1
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Miyanoiri Y, Takeda M, Okuma K, Terauchi T, Kainosho M. Enhancing solution structural analysis of large molecular proteins through optimal stereo array isotope labeling of aromatic amino acids. Biophys Chem 2024; 315:107328. [PMID: 39341158 DOI: 10.1016/j.bpc.2024.107328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2024] [Revised: 08/16/2024] [Accepted: 09/15/2024] [Indexed: 09/30/2024]
Abstract
The observation of side-chain peaks of aromatic amino acids is the prerequisite for a high-resolution three-dimensional structure determination of proteins by NMR. However, it becomes difficult with increasing molecular size due to an increased transverse relaxation and the control of the relaxation pathway is needed to achieve the observation. We demonstrated that even for the large molecular size of 82 kDa Malate synthase G (MSG), the aromatic 13C-1H (CH) peaks of Tryptophan (Trp) and Phenylalanine (Phe) residues can be observed with high quality using a systematic stable isotope labeling scheme, Stereo-Array Isotope Labeling (SAIL) method. However, the sequence specific assignments of these peaks relied on the use of amino acid substitutions, employing an inefficient method that required many isotopes labeled samples. In this study, we developed novel SAIL amino acids that allow for the observation of the aromatic ring δ,ζ and the aliphatic β position peak of Phe residues. The application of TROSY-based experiment to the isolated CH moieties resulted in the successful observation of discernible and resolved CH peaks in Phe residues in MSG. In MSG, the sequence-specific assignments of the backbone and Cβ positions have already been confirmed. Therefore, using this labeling method, the δ and β position peaks of Phe residues can be clearly assigned in a sequence-specific and stereospecific manner through experiments based on intra-residue NOE. Furthermore, the NOESY experiment also allows for the acquisition of information pertaining to the conformation of Phe residues, such as the χ1 dihedral angle, providing valuable insights for the determination of accurate protein structures and in dynamic analysis. This new SAIL amino acids open an avenue to achieve a variety of NMR analysis of large molecular proteins, including a high-resolution structure determination and dynamics and interaction analysis.
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Affiliation(s)
- Yohei Miyanoiri
- Research Center for Next-Generation Protein Sciences, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan; Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.
| | - Mitsuhiro Takeda
- Department of Molecular Biophysics, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Kosuke Okuma
- SAIL Technologies. Inc., 2008-2 Wada, Tama-city, Tokyo 206-0001, Japan
| | - Tsutomu Terauchi
- SAIL Technologies. Inc., 2008-2 Wada, Tama-city, Tokyo 206-0001, Japan
| | - Masatsune Kainosho
- Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minami-ohsawa, Hachioji, Tokyo 192-0397, Japan.
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2
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Van Raad D, Huber T, Otting G. Improved spectral resolution of [ 13C, 1H]-HSQC spectra of aromatic amino acid residues in proteins produced by cell-free synthesis from inexpensive 13C-labelled precursors. JOURNAL OF BIOMOLECULAR NMR 2023; 77:183-190. [PMID: 37338652 PMCID: PMC10406723 DOI: 10.1007/s10858-023-00420-9] [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: 03/08/2023] [Accepted: 05/23/2023] [Indexed: 06/21/2023]
Abstract
Cell-free protein synthesis using eCells allows production of amino acids from inexpensive 13C-labelled precursors. We show that the metabolic pathway converting pyruvate, glucose and erythrose into aromatic amino acids is maintained in eCells. Judicious choice of 13C-labelled starting material leads to proteins, where the sidechains of aromatic amino acids display [13C,1H]-HSQC cross-peaks free of one-bond 13C-13C couplings. Selective 13C-labelling of tyrosine and phenylalanine residues is achieved simply by using different compositions of the reaction buffers.
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Affiliation(s)
- Damian Van Raad
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Thomas Huber
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia.
| | - Gottfried Otting
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia.
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia.
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3
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Akke M, Weininger U. NMR Studies of Aromatic Ring Flips to Probe Conformational Fluctuations in Proteins. J Phys Chem B 2023; 127:591-599. [PMID: 36640108 PMCID: PMC9884080 DOI: 10.1021/acs.jpcb.2c07258] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 12/25/2022] [Indexed: 01/15/2023]
Abstract
Aromatic residues form a significant part of the protein core, where they make tight interactions with multiple surrounding side chains. Despite the dense packing of internal side chains, the aromatic rings of phenylalanine and tyrosine residues undergo 180° rotations, or flips, which are mediated by transient and large-scale "breathing" motions that generate sufficient void volume around the aromatic ring. Forty years after the seminal work by Wagner and Wüthrich, NMR studies of aromatic ring flips are now undergoing a renaissance as a powerful means of probing fundamental dynamic properties of proteins. Recent developments of improved NMR methods and isotope labeling schemes have enabled a number of advances in addressing the mechanisms and energetics of aromatic ring flips. The nature of the transition states associated with ring flips can be described by thermodynamic activation parameters, including the activation enthalpy, activation entropy, activation volume, and also the isothermal volume compressibility of activation. Consequently, it is of great interest to study how ring flip rate constants and activation parameters might vary with protein structure and external conditions like temperature and pressure. The field is beginning to gather such data for aromatic residues in a variety of environments, ranging from surface exposed to buried. In the future, the combination of solution and solid-state NMR spectroscopy together with molecular dynamics simulations and other computational approaches is likely to provide detailed information about the coupled dynamics of aromatic rings and neighboring residues. In this Perspective, we highlight recent developments and provide an outlook toward the future.
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Affiliation(s)
- Mikael Akke
- Division
of Biophysical Chemistry, Center for Molecular Protein Science, Department
of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Ulrich Weininger
- Institute
of Physics, Biophysics, Martin-Luther-University
Halle-Wittenberg, D-06129 Halle (Saale), Germany
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4
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Ahlawat S, Mopidevi SMV, Taware PP, Raran-Kurussi S, Mote KR, Agarwal V. Assignment of aromatic side-chain spins and characterization of their distance restraints at fast MAS. J Struct Biol X 2022; 7:100082. [PMID: 36618437 PMCID: PMC9817166 DOI: 10.1016/j.yjsbx.2022.100082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 11/18/2022] [Accepted: 12/27/2022] [Indexed: 12/30/2022] Open
Abstract
The assignment of aromatic side-chain spins has always been more challenging than assigning backbone and aliphatic spins. Selective labeling combined with mutagenesis has been the approach for assigning aromatic spins. This manuscript reports a method for assigning aromatic spins in a fully protonated protein by connecting them to the backbone atoms using a low-power TOBSY sequence. The pulse sequence employs residual polarization and sequential acquisitions techniques to record HN- and HC-detected spectra in a single experiment. The unambiguous assignment of aromatic spins also enables the characterization of 1H-1H distance restraints involving aromatic spins. Broadband (RFDR) and selective (BASS-SD) recoupling sequences were used to generate HN-ΗC, HC-HN and HC-HC restraints involving the side-chain proton spins of aromatic residues. This approach has been demonstrated on a fully protonated U-[13C,15N] labeled GB1 sample at 95-100 kHz MAS.
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Affiliation(s)
- Sahil Ahlawat
- Tata Institute of Fundamental Research Hyderabad, Sy. No. 36/P, Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad 500 046, India
| | - Subbarao Mohana Venkata Mopidevi
- Tata Institute of Fundamental Research Hyderabad, Sy. No. 36/P, Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad 500 046, India
| | - Pravin P. Taware
- Tata Institute of Fundamental Research Hyderabad, Sy. No. 36/P, Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad 500 046, India
| | - Sreejith Raran-Kurussi
- Tata Institute of Fundamental Research Hyderabad, Sy. No. 36/P, Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad 500 046, India
| | - Kaustubh R. Mote
- Tata Institute of Fundamental Research Hyderabad, Sy. No. 36/P, Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad 500 046, India
| | - Vipin Agarwal
- Tata Institute of Fundamental Research Hyderabad, Sy. No. 36/P, Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad 500 046, India
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5
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Dreydoppel M, Akke M, Weininger U. Characterizing Fast Conformational Exchange of Aromatic Rings Using Residual Dipolar Couplings: Distinguishing Jumplike Flips from Other Exchange Mechanisms. J Phys Chem B 2022; 126:7950-7956. [PMID: 36180044 PMCID: PMC9574926 DOI: 10.1021/acs.jpcb.2c05097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Aromatic ring flips are a hallmark of protein dynamics.
They are
experimentally studied by NMR spectroscopy, where recent advances
have led to improved characterization across a wide range of time
scales. Results on different proteins have been interpreted as continuous
diffusive ring rotations or jumplike flips, leading to diverging views
of the protein interior as being fluidlike or solidlike, respectively.
It is challenging to distinguish between these mechanisms and other
types of conformational exchange because chemical-shift-mediated line
broadening provides only conclusive evidence for ring flips only if
the system can be moved from the slow- to intermediate/fast-exchange
regime. Moreover, whenever the chemical shift difference between the
two symmetry-related sites is close to zero, it is not generally possible
to determine the exchange time scale. Here we resolve these issues
by measuring residual dipolar coupling (RDC)-mediated exchange contributions
using NMR relaxation dispersion experiments on proteins dissolved
in dilute liquid crystalline media. Excellent agreement is found between
the experimental difference in RDC between the two symmetry-related
sites and the value calculated from high-resolution X-ray structures,
demonstrating that dynamics measured for F52 in the B1 domain of protein
G reports on distinct, jumplike flips rather than other types of conformational
exchange.
