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Bartholomew GL, Kraus SL, Karas LJ, Carpaneto F, Bennett R, Sigman MS, Yeung CS, Sarpong R. 14N to 15N Isotopic Exchange of Nitrogen Heteroaromatics through Skeletal Editing. J Am Chem Soc 2024; 146:2950-2958. [PMID: 38286797 DOI: 10.1021/jacs.3c11515] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
The selective modification of nitrogen heteroaromatics enables the development of new chemical tools and accelerates drug discovery. While methods that focus on expanding or contracting the skeletal structures of heteroaromatics are emerging, methods for the direct exchange of single core atoms remain limited. Here, we present a method for 14N → 15N isotopic exchange for several aromatic nitrogen heterocycles. This nitrogen isotope transmutation occurs through activation of the heteroaromatic substrate by triflylation of a nitrogen atom, followed by a ring-opening/ring-closure sequence mediated by 15N-aspartate to effect the isotopic exchange of the nitrogen atom. Key to the success of this transformation is the formation of an isolable 15N-succinyl intermediate, which undergoes elimination to give the isotopically labeled heterocycle. These transformations occur under mild conditions in high chemical and isotopic yields.
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Affiliation(s)
- G Logan Bartholomew
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Samantha L Kraus
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Lucas J Karas
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Filippo Carpaneto
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Raffeal Bennett
- Discovery Analytical Research, Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - Matthew S Sigman
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Charles S Yeung
- Discovery Chemistry, Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - Richmond Sarpong
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
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2
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Craft DL, Schuyler AD. nus-tool: A unified program for generating and analyzing sample schedules for nonuniformly sampled NMR experiments. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 352:107458. [PMID: 37146525 PMCID: PMC10330440 DOI: 10.1016/j.jmr.2023.107458] [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: 02/16/2023] [Revised: 04/11/2023] [Accepted: 04/15/2023] [Indexed: 05/07/2023]
Abstract
Increases in digital resolution achieved by high-field NMR require increases in spectral width. Additionally, the ability to resolve two overlapping peaks requires a sufficiently long acquisition time. These constraints combine, so that achieving high resolution spectra on high-field magnets requires long experiment times when employing uniform sampling and Fourier Transform processing. These limitations may be addressed by using nonuniform sampling (NUS), but the complexity of the parameter space across the variety of available NUS schemes greatly hinders the establishment of optimal approaches and best practices. We address these challenges with nus-tool, which is a software package for generating and analyzing NUS schedules. The nus-tool software internally implements random sampling and exponentially biased sampling. Through pre-configured plug-ins, it also provides access to quantile sampling and Poisson gap sampling. The software computes the relative sensitivity, mean evolution time, point spread function, and peak-to-sidelobe ratio; all of which can be determined for a candidate sample schedule prior to running an experiment to verify expected sensitivity, resolution, and artifact suppression. The nus-tool package is freely available on the NMRbox platform through an interactive GUI and via the command line, which is especially useful for scripted workflows that investigate the effectiveness of various NUS schemes.
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Affiliation(s)
- D Levi Craft
- UConn Health, Molecular Biology and Biophysics, Farmington 06030, CT, USA
| | - Adam D Schuyler
- UConn Health, Molecular Biology and Biophysics, Farmington 06030, CT, USA.
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3
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Abstract
In-cell structural biology aims at extracting structural information about proteins or nucleic acids in their native, cellular environment. This emerging field holds great promise and is already providing new facts and outlooks of interest at both fundamental and applied levels. NMR spectroscopy has important contributions on this stage: It brings information on a broad variety of nuclei at the atomic scale, which ensures its great versatility and uniqueness. Here, we detail the methods, the fundamental knowledge, and the applications in biomedical engineering related to in-cell structural biology by NMR. We finally propose a brief overview of the main other techniques in the field (EPR, smFRET, cryo-ET, etc.) to draw some advisable developments for in-cell NMR. In the era of large-scale screenings and deep learning, both accurate and qualitative experimental evidence are as essential as ever to understand the interior life of cells. In-cell structural biology by NMR spectroscopy can generate such a knowledge, and it does so at the atomic scale. This review is meant to deliver comprehensive but accessible information, with advanced technical details and reflections on the methods, the nature of the results, and the future of the field.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
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4
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Klein A, Vasa SK, Söldner B, Grohe K, Linser R. Unambiguous Side-Chain Assignments for Solid-State NMR Structure Elucidation of Nondeuterated Proteins via a Combined 5D/4D Side-Chain-to-Backbone Experiment. J Phys Chem Lett 2022; 13:1644-1651. [PMID: 35147439 DOI: 10.1021/acs.jpclett.1c04075] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Owing to fast-magic-angle-spinning technology, proton-detected solid-state NMR has been facilitating the analysis of insoluble, crystalline, sedimented, and membrane proteins. However, potential applications have been largely restricted by limited access to side-chain resonances. The recent availability of spinning frequencies exceeding 100 kHz in principle now allows direct probing of all protons without the need for partial deuteration. This potentiates both the number of accessible target proteins and possibilities to exploit side-chain protons as reporters on distances and interactions. Their low dispersion, however, has severely compromised their chemical-shift assignment, which is a prerequisite for their use in downstream applications. Herein, we show that unambiguous correlations are obtained from 5D methodology by which the side-chain resonances are directly connected with the backbone. When further concatenated with simultaneous 4D intra-side-chain correlations, this yields comprehensive assignments in the side chains and hence allows a high density of distance restraints for high-resolution structure calculation from minimal amounts of protein.
