1
|
Locke A, Guarino K, Rule GS. Labeling of methyl groups: a streamlined protocol and guidance for the selection of 2H precursors based on molecular weight. JOURNAL OF BIOMOLECULAR NMR 2024; 78:149-159. [PMID: 38787508 PMCID: PMC11491418 DOI: 10.1007/s10858-024-00441-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 03/21/2024] [Indexed: 05/25/2024]
Abstract
A streamlined one-day protocol is described to produce isotopically methyl-labeled protein with high levels of deuterium for NMR studies. Using this protocol, the D2O and 2H-glucose content of the media and protonation level of ILV labeling precursors (ketobutyrate and ketovalerate) were varied. The relaxation rate of the multiple-quantum (MQ) state that is present during the HMQC-TROSY pulse sequence was measured for different labeling schemes and this rate was used to predict upper limits of molecular weights for various labeling schemes. The use of deuterated solvents (D2O) or deuterated glucose is not required to obtain 1H-13C correlated NMR spectra of a 50 kDa homodimeric protein that are suitable for assignment by mutagenesis. High quality spectra of 100-150 kDa proteins, suitable for most applications, can be obtained without the use of deuterated glucose. The proton on the β-position of ketovalerate appears to undergo partial exchange with deuterium under the growth conditions used in this study.
Collapse
Affiliation(s)
- Alexandra Locke
- Department of Biological Sciences, Carnegie Mellon University, 4400 5th Ave, Pittsburgh, PA, 15213, USA
| | - Kylee Guarino
- Department of Biological Sciences, Carnegie Mellon University, 4400 5th Ave, Pittsburgh, PA, 15213, USA
| | - Gordon S Rule
- Department of Biological Sciences, Carnegie Mellon University, 4400 5th Ave, Pittsburgh, PA, 15213, USA.
| |
Collapse
|
2
|
Beriashvili D, Zhou J, Liu Y, Folkers GE, Baldus M. Cellular Applications of DNP Solid-State NMR - State of the Art and a Look to the Future. Chemistry 2024; 30:e202400323. [PMID: 38451060 DOI: 10.1002/chem.202400323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/08/2024]
Abstract
Sensitivity enhanced dynamic nuclear polarization solid-state NMR is emerging as a powerful technique for probing the structural properties of conformationally homogenous and heterogenous biomolecular species irrespective of size at atomic resolution within their native environments. Herein we detail advancements that have made acquiring such data, specifically within the confines of intact bacterial and eukaryotic cell a reality and further discuss the type of structural information that can presently be garnered by the technique's exploitation. Subsequently, we discuss bottlenecks that have thus far curbed cellular DNP-ssNMR's broader adoption namely due a lack of sensitivity and spectral resolution. We also explore possible solutions ranging from utilization of new pulse sequences, design of better performing polarizing agents, and application of additional biochemical/ cell biological methodologies.
Collapse
Affiliation(s)
- David Beriashvili
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padaulaan 8, 3584 CH, Utrecht, The Netherlands
| | - Jiaxin Zhou
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics, Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, P. R. China
| | - Yangping Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics, Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, P. R. China
| | - Gert E Folkers
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padaulaan 8, 3584 CH, Utrecht, The Netherlands
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padaulaan 8, 3584 CH, Utrecht, The Netherlands
| |
Collapse
|
3
|
Danmaliki GI, Yu S, Braun S, Zhao YY, Moore J, Fahlman RP, West FG, Hwang PM. Cost-effective selective deuteration of aromatic amino acid residues produces long-lived solution 1H NMR magnetization in proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 353:107499. [PMID: 37307676 DOI: 10.1016/j.jmr.2023.107499] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 05/24/2023] [Accepted: 06/01/2023] [Indexed: 06/14/2023]
Abstract
Solution NMR studies of large proteins are hampered by rapid signal decay due to short-range dipolar 1H-1H and 1H-13C interactions. These are attenuated by rapid rotation in methyl groups and by deuteration (2H), so selective 1H,13C-isotope labelling of methyl groups in otherwise perdeuterated proteins, combined with methyl transverse relaxation optimized spectroscopy (methyl-TROSY), is now standard for solution NMR of large protein systems > 25 kDa. For non-methyl positions, long-lived magnetization can be introduced as isolated 1H-12C groups. We have developed a cost-effective chemical synthesis for producing selectively deuterated phenylpyruvate and hydroxyphenylpyruvate. Feeding these amino acid precursors to E. coli in D2O, along with selectively deuterated anthranilate and unlabeled histidine, results in isolated and long-lived 1H magnetization in the aromatic rings of Phe (HD, HZ), Tyr (HD), Trp (HH2, HE3) and His (HD2 and HE1). We are additionally able to obtain stereoselective deuteration of Asp, Asn, and Lys amino acid residues using unlabeled glucose and fumarate as carbon sources and oxalate and malonate as metabolic inhibitors. Combining these approaches produces isolated 1H-12C groups in Phe, Tyr, Trp, His, Asp, Asn, and Lys in a perdeuterated background, which is compatible with standard 1H-13C labeling of methyl groups in Ala, Ile, Leu, Val, Thr, Met. We show that isotope labeling of Ala is improved using the transaminase inhibitor L-cycloserine, and labeling of Thr is improved through addition of Cys and Met, which are known inhibitors of homoserine dehydrogenase. We demonstrate the creation of long-lived 1H NMR signals in most amino acid residues using our model system, the WW domain of human Pin1, as well as the bacterial outer membrane protein PagP.
Collapse
Affiliation(s)
- Gaddafi I Danmaliki
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Shaohui Yu
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Shelly Braun
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Yuan Y Zhao
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Jack Moore
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Richard P Fahlman
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Frederick G West
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Peter M Hwang
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada; Department of Medicine, University of Alberta, Edmonton, Alberta T6G 2R3, Canada.
| |
Collapse
|
4
|
Gordon BH, Liu P, Whittington AC, Silvers R, Miller BG. Biochemical methods to map and quantify allosteric motions in human glucokinase. Methods Enzymol 2023; 685:433-459. [PMID: 37245911 PMCID: PMC10308428 DOI: 10.1016/bs.mie.2023.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Allosteric regulation of protein function is ubiquitous in biology. Allostery originates from ligand-mediated alterations in polypeptide structure and/or dynamics, which produce a cooperative kinetic or thermodynamic response to changing ligand concentrations. Establishing a mechanistic description of individual allosteric events requires both mapping the relevant changes in protein structure and quantifying the rates of differential conformational dynamics in the absence and presence of effectors. In this chapter, we describe three biochemical approaches to understand the dynamic and structural signatures of protein allostery using the well-established cooperative enzyme glucokinase as a case study. The combined application of pulsed proteolysis, biomolecular nuclear magnetic resonance spectroscopy and hydrogen-deuterium exchange mass spectrometry offers complementary information that can used to establish molecular models for allosteric proteins, especially when differential protein dynamics are involved.
Collapse
Affiliation(s)
- Blaine H Gordon
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, United States; Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, United States
| | - Peilu Liu
- Protein Analytical Chemistry, Genentech Inc., South San Francisco, CA, United States
| | - A Carl Whittington
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, United States; Department of Biological Science, Florida State University, Tallahassee, FL, United States
| | - Robert Silvers
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, United States; Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, United States
| | - Brian G Miller
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, United States.
| |
Collapse
|
5
|
Nishikino T, Miyanoiri Y. Site-Specific Isotope Labeling of FliG for Studying Structural Dynamics Using Nuclear Magnetic Resonance Spectroscopy. Methods Mol Biol 2023; 2646:57-70. [PMID: 36842106 DOI: 10.1007/978-1-0716-3060-0_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Abstract
To understand flagella-driven motility of bacteria, it is important to understand the structure and dynamics of the flagellar motor machinery. We have conducted structural dynamics analyses using solution nuclear magnetic resonance (NMR) to elucidate the detailed functions of flagellar motor proteins. Here, we introduce the analysis of the FliG protein, which is a flagellar motor protein, focusing on the preparation method of the original stable isotope-labeled protein.
Collapse
Affiliation(s)
- Tatsuro Nishikino
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Yohei Miyanoiri
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan.
| |
Collapse
|
6
|
Rowlinson B, Crublet E, Kerfah R, Plevin MJ. Specific isotopic labelling and reverse labelling for protein NMR spectroscopy: using metabolic precursors in sample preparation. Biochem Soc Trans 2022; 50:1555-1567. [PMID: 36382942 DOI: 10.1042/bst20210586] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 10/18/2022] [Accepted: 10/24/2022] [Indexed: 11/07/2023]
Abstract
The study of protein structure, dynamics and function by NMR spectroscopy commonly requires samples that have been enriched ('labelled') with the stable isotopes 13C and/or 15N. The standard approach is to uniformly label a protein with one or both of these nuclei such that all C and/or N sites are in principle 'NMR-visible'. NMR spectra of uniformly labelled proteins can be highly complicated and suffer from signal overlap. Moreover, as molecular size increases the linewidths of NMR signals broaden, which decreases sensitivity and causes further spectral congestion. Both effects can limit the type and quality of information available from NMR data. Problems associated with signal overlap and signal broadening can often be alleviated though the use of alternative, non-uniform isotopic labelling patterns. Specific isotopic labelling 'turns on' signals at selected sites while the rest of the protein is NMR-invisible. Conversely, specific isotopic unlabelling (also called 'reverse' labelling) 'turns off' selected signals while the rest of the protein remains NMR-visible. Both approaches can simplify NMR spectra, improve sensitivity, facilitate resonance assignment and permit a range of different NMR strategies when combined with other labelling tools and NMR experiments. Here, we review methods for producing proteins with enrichment of stable NMR-visible isotopes, with particular focus on residue-specific labelling and reverse labelling using Escherichia coli expression systems. We also explore how these approaches can aid NMR studies of proteins.