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Affiliation(s)
- Matthias Dreydoppel
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, D-06120Halle (Saale), Germany
| | - Mikael Akke
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, P.O. Box 124, SE-22100Lund, Sweden
| | - Ulrich Weininger
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, D-06120Halle (Saale), Germany
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6
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Toyama Y, Rangadurai AK, Kay LE. Measurement of 1H α transverse relaxation rates in proteins: application to solvent PREs. JOURNAL OF BIOMOLECULAR NMR 2022; 76:137-152. [PMID: 36018482 DOI: 10.1007/s10858-022-00401-4] [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: 06/06/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
It has recently been demonstrated that accurate near surface electrostatic potentials can be calculated for proteins from solvent paramagnetic relaxation enhancements (PREs) of amide protons measured using spin labels of similar structures but different charges (Yu et al. in Proc Natl Acad Sci 118(25):e2104020118, 2021). Here we develop methodology for extending such measurements to intrinsically disordered proteins at neutral pH where amide spectra are of very poor quality. Under these conditions it is shown that accurate PRE values can be measured using the haCONHA experiment that has been modified for recording 1Hα transverse relaxation rates. The optimal pulse scheme includes a spin-lock relaxation element for suppression of homonuclear scalar coupled evolution for all 1Hα protons, except those derived from Ser and Thr residues, and minimizes the radiation damping field from water magnetization that would otherwise increase measured relaxation rates. The robustness of the experiment is verified by developing a second approach using a band selective adiabatic decoupling scheme for suppression of scalar coupling modulations during 1Hα relaxation and showing that the measured PRE values from the two methods are in excellent agreement. The near surface electrostatic potential of a 103-residue construct comprising the C-terminal intrinsically disordered region of the RNA-binding protein CAPRIN1 is obtained at pH 5.5 using both 1HN and 1Hα-based relaxation rates, and at pH 7.4 where only 1Hα rates can be quantified, with very good agreement between potentials obtained under all experimental conditions.
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Affiliation(s)
- Yuki Toyama
- Department of Molecular Genetics, University of Toronto, Toronto, M5S 1A8, Canada.
- Department of Chemistry, University of Toronto, Toronto, ON, M5S 3H6, Canada.
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.
| | - Atul Kaushik Rangadurai
- Department of Molecular Genetics, University of Toronto, Toronto, M5S 1A8, Canada
- Department of Chemistry, University of Toronto, Toronto, ON, M5S 3H6, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Program in Molecular Medicine, Hospital for Sick Children Research Institute, Toronto, ON, M5G 0A4, Canada
| | - Lewis E Kay
- Department of Molecular Genetics, University of Toronto, Toronto, M5S 1A8, Canada.
- Department of Chemistry, University of Toronto, Toronto, ON, M5S 3H6, Canada.
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.
- Program in Molecular Medicine, Hospital for Sick Children Research Institute, Toronto, ON, M5G 0A4, Canada.
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7
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Abstract
In the last two decades, solid-state nuclear magnetic resonance (ssNMR) spectroscopy has transformed from a spectroscopic technique investigating small molecules and industrial polymers to a potent tool decrypting structure and underlying dynamics of complex biological systems, such as membrane proteins, fibrils, and assemblies, in near-physiological environments and temperatures. This transformation can be ascribed to improvements in hardware design, sample preparation, pulsed methods, isotope labeling strategies, resolution, and sensitivity. The fundamental engagement between nuclear spins and radio-frequency pulses in the presence of a strong static magnetic field is identical between solution and ssNMR, but the experimental procedures vastly differ because of the absence of molecular tumbling in solids. This review discusses routinely employed state-of-the-art static and MAS pulsed NMR methods relevant for biological samples with rotational correlation times exceeding 100's of nanoseconds. Recent developments in signal filtering approaches, proton methodologies, and multiple acquisition techniques to boost sensitivity and speed up data acquisition at fast MAS are also discussed. Several examples of protein structures (globular, membrane, fibrils, and assemblies) solved with ssNMR spectroscopy have been considered. We also discuss integrated approaches to structurally characterize challenging biological systems and some newly emanating subdisciplines in ssNMR spectroscopy.
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Affiliation(s)
- Sahil Ahlawat
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Kaustubh R Mote
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Nils-Alexander Lakomek
- University of Düsseldorf, Institute for Physical Biology, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Vipin Agarwal
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
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8
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The native state conformational heterogeneity in the energy landscape of protein folding. Biophys Chem 2022; 283:106761. [DOI: 10.1016/j.bpc.2022.106761] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/10/2022] [Accepted: 01/14/2022] [Indexed: 11/18/2022]
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9
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Dreydoppel M, Lichtenecker RJ, Akke M, Weininger U. 1H R 1ρ relaxation dispersion experiments in aromatic side chains. JOURNAL OF BIOMOLECULAR NMR 2021; 75:383-392. [PMID: 34510298 PMCID: PMC8642340 DOI: 10.1007/s10858-021-00382-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/03/2021] [Indexed: 06/13/2023]
Abstract
Aromatic side chains are attractive probes of protein dynamic, since they are often key residues in enzyme active sites and protein binding sites. Dynamic processes on microsecond to millisecond timescales can be studied by relaxation dispersion experiments that attenuate conformational exchange contributions to the transverse relaxation rate by varying the refocusing frequency of applied radio-frequency fields implemented as either CPMG pulse trains or continuous spin-lock periods. Here we present an aromatic 1H R1ρ relaxation dispersion experiment enabling studies of two to three times faster exchange processes than achievable by existing experiments for aromatic side chains. We show that site-specific isotope labeling schemes generating isolated 1H-13C spin pairs with vicinal 2H-12C moieties are necessary to avoid anomalous relaxation dispersion profiles caused by Hartmann-Hahn matching due to the 3JHH couplings and limited chemical shift differences among 1H spins in phenylalanine, tyrosine and the six-ring moiety of tryptophan. This labeling pattern is sufficient in that remote protons do not cause additional complications. We validated the approach by measuring ring-flip kinetics in the small protein GB1. The determined rate constants, kflip, agree well with previous results from 13C R1ρ relaxation dispersion experiments, and yield 1H chemical shift differences between the two sides of the ring in good agreement with values measured under slow-exchange conditions. The aromatic1H R1ρ relaxation dispersion experiment in combination with the site-selective 1H-13C/2H-12C labeling scheme enable measurement of exchange rates up to kex = 2kflip = 80,000 s-1, and serve as a useful complement to previously developed 13C-based methods.
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Affiliation(s)
- Matthias Dreydoppel
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | | | - Mikael Akke
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, P.O. Box 124, 22100, Lund, Sweden
| | - Ulrich Weininger
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany.
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10
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Horx P, Geyer A. High five! Methyl probes at five ring positions of phenylalanine explore the hydrophobic core dynamics of zinc finger miniproteins. Chem Sci 2021; 12:11455-11463. [PMID: 34667551 PMCID: PMC8447250 DOI: 10.1039/d1sc02346b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/22/2021] [Indexed: 12/02/2022] Open
Abstract
The elucidation of internal dynamics in proteins is essential for the understanding of their stability and functionality. Breaking the symmetry of the degenerate rotation of the phenyl side chain provides additional structural information and allows a detailed description of the dynamics. Based on this concept, we propose a combination of synthetic and computational methods, to study the rotational mobility of the Phe ring in a sensitive zinc finger motif. The systematic methyl hopping around the phenylalanine ring yields o-, m-, p-tolyl and xylyl side chains that provide a vast array of additional NOE contacts, allowing the precise determination of the orientation of the aromatic ring. MD simulations and metadynamics complement these findings and facilitate the generation of free energy profiles for each derivative. Previous studies used a wide temperature window in combination with NMR spectroscopy to elucidate the side chain mobility of stable proteins. The zinc finger moiety exhibits a limited thermodynamic stability in a temperature range of only 40 K, making this approach impractical for this compound class. Therefore, we have developed a method that can be applied even to thermolabile systems and facilitates the detailed investigation of protein dynamics.
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Affiliation(s)
- Philip Horx
- Philipps-University Marburg 35043 Marburg Germany
| | - Armin Geyer
- Philipps-University Marburg 35043 Marburg Germany
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11
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Dreydoppel M, Dorn B, Modig K, Akke M, Weininger U. Transition-State Compressibility and Activation Volume of Transient Protein Conformational Fluctuations. JACS AU 2021; 1:833-842. [PMID: 34467336 PMCID: PMC8395657 DOI: 10.1021/jacsau.1c00062] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Indexed: 06/13/2023]
Abstract
Proteins are dynamic entities that intermittently depart from their ground-state structures and undergo conformational transitions as a critical part of their functions. Central to understanding such transitions are the structural rearrangements along the connecting pathway, where the transition state plays a special role. Using NMR relaxation at variable temperature and pressure to measure aromatic ring flips inside a protein core, we obtain information on the structure and thermodynamics of the transition state. We show that the isothermal compressibility coefficient of the transition state is similar to that of short-chain hydrocarbon liquids, implying extensive local unfolding of the protein. Our results further indicate that the required local volume expansions of the protein can occur not only with a net positive activation volume of the protein, as expected from previous studies, but also with zero activation volume by compaction of remote void volume, when averaged over the ensemble of states.