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Affiliation(s)
- Alexander Klein
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227 Dortmund, Germany
| | - Suresh K Vasa
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227 Dortmund, Germany
| | - Benedikt Söldner
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227 Dortmund, Germany
| | - Kristof Grohe
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227 Dortmund, Germany
| | - Rasmus Linser
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227 Dortmund, Germany
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5
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Porat G, Lusky OS, Dayan N, Goldbourt A. Nonuniformly sampled exclusively- 13 C/ 15 N 4D solid-state NMR experiments: Assignment and characterization of IKe phage capsid. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:237-246. [PMID: 32603513 DOI: 10.1002/mrc.5072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/11/2020] [Accepted: 06/27/2020] [Indexed: 06/11/2023]
Abstract
An important step in the process of protein research by NMR is the assignment of chemical shifts. In the coat protein of IKe bacteriophage, there are 53 residues making up a long helix resulting in relatively high spectral ambiguity. Assignment thus requires the collection of a set of three-dimensional (3D) experiments and the preparation of sparsely labeled samples. Increasing the dimensionality can facilitate fast and reliable assignment of IKe and of larger proteins. Recent progress in nonuniform sampling techniques made the application of multidimensional NMR solid-state experiments beyond 3D more practical. 4D 1 H-detected experiments have been demonstrated in high-fields and at spinning speeds of 60 kHz and higher but are not practical at spinning speeds of 10-20 kHz for fully protonated proteins. Here, we demonstrate the applicability of a nonuniformly sampled 4D 13 C/15 N-only correlation experiment performed at a moderate field of 14.1 T, which can incorporate sufficiently long acquisition periods in all dimensions. We show how a single CANCOCX experiment, supported by several 2D carbon-based correlation experiments, is utilized for the assignment of heteronuclei in the coat protein of the IKe bacteriophage. One sparsely labeled sample was used to validate sidechain assignment of several hydrophobic-residue sidechains. A comparison to solution NMR studies of isolated IKe coat proteins embedded in micelles points to key residues involved in structural rearrangement of the capsid upon assembly of the virus. The benefits of 4D to a quicker assignment are discussed, and the method may prove useful for studying proteins at relatively low fields.
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Affiliation(s)
- Gal Porat
- School of Chemistry, Tel Aviv University, Ramat Aviv, Tel Aviv, 6997801, Israel
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, 19716, USA
| | - Orr Simon Lusky
- School of Chemistry, Tel Aviv University, Ramat Aviv, Tel Aviv, 6997801, Israel
| | - Nir Dayan
- School of Chemistry, Tel Aviv University, Ramat Aviv, Tel Aviv, 6997801, Israel
- Schulich Faculty of Chemistry, Technion-Institute of Technology, Haifa, Israel
| | - Amir Goldbourt
- School of Chemistry, Tel Aviv University, Ramat Aviv, Tel Aviv, 6997801, Israel
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6
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Kaur M, Lewis CM, Chronister A, Phun GS, Mueller LJ. Non-Uniform Sampling in NMR Spectroscopy and the Preservation of Spectral Knowledge in the Time and Frequency Domains. J Phys Chem A 2020; 124:5474-5486. [PMID: 32496067 DOI: 10.1021/acs.jpca.0c02930] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The increased sensitivity under weighted non-uniform sampling (NUS) is demonstrated and quantified using Monte Carlo simulations of nuclear magnetic resonance (NMR) time- and frequency-domain signals. The concept of spectral knowledge is introduced and shown to be superior to the frequency-domain signal-to-noise ratio for assessing the quality of NMR data. Two methods for rigorously preserving spectral knowledge and the time-domain NUS knowledge enhancement upon transformation to the frequency domain are demonstrated, both theoretically and numerically. The first, non-uniform weighted sampling using consistent root-mean-square noise, is applicable to data sampled on the Nyquist grid, whereas the second, the block Fourier transform using consistent root-mean-square noise, can be used to transform time-domain data acquired with arbitrary, off-grid NUS.
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Affiliation(s)
- Manpreet Kaur
- Department of Chemistry, University of California, Riverside, Riverside, California 92521, United States
| | - Callie M Lewis
- Department of Chemistry, University of California, Riverside, Riverside, California 92521, United States
| | - Aaron Chronister
- Department of Chemistry, University of California, Riverside, Riverside, California 92521, United States
| | - Gabriel S Phun
- Department of Chemistry, University of California, Riverside, Riverside, California 92521, United States
| | - Leonard J Mueller
- Department of Chemistry, University of California, Riverside, Riverside, California 92521, United States
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7
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Zapletal V, Mládek A, Melková K, Louša P, Nomilner E, Jaseňáková Z, Kubáň V, Makovická M, Laníková A, Žídek L, Hritz J. Choice of Force Field for Proteins Containing Structured and Intrinsically Disordered Regions. Biophys J 2020; 118:1621-1633. [PMID: 32367806 DOI: 10.1016/j.bpj.2020.02.019] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 01/06/2020] [Accepted: 02/05/2020] [Indexed: 12/23/2022] Open
Abstract
Biomolecular force fields optimized for globular proteins fail to properly reproduce properties of intrinsically disordered proteins. In particular, parameters of the water model need to be modified to improve applicability of the force fields to both ordered and disordered proteins. Here, we compared performance of force fields recommended for intrinsically disordered proteins in molecular dynamics simulations of three proteins differing in the content of ordered and disordered regions (two proteins consisting of a well-structured domain and of a disordered region with and without a transient helical motif and one disordered protein containing a region of increased helical propensity). The obtained molecular dynamics trajectories were used to predict measurable parameters, including radii of gyration of the proteins and chemical shifts, residual dipolar couplings, paramagnetic relaxation enhancement, and NMR relaxation data of their individual residues. The predicted quantities were compared with experimental data obtained within this study or published previously. The results showed that the NMR relaxation parameters, rarely used for benchmarking, are particularly sensitive to the choice of force-field parameters, especially those defining the water model. Interestingly, the TIP3P water model, leading to an artificial structural collapse, also resulted in unrealistic relaxation properties. The TIP4P-D water model, combined with three biomolecular force-field parameters for the protein part, significantly improved reliability of the simulations. Additional analysis revealed only one particular force field capable of retaining the transient helical motif observed in NMR experiments. The benchmarking protocol used in our study, being more sensitive to imperfections than the commonly used tests, is well suited to evaluate the performance of newly developed force fields.
