliation(s)
| | - Philip Aston
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | | | - James Schouten
- Mologic Ltd, Bedford Technology Park, Thurleigh, Bedford, MK44 2YP, UK
| | - Paul Davis
- Mologic Ltd, Bedford Technology Park, Thurleigh, Bedford, MK44 2YP, UK
| | - Ann M Dixon
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
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McShan AC, Kaur K, Chatterjee S, Knight KM, De Guzman RN. NMR identification of the binding surfaces involved in the Salmonella and Shigella Type III secretion tip-translocon protein-protein interactions. Proteins 2016; 84:1097-107. [PMID: 27093649 DOI: 10.1002/prot.25055] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 03/28/2016] [Accepted: 04/08/2016] [Indexed: 02/04/2023]
Abstract
The type III secretion system (T3SS) is essential for the pathogenesis of many bacteria including Salmonella and Shigella, which together are responsible for millions of deaths worldwide each year. The structural component of the T3SS consists of the needle apparatus, which is assembled in part by the protein-protein interaction between the tip and the translocon. The atomic detail of the interaction between the tip and the translocon proteins is currently unknown. Here, we used NMR methods to identify that the N-terminal domain of the Salmonella SipB translocon protein interacts with the SipD tip protein at a surface at the distal region of the tip formed by the mixed α/β domain and a portion of its coiled-coil domain. Likewise, the Shigella IpaB translocon protein and the IpaD tip protein interact with each other using similar surfaces identified for the Salmonella homologs. Furthermore, removal of the extreme N-terminal residues of the translocon protein, previously thought to be important for the interaction, had little change on the binding surface. Finally, mutations at the binding surface of SipD reduced invasion of Salmonella into human intestinal epithelial cells. Together, these results reveal the binding surfaces involved in the tip-translocon protein-protein interaction and advance our understanding of the assembly of the T3SS needle apparatus. Proteins 2016; 84:1097-1107. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Andrew C McShan
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, 66045
| | - Kawaljit Kaur
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, 66045
| | - Srirupa Chatterjee
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, 63110
| | - Kevin M Knight
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599
| | - Roberto N De Guzman
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, 66045
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Proudfoot A, Frank AO, Ruggiu F, Mamo M, Lingel A. Facilitating unambiguous NMR assignments and enabling higher probe density through selective labeling of all methyl containing amino acids. J Biomol NMR 2016; 65:15-27. [PMID: 27130242 DOI: 10.1007/s10858-016-0032-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 04/19/2016] [Indexed: 05/05/2023]
Abstract
The deuteration of proteins and selective labeling of side chain methyl groups has greatly enhanced the molecular weight range of proteins and protein complexes which can be studied using solution NMR spectroscopy. Protocols for the selective labeling of all six methyl group containing amino acids individually are available, however to date, only a maximum of five amino acids have been labeled simultaneously. Here, we describe a new methodology for the simultaneous, selective labeling of all six methyl containing amino acids using the 115 kDa homohexameric enzyme CoaD from E. coli as a model system. The utility of the labeling protocol is demonstrated by efficiently and unambiguously assigning all methyl groups in the enzymatic active site using a single 4D (13)C-resolved HMQC-NOESY-HMQC experiment, in conjunction with a crystal structure. Furthermore, the six fold labeled protein was employed to characterize the interaction between the substrate analogue (R)-pantetheine and CoaD by chemical shift perturbations, demonstrating the benefit of the increased probe density.
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Affiliation(s)
- Andrew Proudfoot
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, CA, 94608, USA
| | - Andreas O Frank
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, CA, 94608, USA
| | - Fiorella Ruggiu
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, CA, 94608, USA
| | - Mulugeta Mamo
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, CA, 94608, USA
| | - Andreas Lingel
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, CA, 94608, USA.