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Affiliation(s)
- Matthias Dreydoppel
- Institute
of Physics, Biophysics, Martin-Luther-University
Halle-Wittenberg, D-06120 Halle (Saale), Germany
| | - Britta Dorn
- Institute
of Physics, Biophysics, Martin-Luther-University
Halle-Wittenberg, D-06120 Halle (Saale), Germany
| | - Kristofer Modig
- Division
of Biophysical Chemistry, Center for Molecular Protein Science, Department
of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Mikael Akke
- Division
of Biophysical Chemistry, Center for Molecular Protein Science, Department
of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Ulrich Weininger
- Institute
of Physics, Biophysics, Martin-Luther-University
Halle-Wittenberg, D-06120 Halle (Saale), Germany
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12
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Pazicky S, Dhamotharan K, Kaszuba K, Mertens HDT, Gilberger T, Svergun D, Kosinski J, Weininger U, Löw C. Structural role of essential light chains in the apicomplexan glideosome. Commun Biol 2020; 3:568. [PMID: 33051581 PMCID: PMC7555893 DOI: 10.1038/s42003-020-01283-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 09/11/2020] [Indexed: 01/18/2023] Open
Abstract
Gliding, a type of motility based on an actin-myosin motor, is specific to apicomplexan parasites. Myosin A binds two light chains which further interact with glideosome associated proteins and assemble into the glideosome. The role of individual glideosome proteins is unclear due to the lack of structures of larger glideosome assemblies. Here, we investigate the role of essential light chains (ELCs) in Toxoplasma gondii and Plasmodium falciparum and present their crystal structures as part of trimeric sub-complexes. We show that although ELCs bind a conserved MyoA sequence, P. falciparum ELC adopts a distinct structure in the free and MyoA-bound state. We suggest that ELCs enhance MyoA performance by inducing secondary structure in MyoA and thus stiffen its lever arm. Structural and biophysical analysis reveals that calcium binding has no influence on the structure of ELCs. Our work represents a further step towards understanding the mechanism of gliding in Apicomplexa.
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Affiliation(s)
- Samuel Pazicky
- Centre for Structural Systems Biology (CSSB), Notkestrasse 85, D-22607, Hamburg, Germany
- Molecular Biology Laboratory (EMBL), Hamburg Unit c/o Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, D-22607, Hamburg, Germany
| | - Karthikeyan Dhamotharan
- Centre for Structural Systems Biology (CSSB), Notkestrasse 85, D-22607, Hamburg, Germany
- Molecular Biology Laboratory (EMBL), Hamburg Unit c/o Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, D-22607, Hamburg, Germany
| | - Karol Kaszuba
- Centre for Structural Systems Biology (CSSB), Notkestrasse 85, D-22607, Hamburg, Germany
- Molecular Biology Laboratory (EMBL), Hamburg Unit c/o Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, D-22607, Hamburg, Germany
| | - Haydyn D T Mertens
- Molecular Biology Laboratory (EMBL), Hamburg Unit c/o Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, D-22607, Hamburg, Germany
| | - Tim Gilberger
- Centre for Structural Systems Biology (CSSB), Notkestrasse 85, D-22607, Hamburg, Germany
- Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-Strasse 74, D-20359, Hamburg, Germany
- Department of Biology, University of Hamburg, Hamburg, Germany
| | - Dmitri Svergun
- Molecular Biology Laboratory (EMBL), Hamburg Unit c/o Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, D-22607, Hamburg, Germany
| | - Jan Kosinski
- Centre for Structural Systems Biology (CSSB), Notkestrasse 85, D-22607, Hamburg, Germany
- Molecular Biology Laboratory (EMBL), Hamburg Unit c/o Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, D-22607, Hamburg, Germany
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Ulrich Weininger
- Martin-Luther-University Halle-Wittenberg, Institute of Physics, Biophysics, D-06120, Halle (Saale), Germany
| | - Christian Löw
- Centre for Structural Systems Biology (CSSB), Notkestrasse 85, D-22607, Hamburg, Germany.
- Molecular Biology Laboratory (EMBL), Hamburg Unit c/o Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, D-22607, Hamburg, Germany.
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13
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Dreydoppel M, Raum HN, Weininger U. Slow ring flips in aromatic cluster of GB1 studied by aromatic 13C relaxation dispersion methods. JOURNAL OF BIOMOLECULAR NMR 2020; 74:183-191. [PMID: 32016706 PMCID: PMC7080667 DOI: 10.1007/s10858-020-00303-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 01/27/2020] [Indexed: 06/10/2023]
Abstract
Ring flips of phenylalanine and tyrosine are a hallmark of protein dynamics. They report on transient breathing motions of proteins. In addition, flip rates also depend on stabilizing interactions in the ground state, like aromatic stacking or cation-π interaction. So far, experimental studies of ring flips have almost exclusively been performed on aromatic rings without stabilizing interactions. Here we investigate ring flip dynamics of Phe and Tyr in the aromatic cluster in GB1. We found that all four residues of the cluster, Y3, F30, Y45 and F52, display slow ring flips. Interestingly, F52, the central residue of the cluster, which makes aromatic contacts with all three others, is flipping significantly faster, while the other rings are flipping with the same rates within margin of error. Determined activation enthalpies and activation volumes of these processes are in the same range of other reported ring flips of single aromatic rings. There is no correlation of the number of aromatic stacking interactions to the activation enthalpy, and no correlation of the ring's extent of burying to the activation volume. Because of these findings, we speculate that F52 is undergoing concerted ring flips with each of the other rings.
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Affiliation(s)
- Matthias Dreydoppel
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Heiner N Raum
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Ulrich Weininger
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany.
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14
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Recent developments in isotope-aided NMR methods for supramolecular protein complexes –SAIL aromatic TROSY. Biochim Biophys Acta Gen Subj 2020; 1864:129439. [DOI: 10.1016/j.bbagen.2019.129439] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/03/2019] [Accepted: 09/13/2019] [Indexed: 11/18/2022]
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15
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Raum HN, Schörghuber J, Dreydoppel M, Lichtenecker RJ, Weininger U. Site-selective 1H/ 2H labeling enables artifact-free 1H CPMG relaxation dispersion experiments in aromatic side chains. JOURNAL OF BIOMOLECULAR NMR 2019; 73:633-639. [PMID: 31506857 PMCID: PMC6859156 DOI: 10.1007/s10858-019-00275-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 09/05/2019] [Indexed: 06/10/2023]
Abstract
Aromatic side chains are often key residues in enzyme active sites and protein binding sites, making them attractive probes of protein dynamics on the millisecond timescale. Such dynamic processes can be studied by aromatic 13C or 1H CPMG relaxation dispersion experiments. Aromatic 1H CPMG relaxation dispersion experiments in phenylalanine, tyrosine and the six-ring moiety of tryptophan, however, are affected by 3J 1H-1H couplings which are causing anomalous relaxation dispersion profiles. Here we show that this problem can be addressed by site-selective 1H/2H labeling of the aromatic side chains and that artifact-free relaxation dispersion profiles can be acquired. The method has been further validated by measuring folding-unfolding kinetics of the small protein GB1. The determined rate constants and populations agree well with previous results from 13C CPMG relaxation dispersion experiments. Furthermore, the CPMG-derived chemical shift differences between the folded and unfolded states are in excellent agreement with those obtained directly from the spectra. In summary, site-selective 1H/2H labeling enables artifact-free aromatic 1H CPMG relaxation dispersion experiments in phenylalanine and the six-ring moiety of tryptophan, thereby extending the available methods for studying millisecond dynamics in aromatic protein side chains.
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Affiliation(s)
- Heiner N Raum
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, 06120, Halle, Germany
| | - Julia Schörghuber
- Institute of Organic Chemistry, University of Vienna, 1090, Vienna, Austria
| | - Matthias Dreydoppel
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, 06120, Halle, Germany
| | | | - Ulrich Weininger
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, 06120, Halle, Germany.
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16
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Arthanari H, Takeuchi K, Dubey A, Wagner G. Emerging solution NMR methods to illuminate the structural and dynamic properties of proteins. Curr Opin Struct Biol 2019; 58:294-304. [PMID: 31327528 PMCID: PMC6778509 DOI: 10.1016/j.sbi.2019.06.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 06/03/2019] [Accepted: 06/10/2019] [Indexed: 12/20/2022]
Abstract
The first recognition of protein breathing was more than 50 years ago. Today, we are able to detect the multitude of interaction modes, structural polymorphisms, and binding-induced changes in protein structure that direct function. Solution-state NMR spectroscopy has proved to be a powerful technique, not only to obtain high-resolution structures of proteins, but also to provide unique insights into the functional dynamics of proteins. Here, we summarize recent technical landmarks in solution NMR that have enabled characterization of key biological macromolecular systems. These methods have been fundamental to atomic resolution structure determination and quantitative analysis of dynamics over a wide range of time scales by NMR. The ability of NMR to detect lowly populated protein conformations and transiently formed complexes plays a critical role in its ability to elucidate functionally important structural features of proteins and their dynamics.
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Affiliation(s)
- Haribabu Arthanari
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, United States; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, United States.
| | - Koh Takeuchi
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, 135-0064 Tokyo, Japan.
| | - Abhinav Dubey
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, United States; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, United States
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, United States.
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17
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Gauto DF, Macek P, Barducci A, Fraga H, Hessel A, Terauchi T, Gajan D, Miyanoiri Y, Boisbouvier J, Lichtenecker R, Kainosho M, Schanda P. Aromatic Ring Dynamics, Thermal Activation, and Transient Conformations of a 468 kDa Enzyme by Specific 1H- 13C Labeling and Fast Magic-Angle Spinning NMR. J Am Chem Soc 2019; 141:11183-11195. [PMID: 31199882 DOI: 10.1021/jacs.9b04219] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Aromatic residues are located at structurally important sites of many proteins. Probing their interactions and dynamics can provide important functional insight but is challenging in large proteins. Here, we introduce approaches to characterize the dynamics of phenylalanine residues using 1H-detected fast magic-angle spinning (MAS) NMR combined with a tailored isotope-labeling scheme. Our approach yields isolated two-spin systems that are ideally suited for artifact-free dynamics measurements, and allows probing motions effectively without molecular weight limitations. The application to the TET2 enzyme assembly of ∼0.5 MDa size, the currently largest protein assigned by MAS NMR, provides insights into motions occurring on a wide range of time scales (picoseconds to milliseconds). We quantitatively probe ring-flip motions and show the temperature dependence by MAS NMR measurements down to 100 K. Interestingly, favorable line widths are observed down to 100 K, with potential implications for DNP NMR. Furthermore, we report the first 13C R1ρ MAS NMR relaxation-dispersion measurements and detect structural excursions occurring on a microsecond time scale in the entry pore to the catalytic chamber and at a trimer interface that was proposed as the exit pore. We show that the labeling scheme with deuteration at ca. 50 kHz MAS provides superior resolution compared to 100 kHz MAS experiments with protonated, uniformly 13C-labeled samples.