Collapse
Affiliation(s)
- Benjamin Rowlinson
- York Structural Biology Laboratory, York Biomedical Research Institute, Department of Biology, University of York, York YO10 5DD, U.K
| | - Elodie Crublet
- NMR-Bio, World Trade Center- 5 Place Robert Schuman, 38025 Grenoble Cedex 1, France
| | - Rime Kerfah
- NMR-Bio, World Trade Center- 5 Place Robert Schuman, 38025 Grenoble Cedex 1, France
| | - Michael J Plevin
- York Structural Biology Laboratory, York Biomedical Research Institute, Department of Biology, University of York, York YO10 5DD, U.K
| |
Collapse
|
7
|
Henot F, Crublet E, Frech M, Boisbouvier J. NMR assignment of human HSP90 N-terminal domain bound to a long residence time resorcinol ligand. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:257-266. [PMID: 35701717 DOI: 10.1007/s12104-022-10089-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
HSP90 is a major molecular chaperone that helps both folding and stabilization of various client proteins often implicated in growth control and cell survival such as kinases and transcription factors. However, among HSP90 clients are also found numerous oncoproteins and, through its assistance to them, HSP90 has consequently been reported as a promising anticancer target. Several ligand chemotypes, including resorcinol type ligands, were found to inhibit HSP90, most of them in an ATP competitive manner. Binding of some of these ligands modify significantly the NMR spectrum of the HSP90 ATP binding domain compared to the apo protein spectrum, hampering assignment transfer from the previously assigned human HSP90 apo state. Here we report the assignment of the 1HN, 15N, 13C', 13Cα, 13Cβ, 1Hmethyl, and 13Cmethyl chemical shifts of the 29 kDa HSP90 N-terminal domain bound to a long residence time resorcinol type inhibitor: 5-[4-(2-Fluoro-phenyl)-5-oxo-4,5-dihydro-1H-[1,2,4]triazol-3-yl]-N-furan-2-ylmethyl-2,4-dihydroxy-N-methyl-benzamide. 92% of the backbone resonances and 100% of the [1H, 13C]-resonances of Aβ, Mε, Tγ, Lδ2, Vγ2 and Iδ1 methyl groups were successfully assigned, including for the first time the assignment of the segment covering the nucleotide/drug binding site. Secondary structure predictions based on the NMR assignment reveal a structural rearrangement of HSP90 N-terminal domain upon ligand binding. The long residence time ligand induces the formation of a continuous helix covering the ligand binding site of HSP90 N-terminal domain accounting for the large differences observed in the NMR spectra between the apo and bound proteins.
Collapse
Affiliation(s)
- Faustine Henot
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CNRS, CEA, 71, avenue des martyrs, 38044, Grenoble, France.
| | - Elodie Crublet
- NMR-Bio, 5 place Robert Schuman, 38025, Grenoble, France
| | - Matthias Frech
- Discovery Technologies, Merck KGaA, Frankfurter Straße 250, 64293, Darmstadt, Germany
| | - Jerome Boisbouvier
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CNRS, CEA, 71, avenue des martyrs, 38044, Grenoble, France.
| |
Collapse
|
8
|
Kolloff C, Mazur A, Marzinek JK, Bond PJ, Olsson S, Hiller S. Motional clustering in supra-τ c conformational exchange influences NOE cross-relaxation rate. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2022; 338:107196. [PMID: 35367892 DOI: 10.1016/j.jmr.2022.107196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 03/01/2022] [Accepted: 03/13/2022] [Indexed: 06/14/2023]
Abstract
Biomolecular spin relaxation processes, such as the NOE, are commonly modeled by rotational τc-tumbling combined with fast motions on the sub-τc timescale. Motions on the supra-τc timescale, in contrast, are considered to be completely decorrelated to the molecular tumbling and therefore invisible. Here, we show how supra-τc dynamics can nonetheless influence the NOE build-up between methyl groups. This effect arises because supra-τc motions can cluster the fast-motion ensembles into discrete states, affecting distance averaging as well as the fast-motion order parameter and hence the cross-relaxation rate. We present a computational approach to estimate methyl-methyl cross-relaxation rates from extensive (>100×τc) all-atom molecular dynamics (MD) trajectories on the example of the 723-residue protein Malate Synthase G. The approach uses Markov state models (MSMs) to resolve transitions between metastable states and thus to discriminate between sub-τc and supra-τc conformational exchange. We find that supra-τc exchange typically increases NOESY cross-peak intensities. The methods described in this work extend the theory of modeling sub-μs dynamics in spin relaxation and thus contribute to a quantitative estimation of NOE cross-relaxation rates from MD simulations, eventually leading to increased precision in structural and functional studies of large proteins.
Collapse
Affiliation(s)
- Christopher Kolloff
- Biozentrum, Universität Basel, Spitalstrasse 41, Basel 4056, Switzerland; Department of Computer Science and Engineering, Chalmers University of Technology, Rännvägen 6, Göteborg 412 58, Sweden.
| | - Adam Mazur
- Biozentrum, Universität Basel, Spitalstrasse 41, Basel 4056, Switzerland.
| | - Jan K Marzinek
- Bioinformatics Institute (A∗STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore.
| | - Peter J Bond
- Bioinformatics Institute (A∗STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore; National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, Singapore 117543, Singapore.
| | - Simon Olsson
- Department of Computer Science and Engineering, Chalmers University of Technology, Rännvägen 6, Göteborg 412 58, Sweden.
| | - Sebastian Hiller
- Biozentrum, Universität Basel, Spitalstrasse 41, Basel 4056, Switzerland.
| |
Collapse
|
9
|
Abstract
Membrane proteins (MPs) play essential roles in numerous cellular processes. Because around 70% of the currently marketed drugs target MPs, a detailed understanding of their structure, binding properties, and functional dynamics in a physiologically relevant environment is crucial for a more detailed understanding of this important protein class. We here summarize the benefits of using lipid nanodiscs for NMR structural investigations and provide a detailed overview of the currently used lipid nanodisc systems as well as their applications in solution-state NMR. Despite the increasing use of other structural methods for the structure determination of MPs in lipid nanodiscs, solution NMR turns out to be a versatile tool to probe a wide range of MP features, ranging from the structure determination of small to medium-sized MPs to probing ligand and partner protein binding as well as functionally relevant dynamical signatures in a lipid nanodisc setting. We will expand on these topics by discussing recent NMR studies with lipid nanodiscs and work out a key workflow for optimizing the nanodisc incorporation of an MP for subsequent NMR investigations. With this, we hope to provide a comprehensive background to enable an informed assessment of the applicability of lipid nanodiscs for NMR studies of a particular MP of interest.
Collapse
Affiliation(s)
- Umut Günsel
- Bavarian NMR Center (BNMRZ) at the Department of Chemistry, Technical University of Munich, Ernst-Otto-Fischer-Strasse 2, 85748 Garching, Germany
| | - Franz Hagn
- Bavarian NMR Center (BNMRZ) at the Department of Chemistry, Technical University of Munich, Ernst-Otto-Fischer-Strasse 2, 85748 Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| |
Collapse
|
10
|
Törner R, Henot F, Awad R, Macek P, Gans P, Boisbouvier J. Backbone and methyl resonances assignment of the 87 kDa prefoldin from Pyrococcus horikoshii. BIOMOLECULAR NMR ASSIGNMENTS 2021; 15:351-360. [PMID: 33988824 DOI: 10.1007/s12104-021-10029-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 05/04/2021] [Indexed: 06/12/2023]
Abstract
Prefoldin is a heterohexameric protein assembly which acts as a co-chaperonin for the well conserved Hsp60 chaperonin, present in archaebacteria and the eukaryotic cell cytosol. Prefoldin is a holdase, capturing client proteins and subsequently transferring them to the Hsp60 chamber for refolding. The chaperonin family is implicated in the early stages of protein folding and plays an important role in proteostasis in the cytosol. Here, we report the assignment of 1HN, 15N, 13C', 13Cα, 13Cβ, 1Hmethyl, and 13Cmethyl chemical shifts of the 87 kDa prefoldin from the hyperthermophilic archaeon Pyrococcus horikoshii, consisting of two α and four β subunits. 100% of the [13C, 1H]-resonances of Aβ, Iδ1, Iδ2, Tγ2, Vγ2 methyl groups were successfully assigned for both subunits. For the β subunit, showing partial peak doubling, 80% of the backbone resonances were assigned. In the α subunit, large stretches of backbone resonances were not detectable due to slow (μs-ms) time scale dynamics. This conformational exchange limited the backbone sequential assignment of the α subunit to 57% of residues, which corresponds to 84% of visible NMR signals.
Collapse
Affiliation(s)
- Ricarda Törner
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CNRS, CEA, 71, Avenue des Martyrs, 38044, Grenoble, France.
| | - Faustine Henot
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CNRS, CEA, 71, Avenue des Martyrs, 38044, Grenoble, France
| | - Rida Awad
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CNRS, CEA, 71, Avenue des Martyrs, 38044, Grenoble, France
| | - Pavel Macek
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CNRS, CEA, 71, Avenue des Martyrs, 38044, Grenoble, France
| | - Pierre Gans
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CNRS, CEA, 71, Avenue des Martyrs, 38044, Grenoble, France
| | - Jerome Boisbouvier
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CNRS, CEA, 71, Avenue des Martyrs, 38044, Grenoble, France.
| |
Collapse
|
11
|
A Baeyer-Villiger Monooxygenase Gene Involved in the Synthesis of Lysergic Acid Amides Affects the Interaction of the Fungus Metarhizium brunneum with Insects. Appl Environ Microbiol 2021; 87:e0074821. [PMID: 34160271 DOI: 10.1128/aem.00748-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Several fungi, including the plant root symbiont and insect pathogen Metarhizium brunneum, produce lysergic acid amides via a branch of the ergot alkaloid pathway. Lysergic acid amides include important pharmaceuticals and pharmaceutical lead compounds and have potential ecological significance, making knowledge of their biosynthesis relevant. Many steps in the biosynthesis of lysergic acid amides have been determined, but terminal steps in the synthesis of lysergic acid α-hydroxyethylamide (LAH)-by far the most abundant lysergic acid amide in M. brunneum-are unknown. Ergot alkaloid synthesis (eas) genes are clustered in the genomes of fungi that produce these compounds, and the eas clusters of LAH producers contain two uncharacterized genes (easO and easP) not found in fungi that do not produce LAH. Knockout of easO via a CRISPR-Cas9 approach eliminated LAH and resulted in accumulation of the alternate lysergic acid amides lysergyl-alanine and ergonovine. Despite the elimination of LAH, the total concentration of lysergic acid derivatives was not affected significantly by the mutation. Complementation with a wild-type allele of easO restored the ability to synthesize LAH. Substrate feeding studies indicated that neither lysergyl-alanine nor ergonovine were substrates for the product of easO (EasO). EasO had structural similarity to Baeyer-Villiger monooxygenases (BVMOs), and labeling studies with deuterated alanine supported a role for a BVMO in LAH biosynthesis. The easO knockout had reduced virulence to larvae of the insect Galleria mellonella, indicating that LAH contributes to virulence of M. brunneum on insects and that LAH has biological activities different from ergonovine and lysergyl-alanine. IMPORTANCE Fungi in the genus Metarhizium are important plant root symbionts and insect pathogens. They are formulated commercially to protect plants from insect pests. Several Metarhizium species, including M. brunneum, were recently shown to produce ergot alkaloids, a class of specialized metabolites studied extensively in other fungi because of their importance in agriculture and medicine. A biological role for ergot alkaloids in Metarhizium species had not been demonstrated previously. Moreover, the types of ergot alkaloids produced by Metarhizium species are lysergic acid amides, which have served directly or indirectly as important pharmaceutical compounds. The terminal steps in the synthesis of the most abundant lysergic acid amide in Metarhizium species and several other fungi (LAH) have not been determined. The results of this study demonstrate the role of a previously unstudied gene in LAH synthesis and indicate that LAH contributes to virulence of M. brunneum on insects.