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Affiliation(s)
- Vojtěch Zapletal
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic; Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Arnošt Mládek
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Kateřina Melková
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic; Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Petr Louša
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Erik Nomilner
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Zuzana Jaseňáková
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic; Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Vojtěch Kubáň
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic; Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Markéta Makovická
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Alice Laníková
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Lukáš Žídek
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic; Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Jozef Hritz
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
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8
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Orton HW, Stanek J, Schubeis T, Foucaudeau D, Ollier C, Draney AW, Le Marchand T, Cala‐De Paepe D, Felli IC, Pierattelli R, Hiller S, Bermel W, Pintacuda G. Protein‐NMR‐Resonanzzuordnung ohne Spektralanalyse: automatisierte Festkörper‐Projektionsspektroskopie in 5D (SO‐APSY). Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201912211] [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)
- Henry W. Orton
- Research School of ChemistryAustralian National University Canberra ACT 2601 Australien
| | - Jan Stanek
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs (FRE 2034 CNRS, UCBL, ENS Lyon)Université de Lyon 69100 Villeurbanne Frankreich
- Faculty of ChemistryUniversity of Warsaw 02089 Warsaw Polen
| | - Tobias Schubeis
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs (FRE 2034 CNRS, UCBL, ENS Lyon)Université de Lyon 69100 Villeurbanne Frankreich
| | - Dylan Foucaudeau
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs (FRE 2034 CNRS, UCBL, ENS Lyon)Université de Lyon 69100 Villeurbanne Frankreich
| | - Claire Ollier
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs (FRE 2034 CNRS, UCBL, ENS Lyon)Université de Lyon 69100 Villeurbanne Frankreich
| | - Adrian W. Draney
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs (FRE 2034 CNRS, UCBL, ENS Lyon)Université de Lyon 69100 Villeurbanne Frankreich
| | - Tanguy Le Marchand
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs (FRE 2034 CNRS, UCBL, ENS Lyon)Université de Lyon 69100 Villeurbanne Frankreich
| | - Diane Cala‐De Paepe
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs (FRE 2034 CNRS, UCBL, ENS Lyon)Université de Lyon 69100 Villeurbanne Frankreich
| | - Isabella C. Felli
- CERM and Department of ChemistryUniversity of Florence 50019 Sesto Fiorentino Italien
| | - Roberta Pierattelli
- CERM and Department of ChemistryUniversity of Florence 50019 Sesto Fiorentino Italien
| | | | - Wolfgang Bermel
- Bruker BioSpin GmbH Silberstreifen 76287 Rheinstetten Deutschland
| | - Guido Pintacuda
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs (FRE 2034 CNRS, UCBL, ENS Lyon)Université de Lyon 69100 Villeurbanne Frankreich
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9
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Orton HW, Stanek J, Schubeis T, Foucaudeau D, Ollier C, Draney AW, Le Marchand T, Cala‐De Paepe D, Felli IC, Pierattelli R, Hiller S, Bermel W, Pintacuda G. Protein NMR Resonance Assignment without Spectral Analysis: 5D SOlid‐State Automated Projection SpectroscopY (SO‐APSY). Angew Chem Int Ed Engl 2020; 59:2380-2384. [DOI: 10.1002/anie.201912211] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Indexed: 01/18/2023]
Affiliation(s)
- Henry W. Orton
- Research School of ChemistryAustralian National University Canberra ACT 2601 Australia
| | - Jan Stanek
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs (FRE 2034 CNRS, UCBL, ENS Lyon)Université de Lyon 69100 Villeurbanne France
- Faculty of ChemistryUniversity of Warsaw 02089 Warsaw Poland
| | - Tobias Schubeis
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs (FRE 2034 CNRS, UCBL, ENS Lyon)Université de Lyon 69100 Villeurbanne France
| | - Dylan Foucaudeau
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs (FRE 2034 CNRS, UCBL, ENS Lyon)Université de Lyon 69100 Villeurbanne France
| | - Claire Ollier
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs (FRE 2034 CNRS, UCBL, ENS Lyon)Université de Lyon 69100 Villeurbanne France
| | - Adrian W. Draney
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs (FRE 2034 CNRS, UCBL, ENS Lyon)Université de Lyon 69100 Villeurbanne France
| | - Tanguy Le Marchand
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs (FRE 2034 CNRS, UCBL, ENS Lyon)Université de Lyon 69100 Villeurbanne France
| | - Diane Cala‐De Paepe
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs (FRE 2034 CNRS, UCBL, ENS Lyon)Université de Lyon 69100 Villeurbanne France
| | - Isabella C. Felli
- CERM and Department of ChemistryUniversity of Florence 50019 Sesto Fiorentino Italy
| | - Roberta Pierattelli
- CERM and Department of ChemistryUniversity of Florence 50019 Sesto Fiorentino Italy
| | | | - Wolfgang Bermel
- Bruker BioSpin GmbH Silberstreifen 76287 Rheinstetten Germany
| | - Guido Pintacuda
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs (FRE 2034 CNRS, UCBL, ENS Lyon)Université de Lyon 69100 Villeurbanne France
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10