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Affiliation(s)
- Diego F Gauto
- Univ. Grenoble Alpes, CEA, CNRS , Institut de Biologie Structurale (IBS) , 71, avenue des martyrs , F-38044 Grenoble , France
| | - Pavel Macek
- Univ. Grenoble Alpes, CEA, CNRS , Institut de Biologie Structurale (IBS) , 71, avenue des martyrs , F-38044 Grenoble , France
| | - Alessandro Barducci
- Centre de Biochimie Structurale (CBS) , INSERM, CNRS, Université de Montpellier , Montpellier , France
| | - Hugo Fraga
- Univ. Grenoble Alpes, CEA, CNRS , Institut de Biologie Structurale (IBS) , 71, avenue des martyrs , F-38044 Grenoble , France.,Departamento de Biomedicina , Faculdade de Medicina da Universidade do Porto , Porto , Portugal.,i3S, Instituto de Investigação e Inovação em Saúde , Universidade do Porto , Porto , Portugal
| | - Audrey Hessel
- Univ. Grenoble Alpes, CEA, CNRS , Institut de Biologie Structurale (IBS) , 71, avenue des martyrs , F-38044 Grenoble , France
| | - Tsutomu Terauchi
- Graduate School of Science , Tokyo Metropolitan University , 1-1 Minami-ohsawa , Hachioji , Tokyo 192-0397 , Japan.,SI Innovation Center , Taiyo Nippon Sanso Corp. , 2008-2 Wada , Tama-city , Tokyo 206-0001 , Japan
| | - David Gajan
- Université de Lyon , Centre de RMN à Hauts Champs de Lyon CRMN, FRE 2034, Université de Lyon, CNRS, ENS Lyon, UCB Lyon 1 , 69100 Villeurbanne , France
| | - Yohei Miyanoiri
- Institute of Protein Research , Osaka University , 3-2 Yamadaoka , Suita , Osaka 565-0871 , Japan.,Structural Biology Research Center, Graduate School of Sciences , Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8602 , Japan
| | - Jerome Boisbouvier
- Univ. Grenoble Alpes, CEA, CNRS , Institut de Biologie Structurale (IBS) , 71, avenue des martyrs , F-38044 Grenoble , France
| | - Roman Lichtenecker
- Institute of Organic Chemistry , University of Vienna , Währinger Str. 38 , 1090 Vienna , Austria
| | - Masatsune Kainosho
- Graduate School of Science , Tokyo Metropolitan University , 1-1 Minami-ohsawa , Hachioji , Tokyo 192-0397 , Japan.,Structural Biology Research Center, Graduate School of Sciences , Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8602 , Japan
| | - Paul Schanda
- Univ. Grenoble Alpes, CEA, CNRS , Institut de Biologie Structurale (IBS) , 71, avenue des martyrs , F-38044 Grenoble , France
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18
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Raum HN, Dreydoppel M, Weininger U. Conformational exchange of aromatic side chains by 1H CPMG relaxation dispersion. JOURNAL OF BIOMOLECULAR NMR 2018; 72:105-114. [PMID: 30229369 PMCID: PMC6209042 DOI: 10.1007/s10858-018-0210-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 09/14/2018] [Indexed: 06/08/2023]
Abstract
Aromatic side chains are attractive probes of protein dynamics on the millisecond time scale, because they are often key residues in enzyme active sites and protein binding sites. Further they allow to study specific processes, like histidine tautomerization and ring flips. Till now such processes have been studied by aromatic 13C CPMG relaxation dispersion experiments. Here we investigate the possibility of aromatic 1H CPMG relaxation dispersion experiments as a complementary method. Artifact-free dispersions are possible on uniformly 1H and 13C labeled samples for histidine δ2 and ε1, as well as for tryptophan δ1. The method has been validated by measuring fast folding-unfolding kinetics of the small protein CspB under native conditions. The determined rate constants and populations agree well with previous results from 13C CPMG relaxation dispersion experiments. The CPMG-derived chemical shift differences between the folded and unfolded states are in good agreement with those obtained directly from the spectra. In contrast, the 1H relaxation dispersion profiles in phenylalanine, tyrosine and the six-ring moiety of tryptophan, display anomalous behavior caused by 3J 1H-1H couplings and, if present, strong 13C-13C couplings. Therefore they require site-selective 1H/2H and, in case of strong couplings, 13C/12C labeling. In summary, aromatic 1H CPMG relaxation dispersion experiments work on certain positions (His δ2, His ε1 and Trp δ1) in uniformly labeled samples, while other positions require site-selective isotope labeling.
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Affiliation(s)
- Heiner N Raum
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Matthias Dreydoppel
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Ulrich Weininger
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany.
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19
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Weininger U. Optimal Isotope Labeling of Aromatic Amino Acid Side Chains for NMR Studies of Protein Dynamics. Methods Enzymol 2018; 614:67-86. [PMID: 30611433 DOI: 10.1016/bs.mie.2018.08.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Aromatic side chains in proteins are often directly evolved in stabilizing the hydrophobic core, protein binding, or enzymatic activity. They are also responsible for specific local dynamic processes, such as histidine tautomerization or ring flips. Despite their importance, they are often not targeted directly by NMR spectroscopy, because of spectroscopic complications and challenges. This chapter addresses state-of-the-art site-selective 13C-labeling methods for aromatic side chains, and describes how they solve several of the spectroscopic issues. A special emphasis is put on thereby enabled protein dynamics experiments of aromatic side chains.
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Affiliation(s)
- Ulrich Weininger
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, Halle, Germany.
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20
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Analysis of Artifacts Caused by Pulse Imperfections in CPMG Pulse Trains in NMR Relaxation Dispersion Experiments. MAGNETOCHEMISTRY 2018. [DOI: 10.3390/magnetochemistry4030033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Nuclear magnetic resonance relaxation dispersion (rd) experiments provide kinetics and thermodynamics information of molecules undergoing conformational exchange. Rd experiments often use a Carr-Purcell-Meiboom-Gill (CPMG) pulse train equally separated by a spin-state selective inversion element (U-element). Even with measurement parameters carefully set, however, parts of 1H–15N correlations sometimes exhibit large artifacts that may hamper the subsequent analyses. We analyzed such artifacts with a combination of NMR measurements and simulation. We found that particularly the lowest CPMG frequency (νcpmg) can also introduce large artifacts into amide 1H–15N and aromatic 1H–13C correlations whose 15N/13C resonances are very close to the carrier frequencies. The simulation showed that the off-resonance effects and miscalibration of the CPMG π pulses generate artifact maxima at resonance offsets of even and odd multiples of νcpmg, respectively. We demonstrate that a method once introduced into the rd experiments for molecules having residual dipolar coupling significantly reduces artifacts. In the method the 15N/13C π pulse phase in the U-element is chosen between x and y. We show that the correctly adjusted sequence is tolerant to miscalibration of the CPMG π pulse power as large as ±10% for most amide 15N and aromatic 13C resonances of proteins.
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21
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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.
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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.
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22
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Entropy drives selective fluorine recognition in the fluoroacetyl-CoA thioesterase from Streptomyces cattleya. Proc Natl Acad Sci U S A 2018; 115:E2193-E2201. [PMID: 29453276 DOI: 10.1073/pnas.1717077115] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fluorinated small molecules play an important role in the design of bioactive compounds for a broad range of applications. As such, there is strong interest in developing a deeper understanding of how fluorine affects the interaction of these ligands with their targets. Given the small number of fluorinated metabolites identified to date, insights into fluorine recognition have been provided almost entirely by synthetic systems. The fluoroacetyl-CoA thioesterase (FlK) from Streptomyces cattleya thus provides a unique opportunity to study an enzyme-ligand pair that has been evolutionarily optimized for a surprisingly high 106 selectivity for a single fluorine substituent. In these studies, we synthesize a series of analogs of fluoroacetyl-CoA and acetyl-CoA to generate nonhydrolyzable ester, amide, and ketone congeners of the thioester substrate to isolate the role of fluorine molecular recognition in FlK selectivity. Using a combination of thermodynamic, kinetic, and protein NMR experiments, we show that fluorine recognition is entropically driven by the interaction of the fluorine substituent with a key residue, Phe-36, on the lid structure that covers the active site, resulting in an ∼5- to 20-fold difference in binding (KD). Although the magnitude of discrimination is similar to that found in designed synthetic ligand-protein complexes where dipolar interactions control fluorine recognition, these studies show that hydrophobic and solvation effects serve as the major determinant of naturally evolved fluorine selectivity.