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Krishnarjuna B, Lim SS, Devine SM, Debono CO, Lam R, Chandrashekaran IR, Jaipuria G, Yagi H, Atreya HS, Scanlon MJ, MacRaild CA, Scammells PJ, Norton RS. Solution NMR characterization of apical membrane antigen 1 and small molecule interactions as a basis for designing new antimalarials. J Mol Recognit 2016; 29:281-91. [DOI: 10.1002/jmr.2529] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/28/2015] [Indexed: 01/12/2023]
Affiliation(s)
- Bankala Krishnarjuna
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences; Monash University; 381 Royal Parade Parkville Victoria 3052 Australia
| | - San Sui Lim
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences; Monash University; 381 Royal Parade Parkville Victoria 3052 Australia
| | - Shane M. Devine
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences; Monash University; 381 Royal Parade Parkville Victoria 3052 Australia
| | - Cael O. Debono
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences; Monash University; 381 Royal Parade Parkville Victoria 3052 Australia
| | - Raymond Lam
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences; Monash University; 381 Royal Parade Parkville Victoria 3052 Australia
| | - Indu R. Chandrashekaran
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences; Monash University; 381 Royal Parade Parkville Victoria 3052 Australia
| | - Garima Jaipuria
- NMR Research Centre; Indian Institute of Science; Bangalore 560012 India
| | - Hiromasa Yagi
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences; Monash University; 381 Royal Parade Parkville Victoria 3052 Australia
| | | | - Martin J. Scanlon
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences; Monash University; 381 Royal Parade Parkville Victoria 3052 Australia
| | - Christopher A. MacRaild
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences; Monash University; 381 Royal Parade Parkville Victoria 3052 Australia
| | - Peter J. Scammells
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences; Monash University; 381 Royal Parade Parkville Victoria 3052 Australia
| | - Raymond S. Norton
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences; Monash University; 381 Royal Parade Parkville Victoria 3052 Australia
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40
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Dubey A, Kadumuri RV, Jaipuria G, Vadrevu R, Atreya HS. Rapid NMR Assignments of Proteins by Using Optimized Combinatorial Selective Unlabeling. Chembiochem 2016; 17:334-40. [DOI: 10.1002/cbic.201500513] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Abhinav Dubey
- NMR Research Center; Indian Institute of Science, Malleswaram; Bangalore 560012 India
- IISc Mathematics Initiative; Indian Institute of Science, Malleswaram; Bangalore 560012 India
| | - Rajashekar Varma Kadumuri
- Department of Biological Sciences; Birla Institute of Technology and Science-Pilani; Hyderabad Campus Hyderabad 500078 India
| | - Garima Jaipuria
- NMR Research Center; Indian Institute of Science, Malleswaram; Bangalore 560012 India
| | - Ramakrishna Vadrevu
- Department of Biological Sciences; Birla Institute of Technology and Science-Pilani; Hyderabad Campus Hyderabad 500078 India
| | - Hanudatta S. Atreya
- NMR Research Center; Indian Institute of Science, Malleswaram; Bangalore 560012 India
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41
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Ward ME, Ritz E, Ahmed MAM, Bamm VV, Harauz G, Brown LS, Ladizhansky V. Proton detection for signal enhancement in solid-state NMR experiments on mobile species in membrane proteins. J Biomol NMR 2015; 63:375-388. [PMID: 26494649 DOI: 10.1007/s10858-015-9997-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 10/15/2015] [Indexed: 05/09/2023]
Abstract
Direct proton detection is becoming an increasingly popular method for enhancing sensitivity in solid-state nuclear magnetic resonance spectroscopy. Generally, these experiments require extensive deuteration of the protein, fast magic angle spinning (MAS), or a combination of both. Here, we implement direct proton detection to selectively observe the mobile entities in fully-protonated membrane proteins at moderate MAS frequencies. We demonstrate this method on two proteins that exhibit different motional regimes. Myelin basic protein is an intrinsically-disordered, peripherally membrane-associated protein that is highly flexible, whereas Anabaena sensory rhodopsin is composed of seven rigid transmembrane α-helices connected by mobile loop regions. In both cases, we observe narrow proton linewidths and, on average, a 10× increase in sensitivity in 2D insensitive nuclear enhancement of polarization transfer-based HSQC experiments when proton detection is compared to carbon detection. We further show that our proton-detected experiments can be easily extended to three dimensions and used to build complete amino acid systems, including sidechain protons, and obtain inter-residue correlations. Additionally, we detect signals which do not correspond to amino acids, but rather to lipids and/or carbohydrates which interact strongly with membrane proteins.
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Affiliation(s)
- Meaghan E Ward
- Department of Physics, University of Guelph, Guelph, ON, Canada
- Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, Canada
| | - Emily Ritz
- Department of Physics, University of Guelph, Guelph, ON, Canada
- Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, Canada
| | - Mumdooh A M Ahmed
- Department of Physics, University of Guelph, Guelph, ON, Canada
- Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, Canada
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
- The Department of Physics, Faculty of Science, Suez University, Suez, 43533, Egypt
| | - Vladimir V Bamm
- Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, Canada
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - George Harauz
- Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, Canada
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Leonid S Brown
- Department of Physics, University of Guelph, Guelph, ON, Canada
- Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, Canada
| | - Vladimir Ladizhansky
- Department of Physics, University of Guelph, Guelph, ON, Canada.
- Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, Canada.
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42
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Wiesner S, Sprangers R. Methyl groups as NMR probes for biomolecular interactions. Curr Opin Struct Biol 2015; 35:60-7. [DOI: 10.1016/j.sbi.2015.08.010] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 08/26/2015] [Accepted: 08/28/2015] [Indexed: 11/26/2022]
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Rennella E, Huang R, Velyvis A, Kay LE. (13)CHD2-CEST NMR spectroscopy provides an avenue for studies of conformational exchange in high molecular weight proteins. J Biomol NMR 2015; 63:187-99. [PMID: 26271302 DOI: 10.1007/s10858-015-9974-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 07/31/2015] [Indexed: 05/25/2023]
Abstract
An NMR experiment for quantifying slow (millisecond) time-scale exchange processes involving the interconversion between visible ground state and invisible, conformationally excited state conformers is presented. The approach exploits chemical exchange saturation transfer (CEST) and makes use of (13)CHD2 methyl group probes that can be readily incorporated into otherwise highly deuterated proteins. The methodology is validated with an application to a G48A Fyn SH3 domain that exchanges between a folded conformation and a sparsely populated and transiently formed unfolded ensemble. Experiments on a number of different protein systems, including a 360 kDa half-proteasome, establish that the sensitivity of this (13)CHD2 (13)C-CEST technique can be upwards of a factor of 5 times higher than for a previously published (13)CH3 (13)C-CEST approach (Bouvignies and Kay in J Biomol NMR 53:303-310, 2012), suggesting that the methodology will be powerful for studies of conformational exchange in high molecular weight proteins.
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Affiliation(s)
- Enrico Rennella
- Departments of Molecular Genetics, Biochemistry and Chemistry, The University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Rui Huang
- Departments of Molecular Genetics, Biochemistry and Chemistry, The University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Algirdas Velyvis
- Departments of Molecular Genetics, Biochemistry and Chemistry, The University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Lewis E Kay
- Departments of Molecular Genetics, Biochemistry and Chemistry, The University of Toronto, Toronto, ON, M5S 1A8, Canada.
- Program in Molecular Structure and Function, Hospital for Sick Children, 555 University Avenue, Toronto, ON, M5G 1X8, Canada.
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44
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Mazzei P, Piccolo A. Interactions between natural organic matter and organic pollutants as revealed by NMR spectroscopy. Magn Reson Chem 2015; 53:667-678. [PMID: 25783763 DOI: 10.1002/mrc.4209] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 12/13/2014] [Accepted: 12/16/2014] [Indexed: 06/04/2023]
Abstract
Natural organic matter (NOM) plays a critical role in regulating the transport and the fate of organic contaminants in the environment. NMR spectroscopy is a powerful technique for the investigation of the sorption and binding mechanisms between NOM and pollutants, as well as their mutual chemical transformations. Despite NMR relatively low sensibility but due to its wide versatility to investigating samples in the liquid, gel, and solid phases, NMR application to environmental NOM-pollutants relations enables the achievement of specific and complementary molecular information. This report is a brief outline of the potentialities of the different NMR techniques and pulse sequences to elucidate the interactions between NOM and organic pollutants, with and without their labeling with nuclei that enhance NMR sensitivity.
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Affiliation(s)
- Pierluigi Mazzei
- Centro Interdipartimentale per la Risonanza Magnetica Nucleare per l'Ambiente, l'Agro-Alimentare ed i Nuovi Materiali (CERMANU), Università di Napoli Federico II, Via Università 100, 80055, Portici, Italy
| | - Alessandro Piccolo
- Centro Interdipartimentale per la Risonanza Magnetica Nucleare per l'Ambiente, l'Agro-Alimentare ed i Nuovi Materiali (CERMANU), Università di Napoli Federico II, Via Università 100, 80055, Portici, Italy
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45
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Ardenkjaer-Larsen JH, Boebinger GS, Comment A, Duckett S, Edison AS, Engelke F, Griesinger C, Griffin RG, Hilty C, Maeda H, Parigi G, Prisner T, Ravera E, van Bentum J, Vega S, Webb A, Luchinat C, Schwalbe H, Frydman L. Facing and Overcoming Sensitivity Challenges in Biomolecular NMR Spectroscopy. Angew Chem Int Ed Engl 2015; 54:9162-85. [PMID: 26136394 PMCID: PMC4943876 DOI: 10.1002/anie.201410653] [Citation(s) in RCA: 213] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 01/26/2015] [Indexed: 11/07/2022]
Abstract
In the Spring of 2013, NMR spectroscopists convened at the Weizmann Institute in Israel to brainstorm on approaches to improve the sensitivity of NMR experiments, particularly when applied in biomolecular settings. This multi-author interdisciplinary Review presents a state-of-the-art description of the primary approaches that were considered. Topics discussed included the future of ultrahigh-field NMR systems, emerging NMR detection technologies, new approaches to nuclear hyperpolarization, and progress in sample preparation. All of these are orthogonal efforts, whose gains could multiply and thereby enhance the sensitivity of solid- and liquid-state experiments. While substantial advances have been made in all these areas, numerous challenges remain in the quest of endowing NMR spectroscopy with the sensitivity that has characterized forms of spectroscopies based on electrical or optical measurements. These challenges, and the ways by which scientists and engineers are striving to solve them, are also addressed.