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Gołowicz D, Kasprzak P, Orekhov V, Kazimierczuk K. Fast time-resolved NMR with non-uniform sampling. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2020; 116:40-55. [PMID: 32130958 DOI: 10.1016/j.pnmrs.2019.09.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/18/2019] [Accepted: 09/19/2019] [Indexed: 06/10/2023]
Abstract
NMR spectroscopy is a versatile tool for studying time-dependent processes: chemical reactions, phase transitions or macromolecular structure changes. However, time-resolved NMR is usually based on the simplest among available techniques - one-dimensional spectra serving as "snapshots" of the studied process. One of the reasons is that multidimensional experiments are very time-expensive due to costly sampling of evolution time space. In this review we summarize efforts to alleviate the problem of limited applicability of multidimensional NMR in time-resolved studies. We focus on techniques based on sparse or non-uniform sampling (NUS), which lead to experimental time reduction by omitting a significant part of the data during measurement and reconstructing it mathematically, adopting certain assumptions about the spectrum. NUS spectra are faster to acquire than conventional ones and thus better suited to the role of "snapshots", but still suffer from non-stationarity of the signal i.e. amplitude and frequency variations within a dataset. We discuss in detail how these instabilities affect the spectra, and what are the optimal ways of sampling the non-stationary FID signal. Finally, we discuss related areas of NMR where serial experiments are exploited and how they can benefit from the same NUS-based approaches.
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Affiliation(s)
- Dariusz Gołowicz
- Centre of New Technologies, University of Warsaw, Banacha 2C, Warsaw 02-097, Poland; Faculty of Chemistry, University of Warsaw, Pasteura 1, Warsaw 02-093, Poland.
| | - Paweł Kasprzak
- Centre of New Technologies, University of Warsaw, Banacha 2C, Warsaw 02-097, Poland; Department of Mathematical Methods in Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland.
| | - Vladislav Orekhov
- Department of Chemistry & Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden.
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11
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Löhr F, Gebel J, Henrich E, Hein C, Dötsch V. Towards complete polypeptide backbone NH assignment via combinatorial labeling. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 302:50-63. [PMID: 30959416 DOI: 10.1016/j.jmr.2019.03.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 03/27/2019] [Accepted: 03/28/2019] [Indexed: 06/09/2023]
Abstract
Combinatorial selective isotope labeling is a valuable tool to facilitate polypeptide backbone resonance assignment in cases of low sensitivity or extensive chemical shift degeneracy. It involves recording of 15N-HSQC and 2D HN-projections of triple-resonance spectra on a limited set of samples containing different combinations of labeled and unlabeled amino acid types. Using labeling schemes in which the three backbone heteronuclei (amide nitrogen, α-carbon and carbonyl carbon) are enriched in 15N or 13C isotopes - individually as well as simultaneously - usually yields abundant amino-acid type information of consecutive residues i and i - 1. Although this results in a large number of anchor points that can be used in the sequential assignment process, for most amide signals the exact positioning of the corresponding residue the polypeptide sequence still relies on matching intra- and interresidual 13C chemical shifts obtained from 3D spectra. An obvious way to obtain more sequence-specific assignments directly with combinatorial labeling would be to increase the number of samples. This is, however, undesirable because of increased sample preparation efforts and costs. Irrespective of the number of samples, unambiguous assignments cannot be accomplished for i - 1/i pairs that are not unique in the sequence. Here we show that the ambiguity for non-unique pairs can be resolved by including information about the labeling state of residues i + 1 and i - 2. Application to a 35-residue peptide resulted in complete assignments of all detectable signals in the 15N HSQC which, due to its repetitive sequence and 13C chemical shift degeneracies, was difficult to achieve by other means. For a medium-sized protein (165 residues, rotational correlation time 8.2 ns) the improved protocol allowed the extent of backbone amide assignment to be expanded to 88% solely using a suite of 2D 1H-15N correlated spectra.
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Affiliation(s)
- Frank Löhr
- Institute of Biophysical Chemistry & Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Jakob Gebel
- Institute of Biophysical Chemistry & Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Erik Henrich
- Institute of Biophysical Chemistry & Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Christopher Hein
- Institute of Biophysical Chemistry & Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry & Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany.
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12
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Deev SL, Khalymbadzha IA, Shestakova TS, Charushin VN, Chupakhin ON. 15N labeling and analysis of 13C–15N and 1H–15N couplings in studies of the structures and chemical transformations of nitrogen heterocycles. RSC Adv 2019; 9:26856-26879. [PMID: 35528595 PMCID: PMC9070671 DOI: 10.1039/c9ra04825a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 08/19/2019] [Indexed: 11/21/2022] Open
Abstract
This review provides a generalization of effective examples of 15N labeling followed by an analysis of JCN and JHN couplings in solution as a tool to study the structural aspects and pathways of chemical transformations in nitrogen heterocycles.