Collapse
|
12
|
Henot F, Kerfah R, Törner R, Macek P, Crublet E, Gans P, Frech M, Hamelin O, Boisbouvier J. Optimized precursor to simplify assignment transfer between backbone resonances and stereospecifically labelled valine and leucine methyl groups: application to human Hsp90 N-terminal domain. JOURNAL OF BIOMOLECULAR NMR 2021; 75:221-232. [PMID: 34041691 DOI: 10.1007/s10858-021-00370-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/20/2021] [Indexed: 06/12/2023]
Abstract
Methyl moieties are highly valuable probes for quantitative NMR studies of large proteins. Hence, their assignment is of the utmost interest to obtain information on both interactions and dynamics of proteins in solution. Here, we present the synthesis of a new precursor that allows connection of leucine and valine pro-S methyl moieties to backbone atoms by linear 13C-chains. This optimized 2H/13C-labelled acetolactate precursor can be combined with existing 13C/2H-alanine and isoleucine precursors in order to directly transfer backbone assignment to the corresponding methyl groups. Using this simple approach leucine and valine pro-S methyl groups can be assigned using a single sample without requiring correction of 1H/2H isotopic shifts on 13C resonances. The approach was demonstrated on the N-terminal domain of human HSP90, for which complete assignment of Ala-β, Ile-δ1, Leu-δ2, Met-ε, Thr-γ and Val-γ2 methyl groups was obtained.
Collapse
Affiliation(s)
- Faustine Henot
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71, Avenue des martyrs, 38044, Grenoble, France
| | - Rime Kerfah
- NMR-Bio, 5 place Robert Schuman, 38025, Grenoble, France
| | - Ricarda Törner
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71, Avenue des martyrs, 38044, Grenoble, France
| | - Pavel Macek
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71, Avenue des martyrs, 38044, Grenoble, France
- NMR-Bio, 5 place Robert Schuman, 38025, Grenoble, France
| | - Elodie Crublet
- NMR-Bio, 5 place Robert Schuman, 38025, Grenoble, France
| | - Pierre Gans
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71, Avenue des martyrs, 38044, Grenoble, France
| | - Matthias Frech
- Discovery Technologies, Merck KGaA, Frankfurter Straße 250, 64293, Darmstadt, Germany
| | - Olivier Hamelin
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, CBM, 38000, Grenoble, France
| | - Jerome Boisbouvier
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71, Avenue des martyrs, 38044, Grenoble, France.
| |
Collapse
|
13
|
Rogals MJ, Yang JY, Williams RV, Moremen KW, Amster IJ, Prestegard JH. Sparse isotope labeling for nuclear magnetic resonance (NMR) of glycoproteins using 13C-glucose. Glycobiology 2021; 31:425-435. [PMID: 32902634 PMCID: PMC8091466 DOI: 10.1093/glycob/cwaa071] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 07/22/2020] [Accepted: 07/24/2020] [Indexed: 01/02/2023] Open
Abstract
Preparation of samples for nuclear magnetic resonance (NMR) characterization of larger proteins requires enrichment with less abundant, NMR-active, isotopes such as 13C and 15N. This is routine for proteins that can be expressed in bacterial culture where low-cost isotopically enriched metabolic substrates can be used. However, it can be expensive for glycosylated proteins expressed in mammalian culture where more costly isotopically enriched amino acids are usually used. We describe a simple, relatively inexpensive procedure in which standard commercial media is supplemented with 13C-enriched glucose to achieve labeling of all glycans plus all alanines of the N-terminal domain of the highly glycosylated protein, CEACAM1. We demonstrate an ability to detect partially occupied N-glycan sites, sites less susceptible to processing by an endoglycosidase, and some unexpected truncation of the amino acid sequence. The labeling of both the protein (through alanines) and the glycans in a single culture requiring no additional technical expertise past standard mammalian expression requirements is anticipated to have several applications, including structural and functional screening of the many glycosylated proteins important to human health.
Collapse
Affiliation(s)
- Monique J Rogals
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd., Athens, GA 30602, USA
| | - Jeong-Yeh Yang
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd., Athens, GA 30602, USA
| | - Robert V Williams
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd., Athens, GA 30602, USA
- Department of Chemistry
| | - Kelley W Moremen
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd., Athens, GA 30602, USA
- Department of Biochemistry and Molecular Biology
| | | | - James H Prestegard
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd., Athens, GA 30602, USA
- Department of Chemistry
- Department of Biochemistry and Molecular Biology
| |
Collapse
|
14
|
Pritišanac I, Alderson TR, Güntert P. Automated assignment of methyl NMR spectra from large proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2020; 118-119:54-73. [PMID: 32883449 DOI: 10.1016/j.pnmrs.2020.04.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/15/2020] [Accepted: 04/17/2020] [Indexed: 05/05/2023]
Abstract
As structural biology trends towards larger and more complex biomolecular targets, a detailed understanding of their interactions and underlying structures and dynamics is required. The development of methyl-TROSY has enabled NMR spectroscopy to provide atomic-resolution insight into the mechanisms of large molecular assemblies in solution. However, the applicability of methyl-TROSY has been hindered by the laborious and time-consuming resonance assignment process, typically performed with domain fragmentation, site-directed mutagenesis, and analysis of NOE data in the context of a crystal structure. In response, several structure-based automatic methyl assignment strategies have been developed over the past decade. Here, we present a comprehensive analysis of all available methods and compare their input data requirements, algorithmic strategies, and reported performance. In general, the methods fall into two categories: those that primarily rely on inter-methyl NOEs, and those that utilize methyl PRE- and PCS-based restraints. We discuss their advantages and limitations, and highlight the potential benefits from standardizing and combining different methods.
Collapse
Affiliation(s)
- Iva Pritišanac
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | - T Reid Alderson
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter Güntert
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany; Laboratory of Physical Chemistry, ETH Zürich, 8093 Zürich, Switzerland; Department of Chemistry, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan.
| |
Collapse
|
15
|
Danmaliki GI, Hwang PM. Solution NMR spectroscopy of membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183356. [PMID: 32416193 DOI: 10.1016/j.bbamem.2020.183356] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 05/08/2020] [Accepted: 05/10/2020] [Indexed: 02/06/2023]
Abstract
Integral membrane proteins (IMPs) perform unique and indispensable functions in the cell, making them attractive targets for fundamental research and drug discovery. Developments in protein production, isotope labeling, sample preparation, and pulse sequences have extended the utility of solution NMR spectroscopy for studying IMPs with multiple transmembrane segments. Here we review some recent applications of solution NMR for studying structure, dynamics, and interactions of polytopic IMPs, emphasizing strategies used to overcome common technical challenges.
Collapse
Affiliation(s)
- Gaddafi I Danmaliki
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Peter M Hwang
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada; Department of Medicine, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.
| |
Collapse
|
16
|
Ayala I, Chiari L, Kerfah R, Boisbouvier J, Gans P, Hamelin O. Asymmetric Synthesis of Methyl Specifically Labelled
L
‐Threonine and Application to the NMR Studies of High Molecular Weight Proteins. ChemistrySelect 2020. [DOI: 10.1002/slct.202000827] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Isabel Ayala
- Univ. Grenoble Alpes, CNRS, CEAInstitut de Biologie Structurale (IBS), 71, avenue des martyrs F-38044 Grenoble France
| | - Lucile Chiari
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, CBM- F-38000 Grenoble France
| | - Rime Kerfah
- NMR-Bio 5 place Robert Schuman F-38025 Grenoble France
| | - Jerome Boisbouvier
- Univ. Grenoble Alpes, CNRS, CEAInstitut de Biologie Structurale (IBS), 71, avenue des martyrs F-38044 Grenoble France
| | - Pierre Gans
- Univ. Grenoble Alpes, CNRS, CEAInstitut de Biologie Structurale (IBS), 71, avenue des martyrs F-38044 Grenoble France
| | - Olivier Hamelin
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, CBM- F-38000 Grenoble France
| |
Collapse
|
17
|
Schütz S, Sprangers R. Methyl TROSY spectroscopy: A versatile NMR approach to study challenging biological systems. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2020; 116:56-84. [PMID: 32130959 DOI: 10.1016/j.pnmrs.2019.09.004] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 09/09/2019] [Accepted: 09/25/2019] [Indexed: 05/21/2023]
Abstract
A major goal in structural biology is to unravel how molecular machines function in detail. To that end, solution-state NMR spectroscopy is ideally suited as it is able to study biological assemblies in a near natural environment. Based on methyl TROSY methods, it is now possible to record high-quality data on complexes that are far over 100 kDa in molecular weight. In this review, we discuss the theoretical background of methyl TROSY spectroscopy, the information that can be extracted from methyl TROSY spectra and approaches that can be used to assign methyl resonances in large complexes. In addition, we touch upon insights that have been obtained for a number of challenging biological systems, including the 20S proteasome, the RNA exosome, molecular chaperones and G-protein-coupled receptors. We anticipate that methyl TROSY methods will be increasingly important in modern structural biology approaches, where information regarding static structures is complemented with insights into conformational changes and dynamic intermolecular interactions.
Collapse
Affiliation(s)
- Stefan Schütz
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Remco Sprangers
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany.
| |
Collapse
|
18
|
Törner R, Awad R, Gans P, Brutscher B, Boisbouvier J. Spectral editing of intra- and inter-chain methyl-methyl NOEs in protein complexes. JOURNAL OF BIOMOLECULAR NMR 2020; 74:83-94. [PMID: 31897934 DOI: 10.1007/s10858-019-00293-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 12/10/2019] [Indexed: 06/10/2023]
Abstract
Specific isotopic labeling of methyl groups in a perdeuterated protein background enables the detection of long range NOEs in proteins or high molecular weight complexes. We introduce here an approach, combining an optimized isotopic labeling scheme with a specifically tailored NMR pulse sequence, to distinguish between intramolecular and intermolecular NOE connectivities. In hetero-oligomeric complexes, this strategy enables sign encoding of intra-subunit and inter-subunit NOEs. For homo-oligomeric assemblies, our strategy allows the specific detection of intra-chain NOEs in high resolution 3D NOESY spectra. The general principles, possibilities and limitations of this approach are presented. Applications of this approach for the detection of intermolecular NOEs in a hetero-hexamer, and the assignment of methyl 1H and 13C resonances in a homo-tetrameric protein complex are shown.
