1
|
Kiraly P, Dal Poggetto G, Castañar L, Nilsson M, Deák A, Morris GA. Broadband measurement of true transverse relaxation rates in systems with coupled protons: application to the study of conformational exchange. Chem Sci 2021; 12:11538-11547. [PMID: 34667556 PMCID: PMC8447259 DOI: 10.1039/d1sc03391c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 07/25/2021] [Indexed: 12/02/2022] Open
Abstract
Accurate measurement of transverse relaxation rates in coupled spin systems is important in the study of molecular dynamics, but is severely complicated by the signal modulations caused by scalar couplings in spin echo experiments. The most widely used experiments for measuring transverse relaxation in coupled systems, CPMG and PROJECT, can suppress such modulations, but they also both suppress some relaxation contributions, and average relaxation rates between coupled spins. Here we introduce a new experiment which for the first time allows accurate broadband measurement of transverse relaxation rates of coupled protons, and hence the determination of exchange rate constants in slow exchange from relaxation measurements. The problems encountered with existing methods are illustrated, and the use of the new method is demonstrated for the classic case of hindered amide rotation and for the more challenging problem of exchange between helical enantiomers of a gold(i) complex.
Collapse
Affiliation(s)
- Peter Kiraly
- Department of Chemistry, University of Manchester Oxford Road Manchester M13 9PL UK
| | | | - Laura Castañar
- Department of Chemistry, University of Manchester Oxford Road Manchester M13 9PL UK
| | - Mathias Nilsson
- Department of Chemistry, University of Manchester Oxford Road Manchester M13 9PL UK
| | - Andrea Deák
- Eötvös Loránd Research Network (ELKH), Research Centre for Natural Sciences, Institute of Materials and Environmental Chemistry, Supramolecular Chemistry Research Group Magyar Tudósok körútja 2 1117 Budapest Hungary
| | - Gareth A Morris
- Department of Chemistry, University of Manchester Oxford Road Manchester M13 9PL UK
| |
Collapse
|
2
|
Altincekic N, Löhr F, Meier-Credo J, Langer JD, Hengesbach M, Richter C, Schwalbe H. Site-Specific Detection of Arginine Methylation in Highly Repetitive Protein Motifs of Low Sequence Complexity by NMR. J Am Chem Soc 2020; 142:7647-7654. [PMID: 32233470 DOI: 10.1021/jacs.0c02308] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Post-translational modifications of proteins are widespread in eukaryotes. To elucidate the functional role of these modifications, detection methods need to be developed that provide information at atomic resolution. Here, we report on the development of a novel Arg-specific NMR experiment that detects the methylation status and symmetry of each arginine side chain even in highly repetitive RGG amino acid sequence motifs found in numerous proteins within intrinsically disordered regions. The experiment relies on the excellent resolution of the backbone H,N correlation spectra even in these low complexity sequences. It requires 13C, 15N labeled samples.
Collapse
Affiliation(s)
- Nadide Altincekic
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Frankfurt 60438, Germany.,Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Frankfurt 60438, Germany
| | - Frank Löhr
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Frankfurt 60438, Germany.,Institute of Biophysical Chemistry, Goethe University Frankfurt am Main, Frankfurt 60438, Germany
| | - Jakob Meier-Credo
- Max Planck Institute of Biophysics, Frankfurt am Main, 60438, Germany
| | - Julian D Langer
- Max Planck Institute of Biophysics, Frankfurt am Main, 60438, Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Frankfurt 60438, Germany
| | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Frankfurt 60438, Germany.,Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Frankfurt 60438, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Frankfurt 60438, Germany.,Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Frankfurt 60438, Germany
| |
Collapse
|
3
|
Nguyen D, Chen C, Pettitt BM, Iwahara J. NMR Methods for Characterizing the Basic Side Chains of Proteins: Electrostatic Interactions, Hydrogen Bonds, and Conformational Dynamics. Methods Enzymol 2018; 615:285-332. [PMID: 30638532 DOI: 10.1016/bs.mie.2018.08.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
NMR spectroscopy is a powerful tool for studying protein dynamics. Conventionally, NMR studies on protein dynamics have probed motions of protein backbone NH, side-chain aromatic, and CH3 groups. Recently, there has been remarkable progress in NMR methodologies that can characterize motions of cationic groups in protein side chains. These NMR methods allow investigations of the dynamics of positively charged lysine (Lys) and arginine (Arg) side chains and their hydrogen bonds as well as their electrostatic interactions important for protein function. Here, describing various practical aspects, we provide an overview of the NMR methods for dynamics studies of Lys and Arg side chains. Some example data on protein-DNA complexes are shown. We will also explain how molecular dynamics (MD) simulations can facilitate the interpretation of the NMR data on these basic side chains. Studies combining NMR and MD have revealed the highly dynamic nature of short-range electrostatic interactions via ion pairs, especially those involving Lys side chains.
Collapse
Affiliation(s)
- Dan Nguyen
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, United States
| | - Chuanying Chen
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, United States
| | - B Montgomery Pettitt
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, United States
| | - Junji Iwahara
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, United States.
| |
Collapse
|