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Affiliation(s)
- Sergey L. Deev
- Ural Federal University
- 620002 Yekaterinburg
- Russian Federation
- I. Ya. Postovsky Institute of Organic Synthesis
- 620219 Yekaterinburg
| | | | | | - Valery N. Charushin
- Ural Federal University
- 620002 Yekaterinburg
- Russian Federation
- I. Ya. Postovsky Institute of Organic Synthesis
- 620219 Yekaterinburg
| | - Oleg N. Chupakhin
- Ural Federal University
- 620002 Yekaterinburg
- Russian Federation
- I. Ya. Postovsky Institute of Organic Synthesis
- 620219 Yekaterinburg
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13
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Klein A, Vasa SK, Linser R. Automated projection spectroscopy in solid-state NMR. JOURNAL OF BIOMOLECULAR NMR 2018; 72:163-170. [PMID: 30430291 DOI: 10.1007/s10858-018-0215-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 11/06/2018] [Indexed: 06/09/2023]
Abstract
Given that solid-state NMR is being used for protein samples of increasing molecular weight and complexity, higher-dimensionality methods are likely to be more and more indispensable for unambiguous chemical shift assignments in the near future. In addition, solid-state NMR spectral properties are increasingly comparable with solution NMR, allowing adaptation of more sophisticated solution NMR strategies for the solid state in addition to the conventional methodology. Assessing first principles, here we demonstrate the application of automated projection spectroscopy for a micro-crystalline protein in the solid state.
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Affiliation(s)
- Alexander Klein
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany
- Center for Integrated Protein Science (CiPSM), Munich, Germany
| | - Suresh K Vasa
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany
- Center for Integrated Protein Science (CiPSM), Munich, Germany
| | - Rasmus Linser
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany.
- Center for Integrated Protein Science (CiPSM), Munich, Germany.
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Straße 4a, 44227, Dortmund, Germany.
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14
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Grudziąż K, Zawadzka-Kazimierczuk A, Koźmiński W. High-dimensional NMR methods for intrinsically disordered proteins studies. Methods 2018; 148:81-87. [PMID: 29705209 DOI: 10.1016/j.ymeth.2018.04.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 04/24/2018] [Indexed: 01/16/2023] Open
Abstract
Intrinsically disordered proteins (IDPs) are getting more and more interest of the scientific community. Nuclear magnetic resonance (NMR) is often a technique of choice for these studies, as it provides atomic-resolution information on structure, dynamics and interactions of IDPs. Nonetheless, NMR spectra of IDPs are typically extraordinary crowded, comparing to those of structured proteins. To overcome this problem, high-dimensional NMR experiments can be used, which allow for a better peak separation. In the present review different aspects of such experiments are discussed, from data acquisition and processing to analysis, focusing on experiments for resonance assignment.
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Affiliation(s)
- Katarzyna Grudziąż
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Anna Zawadzka-Kazimierczuk
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Wiktor Koźmiński
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland.
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15
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Kosiński K, Stanek J, Górka MJ, Żerko S, Koźmiński W. Reconstruction of non-uniformly sampled five-dimensional NMR spectra by signal separation algorithm. JOURNAL OF BIOMOLECULAR NMR 2017; 68:129-138. [PMID: 28243768 PMCID: PMC5504137 DOI: 10.1007/s10858-017-0095-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 02/08/2017] [Indexed: 05/31/2023]
Abstract
A method for five-dimensional spectral reconstruction of non-uniformly sampled NMR data sets is proposed. It is derived from the previously published signal separation algorithm, with major alterations to avoid unfeasible processing of an entire five-dimensional spectrum. The proposed method allows credible reconstruction of spectra from as little as a few hundred data points and enables sensitive resonance detection in experiments with a high dynamic range of peak intensities. The efficiency of the method is demonstrated on two high-resolution spectra for rapid sequential assignment of intrinsically disordered proteins, namely 5D HN(CA)CONH and 5D (HACA)CON(CO)CONH.
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Affiliation(s)
- Krzysztof Kosiński
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Jan Stanek
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Michał J Górka
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
- Faculty of Physics, Division of Biophysics, Institute of Experimental Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Szymon Żerko
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Wiktor Koźmiński
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland.
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16
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Ying J, Delaglio F, Torchia DA, Bax A. Sparse multidimensional iterative lineshape-enhanced (SMILE) reconstruction of both non-uniformly sampled and conventional NMR data. JOURNAL OF BIOMOLECULAR NMR 2017; 68:101-118. [PMID: 27866371 PMCID: PMC5438302 DOI: 10.1007/s10858-016-0072-7] [Citation(s) in RCA: 197] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 10/25/2016] [Indexed: 05/03/2023]
Abstract
Implementation of a new algorithm, SMILE, is described for reconstruction of non-uniformly sampled two-, three- and four-dimensional NMR data, which takes advantage of the known phases of the NMR spectrum and the exponential decay of underlying time domain signals. The method is very robust with respect to the chosen sampling protocol and, in its default mode, also extends the truncated time domain signals by a modest amount of non-sampled zeros. SMILE can likewise be used to extend conventional uniformly sampled data, as an effective multidimensional alternative to linear prediction. The program is provided as a plug-in to the widely used NMRPipe software suite, and can be used with default parameters for mainstream application, or with user control over the iterative process to possibly further improve reconstruction quality and to lower the demand on computational resources. For large data sets, the method is robust and demonstrated for sparsities down to ca 1%, and final all-real spectral sizes as large as 300 Gb. Comparison between fully sampled, conventionally processed spectra and randomly selected NUS subsets of this data shows that the reconstruction quality approaches the theoretical limit in terms of peak position fidelity and intensity. SMILE essentially removes the noise-like appearance associated with the point-spread function of signals that are a default of five-fold above the noise level, but impacts the actual thermal noise in the NMR spectra only minimally. Therefore, the appearance and interpretation of SMILE-reconstructed spectra is very similar to that of fully sampled spectra generated by Fourier transformation.