Collapse
Affiliation(s)
- Ricarda Törner
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, 38044, Grenoble, France
| | - Rida Awad
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, 38044, Grenoble, France
| | - Pierre Gans
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, 38044, Grenoble, France
| | - Bernhard Brutscher
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, 38044, Grenoble, France
| | - Jerome Boisbouvier
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, 38044, Grenoble, France.
| |
Collapse
|
19
|
Kaur H, Grahl A, Hartmann JB, Hiller S. Sample Preparation and Technical Setup for NMR Spectroscopy with Integral Membrane Proteins. Methods Mol Biol 2020; 2127:373-396. [PMID: 32112334 DOI: 10.1007/978-1-0716-0373-4_24] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
NMR spectroscopy is a method of choice to characterize structure, function, and dynamics of integral membrane proteins at atomic resolution. Here, we describe protocols for sample preparation and characterization by NMR spectroscopy of two integral membrane proteins with different architecture, the α-helical membrane protein MsbA and the β-barrel membrane protein BamA. The protocols describe recombinant expression in E. coli, protein refolding, purification, and reconstitution in suitable membrane mimetics, as well as key setup steps for basic NMR experiments. These include experiments on protein samples in the solid state under magic angle spinning (MAS) conditions and experiments on protein samples in aqueous solution. Since MsbA and BamA are typical examples of their respective architectural classes, the protocols presented here can also serve as a reference for other integral membrane proteins.
Collapse
Affiliation(s)
- Hundeep Kaur
- Biozentrum, University of Basel, Basel, Switzerland
| | - Anne Grahl
- Biozentrum, University of Basel, Basel, Switzerland
| | | | | |
Collapse
|
20
|
Kano H, Toyama Y, Imai S, Iwahashi Y, Mase Y, Yokogawa M, Osawa M, Shimada I. Structural mechanism underlying G protein family-specific regulation of G protein-gated inwardly rectifying potassium channel. Nat Commun 2019; 10:2008. [PMID: 31043612 PMCID: PMC6494913 DOI: 10.1038/s41467-019-10038-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 04/12/2019] [Indexed: 01/26/2023] Open
Abstract
G protein-gated inwardly rectifying potassium channel (GIRK) plays a key role in regulating neurotransmission. GIRK is opened by the direct binding of the G protein βγ subunit (Gβγ), which is released from the heterotrimeric G protein (Gαβγ) upon the activation of G protein-coupled receptors (GPCRs). GIRK contributes to precise cellular responses by specifically and efficiently responding to the Gi/o-coupled GPCRs. However, the detailed mechanisms underlying this family-specific and efficient activation are largely unknown. Here, we investigate the structural mechanism underlying the Gi/o family-specific activation of GIRK, by combining cell-based BRET experiments and NMR analyses in a reconstituted membrane environment. We show that the interaction formed by the αA helix of Gαi/o mediates the formation of the Gαi/oβγ-GIRK complex, which is responsible for the family-specific activation of GIRK. We also present a model structure of the Gαi/oβγ-GIRK complex, which provides the molecular basis underlying the specific and efficient regulation of GIRK.
Collapse
Affiliation(s)
- Hanaho Kano
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yuki Toyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Shunsuke Imai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yuta Iwahashi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yoko Mase
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Mariko Yokogawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,Faculty of Pharmacy, Keio University, Shibakoen, Minato-ku, Tokyo, 105-8512, Japan
| | - Masanori Osawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,Faculty of Pharmacy, Keio University, Shibakoen, Minato-ku, Tokyo, 105-8512, Japan
| | - Ichio Shimada
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| |
Collapse
|
21
|
Goricanec D, Hagn F. NMR backbone and methyl resonance assignments of an inhibitory G-alpha subunit in complex with GDP. BIOMOLECULAR NMR ASSIGNMENTS 2019; 13:131-137. [PMID: 30539422 DOI: 10.1007/s12104-018-9865-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 12/06/2018] [Indexed: 06/09/2023]
Abstract
G-proteins are essential switch points at the cell membrane that control downstream signaling by their ability to adopt an inactive, GDP-bound or an active, GTP-bound state. Among other exchange factors, G-protein coupled receptors (GPCRs) induce exchange of GDP to GTP and thus promote the active state of the G-protein. The nucleotide-binding α subunit of the G-protein undergoes major conformational changes upon nucleotide binding. Thus, an NMR analysis of the two distinct nucleotide-bound states is essential for a more detailed understanding of associated structural changes. Here, we provide an NMR backbone as well as methyl group resonance assignment of an inhibitory G-alpha subunit subtype 1 (Gαi,1) in the GDP-bound form and show that, in contrast to the GTP-bound form, large parts of the protein are mobile, presumably caused by a loose arrangement of the two subdomains in Gα that tightly interact with each other only in the GTP-bound state. As the GDP-bound form represents the GPCR-binding-competent state, the presented NMR data will be essential for further studies on G-protein-GPCR interactions and dynamics in solution for receptor systems that couple to G-proteins containing an inhibitory Gα,1 subunit.
Collapse
Affiliation(s)
- David Goricanec
- Bavarian NMR Center at the Department of Chemistry and Institute for Advanced Study, Technical University of Munich, Ernst-Otto-Fischer-Str. 2, 85748, Garching, Germany
- Institute of Structural Biology, Helmholtz Center Munich, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Franz Hagn
- Bavarian NMR Center at the Department of Chemistry and Institute for Advanced Study, Technical University of Munich, Ernst-Otto-Fischer-Str. 2, 85748, Garching, Germany.
- Institute of Structural Biology, Helmholtz Center Munich, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany.
| |
Collapse
|
22
|
Williams RV, Yang JY, Moremen KW, Amster IJ, Prestegard JH. Measurement of residual dipolar couplings in methyl groups via carbon detection. JOURNAL OF BIOMOLECULAR NMR 2019; 73:191-198. [PMID: 31041649 PMCID: PMC7020099 DOI: 10.1007/s10858-019-00245-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 03/30/2019] [Indexed: 06/09/2023]
Abstract
Residual dipolar couplings (RDCs) provide both structural and dynamical information useful in the characterization of biological macromolecules. While most data come from the interaction of simple pairs of directly bonded spin-1/2 nuclei (1H-15N, 1H-13C, 1H-1H), it is possible to acquire data from interactions among the multiple spins of 13C-labeled methyl groups (1H3-13C). This is especially important because of the advantages that observation of 13C-labeled methyl groups offers in working with very large molecules. Here we consider some of the options for measurement of methyl RDCs in large and often fully protonated proteins and arrive at a pulse sequence that exploits both J-modulation and direct detection of 13C. Its utility is illustrated by application to a fully protonated two domain fragment from the mammalian glycoprotein, Robo1, 13C-methyl-labeled in all valines.
Collapse
Affiliation(s)
- Robert V Williams
- Department of Chemistry, University of Georgia, Athens, GA, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Jeong-Yeh Yang
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Kelley W Moremen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | | | - James H Prestegard
- Department of Chemistry, University of Georgia, Athens, GA, USA.
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA.
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA.
| |
Collapse
|
23
|
|
24
|
Proudfoot A, Frank AO, Frommlet A, Lingel A. Selective Methyl Labeling of Proteins: Enabling Structural and Mechanistic Studies As Well As Drug Discovery Applications by Solution-State NMR. Methods Enzymol 2018; 614:1-36. [PMID: 30611421 DOI: 10.1016/bs.mie.2018.08.035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Escherichia coli expression protocols for selective labeling of methyl groups in proteins have been essential in expanding the size range of targets that can be studied by biomolecular NMR. Based on the initial work achieving selective labeling of isoleucine, leucine, and valine residues, additional methods were developed over the past years which enabled the individual and/or simultaneous combinatorial labeling of all methyl containing amino acids. Together with the introduction of new methyl-optimized NMR experiments, this now allows the detailed characterization of protein-ligand interactions as well as mechanistic and dynamic processes of protein-protein complexes up to 1MDa in size. In this chapter, we provide a general introduction to selective labeling of proteins using E. coli-based expression systems, describe the considerations taken into account prior to the selective labeling of a protein, and include the protocols used to produce such proteins. An overview of applications using selectively labeled proteins with an emphasis on examples relevant to the drug discovery process is then presented.
Collapse
Affiliation(s)
- Andrew Proudfoot
- Structural and Biophysical Chemistry, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Emeryville, CA, United States
| | - Andreas O Frank
- Structural and Biophysical Chemistry, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Emeryville, CA, United States
| | - Alexandra Frommlet
- Structural and Biophysical Chemistry, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Emeryville, CA, United States
| | - Andreas Lingel
- Structural and Biophysical Chemistry, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Emeryville, CA, United States; Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, Basel, Switzerland.
| |
Collapse
|
25
|
Demers JP, Fricke P, Shi C, Chevelkov V, Lange A. Structure determination of supra-molecular assemblies by solid-state NMR: Practical considerations. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018; 109:51-78. [PMID: 30527136 DOI: 10.1016/j.pnmrs.2018.06.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 06/15/2018] [Accepted: 06/15/2018] [Indexed: 05/26/2023]
Abstract
In the cellular environment, biomolecules assemble in large complexes which can act as molecular machines. Determining the structure of intact assemblies can reveal conformations and inter-molecular interactions that are only present in the context of the full assembly. Solid-state NMR (ssNMR) spectroscopy is a technique suitable for the study of samples with high molecular weight that allows the atomic structure determination of such large protein assemblies under nearly physiological conditions. This review provides a practical guide for the first steps of studying biological supra-molecular assemblies using ssNMR. The production of isotope-labeled samples is achievable via several means, which include recombinant expression, cell-free protein synthesis, extraction of assemblies directly from cells, or even the study of assemblies in whole cells in situ. Specialized isotope labeling schemes greatly facilitate the assignment of chemical shifts and the collection of structural data. Advanced strategies such as mixed, diluted, or segmental subunit labeling offer the possibility to study inter-molecular interfaces. Detailed and practical considerations are presented with respect to first setting up magic-angle spinning (MAS) ssNMR experiments, including the selection of the ssNMR rotor, different methods to best transfer the sample and prepare the rotor, as well as common and robust procedures for the calibration of the instrument. Diagnostic spectra to evaluate the resolution and sensitivity of the sample are presented. Possible improvements that can reduce sample heterogeneity and improve the quality of ssNMR spectra are reviewed.