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23
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Abstract
Molecular recognition by proteins is fundamental to the molecular basis of biology. Dissection of the thermodynamic landscape governing protein-ligand interactions has proven difficult because determination of various entropic contributions is quite challenging. Nuclear magnetic resonance relaxation measurements, theory, and simulations suggest that conformational entropy can be accessed through a dynamical proxy. Here, we review the relationship between measures of fast side-chain motion and the underlying conformational entropy. The dynamical proxy reveals that the contribution of conformational entropy can range from highly favorable to highly unfavorable and demonstrates the potential of this key thermodynamic variable to modulate protein-ligand interactions. The dynamical so-called entropy meter also refines the role of solvent entropy and directly determines the loss in rotational-translational entropy that occurs upon formation of high-affinity complexes. The ability to quantify the roles of entropy through an entropy meter based on measurable dynamical properties promises to highlight its role in protein function.
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Affiliation(s)
- A Joshua Wand
- Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104-6059, USA; ,
| | - Kim A Sharp
- Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104-6059, USA; ,
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24
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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.
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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.
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25
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Schörghuber J, Geist L, Bisaccia M, Weber F, Konrat R, Lichtenecker RJ. Anthranilic acid, the new player in the ensemble of aromatic residue labeling precursor compounds. JOURNAL OF BIOMOLECULAR NMR 2017; 69:13-22. [PMID: 28861670 PMCID: PMC5626795 DOI: 10.1007/s10858-017-0129-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 08/28/2017] [Indexed: 06/07/2023]
Abstract
The application of metabolic precursors for selective stable isotope labeling of aromatic residues in cell-based protein overexpression has already resulted in numerous NMR probes to study the structural and dynamic characteristics of proteins. With anthranilic acid, we present the structurally simplest precursor for exclusive tryptophan side chain labeling. A synthetic route to 13C, 2H isotopologues allows the installation of isolated 13C-1H spin systems in the indole ring of tryptophan, representing a versatile tool to investigate side chain motion using relaxation-based experiments without the loss of magnetization due to strong 1JCC and weaker 2JCH scalar couplings, as well as dipolar interactions with remote hydrogens. In this article, we want to introduce this novel precursor in the context of hitherto existing techniques of in vivo aromatic residue labeling.
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Affiliation(s)
- Julia Schörghuber
- Institute of Organic Chemistry, University of Vienna, Währingerstr. 38, 1090, Vienna, Austria
| | - Leonhard Geist
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Dr-Bohr-Gasse 9, 1030, Vienna, Austria
| | - Marilena Bisaccia
- Institute of Organic Chemistry, University of Vienna, Währingerstr. 38, 1090, Vienna, Austria
| | - Frederik Weber
- Institute of Organic Chemistry, University of Vienna, Währingerstr. 38, 1090, Vienna, Austria
| | - Robert Konrat
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Dr-Bohr-Gasse 9, 1030, Vienna, Austria
| | - Roman J Lichtenecker
- Institute of Organic Chemistry, University of Vienna, Währingerstr. 38, 1090, Vienna, Austria.
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26
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Weininger U. Site-selective 13C labeling of histidine and tryptophan using ribose. JOURNAL OF BIOMOLECULAR NMR 2017; 69:23-30. [PMID: 28856561 PMCID: PMC5626788 DOI: 10.1007/s10858-017-0130-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 08/28/2017] [Indexed: 06/07/2023]
Abstract
Experimental studies on protein dynamics at atomic resolution by NMR-spectroscopy in solution require isolated 1H-X spin pairs. This is the default scenario in standard 1H-15N backbone experiments. Side chain dynamic experiments, which allow to study specific local processes like proton-transfer, or tautomerization, require isolated 1H-13C sites which must be produced by site-selective 13C labeling. In the most general way this is achieved by using site-selectively 13C-enriched glucose as the carbon source in bacterial expression systems. Here we systematically investigate the use of site-selectively 13C-enriched ribose as a suitable precursor for 13C labeled histidines and tryptophans. The 13C incorporation in nearly all sites of all 20 amino acids was quantified and compared to glucose based labeling. In general the ribose approach results in more selective labeling. 1-13C ribose exclusively labels His δ2 and Trp δ1 in aromatic side chains and helps to resolve possible overlap problems. The incorporation yield is however only 37% in total and 72% compared to yields of 2-13C glucose. A combined approach of 1-13C ribose and 2-13C glucose maximizes 13C incorporation to 75% in total and 150% compared to 2-13C glucose only. Further histidine positions β, α and CO become significantly labeled at around 50% in total by 3-, 4- or 5-13C ribose. Interestingly backbone CO of Gly, Ala, Cys, Ser, Val, Phe and Tyr are labeled at 40-50% in total with 3-13C ribose, compared to 5% and below for 1-13C and 2-13C glucose. Using ribose instead of glucose as a source for site-selective 13C labeling enables a very selective labeling of certain positions and thereby expanding the toolbox for customized isotope labeling of amino-acids.
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Affiliation(s)
- Ulrich Weininger
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, P. O. Box 124, 22100, Lund, Sweden.
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany.
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27
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Jiang Y, Kalodimos CG. NMR Studies of Large Proteins. J Mol Biol 2017; 429:2667-2676. [PMID: 28728982 DOI: 10.1016/j.jmb.2017.07.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 07/06/2017] [Accepted: 07/06/2017] [Indexed: 01/08/2023]
Abstract
Recent breakthroughs in isotope-labeling and pulse sequence techniques have enabled the NMR characterization of large protein systems with molecular masses of hundreds of kilodaltons. NMR studies of a great variety of large proteins have provided unique insights into the binding, dynamic, and allosteric mechanisms. Here we present a brief summary of these developments by highlighting few cases that exemplify the uniqueness of NMR in providing atomic resolution information into key dynamic processes and structures of protein complexes with high degree of flexibility.
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Affiliation(s)
- Yajun Jiang
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455, United States; Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, United States
| | - Charalampos G Kalodimos
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455, United States; Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, United States.
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28
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Schörghuber J, Geist L, Platzer G, Konrat R, Lichtenecker RJ. Highly Selective Stable Isotope Labeling of Histidine Residues by Using a Novel Precursor in E. coli-Based Overexpression Systems. Chembiochem 2017; 18:1487-1491. [PMID: 28489326 DOI: 10.1002/cbic.201700192] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Indexed: 12/14/2022]
Abstract
The importance of NMR spectroscopy in unraveling the structural and dynamic properties of proteins is ever-expanding owing to progress in experimental techniques, hardware development, and novel labeling approaches. Multiple sophisticated methods of aliphatic residue labeling can be found in the literature, whereas the selective incorporation of NMR active isotopes into other amino acids still holds the potential for improvement. In order to close this methodological gap, we present a novel metabolic precursor for cell-based protein overexpression to assemble 13 C/2 H isotope patterns in the peptide backbone, as well as in side chain positions of a mechanistically distinguished histidine residue.
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Affiliation(s)
- Julia Schörghuber
- Institute of Organic Chemistry, University of Vienna, Währingerstrasse 38, 1090, Vienna, Austria
| | - Leonhard Geist
- Christian Doppler Laboratory for High-Content Structural Biology, and Biotechnology/Department of Structural and Computational Biology, University of Vienna, 1090, Vienna, Austria
| | - Gerald Platzer
- Christian Doppler Laboratory for High-Content Structural Biology, and Biotechnology/Department of Structural and Computational Biology, University of Vienna, 1090, Vienna, Austria
| | - Robert Konrat
- Christian Doppler Laboratory for High-Content Structural Biology, and Biotechnology/Department of Structural and Computational Biology, University of Vienna, 1090, Vienna, Austria
| | - Roman J Lichtenecker
- Institute of Organic Chemistry, University of Vienna, Währingerstrasse 38, 1090, Vienna, Austria
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29
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Huang C, Kalodimos CG. Structures of Large Protein Complexes Determined by Nuclear Magnetic Resonance Spectroscopy. Annu Rev Biophys 2017; 46:317-336. [DOI: 10.1146/annurev-biophys-070816-033701] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Chengdong Huang
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455
| | - Charalampos G. Kalodimos
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455
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30
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Vallurupalli P, Sekhar A, Yuwen T, Kay LE. Probing conformational dynamics in biomolecules via chemical exchange saturation transfer: a primer. JOURNAL OF BIOMOLECULAR NMR 2017; 67:243-271. [PMID: 28317074 DOI: 10.1007/s10858-017-0099-4] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 02/20/2017] [Indexed: 05/25/2023]
Abstract
Although Chemical Exchange Saturation Transfer (CEST) type NMR experiments have been used to study chemical exchange processes in molecules since the early 1960s, there has been renewed interest in the past several years in using this approach to study biomolecular conformational dynamics. The methodology is particularly powerful for the study of sparsely populated, transiently formed conformers that are recalcitrant to investigation using traditional biophysical tools, and it is complementary to relaxation dispersion and magnetization transfer experiments that have traditionally been used to study chemical exchange processes. Here we discuss the concepts behind the CEST experiment, focusing on practical aspects as well, we review some of the pulse sequences that have been developed to characterize protein and RNA conformational dynamics, and we discuss a number of examples where the CEST methodology has provided important insights into the role of dynamics in biomolecular function.
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Affiliation(s)
| | - Ashok Sekhar
- Departments of Molecular Genetics, Biochemistry and Chemistry, University of Toronto, Toronto, ON, Canada
| | - Tairan Yuwen
- Departments of Molecular Genetics, Biochemistry and Chemistry, University of Toronto, Toronto, ON, Canada
| | - Lewis E Kay
- Departments of Molecular Genetics, Biochemistry and Chemistry, University of Toronto, Toronto, ON, Canada.
- Hospital for Sick Children, Program in Molecular Structure and Function, Toronto, ON, Canada.