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Affiliation(s)
- Jinfa Ying
- Laboratory of Chemical Physics, National Institute of Digestive and Diabetic and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Frank Delaglio
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD, 20850, USA
| | - Dennis A Torchia
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Digestive and Diabetic and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
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17
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Göbl C, Resch M, Strickland M, Hartlmüller C, Viertler M, Tjandra N, Madl T. Verbesserung der Dispersion der chemischen Verschiebungen von unstrukturierten Proteinen durch einen kovalent gebundenen Lanthanoidkomplex. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201607261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Christoph Göbl
- Center for Integrated Protein Science Munich; Technische Universität München; Fakultät für Chemie; Lichtenbergstraße 4 85748 Garching Deutschland
- Institut für Strukturbiologie; Helmholtz Zentrum München; Ingolstädter Landstr. 1 85764 Neuherberg Deutschland
| | - Moritz Resch
- Center for Integrated Protein Science Munich; Technische Universität München; Fakultät für Chemie; Lichtenbergstraße 4 85748 Garching Deutschland
- Institut für Strukturbiologie; Helmholtz Zentrum München; Ingolstädter Landstr. 1 85764 Neuherberg Deutschland
| | - Madeleine Strickland
- Laboratory of Structural Biophysics Biochemistry and Biophysics Center; National Heart, Lung, and Blood Institute; National Institutes of Health; Building 50 Bethesda MD 20814 USA
| | - Christoph Hartlmüller
- Center for Integrated Protein Science Munich; Technische Universität München; Fakultät für Chemie; Lichtenbergstraße 4 85748 Garching Deutschland
- Institut für Strukturbiologie; Helmholtz Zentrum München; Ingolstädter Landstr. 1 85764 Neuherberg Deutschland
| | - Martin Viertler
- Institut für Strukturbiologie; Helmholtz Zentrum München; Ingolstädter Landstr. 1 85764 Neuherberg Deutschland
| | - Nico Tjandra
- Laboratory of Structural Biophysics Biochemistry and Biophysics Center; National Heart, Lung, and Blood Institute; National Institutes of Health; Building 50 Bethesda MD 20814 USA
| | - Tobias Madl
- Center for Integrated Protein Science Munich; Technische Universität München; Fakultät für Chemie; Lichtenbergstraße 4 85748 Garching Deutschland
- Institut für Strukturbiologie; Helmholtz Zentrum München; Ingolstädter Landstr. 1 85764 Neuherberg Deutschland
- Institut für Molekularbiologie & Biochemie; Zentrum für Medizinische Forschung; Medizinische Universität Graz; 8010 Graz Österreich
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18
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Göbl C, Resch M, Strickland M, Hartlmüller C, Viertler M, Tjandra N, Madl T. Increasing the Chemical-Shift Dispersion of Unstructured Proteins with a Covalent Lanthanide Shift Reagent. Angew Chem Int Ed Engl 2016; 55:14847-14851. [PMID: 27763708 PMCID: PMC5146990 DOI: 10.1002/anie.201607261] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/16/2016] [Indexed: 01/19/2023]
Abstract
The study of intrinsically disordered proteins (IDPs) by NMR often suffers from highly overlapped resonances that prevent unambiguous chemical-shift assignments, and data analysis that relies on well-separated resonances. We present a covalent paramagnetic lanthanide-binding tag (LBT) for increasing the chemical-shift dispersion and facilitating the chemical-shift assignment of challenging, repeat-containing IDPs. Linkage of the DOTA-based LBT to a cysteine residue induces pseudo-contact shifts (PCS) for resonances more than 20 residues from the spin-labeling site. This leads to increased chemical-shift dispersion and decreased signal overlap, thereby greatly facilitating chemical-shift assignment. This approach is applicable to IDPs of varying sizes and complexity, and is particularly helpful for repeat-containing IDPs and low-complexity regions. This results in improved efficiency for IDP analysis and binding studies.
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Affiliation(s)
- Christoph Göbl
- Center for Integrated Protein Science Munich, Technische Universität München, Department of Chemistry, Lichtenbergstraße 4, 85748, Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Moritz Resch
- Center for Integrated Protein Science Munich, Technische Universität München, Department of Chemistry, Lichtenbergstraße 4, 85748, Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Madeleine Strickland
- Laboratory of Structural Biophysics Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Building 50, Bethesda, MD, 20814, USA
| | - Christoph Hartlmüller
- Center for Integrated Protein Science Munich, Technische Universität München, Department of Chemistry, Lichtenbergstraße 4, 85748, Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Martin Viertler
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Nico Tjandra
- Laboratory of Structural Biophysics Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Building 50, Bethesda, MD, 20814, USA
| | - Tobias Madl
- Center for Integrated Protein Science Munich, Technische Universität München, Department of Chemistry, Lichtenbergstraße 4, 85748, Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Institute of Molecular Biology & Biochemistry, Center of Molecular Medicine, Medical University of Graz, 8010, Graz, Austria
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19
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Żerko S, Byrski P, Włodarczyk-Pruszyński P, Górka M, Ledolter K, Masliah E, Konrat R, Koźmiński W. Five and four dimensional experiments for robust backbone resonance assignment of large intrinsically disordered proteins: application to Tau3x protein. JOURNAL OF BIOMOLECULAR NMR 2016; 65:193-203. [PMID: 27430223 PMCID: PMC4983291 DOI: 10.1007/s10858-016-0048-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 07/09/2016] [Indexed: 05/04/2023]
Abstract
New experiments dedicated for large IDPs backbone resonance assignment are presented. The most distinctive feature of all described techniques is the employment of MOCCA-XY16 mixing sequences to obtain effective magnetization transfers between carbonyl carbon backbone nuclei. The proposed 4 and 5 dimensional experiments provide a high dispersion of obtained signals making them suitable for use in the case of large IDPs (application to 354 a. a. residues of Tau protein 3x isoform is presented) as well as provide both forward and backward connectivities. What is more, connecting short chains interrupted with proline residues is also possible. All the experiments employ non-uniform sampling.