Collapse
Affiliation(s)
- Jean-Philippe Demers
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; Laboratory of Cell Biology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Pascal Fricke
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Chaowei Shi
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Veniamin Chevelkov
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Adam Lange
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany.
| |
Collapse
|
26
|
An Evaluation of the Potential of NMR Spectroscopy and Computational Modelling Methods to Inform Biopharmaceutical Formulations. Pharmaceutics 2018; 10:pharmaceutics10040165. [PMID: 30248922 PMCID: PMC6320905 DOI: 10.3390/pharmaceutics10040165] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 09/11/2018] [Accepted: 09/17/2018] [Indexed: 12/22/2022] Open
Abstract
Protein-based therapeutics are considered to be one of the most important classes of pharmaceuticals on the market. The growing need to prolong stability of high protein concentrations in liquid form has proven to be challenging. Therefore, significant effort is being made to design formulations which can enable the storage of these highly concentrated protein therapies for up to 2 years. Currently, the excipient selection approach involves empirical high-throughput screening, but does not reveal details on aggregation mechanisms or the molecular-level effects of the formulations under storage conditions. Computational modelling approaches have the potential to elucidate such mechanisms, and rapidly screen in silico prior to experimental testing. Nuclear Magnetic Resonance (NMR) spectroscopy can also provide complementary insights into excipient–protein interactions. This review will highlight the underpinning principles of molecular modelling and NMR spectroscopy. It will also discuss the advancements in the applications of computational and NMR approaches in investigating excipient–protein interactions.
Collapse
|
27
|
Suzuki R, Sakakura M, Mori M, Fujii M, Akashi S, Takahashi H. Methyl-selective isotope labeling using α-ketoisovalerate for the yeast Pichia pastoris recombinant protein expression system. JOURNAL OF BIOMOLECULAR NMR 2018; 71:213-223. [PMID: 29869771 DOI: 10.1007/s10858-018-0192-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 05/29/2018] [Indexed: 06/08/2023]
Abstract
Methyl-detected NMR spectroscopy is a useful tool for investigating the structures and interactions of large macromolecules such as membrane proteins. The procedures for preparation of methyl-specific isotopically-labeled proteins were established for the Escherichia coli (E. coli) expression system, but typically it is not feasible to express eukaryotic proteins using E. coli. The Pichia pastoris (P. pastoris) expression system is the most common yeast expression system, and is known to be superior to the E. coli system for the expression of mammalian proteins, including secretory and membrane proteins. However, this system has not yet been optimized for methyl-specific isotope labeling, especially for Val/Leu-methyl specific isotope incorporation. To overcome this difficulty, we explored various culture conditions for the yeast cells to efficiently uptake Val/Leu precursors. Among the searched conditions, we found that the cultivation pH has a critical effect on Val/Leu precursor uptake. At an acidic cultivation pH, the uptake of the Val/Leu precursor was increased, and methyl groups of Val and Leu in the synthesized recombinant protein yielded intense 1H-13C correlation signals. Based on these results, we present optimized protocols for the Val/Leu-methyl-selective 13C incorporation by the P. pastoris expression system.
Collapse
Affiliation(s)
- Rika Suzuki
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Masayoshi Sakakura
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Masaki Mori
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Moe Fujii
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Satoko Akashi
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Hideo Takahashi
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.
| |
Collapse
|
28
|
Lacabanne D, Meier BH, Böckmann A. Selective labeling and unlabeling strategies in protein solid-state NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2018; 71:141-150. [PMID: 29197975 DOI: 10.1007/s10858-017-0156-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 11/23/2017] [Indexed: 06/07/2023]
Abstract
Selective isotope labeling is central in NMR experiments and often allows to push the limits on the systems investigated. It has the advantage to supply additional resolution by diminishing the number of signals in the spectra. This is particularly interesting when dealing with the large protein systems which are currently becoming accessible to solid-state NMR studies. Isotope labeled proteins for NMR experiments are most often expressed in E. coli systems, where bacteria are grown in minimal media supplemented with 15NH4Cl and 13C-glucose as sole source of nitrogen and carbon. For amino acids selective labeling or unlabeling, specific amino acids are supplemented in the minimal medium. The aim is that they will be incorporated in the protein by the bacteria. However, E. coli amino-acid anabolism and catabolism tend to interconnect different pathways, remnant of a subway system. These connections lead to inter conversion between amino acids, called scrambling. A thorough understanding of the involved pathways is thus important to obtain the desired labeling schemes, as not all combinations of amino acids are adapted. We present here a detailed overview of amino-acid metabolism in this context. Each amino-acid pathway is described in order to define accessible combinations for 13C or 15N specific labeling or unlabeling. Using as example the ABC transporter BmrA, a membrane protein of 600 residues, we demonstrate how these strategies can be applied. Indeed, even though there is no size limit in solid-state NMR, large (membrane) proteins are still a challenge due to heavy signal overlap. To initiate resonance assignment in these large systems, we describe how selectively labeled samples can be obtained with the addition of labeled or unlabeled amino acids in the medium. The reduced spectral overlap enabled us to identify typical spectral fingerprints and to initiate sequential assignment using the more sensitive 2D DARR experiments with long mixing time showing inter-residue correlations.
Collapse
Affiliation(s)
- Denis Lacabanne
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367, Lyon, France
| | - Beat H Meier
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367, Lyon, France.
| |
Collapse
|
29
|
Schörghuber J, Geist L, Platzer G, Feichtinger M, Bisaccia M, Scheibelberger L, Weber F, Konrat R, Lichtenecker RJ. Late metabolic precursors for selective aromatic residue labeling. JOURNAL OF BIOMOLECULAR NMR 2018; 71:129-140. [PMID: 29808436 PMCID: PMC6096522 DOI: 10.1007/s10858-018-0188-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/19/2018] [Indexed: 06/08/2023]
Abstract
In recent years, we developed a toolbox of heavy isotope containing compounds, which serve as metabolic amino acid precursors in the E. coli-based overexpression of aromatic residue labeled proteins. Our labeling techniques show excellent results both in terms of selectivity and isotope incorporation levels. They are additionally distinguished by low sample production costs and meet the economic demands to further implement protein NMR spectroscopy as a routinely used method in drug development processes. Different isotopologues allow for the assembly of optimized protein samples, which fulfill the requirements of various NMR experiments to elucidate protein structures, analyze conformational dynamics, or probe interaction surfaces. In the present article, we want to summarize the precursors we developed so far and give examples of their special value in the probing of protein-ligand interaction.
Collapse
Affiliation(s)
- Julia Schörghuber
- Institute of Organic Chemistry, University of Vienna, Währinger Str. 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
| | - Gerald Platzer
- 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
| | - Michael Feichtinger
- 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, Währinger Str. 38, 1090, Vienna, Austria
| | - Lukas Scheibelberger
- Institute of Organic Chemistry, University of Vienna, Währinger Str. 38, 1090, Vienna, Austria
| | - Frederik Weber
- Institute of Organic Chemistry, University of Vienna, Währinger Str. 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, Währinger Str. 38, 1090, Vienna, Austria.
| |
Collapse
|
30
|
Gorman SD, Sahu D, O'Rourke KF, Boehr DD. Assigning methyl resonances for protein solution-state NMR studies. Methods 2018; 148:88-99. [PMID: 29958930 DOI: 10.1016/j.ymeth.2018.06.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 06/16/2018] [Accepted: 06/18/2018] [Indexed: 10/28/2022] Open
Abstract
Solution-state NMR is an important tool for studying protein structure and function. The ability to probe methyl groups has substantially expanded the scope of proteins accessible by NMR spectroscopy, including facilitating study of proteins and complexes greater than 100 kDa in size. While the toolset for studying protein structure and dynamics by NMR continues to grow, a major rate-limiting step in these studies is the initial resonance assignments, especially for larger (>50 kDa) proteins. In this practical review, we present strategies to efficiently isotopically label proteins, delineate NMR pulse sequences that can be used to determine methyl resonance assignments in the presence and absence of backbone assignments, and outline computational methods for NMR data analysis. We use our experiences from assigning methyl resonances for the aromatic biosynthetic enzymes tryptophan synthase and chorismate mutase to provide advice for all stages of experimental set-up and data analysis.
Collapse
Affiliation(s)
- Scott D Gorman
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Debashish Sahu
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Kathleen F O'Rourke
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - David D Boehr
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA.
| |
Collapse
|
31
|
Sugiki T, Furuita K, Fujiwara T, Kojima C. Amino Acid Selective 13C Labeling and 13C Scrambling Profile Analysis of Protein α and Side-Chain Carbons in Escherichia coli Utilized for Protein Nuclear Magnetic Resonance. Biochemistry 2018; 57:3576-3589. [PMID: 29924600 DOI: 10.1021/acs.biochem.8b00182] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Amino acid selective isotope labeling is an important nuclear magnetic resonance technique, especially for larger proteins, providing strong bases for the unambiguous resonance assignments and information concerning the structure, dynamics, and intermolecular interactions. Amino acid selective 15N labeling suffers from isotope dilution caused by metabolic interconversion of the amino acids, resulting in isotope scrambling within the target protein. Carbonyl 13C atoms experience less isotope scrambling than the main-chain 15N atoms do. However, little is known about the side-chain 13C atoms. Here, the 13C scrambling profiles of the Cα and side-chain carbons were investigated for 15N scrambling-prone amino acids, such as Leu, Ile, Tyr, Phe, Thr, Val, and Ala. The level of isotope scrambling was substantially lower in 13Cα and 13C side-chain labeling than in 15N labeling. We utilized this reduced scrambling-prone character of 13C as a simple and efficient method for amino acid selective 13C labeling using an Escherichia coli cold-shock expression system and high-cell density fermentation. Using this method, the 13C labeling efficiency was >80% for Leu and Ile, ∼60% for Tyr and Phe, ∼50% for Thr, ∼40% for Val, and 30-40% for Ala. 1H-15N heteronuclear single-quantum coherence signals of the 15N scrambling-prone amino acid were also easily filtered using 15N-{13Cα} spin-echo difference experiments. Our method could be applied to the assignment of the 55 kDa protein.