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31
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Weininger U. Site-selective 13C labeling of proteins using erythrose. JOURNAL OF BIOMOLECULAR NMR 2017; 67:191-200. [PMID: 28247186 PMCID: PMC5388708 DOI: 10.1007/s10858-017-0096-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Accepted: 02/10/2017] [Indexed: 06/06/2023]
Abstract
NMR-spectroscopy enables unique experimental studies on protein dynamics at atomic resolution. In order to obtain a full atom view on protein dynamics, and to study specific local processes like ring-flips, proton-transfer, or tautomerization, one has to perform studies on amino-acid side chains. A key requirement for these studies is site-selective labeling with 13C and/or 1H, which is achieved in the most general way by using site-selectively 13C-enriched glucose (1- and 2-13C) as the carbon source in bacterial expression systems. Using this strategy, multiple sites in side chains, including aromatics, become site-selectively labeled and suitable for relaxation studies. Here we systematically investigate the use of site-selectively 13C-enriched erythrose (1-, 2-, 3- and 4-13C) as a suitable precursor for 13C labeled aromatic side chains. We quantify 13C incorporation in nearly all sites in all 20 amino acids and compare the results to glucose based labeling. In general the erythrose approach results in more selective labeling. While there is only a minor gain for phenylalanine and tyrosine side-chains, the 13C incorporation level for tryptophan is at least doubled. Additionally, the Phe ζ and Trp η2 positions become labeled. In the aliphatic side chains, labeling using erythrose yields isolated 13C labels for certain positions, like Ile β and His β, making these sites suitable for dynamics studies. Using erythrose instead of glucose as a source for site-selective 13C labeling enables unique or superior labeling for certain positions and is thereby expanding the toolbox for customized isotope labeling of amino-acid side-chains.
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Affiliation(s)
- Ulrich Weininger
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, P.O. Box 124, 22100, Lund, Sweden.
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany.
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32
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Ramaraju B, McFeeters H, Vogler B, McFeeters RL. Bacterial production of site specific 13C labeled phenylalanine and methodology for high level incorporation into bacterially expressed recombinant proteins. JOURNAL OF BIOMOLECULAR NMR 2017; 67:23-34. [PMID: 28028744 PMCID: PMC5311020 DOI: 10.1007/s10858-016-0081-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 12/11/2016] [Indexed: 06/06/2023]
Abstract
Nuclear magnetic resonance spectroscopy studies of ever larger systems have benefited from many different forms of isotope labeling, in particular, site specific isotopic labeling. Site specific 13C labeling of methyl groups has become an established means of probing systems not amenable to traditional methodology. However useful, methyl reporter sites can be limited in number and/or location. Therefore, new complementary site specific isotope labeling strategies are valuable. Aromatic amino acids make excellent probes since they are often found at important interaction interfaces and play significant structural roles. Aromatic side chains have many of the same advantages as methyl containing amino acids including distinct 13C chemical shifts and multiple magnetically equivalent 1H positions. Herein we report economical bacterial production and one-step purification of phenylalanine with 13C incorporation at the Cα, Cγ and Cε positions, resulting in two isolated 1H-13C spin systems. We also present methodology to maximize incorporation of phenylalanine into recombinantly overexpressed proteins in bacteria and demonstrate compatibility with ILV-methyl labeling. Inexpensive, site specific isotope labeled phenylalanine adds another dimension to biomolecular NMR, opening new avenues of study.
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Affiliation(s)
- Bhargavi Ramaraju
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL, 35899, USA
| | - Hana McFeeters
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL, 35899, USA
| | - Bernhard Vogler
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL, 35899, USA
| | - Robert L McFeeters
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL, 35899, USA.
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33
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Weininger U, Modig K, Geitner AJ, Schmidpeter PAM, Koch JR, Akke M. Dynamics of Aromatic Side Chains in the Active Site of FKBP12. Biochemistry 2016; 56:334-343. [DOI: 10.1021/acs.biochem.6b01157] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Ulrich Weininger
- Department
of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, P.O.
Box 124, SE-22100 Lund, Sweden
- Institute
of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, D-06120 Halle (Saale), Germany
| | - Kristofer Modig
- Department
of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, P.O.
Box 124, SE-22100 Lund, Sweden
| | - Anne-Juliane Geitner
- Laboratorium
für Biochemie, Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, D-95440 Bayreuth, Germany
| | - Philipp A. M. Schmidpeter
- Laboratorium
für Biochemie, Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, D-95440 Bayreuth, Germany
| | - Johanna R. Koch
- Laboratorium
für Biochemie, Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, D-95440 Bayreuth, Germany
| | - Mikael Akke
- Department
of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, P.O.
Box 124, SE-22100 Lund, Sweden
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34
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Longhini AP, LeBlanc RM, Becette O, Salguero C, Wunderlich CH, Johnson BA, D'Souza VM, Kreutz C, Dayie TK. Chemo-enzymatic synthesis of site-specific isotopically labeled nucleotides for use in NMR resonance assignment, dynamics and structural characterizations. Nucleic Acids Res 2015; 44:e52. [PMID: 26657632 PMCID: PMC4824079 DOI: 10.1093/nar/gkv1333] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 11/16/2015] [Indexed: 11/12/2022] Open
Abstract
Stable isotope labeling is central to NMR studies of nucleic acids. Development of methods that incorporate labels at specific atomic positions within each nucleotide promises to expand the size range of RNAs that can be studied by NMR. Using recombinantly expressed enzymes and chemically synthesized ribose and nucleobase, we have developed an inexpensive, rapid chemo-enzymatic method to label ATP and GTP site specifically and in high yields of up to 90%. We incorporated these nucleotides into RNAs with sizes ranging from 27 to 59 nucleotides using in vitro transcription: A-Site (27 nt), the iron responsive elements (29 nt), a fluoride riboswitch from Bacillus anthracis (48 nt), and a frame-shifting element from a human corona virus (59 nt). Finally, we showcase the improvement in spectral quality arising from reduced crowding and narrowed linewidths, and accurate analysis of NMR relaxation dispersion (CPMG) and TROSY-based CEST experiments to measure μs-ms time scale motions, and an improved NOESY strategy for resonance assignment. Applications of this selective labeling technology promises to reduce difficulties associated with chemical shift overlap and rapid signal decay that have made it challenging to study the structure and dynamics of large RNAs beyond the 50 nt median size found in the PDB.
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Affiliation(s)
- Andrew P Longhini
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USAfi
| | - Regan M LeBlanc
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USAfi
| | - Owen Becette
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USAfi
| | - Carolina Salguero
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Christoph H Wunderlich
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria
| | - Bruce A Johnson
- Structural Biology Initiative, CUNY Advanced Science Research Center, 85 St. Nicholas Terrace, New York, NY 10031, USA One Moon Scientific, Inc., 839 Grant Avenue, Westfield, NJ 07090-2322, USA
| | - Victoria M D'Souza
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria
| | - T Kwaku Dayie
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USAfi
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35
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Yang CJ, Takeda M, Terauchi T, Jee J, Kainosho M. Differential Large-Amplitude Breathing Motions in the Interface of FKBP12–Drug Complexes. Biochemistry 2015; 54:6983-95. [DOI: 10.1021/acs.biochem.5b00820] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Chun-Jiun Yang
- Department
of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 minami-ohsawa, Hachioji,
Tokyo 192-0397, Japan
| | - Mitsuhiro Takeda
- Structural
Biology Research Center, Graduate School of Science, Nagoya University, Furo-cho,
Chikusa-ku, Nagoya 464-8602, Japan
| | - Tsutomu Terauchi
- Department
of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 minami-ohsawa, Hachioji,
Tokyo 192-0397, Japan
| | - JunGoo Jee
- Department
of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 minami-ohsawa, Hachioji,
Tokyo 192-0397, Japan
| | - Masatsune Kainosho
- Department
of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 minami-ohsawa, Hachioji,
Tokyo 192-0397, Japan
- Structural
Biology Research Center, Graduate School of Science, Nagoya University, Furo-cho,
Chikusa-ku, Nagoya 464-8602, Japan
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36
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Milbradt AG, Arthanari H, Takeuchi K, Boeszoermenyi A, Hagn F, Wagner G. Increased resolution of aromatic cross peaks using alternate 13C labeling and TROSY. JOURNAL OF BIOMOLECULAR NMR 2015; 62:291-301. [PMID: 25957757 PMCID: PMC4782774 DOI: 10.1007/s10858-015-9944-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 05/02/2015] [Indexed: 05/21/2023]
Abstract
For typical globular proteins, contacts involving aromatic side chains would constitute the largest number of distance constraints that could be used to define the structure of proteins and protein complexes based on NOE contacts. However, the (1)H NMR signals of aromatic side chains are often heavily overlapped, which hampers extensive use of aromatic NOE cross peaks. Some of this overlap can be overcome by recording (13)C-dispersed NOESY spectra. However, the resolution in the carbon dimension is rather low due to the narrow dispersion of the carbon signals, large one-bond carbon-carbon (C-C) couplings, and line broadening due to chemical shift anisotropy (CSA). Although it has been noted that the CSA of aromatic carbons could be used in TROSY experiments for enhancing resolution, this has not been used much in practice because of complications arising from large aromatic one-bond C-C couplings, and 3D or 4D carbon dispersed NOESY are typically recorded at low resolution hampering straightforward peak assignments. Here we show that the aromatic TROSY effect can optimally be used when employing alternate (13)C labeling using 2-(13)C glycerol, 2-(13)C pyruvate, or 3-(13)C pyruvate as the carbon source. With the elimination of the strong one-bond C-C coupling, the TROSY effect can easily be exploited. We show that (1)H-(13)C TROSY spectra of alternately (13)C labeled samples can be recorded at high resolution, and we employ 3D NOESY aromatic-TROSY spectra to obtain valuable intramolecular and intermolecular cross peaks on a protein complex.