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Affiliation(s)
- Szymon Żerko
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 02093, Warsaw, Poland
| | - Piotr Byrski
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 02093, Warsaw, Poland
| | | | - Michał Górka
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 02093, Warsaw, Poland
- Section of Biophysics, Faculty of Physics, University of Warsaw, 02093, Warsaw, Poland
| | - Karin Ledolter
- Department of Computational and Structural Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Eliezer Masliah
- Departments of Neuroscience and Pathology, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Robert Konrat
- Department of Computational and Structural Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Wiktor Koźmiński
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 02093, Warsaw, Poland.
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20
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Wiedemann C, Bellstedt P, Häfner S, Herbst C, Bordusa F, Görlach M, Ohlenschläger O, Ramachandran R. A Set of Efficient nD NMR Protocols for Resonance Assignments of Intrinsically Disordered Proteins. Chemphyschem 2016; 17:1961-8. [PMID: 27061973 DOI: 10.1002/cphc.201600155] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Indexed: 11/07/2022]
Abstract
The RF pulse scheme RN[N-CA HEHAHA]NH, which provides a convenient approach to the acquisition of different multidimensional chemical shift correlation NMR spectra leading to backbone resonance assignments, including those of the proline residues of intrinsically disordered proteins (IDPs), is experimentally demonstrated. Depending on the type of correlation data required, the method involves the generation of in-phase ((15) N)(x) magnetisation via different magnetisation transfer pathways such as H→N→CO→N, HA→CA→CO→N, H→N→CA→N and H→CA→N, the subsequent application of (15) N-(13) C(α) heteronuclear Hartmann-Hahn mixing over a period of ≈100 ms, chemical-shift labelling of relevant nuclei before and after the heteronuclear mixing step and amide proton detection in the acquisition dimension. It makes use of the favourable relaxation properties of IDPs and the presence of (1) JCαN and (2) JCαN couplings to achieve efficient correlation of the backbone resonances of each amino acid residue "i" with the backbone amide resonances of residues "i-1" and "i+1". It can be implemented in a straightforward way through simple modifications of the RF pulse schemes commonly employed in protein NMR studies. The efficacy of the approach is demonstrated using a uniformly ((15) N,(13) C) labelled sample of α-synuclein. The different possibilities for obtaining the amino-acid-type information, simultaneously with the connectivity data between the backbone resonances of sequentially neighbouring residues, have also been outlined.
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Affiliation(s)
- Christoph Wiedemann
- Institute of Biochemistry/Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle/Saale, Germany
| | - Peter Bellstedt
- Faculty of Chemistry and Earth Sciences, Friedrich Schiller University Jena, Humboldstr. 10, 07743, Jena, Germany
| | - Sabine Häfner
- Leibniz Institute on Aging/Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany
| | - Christian Herbst
- Department of Physics, Faculty of Science, Ubon Ratchathani University, 34190, Ubon Ratchathani, Thailand
| | - Frank Bordusa
- Institute of Biochemistry/Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle/Saale, Germany
| | - Matthias Görlach
- Leibniz Institute on Aging/Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany
| | - Oliver Ohlenschläger
- Leibniz Institute on Aging/Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany
| | - Ramadurai Ramachandran
- Leibniz Institute on Aging/Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany.
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21
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Piai A, Gonnelli L, Felli IC, Pierattelli R, Kazimierczuk K, Grudziąż K, Koźmiński W, Zawadzka-Kazimierczuk A. Amino acid recognition for automatic resonance assignment of intrinsically disordered proteins. JOURNAL OF BIOMOLECULAR NMR 2016; 64:239-53. [PMID: 26891900 PMCID: PMC4824835 DOI: 10.1007/s10858-016-0024-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 02/11/2016] [Indexed: 05/07/2023]
Abstract
Resonance assignment is a prerequisite for almost any NMR-based study of proteins. It can be very challenging in some cases, however, due to the nature of the protein under investigation. This is the case with intrinsically disordered proteins, for example, whose NMR spectra suffer from low chemical shifts dispersion and generally low resolution. For these systems, sequence specific assignment is highly time-consuming, so the prospect of using automatic strategies for their assignment is very attractive. In this article we present a new version of the automatic assignment program TSAR dedicated to intrinsically disordered proteins. In particular, we demonstrate how the automatic procedure can be improved by incorporating methods for amino acid recognition and information on chemical shifts in selected amino acids. The approach was tested in silico on 16 disordered proteins and experimentally on α-synuclein, with remarkably good results.