Collapse
Affiliation(s)
- Toshihiko Sugiki
- Institute for Protein Research , Osaka University , 3-2 Yamadaoka , Suita , Osaka 565-0871 , Japan
| | - Kyoko Furuita
- Institute for Protein Research , Osaka University , 3-2 Yamadaoka , Suita , Osaka 565-0871 , Japan
| | - Toshimichi Fujiwara
- Institute for Protein Research , Osaka University , 3-2 Yamadaoka , Suita , Osaka 565-0871 , Japan
| | - Chojiro Kojima
- Institute for Protein Research , Osaka University , 3-2 Yamadaoka , Suita , Osaka 565-0871 , Japan.,Graduate School of Engineering Science , Yokohama National University , 79-5 Tokiwadai , Hodogaya-ku, Yokohama 240-8501 , Japan
| |
Collapse
|
32
|
Methyl NMR spectroscopy: Measurement of dynamics in viral RNA-directed RNA polymerases. Methods 2018; 148:100-114. [PMID: 29857193 DOI: 10.1016/j.ymeth.2018.05.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 05/22/2018] [Accepted: 05/23/2018] [Indexed: 11/23/2022] Open
Abstract
Measurement of nuclear spin relaxation provides a powerful approach to access information about biomolecular conformational dynamics over several orders of magnitude in timescale. In several cases this knowledge in combination with spatial information from three-dimensional structures yields unique insight into protein stability and the kinetics and thermodynamics of their interactions and function. However, due to intrinsic difficulties in studying large systems using solution state nuclear magnetic resonance (NMR) approaches, until recently these measurements were limited to small-to-medium-sized systems. However, the development of a wide range of novel strategies that allow the selective isotope labeling of methyl groups in proteins have allowed the exploitation of the unique relaxation properties of this spin-system. This has in turn enabled the extension of NMR approaches to high molecular weight proteins including a variety of enzymes and their complexes. Here, we recount our experiences in obtaining assignments of the methyl resonances for two representative members of a class of RNA-directed RNA polymerases (RdRps) encoded by bacteriophages of the Cystoviridae family. We demonstrate the utility of these methyl probes, limited in number for one case and more numerous for the other, to investigate the conformational dynamics of RdRps on the fast (ps-ns) and slow (μs-ms) timescales.
Collapse
|
33
|
Flügge F, Peters T. Complete assignment of Ala, Ile, Leu, Met and Val methyl groups of human blood group A and B glycosyltransferases using lanthanide-induced pseudocontact shifts and methyl-methyl NOESY. JOURNAL OF BIOMOLECULAR NMR 2018; 70:245-259. [PMID: 29700756 DOI: 10.1007/s10858-018-0183-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 04/21/2018] [Indexed: 05/05/2023]
Abstract
Human blood group A and B glycosyltransferases (GTA, GTB) are highly homologous glycosyltransferases. A number of high-resolution crystal structures is available showing that these enzymes convert from an open conformation into a catalytically active closed conformation upon substrate binding. However, the mechanism of glycosyltransfer is still under debate, and the precise nature as well as the time scales of conformational transitions are unknown. NMR offers a variety of experiments to shine more light on these unresolved questions. Therefore, in a first step we have assigned all methyl resonance signals in MILVA labeled samples of GTA and GTB, still a challenging task for 70 kDa homodimeric proteins. Assignments were obtained from methyl-methyl NOESY experiments, and from measurements of lanthanide-induced pseudocontact shifts (PCS) using high resolution crystal structures as templates. PCSs and chemical shift perturbations, induced by substrate analogue binding, suggest that the fully closed state is not adopted in the presence of lanthanide ions.
Collapse
Affiliation(s)
- Friedemann Flügge
- Institute for Chemistry and Metabolomics, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Thomas Peters
- Institute for Chemistry and Metabolomics, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany.
| |
Collapse
|
34
|
Structural basis for the ethanol action on G-protein-activated inwardly rectifying potassium channel 1 revealed by NMR spectroscopy. Proc Natl Acad Sci U S A 2018; 115:3858-3863. [PMID: 29581303 DOI: 10.1073/pnas.1722257115] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Ethanol consumption leads to a wide range of pharmacological effects by acting on the signaling proteins in the human nervous system, such as ion channels. Despite its familiarity and biological importance, very little is known about the molecular mechanisms underlying the ethanol action, due to extremely weak binding affinity and the dynamic nature of the ethanol interaction. In this research, we focused on the primary in vivo target of ethanol, G-protein-activated inwardly rectifying potassium channel (GIRK), which is responsible for the ethanol-induced analgesia. By utilizing solution NMR spectroscopy, we characterized the changes in the structure and dynamics of GIRK induced by ethanol binding. We demonstrated here that ethanol binds to GIRK with an apparent dissociation constant of 1.0 M and that the actual physiological binding site of ethanol is located on the cavity formed between the neighboring cytoplasmic regions of the GIRK tetramer. From the methyl-based NMR relaxation analyses, we revealed that ethanol activates GIRK by shifting the conformational equilibrium processes, which are responsible for the gating of GIRK, to stabilize an open conformation of the cytoplasmic ion gate. We suggest that the dynamic molecular mechanism of the ethanol-induced activation of GIRK represents a general model of the ethanol action on signaling proteins in the human nervous system.
Collapse
|
35
|
Mochizuki A, Saso A, Zhao Q, Kubo S, Nishida N, Shimada I. Balanced Regulation of Redox Status of Intracellular Thioredoxin Revealed by in-Cell NMR. J Am Chem Soc 2018; 140:3784-3790. [PMID: 29509009 DOI: 10.1021/jacs.8b00426] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
To understand how intracellular proteins respond to oxidative stresses, the redox status of the target protein, as well as the intracellular redox potential ( EGSH), which is defined by the concentrations of reduced and oxidized glutathione, should be observed simultaneously within living cells. In this study, we developed a method that can monitor the redox status of thioredoxin (Trx) and EGSH by direct NMR observation of Trx and glutathione within living cells. Unlike the midpoint potential of Trx measured in vitro (∼ -300 mV), the intracellular Trx exhibited the redox transition at EGSH between -250 and -200 mV, the range known to trigger the oxidative stress-mediated signalings. Furthermore, we quantified the contribution of Trx reductase to the redox status of Trx, demonstrating that the redox profile of Trx is determined by the interplay between the elevation of EGSH and the reduction by Trx reductase and other endogenous molecules.
Collapse
Affiliation(s)
- Ayano Mochizuki
- Graduate School of Pharmaceutical Sciences , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-0033 , Japan
| | - Arata Saso
- Graduate School of Pharmaceutical Sciences , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-0033 , Japan
| | - Qingci Zhao
- Graduate School of Pharmaceutical Sciences , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-0033 , Japan
| | - Satoshi Kubo
- Graduate School of Pharmaceutical Sciences , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-0033 , Japan
| | - Noritaka Nishida
- Graduate School of Pharmaceutical Sciences , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-0033 , Japan
| | - Ichio Shimada
- Graduate School of Pharmaceutical Sciences , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-0033 , Japan
| |
Collapse
|
36
|
Sugiki T, Furuita K, Fujiwara T, Kojima C. Current NMR Techniques for Structure-Based Drug Discovery. Molecules 2018; 23:molecules23010148. [PMID: 29329228 PMCID: PMC6017608 DOI: 10.3390/molecules23010148] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 12/28/2017] [Accepted: 01/09/2018] [Indexed: 12/22/2022] Open
Abstract
A variety of nuclear magnetic resonance (NMR) applications have been developed for structure-based drug discovery (SBDD). NMR provides many advantages over other methods, such as the ability to directly observe chemical compounds and target biomolecules, and to be used for ligand-based and protein-based approaches. NMR can also provide important information about the interactions in a protein-ligand complex, such as structure, dynamics, and affinity, even when the interaction is too weak to be detected by ELISA or fluorescence resonance energy transfer (FRET)-based high-throughput screening (HTS) or to be crystalized. In this study, we reviewed current NMR techniques. We focused on recent progress in NMR measurement and sample preparation techniques that have expanded the potential of NMR-based SBDD, such as fluorine NMR (19F-NMR) screening, structure modeling of weak complexes, and site-specific isotope labeling of challenging targets.
Collapse
Affiliation(s)
- Toshihiko Sugiki
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan.
| | - Kyoko Furuita
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan.
| | | | - Chojiro Kojima
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan.
- Graduate School of Engineering, Yokohama National University, Yokohama 240-8501, Japan.
| |
Collapse
|
37
|
Assembly of phospholipid nanodiscs of controlled size for structural studies of membrane proteins by NMR. Nat Protoc 2017; 13:79-98. [PMID: 29215632 DOI: 10.1038/nprot.2017.094] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Suitable membrane mimetics are crucial to the performance of structural and functional studies of membrane proteins. Phospholipid nanodiscs (formed when a membrane scaffold protein encircles a small portion of a lipid bilayer) have native-like membrane properties. These have been used for a variety of functional studies, but structural studies by high-resolution solution-state NMR spectroscopy of membrane proteins in commonly used nanodiscs of 10-nm diameter were limited by the high molecular weight of these particles, which caused unfavorably large NMR line widths. We have recently constructed truncated versions of the membrane scaffold protein, allowing the preparation of a range of stepwise-smaller nanodiscs (6- to 8-nm diameter) to overcome this limitation. Here, we present a protocol on the assembly of phospholipid nanodiscs of various sizes for structural studies of membrane proteins with solution-state NMR spectroscopy. We describe specific isotope-labeling schemes required for working with large membrane protein systems in nanodiscs, and provide guidelines on the setup of NMR non-uniform sampling (NUS) data acquisition and high-resolution NMR spectra reconstruction. We discuss critical points and pitfalls relating to optimization of nanodiscs for NMR spectroscopy and outline a strategy for the high-resolution structure determination and positioning of isotope-labeled membrane proteins in nanodiscs using nuclear Overhauser enhancement spectroscopy (NOESY) spectroscopy, residual dipolar couplings (RDCs) and paramagnetic relaxation enhancements (PREs). Depending on the target protein of interest, nanodisc assembly and purification can be achieved within 12-24 h. Although the focus of this protocol is on protein NMR, these nanodiscs can also be used for (cryo-) electron microscopy (EM) and small-angle X-ray and neutron-scattering studies.
Collapse
|
38
|
Monneau YR, Rossi P, Bhaumik A, Huang C, Jiang Y, Saleh T, Xie T, Xing Q, Kalodimos CG. Automatic methyl assignment in large proteins by the MAGIC algorithm. JOURNAL OF BIOMOLECULAR NMR 2017; 69:215-227. [PMID: 29098507 PMCID: PMC5764113 DOI: 10.1007/s10858-017-0149-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 10/23/2017] [Indexed: 05/03/2023]
Abstract
Selective methyl labeling is an extremely powerful approach to study the structure, dynamics and function of biomolecules by NMR. Despite spectacular progress in the field, such studies remain rather limited in number. One of the main obstacles remains the assignment of the methyl resonances, which is labor intensive and error prone. Typically, NOESY crosspeak patterns are manually correlated to the available crystal structure or an in silico template model of the protein. Here, we propose methyl assignment by graphing inference construct, an exhaustive search algorithm with no peak network definition requirement. In order to overcome the combinatorial problem, the exhaustive search is performed locally, i.e. for a small number of methyls connected through-space according to experimental 3D methyl NOESY data. The local network approach drastically reduces the search space. Only the best local assignments are combined to provide the final output. Assignments that match the data with comparable scores are made available to the user for cross-validation by additional experiments such as methyl-amide NOEs. Several NMR datasets for proteins in the 25-50 kDa range were used during development and for performance evaluation against the manually assigned data. We show that the algorithm is robust, reliable and greatly speeds up the methyl assignment task.