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Affiliation(s)
- Jan-Henrik Ardenkjaer-Larsen
- GE Healthcare, Broendby, Denmark; Department of Electrical Engineering, Technical University of Denmark, Danish Research Centre for Magnetic Resonance, Copenhagen University Hospital Hvidovre (Denmark)
| | - Gregory S Boebinger
- U.S. National High Magnetic Field Lab, Florida State University, Tallahassee, FL 32310 (USA)
| | - Arnaud Comment
- Institute of Physics of Biological Systems, Ecole Polytechnique Fédérale de Lausanne, Lausanne (Switzerland)
| | - Simon Duckett
- Department of Chemistry, University of York, Heslington, York, YO10 5DD (UK)
| | - Arthur S Edison
- Department of Biochemistry & Molecular Biology, University of Florida, Gainesville, FL 32610 (USA)
| | | | | | - Robert G Griffin
- Department of Chemistry and Francis Bitter Magnet Lab, MIT, Cambridge, MA 02139-4703 (USA)
| | - Christian Hilty
- Department of Chemistry, Texas A&M University, College Station (USA)
| | - Hidaeki Maeda
- Riken Center for Life Science Technologies, Yokohama, Kanagawa (Japan)
| | - Giacomo Parigi
- CERM and Department of Chemistry, University of Florence, Sesto Fiorentino (Italy)
| | - Thomas Prisner
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main (Germany)
| | - Enrico Ravera
- CERM and Department of Chemistry, University of Florence, Sesto Fiorentino (Italy)
| | | | - Shimon Vega
- Chemical Physics Department, Weizmann Institute of Science, Rehovot (Israel)
| | - Andrew Webb
- Department of Radiology, C. J. Gorter Center for High Field MRI, Leiden University Medical Center (The Netherlands)
| | - Claudio Luchinat
- CERM and Department of Chemistry, University of Florence, Sesto Fiorentino (Italy).
| | - Harald Schwalbe
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main (Germany).
| | - Lucio Frydman
- Chemical Physics Department, Weizmann Institute of Science, Rehovot (Israel).
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Ardenkjaer-Larsen JH, Boebinger GS, Comment A, Duckett S, Edison AS, Engelke F, Griesinger C, Griffin RG, Hilty C, Maeda H, Parigi G, Prisner T, Ravera E, van Bentum J, Vega S, Webb A, Luchinat C, Schwalbe H, Frydman L. Neue Ansätze zur Empfindlichkeitssteigerung in der biomolekularen NMR-Spektroskopie. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201410653] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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47
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Brown LS, Ladizhansky V. Membrane proteins in their native habitat as seen by solid-state NMR spectroscopy. Protein Sci 2015; 24:1333-46. [PMID: 25973959 DOI: 10.1002/pro.2700] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 04/07/2015] [Accepted: 04/09/2015] [Indexed: 12/21/2022]
Abstract
Membrane proteins play many critical roles in cells, mediating flow of material and information across cell membranes. They have evolved to perform these functions in the environment of a cell membrane, whose physicochemical properties are often different from those of common cell membrane mimetics used for structure determination. As a result, membrane proteins are difficult to study by traditional methods of structural biology, and they are significantly underrepresented in the protein structure databank. Solid-state Nuclear Magnetic Resonance (SSNMR) has long been considered as an attractive alternative because it allows for studies of membrane proteins in both native-like membranes composed of synthetic lipids and in cell membranes. Over the past decade, SSNMR has been rapidly developing into a major structural method, and a growing number of membrane protein structures obtained by this technique highlights its potential. Here we discuss membrane protein sample requirements, review recent progress in SSNMR methodologies, and describe recent advances in characterizing membrane proteins in the environment of a cellular membrane.