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Affiliation(s)
- Alessandro Piai
- CERM and Department of Chemistry Ugo Schiff, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019, Florence, Italy
| | - Leonardo Gonnelli
- CERM and Department of Chemistry Ugo Schiff, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019, Florence, Italy
| | - Isabella C Felli
- CERM and Department of Chemistry Ugo Schiff, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019, Florence, Italy
| | - Roberta Pierattelli
- CERM and Department of Chemistry Ugo Schiff, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019, Florence, Italy
| | | | - Katarzyna Grudziąż
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Wiktor Koźmiński
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Anna Zawadzka-Kazimierczuk
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland.
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22
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Dubey A, Kadumuri RV, Jaipuria G, Vadrevu R, Atreya HS. Rapid NMR Assignments of Proteins by Using Optimized Combinatorial Selective Unlabeling. Chembiochem 2016; 17:334-40. [DOI: 10.1002/cbic.201500513] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Abhinav Dubey
- NMR Research Center; Indian Institute of Science, Malleswaram; Bangalore 560012 India
- IISc Mathematics Initiative; Indian Institute of Science, Malleswaram; Bangalore 560012 India
| | - Rajashekar Varma Kadumuri
- Department of Biological Sciences; Birla Institute of Technology and Science-Pilani; Hyderabad Campus Hyderabad 500078 India
| | - Garima Jaipuria
- NMR Research Center; Indian Institute of Science, Malleswaram; Bangalore 560012 India
| | - Ramakrishna Vadrevu
- Department of Biological Sciences; Birla Institute of Technology and Science-Pilani; Hyderabad Campus Hyderabad 500078 India
| | - Hanudatta S. Atreya
- NMR Research Center; Indian Institute of Science, Malleswaram; Bangalore 560012 India
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23
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Cousin SF, Charlier C, Kadeřávek P, Marquardsen T, Tyburn JM, Bovier PA, Ulzega S, Speck T, Wilhelm D, Engelke F, Maas W, Sakellariou D, Bodenhausen G, Pelupessy P, Ferrage F. High-resolution two-field nuclear magnetic resonance spectroscopy. Phys Chem Chem Phys 2016; 18:33187-33194. [DOI: 10.1039/c6cp05422f] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two-field NMR provides correlations of nuclear spins at the most favourable magnetic fields in a single experiment.
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Affiliation(s)
- Samuel F. Cousin
- Département de Chimie
- Ecole Normale Supérieure
- PSL Research University
- UPMC Univ Paris 06
- CNRS
| | - Cyril Charlier
- Département de Chimie
- Ecole Normale Supérieure
- PSL Research University
- UPMC Univ Paris 06
- CNRS
| | - Pavel Kadeřávek
- Département de Chimie
- Ecole Normale Supérieure
- PSL Research University
- UPMC Univ Paris 06
- CNRS
| | | | | | | | | | | | | | | | | | | | - Geoffrey Bodenhausen
- Département de Chimie
- Ecole Normale Supérieure
- PSL Research University
- UPMC Univ Paris 06
- CNRS
| | - Philippe Pelupessy
- Département de Chimie
- Ecole Normale Supérieure
- PSL Research University
- UPMC Univ Paris 06
- CNRS
| | - Fabien Ferrage
- Département de Chimie
- Ecole Normale Supérieure
- PSL Research University
- UPMC Univ Paris 06
- CNRS
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24
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Saxena S, Stanek J, Cevec M, Plavec J, Koźmiński W. High resolution 4D HPCH experiment for sequential assignment of (13)C-labeled RNAs via phosphodiester backbone. JOURNAL OF BIOMOLECULAR NMR 2015; 63:291-298. [PMID: 26409925 PMCID: PMC4642592 DOI: 10.1007/s10858-015-9989-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Accepted: 09/20/2015] [Indexed: 06/05/2023]
Abstract
The three-dimensional structure determination of RNAs by NMR spectroscopy requires sequential resonance assignment, often hampered by assignment ambiguities and limited dispersion of (1)H and (13)C chemical shifts, especially of C4'/H4'. Here we present a novel through-bond 4D HPCH NMR experiment involving phosphate backbone where C4'-H4' correlations are resolved along the (1)H3'-(31)P spectral planes. The experiment provides high peak resolution and effectively removes ambiguities encountered during assignments. Enhanced peak dispersion is provided by the inclusion of additional (31)P and (1)H3' dimensions and constant-time evolution of chemical shifts. High spectral resolution is obtained by using non-uniform sampling in three indirect dimensions. The experiment fully utilizes the isotopic (13)C-labeling with evolution of C4' carbons. Band selective (13)C inversion pulses are used to achieve selectivity and prevent signal dephasing due to the C4'-C3' and C4'-C5' homonuclear couplings. Multiple quantum line narrowing is employed to minimize sensitivity loses. The 4D HPCH experiment is verified and successfully applied to a non-coding 34-nt RNA consisting typical structure elements and a 14-nt RNA hairpin capped by cUUCGg tetraloop.
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Affiliation(s)
- Saurabh Saxena
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02089, Warsaw, Poland
| | - Jan Stanek
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02089, Warsaw, Poland
| | - Mirko Cevec
- Slovenian NMR Centre, National Institute of Chemistry, 1000, Ljubljana, Slovenia
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, 1000, Ljubljana, Slovenia
- EN-FIST Centre of Excellence, 1000, Ljubljana, Slovenia
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Wiktor Koźmiński
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02089, Warsaw, Poland.
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