Collapse
Affiliation(s)
- Yoan R Monneau
- Université Grenoble Alpes, CEA, CNRS, IBS, 38000, Grenoble, France
| | - Paolo Rossi
- Deparment of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
| | - Anusarka Bhaumik
- Deparment of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Chengdong Huang
- Deparment of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Yajun Jiang
- Deparment of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Tamjeed Saleh
- Deparment of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Tao Xie
- Deparment of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Qiong Xing
- Deparment of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Charalampos G Kalodimos
- Deparment of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
| |
Collapse
|
39
|
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] [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
| |
Collapse
|
40
|
Laguri C, Sperandeo P, Pounot K, Ayala I, Silipo A, Bougault CM, Molinaro A, Polissi A, Simorre JP. Interaction of lipopolysaccharides at intermolecular sites of the periplasmic Lpt transport assembly. Sci Rep 2017; 7:9715. [PMID: 28852068 PMCID: PMC5575297 DOI: 10.1038/s41598-017-10136-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 08/02/2017] [Indexed: 01/14/2023] Open
Abstract
Transport of lipopolysaccharides (LPS) to the surface of the outer membrane is essential for viability of Gram-negative bacteria. Periplasmic LptC and LptA proteins of the LPS transport system (Lpt) are responsible for LPS transfer between the Lpt inner and outer membrane complexes. Here, using a monomeric E. coli LptA mutant, we first show in vivo that a stable LptA oligomeric form is not strictly essential for bacteria. The LptC-LptA complex was characterized by a combination of SAXS and NMR methods and a low resolution model of the complex was determined. We were then able to observe interaction of LPS with LptC, the monomeric LptA mutant as well as with the LptC-LptA complex. A LptC-LPS complex was built based on NMR data in which the lipid moiety of the LPS is buried at the interface of the two β-jellyrolls of the LptC dimer. The selectivity of LPS for this intermolecular surface and the observation of such cavities at homo- or heteromolecular interfaces in LptC and LptA suggests that intermolecular sites are essential for binding LPS during its transport.
Collapse
Affiliation(s)
- Cedric Laguri
- Université Grenoble Alpes, Institut de Biologie Structurale, 71 avenue des Martyrs - CS10090, 38044, Grenoble cedex 9, France. .,CEA, DSV, Institut de Biologie Structurale, 71 avenue des Martyrs - CS10090, 38044, Grenoble cedex 9, France. .,CNRS, Institut de Biologie Structurale, 71 avenue des Martyrs - CS10090, 38044, Grenoble cedex 9, France.
| | - Paola Sperandeo
- University of Milano, Department of Pharmacological and Biomolecular Sciences, Via Balzaretti 9, Milano, Italy
| | - Kevin Pounot
- Université Grenoble Alpes, Institut de Biologie Structurale, 71 avenue des Martyrs - CS10090, 38044, Grenoble cedex 9, France.,CEA, DSV, Institut de Biologie Structurale, 71 avenue des Martyrs - CS10090, 38044, Grenoble cedex 9, France.,CNRS, Institut de Biologie Structurale, 71 avenue des Martyrs - CS10090, 38044, Grenoble cedex 9, France
| | - Isabel Ayala
- Université Grenoble Alpes, Institut de Biologie Structurale, 71 avenue des Martyrs - CS10090, 38044, Grenoble cedex 9, France.,CEA, DSV, Institut de Biologie Structurale, 71 avenue des Martyrs - CS10090, 38044, Grenoble cedex 9, France.,CNRS, Institut de Biologie Structurale, 71 avenue des Martyrs - CS10090, 38044, Grenoble cedex 9, France
| | - Alba Silipo
- University of Naples Federico II, Department of Chemical Sciences, via cinthia 4, Napoli, Italy
| | - Catherine M Bougault
- Université Grenoble Alpes, Institut de Biologie Structurale, 71 avenue des Martyrs - CS10090, 38044, Grenoble cedex 9, France.,CEA, DSV, Institut de Biologie Structurale, 71 avenue des Martyrs - CS10090, 38044, Grenoble cedex 9, France.,CNRS, Institut de Biologie Structurale, 71 avenue des Martyrs - CS10090, 38044, Grenoble cedex 9, France
| | - Antonio Molinaro
- University of Naples Federico II, Department of Chemical Sciences, via cinthia 4, Napoli, Italy
| | - Alessandra Polissi
- University of Milano, Department of Pharmacological and Biomolecular Sciences, Via Balzaretti 9, Milano, Italy.
| | - Jean-Pierre Simorre
- Université Grenoble Alpes, Institut de Biologie Structurale, 71 avenue des Martyrs - CS10090, 38044, Grenoble cedex 9, France.,CEA, DSV, Institut de Biologie Structurale, 71 avenue des Martyrs - CS10090, 38044, Grenoble cedex 9, France.,CNRS, Institut de Biologie Structurale, 71 avenue des Martyrs - CS10090, 38044, Grenoble cedex 9, France
| |
Collapse
|
41
|
Ikeya T, Ban D, Lee D, Ito Y, Kato K, Griesinger C. Solution NMR views of dynamical ordering of biomacromolecules. Biochim Biophys Acta Gen Subj 2017; 1862:287-306. [PMID: 28847507 DOI: 10.1016/j.bbagen.2017.08.020] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/22/2017] [Accepted: 08/24/2017] [Indexed: 01/01/2023]
Abstract
BACKGROUND To understand the mechanisms related to the 'dynamical ordering' of macromolecules and biological systems, it is crucial to monitor, in detail, molecular interactions and their dynamics across multiple timescales. Solution nuclear magnetic resonance (NMR) spectroscopy is an ideal tool that can investigate biophysical events at the atomic level, in near-physiological buffer solutions, or even inside cells. SCOPE OF REVIEW In the past several decades, progress in solution NMR has significantly contributed to the elucidation of three-dimensional structures, the understanding of conformational motions, and the underlying thermodynamic and kinetic properties of biomacromolecules. This review discusses recent methodological development of NMR, their applications and some of the remaining challenges. MAJOR CONCLUSIONS Although a major drawback of NMR is its difficulty in studying the dynamical ordering of larger biomolecular systems, current technologies have achieved considerable success in the structural analysis of substantially large proteins and biomolecular complexes over 1MDa and have characterised a wide range of timescales across which biomolecular motion exists. While NMR is well suited to obtain local structure information in detail, it contributes valuable and unique information within hybrid approaches that combine complementary methodologies, including solution scattering and microscopic techniques. GENERAL SIGNIFICANCE For living systems, the dynamic assembly and disassembly of macromolecular complexes is of utmost importance for cellular homeostasis and, if dysregulated, implied in human disease. It is thus instructive for the advancement of the study of the dynamical ordering to discuss the potential possibilities of solution NMR spectroscopy and its applications. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato.
Collapse
Affiliation(s)
- Teppei Ikeya
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, Tokyo 192-0373, Japan; CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.
| | - David Ban
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - Donghan Lee
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - Yutaka Ito
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, Tokyo 192-0373, Japan; CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Koichi Kato
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan; Graduate School of Pharmaceutical Sciences, Nagoya City University, Tanabe-dori 3-1, Mizuho-ku, Nagoya 467-8603, Japan
| | - Christian Griesinger
- Department of Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany.
| |
Collapse
|
42
|
Pederson K, Chalmers GR, Gao Q, Elnatan D, Ramelot TA, Ma LC, Montelione GT, Kennedy MA, Agard DA, Prestegard JH. NMR characterization of HtpG, the E. coli Hsp90, using sparse labeling with 13C-methyl alanine. JOURNAL OF BIOMOLECULAR NMR 2017; 68:225-236. [PMID: 28653216 PMCID: PMC5546222 DOI: 10.1007/s10858-017-0123-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 06/22/2017] [Indexed: 05/03/2023]
Abstract
A strategy for acquiring structural information from sparsely isotopically labeled large proteins is illustrated with an application to the E. coli heat-shock protein, HtpG (high temperature protein G), a 145 kDa dimer. It uses 13C-alanine methyl labeling in a perdeuterated background to take advantage of the sensitivity and resolution of Methyl-TROSY spectra, as well as the backbone-centered structural information from 1H-13C residual dipolar couplings (RDCs) of alanine methyl groups. In all, 40 of the 47 expected crosspeaks were resolved and 36 gave RDC data. Assignments of crosspeaks were partially achieved by transferring assignments from those made on individual domains using triple resonance methods. However, these were incomplete and in many cases the transfer was ambiguous. A genetic algorithm search for consistency between predictions based on domain structures and measurements for chemical shifts and RDCs allowed 60% of the 40 resolved crosspeaks to be assigned with confidence. Chemical shift changes of these crosspeaks on adding an ATP analog to the apo-protein are shown to be consistent with structural changes expected on comparing previous crystal structures for apo- and complex- structures. RDCs collected on the assigned alanine methyl peaks are used to generate a new solution model for the apo-protein structure.
Collapse
Affiliation(s)
- Kari Pederson
- Complex Carbohydrate Research Center, University of Georgia, Athens, USA
| | - Gordon R Chalmers
- Complex Carbohydrate Research Center, University of Georgia, Athens, USA
- Department of Computer Science, University of Georgia, Athens, USA
| | - Qi Gao
- Complex Carbohydrate Research Center, University of Georgia, Athens, USA
| | - Daniel Elnatan
- Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California, San Francisco, USA
| | - Theresa A Ramelot
- Department of Chemistry and Biochemistry, Miami University, Oxford, USA
| | - Li-Chung Ma
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, The State University of New Jersey, Piscataway, USA
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, USA
| | - Gaetano T Montelione
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, The State University of New Jersey, Piscataway, USA
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, USA
| | - Michael A Kennedy
- Department of Chemistry and Biochemistry, Miami University, Oxford, USA
| | - David A Agard
- Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California, San Francisco, USA
| | - James H Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, USA.
| |
Collapse
|
43
|
Pilla KB, Gaalswyk K, MacCallum JL. Molecular modeling of biomolecules by paramagnetic NMR and computational hybrid methods. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017. [PMID: 28648524 DOI: 10.1016/j.bbapap.2017.06.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The 3D atomic structures of biomolecules and their complexes are key to our understanding of biomolecular function, recognition, and mechanism. However, it is often difficult to obtain structures, particularly for systems that are complex, dynamic, disordered, or exist in environments like cell membranes. In such cases sparse data from a variety of paramagnetic NMR experiments offers one possible source of structural information. These restraints can be incorporated in computer modeling algorithms that can accurately translate the sparse experimental data into full 3D atomic structures. In this review, we discuss various types of paramagnetic NMR/computational hybrid modeling techniques that can be applied to successful modeling of not only the atomic structure of proteins but also their interacting partners. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.