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Affiliation(s)
- Alexander G. Milbradt
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA
| | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA
| | - Koh Takeuchi
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA
| | - Andras Boeszoermenyi
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA
| | - Franz Hagn
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA
- Dept. of Chemistry and Institute for Advanced Study, Technische Universität München, 85748 Garching, Germany
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA
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37
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Colvin MT, Silvers R, Frohm B, Su Y, Linse S, Griffin RG. High resolution structural characterization of Aβ42 amyloid fibrils by magic angle spinning NMR. J Am Chem Soc 2015; 137:7509-18. [PMID: 26001057 PMCID: PMC4623963 DOI: 10.1021/jacs.5b03997] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
![]()
The presence of amyloid plaques composed
of amyloid beta (Aβ)
fibrils is a hallmark of Alzheimer’s disease (AD). The Aβ
peptide is present as several length variants with two common alloforms
consisting of 40 and 42 amino acids, denoted Aβ1–40 and Aβ1–42, respectively. While there have
been numerous reports that structurally characterize fibrils of Aβ1–40, very little is known about the structure of amyloid
fibrils of Aβ1–42, which are considered the
more toxic alloform involved in AD. We have prepared isotopically 13C/15N labeled AβM01–42 fibrils in vitro from recombinant protein and examined their 13C–13C and 13C–15N magic angle spinning (MAS) NMR spectra. In contrast to several
other studies of Aβ fibrils, we observe spectra with excellent
resolution and a single set of chemical shifts, suggesting the presence
of a single fibril morphology. We report the initial structural characterization
of AβM01–42 fibrils utilizing 13C and 15N shift assignments of 38 of the 43 residues,
including the backbone and side chains, obtained through a series
of cross-polarization based 2D and 3D 13C–13C, 13C–15N MAS NMR experiments for rigid
residues along with J-based 2D TOBSY experiments for dynamic residues.
We find that the first ∼5 residues are dynamic and most efficiently
detected in a J-based TOBSY spectrum. In contrast, residues 16–42
are easily observed in cross-polarization experiments and most likely
form the amyloid core. Calculation of ψ and φ dihedral
angles from the chemical shift assignments indicate that 4 β-strands
are present in the fibril’s secondary structure.
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Affiliation(s)
- Michael T Colvin
- †Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Robert Silvers
- †Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Birgitta Frohm
- ‡Department of Biochemistry and Structural Biology, Lund University, SE22100 Lund, Sweden
| | - Yongchao Su
- †Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Sara Linse
- ‡Department of Biochemistry and Structural Biology, Lund University, SE22100 Lund, Sweden
| | - Robert G Griffin
- †Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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38
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Kasinath V, Fu Y, Sharp KA, Wand AJ. A Sharp Thermal Transition of Fast Aromatic‐Ring Dynamics in Ubiquitin. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201408220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Vignesh Kasinath
- Department of Biochemistry & Biophysics, University of Pennsylvania, Philadelphia, PA 19104 (USA)
| | - Yinan Fu
- Department of Biochemistry & Biophysics, University of Pennsylvania, Philadelphia, PA 19104 (USA)
| | - Kim A. Sharp
- Department of Biochemistry & Biophysics, University of Pennsylvania, Philadelphia, PA 19104 (USA)
| | - A. Joshua Wand
- Department of Biochemistry & Biophysics, University of Pennsylvania, Philadelphia, PA 19104 (USA)
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39
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Kasinath V, Fu Y, Sharp KA, Wand AJ. A sharp thermal transition of fast aromatic-ring dynamics in ubiquitin. Angew Chem Int Ed Engl 2014; 54:102-7. [PMID: 25476230 DOI: 10.1002/anie.201408220] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Indexed: 11/06/2022]
Abstract
Aromatic amino acid side chains have a rich role within proteins and are often central to their structure and function. Suitable isotopic-labelling strategies enable studies of sub-nanosecond aromatic-ring dynamics using solution NMR relaxation methods. Surprisingly, it was found that the three aromatic side chains in human ubiquitin show a sharp thermal dynamical transition at approximately 312 K. Hydrostatic pressure has little effect on the low-temperature behavior, but somewhat decreases the amplitude of motion in the high-temperature regime. Therefore, below the transition temperature, ring motion is largely librational. Above this temperature, a complete ring-rotation process that is fully consistent with a continuous diffusion not requiring the transient creation of a large activated free volume occurs. Molecular dynamics simulations qualitatively corroborate this view and reinforce the notion that the dynamical character of the protein interior has much more liquid-alkane-like properties than previously appreciated.
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Affiliation(s)
- Vignesh Kasinath
- Department of Biochemistry & Biophysics, University of Pennsylvania, Philadelphia, PA 19104 (USA)
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40
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Weininger U, Modig K, Akke M. Ring Flips Revisited: 13C Relaxation Dispersion Measurements of Aromatic Side Chain Dynamics and Activation Barriers in Basic Pancreatic Trypsin Inhibitor. Biochemistry 2014; 53:4519-25. [DOI: 10.1021/bi500462k] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ulrich Weininger
- Department of Biophysical
Chemistry, Center for Molecular Protein Science, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Kristofer Modig
- Department of Biophysical
Chemistry, Center for Molecular Protein Science, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Mikael Akke
- Department of Biophysical
Chemistry, Center for Molecular Protein Science, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
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41
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Weininger U, Brath U, Modig K, Teilum K, Akke M. Off-resonance rotating-frame relaxation dispersion experiment for 13C in aromatic side chains using L-optimized TROSY-selection. JOURNAL OF BIOMOLECULAR NMR 2014; 59:23-9. [PMID: 24706175 PMCID: PMC4003406 DOI: 10.1007/s10858-014-9826-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 03/25/2014] [Indexed: 05/04/2023]
Abstract
Protein dynamics on the microsecond-millisecond time scales often play a critical role in biological function. NMR relaxation dispersion experiments are powerful approaches for investigating biologically relevant dynamics with site-specific resolution, as shown by a growing number of publications on enzyme catalysis, protein folding, ligand binding, and allostery. To date, the majority of studies has probed the backbone amides or side-chain methyl groups, while experiments targeting other sites have been used more sparingly. Aromatic side chains are useful probes of protein dynamics, because they are over-represented in protein binding interfaces, have important catalytic roles in enzymes, and form a sizable part of the protein interior. Here we present an off-resonance R 1ρ experiment for measuring microsecond to millisecond conformational exchange of aromatic side chains in selectively (13)C labeled proteins by means of longitudinal- and transverse-relaxation optimization. Using selective excitation and inversion of the narrow component of the (13)C doublet, the experiment achieves significant sensitivity enhancement in terms of both signal intensity and the fractional contribution from exchange to transverse relaxation; additional signal enhancement is achieved by optimizing the longitudinal relaxation recovery of the covalently attached (1)H spins. We validated the L-TROSY-selected R 1ρ experiment by measuring exchange parameters for Y23 in bovine pancreatic trypsin inhibitor at a temperature of 328 K, where the ring flip is in the fast exchange regime with a mean waiting time between flips of 320 μs. The determined chemical shift difference matches perfectly with that measured from the NMR spectrum at lower temperatures, where separate peaks are observed for the two sites. We further show that potentially complicating effects of strong scalar coupling between protons (Weininger et al. in J Phys Chem B 117: 9241-9247, 2013b) can be accounted for using a simple expression, and provide recommendations for data acquisition when the studied system exhibits this behavior. The present method extends the repertoire of relaxation methods tailored for aromatic side chains by enabling studies of faster processes and improved control over artifacts due to strong coupling.
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Affiliation(s)
- Ulrich Weininger
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, P.O. Box 124, 22100 Lund, Sweden
| | - Ulrika Brath
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, P.O. Box 124, 22100 Lund, Sweden
- Present Address: Department of Chemistry and Molecular Biology, University of Gothenburg, 41296 Göteborg, Sweden
| | - Kristofer Modig
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, P.O. Box 124, 22100 Lund, Sweden
| | - Kaare Teilum
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Mikael Akke
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, P.O. Box 124, 22100 Lund, Sweden
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42
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Xu G, Ye Y, Liu X, Cao S, Wu Q, Cheng K, Liu M, Pielak GJ, Li C. Strategies for Protein NMR in Escherichia coli. Biochemistry 2014; 53:1971-81. [DOI: 10.1021/bi500079u] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Guohua Xu
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Yansheng Ye
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China
- Graduate University of Chinese Academy of Sciences, Beijing 100029, P. R. China
| | - Xiaoli Liu
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Shufen Cao
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Qiong Wu
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Kai Cheng
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China
- Graduate University of Chinese Academy of Sciences, Beijing 100029, P. R. China
| | - Maili Liu
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Gary J. Pielak
- Department
of Chemistry and Department of Biochemistry and Biophysics, University of North Carolina−Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Conggang Li
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China
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43
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Villali J, Pontiggia F, Clarkson MW, Hagan MF, Kern D. Evidence against the "Y-T coupling" mechanism of activation in the response regulator NtrC. J Mol Biol 2014; 426:1554-67. [PMID: 24406745 DOI: 10.1016/j.jmb.2013.12.027] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 12/18/2013] [Accepted: 12/24/2013] [Indexed: 01/17/2023]
Abstract
The dominant theory on the mechanism of response regulators activation in two-component bacterial signaling systems is the "Y-T coupling" mechanism, wherein the χ1 rotameric state of a highly conserved aromatic residue correlates with the activation of the protein via structural rearrangements coupled to a conserved tyrosine. In this paper, we present evidence that, in the receiver domain of the response regulator nitrogen regulatory protein C (NtrC(R)), the interconversion of this tyrosine (Y101) between its rotameric states is actually faster than the rate of inactive/active conversion and is not correlated to the activation process. Data gathered from NMR relaxation dispersion experiments show that a subset of residues surrounding the conserved tyrosine sense a process that is occurring at a faster rate than the inactive/active conformational transition. We show that this process is related to χ1 rotamer exchange of Y101 and that mutation of this aromatic residue to a leucine eliminated this second faster process without affecting activation. Computational simulations of NtrC(R) in its active conformation further demonstrate that the rotameric state of Y101 is uncorrelated with the global conformational transition during activation. Moreover, the tyrosine does not appear to be involved in the stabilization of the active form upon phosphorylation and is not essential in propagating the signal downstream for ATPase activity of the central domain. Our data provide experimental evidence against the generally accepted "Y-T coupling" mechanism of activation in NtrC(R).