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Affiliation(s)
- Leonid S Brown
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - Vladimir Ladizhansky
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
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48
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Abstract
When the first version of this unit was written in 1995, protein purification of recombinant proteins was based on a variety of standard chromatographic methods and approaches, many of which were described and mentioned throughout Current Protocols in Protein Science. In the interim, there has been a shift toward an almost universal usage of the affinity or fusion tag. This may not be the case for biotechnology manufacture where affinity tags can complicate producing proteins under regulatory conditions. Regardless of the protein expression system, questions are asked as to which and how many affinity tags to use, where to attach them in the protein, and whether to engineer a self-cleavage system or simply leave them on. We will briefly address some of these issues. Also, although this overview focuses on E.coli, protein expression and purification, other commonly used expression systems are mentioned and, apart from cell-breakage methods, protein purification methods and strategies are essentially the same.
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Affiliation(s)
- Paul T. Wingfield
- Protein Expression Laboratory, NIAMS - NIH, Building 6B, Room 1B130, 6 Center Drive, Bethesda, MD 20814, Tel: 301-594-1313,
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49
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Schörghuber J, Sára T, Bisaccia M, Schmid W, Konrat R, Lichtenecker RJ. Novel approaches in selective tryptophan isotope labeling by using Escherichia coli overexpression media. Chembiochem 2015; 16:746-51. [PMID: 25703586 DOI: 10.1002/cbic.201402677] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Indexed: 01/25/2023]
Abstract
NMR-based investigations of large protein complexes require optimized isotopic labeling schemes. We report new methods to introduce stable isotopes into tryptophan residues; these are fine-tuned to the requirements of the particular protein NMR experiment. Selective backbone labeling was performed by using a new α-ketoacid precursor as an additive in cell-based overexpression media. Additionally, we developed synthetic routes to certain isotopologues of indole with (13)C-(1)H spin systems surrounded by (12)C and (2)H. The corresponding proteins, overexpressed in the presence of these precursor compounds, can be effectively analyzed for conformational changes in tryptophan residues in response to external stimuli, such as interaction with other proteins or small molecules.
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Affiliation(s)
- Julia Schörghuber
- Institute of Organic Chemistry, University of Vienna, Währingerstrasse 38, 1090 Vienna (Austria)
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50
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Chimenti MS, Bulfer SL, Neitz RJ, Renslo AR, Jacobson MP, James TL, Arkin MR, Kelly MJS. A Fragment-Based Ligand Screen Against Part of a Large Protein Machine: The ND1 Domains of the AAA+ ATPase p97/VCP. ACTA ACUST UNITED AC 2015; 20:788-800. [PMID: 25690569 DOI: 10.1177/1087057115570550] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 01/02/2015] [Indexed: 01/25/2023]
Abstract
The ubiquitous AAA+ ATPase p97 functions as a dynamic molecular machine driving several cellular processes. It is essential in regulating protein homeostasis, and it represents a potential drug target for cancer, particularly when there is a greater reliance on the endoplasmic reticulum-associated protein degradation pathway and ubiquitin-proteasome pathway to degrade an overabundance of secreted proteins. Here, we report a case study for using fragment-based ligand design approaches against this large and dynamic hexamer, which has multiple potential binding sites for small molecules. A screen of a fragment library was conducted by surface plasmon resonance (SPR) and followed up by nuclear magnetic resonance (NMR), two complementary biophysical techniques. Virtual screening was also carried out to examine possible binding sites for the experimental hits and evaluate the potential utility of fragment docking for this target. Out of this effort, 13 fragments were discovered that showed reversible binding with affinities between 140 µM and 1 mM, binding stoichiometries of 1:1 or 2:1, and good ligand efficiencies. Structural data for fragment-protein interactions were obtained with residue-specific [U-(2)H] (13)CH3-methyl-labeling NMR strategies, and these data were compared to poses from docking. The combination of virtual screening, SPR, and NMR enabled us to find and validate a number of interesting fragment hits and allowed us to gain an understanding of the structural nature of fragment binding.
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Affiliation(s)
- Michael S Chimenti
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA Co-first authors
| | - Stacie L Bulfer
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA Small Molecule Discovery Center, University of California San Francisco, San Francisco, CA, USA Co-first authors
| | - R Jeffrey Neitz
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA Small Molecule Discovery Center, University of California San Francisco, San Francisco, CA, USA
| | - Adam R Renslo
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA Small Molecule Discovery Center, University of California San Francisco, San Francisco, CA, USA
| | - Matthew P Jacobson
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Thomas L James
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Michelle R Arkin
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA Small Molecule Discovery Center, University of California San Francisco, San Francisco, CA, USA
| | - Mark J S Kelly
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
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