Collapse
Affiliation(s)
| | - Kari Gaalswyk
- Department of Chemistry, University of Calgary, Calgary, AB, Canada
| | | |
Collapse
|
44
|
Macek P, Kerfah R, Boeri Erba E, Crublet E, Moriscot C, Schoehn G, Amero C, Boisbouvier J. Unraveling self-assembly pathways of the 468-kDa proteolytic machine TET2. SCIENCE ADVANCES 2017; 3:e1601601. [PMID: 28435872 PMCID: PMC5384809 DOI: 10.1126/sciadv.1601601] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 02/10/2017] [Indexed: 05/03/2023]
Abstract
The spontaneous formation of biological higher-order structures from smaller building blocks, called self-assembly, is a fundamental attribute of life. Although the protein self-assembly is a time-dependent process that occurs at the molecular level, its current understanding originates either from static structures of trapped intermediates or from modeling. Nuclear magnetic resonance (NMR) spectroscopy has the unique ability to monitor structural changes in real time; however, its size limitation and time-resolution constraints remain a challenge when studying the self-assembly of large biological particles. We report the application of methyl-specific isotopic labeling combined with relaxation-optimized NMR spectroscopy to overcome both size- and time-scale limitations. We report for the first time the self-assembly process of a half-megadalton protein complex that was monitored at the structural level, including the characterization of intermediate states, using a mutagenesis-free strategy. NMR was used to obtain individual kinetics data on the different transient intermediates and the formation of final native particle. In addition, complementary time-resolved electron microscopy and native mass spectrometry were used to characterize the low-resolution structures of oligomerization intermediates.
Collapse
Affiliation(s)
- Pavel Macek
- Université Grenoble Alpes, Institut de
Biologie Structurale (IBS), Grenoble, France
- CEA, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
| | - Rime Kerfah
- Université Grenoble Alpes, Institut de
Biologie Structurale (IBS), Grenoble, France
- CEA, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
| | - Elisabetta Boeri Erba
- Université Grenoble Alpes, Institut de
Biologie Structurale (IBS), Grenoble, France
- CEA, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
| | - Elodie Crublet
- Université Grenoble Alpes, Institut de
Biologie Structurale (IBS), Grenoble, France
- CEA, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
| | - Christine Moriscot
- Université Grenoble Alpes, Institut de
Biologie Structurale (IBS), Grenoble, France
- CEA, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
| | - Guy Schoehn
- Université Grenoble Alpes, Institut de
Biologie Structurale (IBS), Grenoble, France
- CEA, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
| | - Carlos Amero
- Centro de Investigaciones Químicas, IICBA,
Universidad Autónoma del Estado de Morelos, México
- Corresponding author. (C.A.);
(J.B.)
| | - Jerome Boisbouvier
- Université Grenoble Alpes, Institut de
Biologie Structurale (IBS), Grenoble, France
- CEA, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
- Corresponding author. (C.A.);
(J.B.)
| |
Collapse
|
45
|
Abstract
Methyl groups are very useful probes of structure, dynamics, and interactions in protein NMR spectroscopy. In particular, methyl-directed experiments provide high sensitivity even in very large proteins, such as membrane proteins in a membrane-mimicking environment. In this chapter, we discuss the approach for labeling methyl groups in E. coli-based protein expression, as exemplified with the mitochondrial carrier GGC.
Collapse
|
46
|
Mohanty B, Williams ML, Doak BC, Vazirani M, Ilyichova O, Wang G, Bermel W, Simpson JS, Chalmers DK, King GF, Mobli M, Scanlon MJ. Determination of ligand binding modes in weak protein-ligand complexes using sparse NMR data. JOURNAL OF BIOMOLECULAR NMR 2016; 66:195-208. [PMID: 27778134 DOI: 10.1007/s10858-016-0067-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 09/29/2016] [Indexed: 06/06/2023]
Abstract
We describe a general approach to determine the binding pose of small molecules in weakly bound protein-ligand complexes by deriving distance constraints between the ligand and methyl groups from all methyl-containing residues of the protein. We demonstrate that using a single sample, which can be prepared without the use of expensive precursors, it is possible to generate high-resolution data rapidly and obtain the resonance assignments of Ile, Leu, Val, Ala and Thr methyl groups using triple resonance scalar correlation data. The same sample may be used to obtain Met εCH3 assignments using NOESY-based methods, although the superior sensitivity of NOESY using [U-13C,15N]-labeled protein makes the use of this second sample more efficient. We describe a structural model for a weakly binding ligand bound to its target protein, DsbA, derived from intermolecular methyl-to-ligand nuclear Overhauser enhancements, and demonstrate that the ability to assign all methyl resonances in the spectrum is essential to derive an accurate model of the structure. Once the methyl assignments have been obtained, this approach provides a rapid means to generate structural models for weakly bound protein-ligand complexes. Such weak complexes are often found at the beginning of programs of fragment based drug design and can be challenging to characterize using X-ray crystallography.
Collapse
Affiliation(s)
- Biswaranjan Mohanty
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Martin L Williams
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Bradley C Doak
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Mansha Vazirani
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Olga Ilyichova
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Geqing Wang
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
- La Trobe Institute for Molecular Bioscience, La Trobe University, Bundoora, VIC, 3083, Australia
| | - Wolfgang Bermel
- Bruker Biospin GmbH, Silberstreifen, 76287, Rheinstetten, Germany
| | - Jamie S Simpson
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - David K Chalmers
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Glenn F King
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Mehdi Mobli
- Centre for Advanced Imaging, The University of Queensland, St Lucia, QLD, 4072, Australia.
| | - Martin J Scanlon
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia.
| |
Collapse
|
47
|
Zhang H, van Ingen H. Isotope-labeling strategies for solution NMR studies of macromolecular assemblies. Curr Opin Struct Biol 2016; 38:75-82. [PMID: 27295425 DOI: 10.1016/j.sbi.2016.05.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 05/20/2016] [Accepted: 05/22/2016] [Indexed: 12/21/2022]
Abstract
Proteins come together in macromolecular assemblies, recognizing and binding to each other through their structures, and operating on their substrates through their motions. Detailed characterization of these processes is particularly suited to NMR, a high-resolution technique sensitive to structure, dynamics, and interactions. Advances in isotope-labeling have enabled such studies to an ever-increasing range of systems. Here we highlight recent applications and bring to the fore the range of options to produce labeled proteins and to control the specific placement of isotopes. The increased labeling control and affordability, together with the possibility to combine strategies will further deepen and extend the range of protein assembly investigations.
Collapse
Affiliation(s)
- Heyi Zhang
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden, The Netherlands
| | - Hugo van Ingen
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden, The Netherlands.
| |
Collapse
|
48
|
Monneau YR, Ishida Y, Rossi P, Saio T, Tzeng SR, Inouye M, Kalodimos CG. Exploiting E. coli auxotrophs for leucine, valine, and threonine specific methyl labeling of large proteins for NMR applications. JOURNAL OF BIOMOLECULAR NMR 2016; 65:99-108. [PMID: 27255761 PMCID: PMC4936824 DOI: 10.1007/s10858-016-0041-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 05/25/2016] [Indexed: 05/03/2023]
Abstract
A simple and cost effective method to independently and stereo-specifically incorporate [(1)H,(13)C]-methyls in Leu and Val in proteins is presented. Recombinant proteins for NMR studies are produced using a tailored set of auxotrophic E. coli strains. NMR active isotopes are routed to either Leu or Val methyl groups from the commercially available and scrambling-free precursors α-ketoisovalerate and acetolactate. The engineered strains produce deuterated proteins with stereospecific [(1)H,(13)C]-methyl labeling separately at Leu or Val amino acids. This is the first method that achieves Leu-specific stereospecific [(1)H,(13)C]-methyl labeling of proteins and scramble-free Val-specific labeling. Use of auxotrophs drastically decreases the amount of labeled precursor required for expression without impacting the yield. The concept is extended to Thr methyl labeling by means of a Thr-specific auxotroph that provides enhanced efficiency for use with the costly L-[4-(13)C,2,3-(2)H2,(15)N]-Thr reagent. The Thr-specific strain allows for the production of Thr-[(13)CH3](γ2) labeled protein with an optimal isotope incorporation using up to 50 % less labeled Thr than the traditional E. coli strain without the need for (2)H-glycine to prevent scrambling.
Collapse
Affiliation(s)
- Yoan R Monneau
- Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, 08854, USA
| | - Yojiro Ishida
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, 08854, USA
| | - Paolo Rossi
- Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, 08854, USA
- Deparment of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Tomohide Saio
- Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, 08854, USA
| | - Shiou-Ru Tzeng
- Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, 08854, USA
| | - Masayori Inouye
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, 08854, USA.
| | - Charalampos G Kalodimos
- Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, 08854, USA.
- Deparment of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA.
| |
Collapse
|
49
|
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. JOURNAL OF BIOMOLECULAR 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] [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.
Collapse
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.
| |
Collapse
|
50
|
Namanja AT, Wang J, Buettner R, Colson L, Chen Y. Allosteric Communication across STAT3 Domains Associated with STAT3 Function and Disease-Causing Mutation. J Mol Biol 2016; 428:579-589. [PMID: 26774853 DOI: 10.1016/j.jmb.2016.01.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Revised: 01/03/2016] [Accepted: 01/06/2016] [Indexed: 01/10/2023]
Abstract
STAT3 is a member of STAT (signal transducer and activator of transcription) transcription activators. Aberration in STAT3 activity due to constitutive activation or mutations leads to diseases such as cancer and hyper-immunoglobulin E syndrome (HIES). STAT3 contains several structured domains including the Src homology 2 domain (SH2), linker domain (LD), DNA-binding domain (DBD) and the coiled-coil domain. Here we report the discovery of inter-domain allosteric communications in STAT3 from studies using nuclear magnetic resonance (NMR) and other methods. We found that pTyr-peptide interactions with SH2 cause structural and dynamics changes in LD and DBD. The inter-domain allosteric effect is likely mediated by the flexibility in the hydrophobic core. In addition, a mutation in LD found in HIES (I568F) induces NMR chemical shift perturbation in SH2, DBD and the coiled-coil domain, suggesting conformational changes in these domains. Consistent with conformational changes in SH2, the I568F mutant reduces SH2's binding affinity to a pTyr-containing peptide. This study provides an example of dynamics-dependent allosteric effects, and due to the structural conservation of the STAT family of proteins, the inter-domain allosteric communication observed in STAT3 likely occurs in other STATs.
Collapse
Affiliation(s)
- Andrew T Namanja
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Jianghai Wang
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Ralf Buettner
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Loren Colson
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Yuan Chen
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA.
| |
Collapse
|