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Affiliation(s)
- Janice Villali
- Department of Biochemistry and Howard Hughes Medical Institute, Waltham, MA 02452, USA
| | - Francesco Pontiggia
- Department of Biochemistry and Howard Hughes Medical Institute, Waltham, MA 02452, USA
| | - Michael W Clarkson
- Department of Biochemistry and Howard Hughes Medical Institute, Waltham, MA 02452, USA
| | - Michael F Hagan
- Department of Physics, Brandeis University, Waltham, MA 02452, USA
| | - Dorothee Kern
- Department of Biochemistry and Howard Hughes Medical Institute, Waltham, MA 02452, USA.
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44
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Lichtenecker RJ. Synthesis of aromatic 13C/2H-α-ketoacid precursors to be used in selective phenylalanine and tyrosine protein labelling. Org Biomol Chem 2014; 12:7551-60. [DOI: 10.1039/c4ob01129e] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A synthetic concept to access various 13C/2H patterns of phenylalanine and tyrosine precursors for cell-based protein overexpression systems is presented. The target compounds feature isolated 13C–1H spin systems to be used in NMR probing of protein structure and dynamics.
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Affiliation(s)
- R. J. Lichtenecker
- Institute of Organic Chemistry
- University of Vienna
- A-1090 Vienna, Austria
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45
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Lichtenecker RJ, Weinhäupl K, Schmid W, Konrat R. α-Ketoacids as precursors for phenylalanine and tyrosine labelling in cell-based protein overexpression. JOURNAL OF BIOMOLECULAR NMR 2013; 57:327-331. [PMID: 24264768 DOI: 10.1007/s10858-013-9796-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 11/14/2013] [Indexed: 06/02/2023]
Abstract
(13)C-α-ketoacid metabolic precursors of phenylalanine and tyrosine effectively enter the metabolism of a protein overexpressing E. coli strain to label Phe- and Tyr-residues devoid of any cross-labelling. The methodology gives access to highly selective labelling patterns as valuable tools in protein NMR spectroscopy without the need of (15)N-chiral amino acid synthesis using organic chemistry.
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Affiliation(s)
- Roman J Lichtenecker
- Institute of Organic Chemistry, University of Vienna, Währingerstr. 38, 1090, Vienna, Austria,
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46
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Kasinath V, Valentine KG, Wand AJ. A 13C labeling strategy reveals a range of aromatic side chain motion in calmodulin. J Am Chem Soc 2013; 135:9560-3. [PMID: 23767407 DOI: 10.1021/ja4001129] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
NMR relaxation experiments often require site-specific isotopic enrichment schemes in order to allow for quantitative interpretation. Here we describe a new labeling scheme for site-specific (13)C-(1)H enrichment of a single ortho position of aromatic amino acid side chains in an otherwise perdeuterated background by employing a combination of [4-(13)C]erythrose and deuterated pyruvate during growth on deuterium oxide. This labeling scheme largely eliminates undesired contributions to (13)C relaxation and greatly simplifies the fitting of relaxation data using the Lipari-Szabo model-free formalism. This approach is illustrated with calcium-saturated vertebrate calmodulin and oxidized flavodoxin from Cyanobacterium anabaena . Analysis of (13)C relaxation in the aromatic groups of calcium-saturated calmodulin indicates a wide range of motion in the subnanosecond time regime.
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Affiliation(s)
- Vignesh Kasinath
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
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47
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Lundström P, Ahlner A, Blissing AT. Isotope labeling methods for relaxation measurements. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 992:63-82. [PMID: 23076579 DOI: 10.1007/978-94-007-4954-2_4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Nuclear magnetic spin relaxation has emerged as a powerful technique for probing molecular dynamics. Not only is it possible to use it for determination of time constant(s) for molecular reorientation but it can also be used to characterize internal motions on time scales from picoseconds to seconds. Traditionally, uniformly (15)N labeled samples have been used for these experiments but it is clear that this limits the applications. For instance, sensitivity for large systems is dramatically increased if dynamics is probed at methyl groups and structural characterization of low-populated states requires measurements on (13)Cα, (13)Cβ or (13)CO or (1)Hα. Unfortunately, homonuclear scalar couplings may lead to artifacts in the latter types of experiments and selective isotopic labeling schemes that only label the desired position are necessary. Both selective and uniform labeling schemes for measurements of relaxation rates for a large number of positions in proteins are discussed in this chapter.
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Affiliation(s)
- Patrik Lundström
- Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden.
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48
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Hiroaki H. Recent applications of isotopic labeling for protein NMR in drug discovery. Expert Opin Drug Discov 2013; 8:523-36. [PMID: 23480844 DOI: 10.1517/17460441.2013.779665] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Nuclear magnetic resonance (NMR) applications in drug discovery are classified into two categories: ligand-based methods and protein-based methods. The latter is based on the observation of the (1)H-(15)N HSQC spectra of a protein with and without lead compounds. However, in order to take this strategy, isotopic labeling is an absolute necessity. Given that each (1)H-(15)N HSQC signal corresponds to a residue of the target protein, signal changes provide specific information on whether a compound will fit into a pocket. Thus, this protein-based method is particularly suitable for fragment-based approaches, such as "SAR-by-NMR" and "fragment-growing." Alternatively, the information from a protein interface may be used to develop inhibitors for protein-protein interactions. AREAS COVERED This review discusses at the experimental procedures for preparing isotopically labeled protein and introduces selected topics on atom-specific and residue-selective isotope labeling, which may facilitate the development of PPI/PA inhibitors. Furthermore, the author reviews the recent applications of "in-cell" NMR spectroscopy, which is now considered as an important tool in drug delivery research. EXPERT OPINION Many recent advances in labeling methods have succeeded in expanding NMR's potential for drug discovery. In addition to those methods, another new technique called "in-cell NMR" allows the observation of protein-ligand interactions inside living cells. In other words, "in-cell NMR" may become a pharmaceutical NMR technique for drug delivery.
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Affiliation(s)
- Hidekazu Hiroaki
- Nagoya University, Graduate School of Pharmaceutical Sciences, Furocho, Chikusa-kum, Koto-kenkyu-kan, Nagoya, 464-8601, Japan.
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Kjaergaard M, Andersen L, Nielsen LD, Teilum K. A Folded Excited State of Ligand-Free Nuclear Coactivator Binding Domain (NCBD) Underlies Plasticity in Ligand Recognition. Biochemistry 2013; 52:1686-93. [DOI: 10.1021/bi4001062] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Magnus Kjaergaard
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200
Copenhagen N, Denmark
| | - Lisbeth Andersen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200
Copenhagen N, Denmark
| | - Lau Dalby Nielsen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200
Copenhagen N, Denmark
| | - Kaare Teilum
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200
Copenhagen N, Denmark
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50
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Weininger U, Respondek M, Akke M. Conformational exchange of aromatic side chains characterized by L-optimized TROSY-selected ¹³C CPMG relaxation dispersion. JOURNAL OF BIOMOLECULAR NMR 2012; 54:9-14. [PMID: 22833056 PMCID: PMC3427480 DOI: 10.1007/s10858-012-9656-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Accepted: 07/12/2012] [Indexed: 05/12/2023]
Abstract
Protein dynamics on the millisecond time scale commonly reflect conformational transitions between distinct functional states. NMR relaxation dispersion experiments have provided important insights into biologically relevant dynamics with site-specific resolution, primarily targeting the protein backbone and methyl-bearing side chains. Aromatic side chains represent attractive probes of protein dynamics because they are over-represented in protein binding interfaces, play critical roles in enzyme catalysis, and form an important part of the core. Here we introduce a method to characterize millisecond conformational exchange of aromatic side chains in selectively (13)C labeled proteins by means of longitudinal- and transverse-relaxation optimized CPMG relaxation dispersion. By monitoring (13)C relaxation in a spin-state selective manner, significant sensitivity enhancement can be achieved in terms of both signal intensity and the relative exchange contribution to transverse relaxation. Further signal enhancement results from optimizing the longitudinal relaxation recovery of the covalently attached (1)H spins. We validated the L-TROSY-CPMG experiment by measuring fast folding-unfolding kinetics of the small protein CspB under native conditions. The determined unfolding rate matches perfectly with previous results from stopped-flow kinetics. The CPMG-derived chemical shift differences between the folded and unfolded states are in excellent agreement with those obtained by urea-dependent chemical shift analysis. The present method enables characterization of conformational exchange involving aromatic side chains and should serve as a valuable complement to methods developed for other types of protein side chains.
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Affiliation(s)
- Ulrich Weininger
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, P.O. Box 124, 22100 Lund, Sweden
| | - Michal Respondek
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, P.O. Box 124, 22100 Lund, Sweden
| | - Mikael Akke
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, P.O. Box 124, 22100 Lund, Sweden
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