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Han R, Borcik CG, Wang S, Warmuth OA, Geohring K, Mullen C, Incitti M, Stringer JA, Rienstra CM. Solid-State NMR 13C sensitivity at high magnetic field. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2024; 365:107709. [PMID: 38991265 PMCID: PMC11391299 DOI: 10.1016/j.jmr.2024.107709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 06/05/2024] [Accepted: 06/06/2024] [Indexed: 07/13/2024]
Abstract
Sensitivity is the foundation of every NMR experiment, and the signal-to-noise ratio (SNR) should increase with static (B0) magnetic field, by a proportionality that primarily depends on the design of the NMR probe and receiver. In the low B0 field limit, where the coil geometry is much smaller than the wavelength of the NMR frequency, SNR can increase in proportion to B0 to the power 7/4. For modern magic-angle spinning (MAS) probes, this approximation holds for rotor sizes up to 3.2 mm at 14.1 Tesla (T), corresponding to 600 MHz 1H and 151 MHz 13C Larmor frequencies. To obtain the anticipated benefit of larger coils and/or higher B0 fields requires a quantitative understanding of the contributions to SNR, utilizing standard samples and protocols that reproduce SNR measurements with high accuracy and precision. Here, we present such a systematic and comprehensive study of 13C SNR under MAS over the range of 14.1 to 21.1 T. We evaluate a range of probe designs utilizing 1.6, 2.5 and 3.2 mm rotors, including 24 different sets of measurements on 17 probe configurations using five spectrometers. We utilize N-acetyl valine as the primary standard and compare and contrast with other commonly used standard samples (adamantane, glycine, hexamethylbenzene, and 3-methylglutaric acid). These robust approaches and standard operating procedures provide an improved understanding of the contributions from probe efficiency, receiver noise figure, and B0 dependence in a range of custom-designed and commercially available probes. We find that the optimal raw SNR is obtained with balanced 3.2 mm design at 17.6 T, that the best mass-limited SNR is achieved with a balanced 1.6 mm design at 21.1 T, and that the raw SNR at 21.1 T reaches diminishing returns with rotors larger than 2.5 mm.
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Affiliation(s)
- Ruixian Han
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Collin G Borcik
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Songlin Wang
- National Magnetic Resonance Facility at Madison (NMRFAM), University of Wisconsin-Madison, Madison, WI, United States
| | - Owen A Warmuth
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, United States
| | | | | | | | | | - Chad M Rienstra
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, United States; National Magnetic Resonance Facility at Madison (NMRFAM), University of Wisconsin-Madison, Madison, WI, United States.
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Mironenko A, de Groot BL, Kopec W. Selectivity filter mutations shift ion permeation mechanism in potassium channels. PNAS NEXUS 2024; 3:pgae272. [PMID: 39015549 PMCID: PMC11251424 DOI: 10.1093/pnasnexus/pgae272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 06/26/2024] [Indexed: 07/18/2024]
Abstract
Potassium (K+) channels combine high conductance with high ion selectivity. To explain this efficiency, two molecular mechanisms have been proposed. The "direct knock-on" mechanism is defined by water-free K+ permeation and formation of direct ion-ion contacts in the highly conserved selectivity filter (SF). The "soft knock-on" mechanism involves co-permeation of water and separation of K+ by water molecules. With the aim to distinguish between these mechanisms, crystal structures of the KcsA channel with mutations in two SF residues-G77 and T75-were published, where the arrangements of K+ ions and water display canonical soft knock-on configurations. These data were interpreted as evidence of the soft knock-on mechanism in wild-type channels. Here, we test this interpretation using molecular dynamics simulations of KcsA and its mutants. We show that while a strictly water-free direct knock-on permeation is observed in the wild type, conformational changes induced by these mutations lead to distinct ion permeation mechanisms, characterized by co-permeation of K+ and water. These mechanisms are characterized by reduced conductance and impaired potassium selectivity, supporting the importance of full dehydration of potassium ions for the hallmark high conductance and selectivity of K+ channels. In general, we present a case where mutations introduced at the critical points of the permeation pathway in an ion channel drastically change its permeation mechanism in a nonintuitive manner.
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Affiliation(s)
- Andrei Mironenko
- Computational Biomolecular Dynamics Group, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
| | - Bert L de Groot
- Computational Biomolecular Dynamics Group, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
| | - Wojciech Kopec
- Computational Biomolecular Dynamics Group, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
- Department of Chemistry, Queen Mary University of London, 327 Mile End Road, London E1 4NS, UK
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Zhang M, Hillegass WB, Yu X, Majumdar S, Daryl Pollard J, Jackson E, Knudson J, Wolfe D, Kato GJ, Maher JF, Mei H. Genetic variants and effect modifiers of QT interval prolongation in patients with sickle cell disease. Gene 2024; 890:147824. [PMID: 37741592 DOI: 10.1016/j.gene.2023.147824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/17/2023] [Accepted: 09/20/2023] [Indexed: 09/25/2023]
Abstract
BACKGROUND Sickle cell disease (SCD) is a common inherited blood disorder among African Americans (AA), with premature mortality which has been associated with prolongation of the heart rate-corrected QT interval (QTc), a known risk factor for sudden cardiac death. Although numerous genetic variants have been identified as contributors to QT interval prolongation in the general population, their impact on SCD patients remains unclear. This study used an unweighted polygenic risk score (PRS) to validate the previously identified associations between SNPs and QTc interval in SCD patients, and to explore possible interactions with other factors that prolong QTc interval in AA individuals with SCD. METHODS In SCD patients, candidate genetic variants associated with the QTc interval were genotyped. To identify any risk SNPs that may be correlated with QTc interval prolongation, linear regression was employed, and an unweighted PRS was subsequently constructed. The effect of PRS on the QTc interval was evaluated using linear regression, while stratification analysis was used to assess the influence of serum alanine transaminase (ALT), a biomarker for liver disease, on the PRS effect. We also evaluated the PRS with the two subcomponents of QTc, the QRS and JTc intervals. RESULTS Out of 26 candidate SNPs, five risk SNPs were identified for QTc duration under the recessive model. For every unit increase in PRS, the QTc interval prolonged by 4.0 ms (95% CI: [2.0, 6.1]; p-value: <0.001) in the additive model and 9.4 ms in the recessive model (95% CI: [4.6, 14.1]; p-value: <0.001). Serum ALT showed a modification effect on PRS-QTc prolongation under the recessive model. In the normal ALT group, each PRS unit increased QTc interval by 11.7 ms (95% CI: [6.3, 17.1]; p-value: 2.60E-5), whereas this effect was not observed in the elevated ALT group (0.9 ms; 95% CI: [-7.0, 8.8]; p-value: 0.823). CONCLUSION Several candidate genetic variants are associated with QTc interval prolongation in SCD patients, and serum ALT acts as a modifying factor. The association of a CPS1 gene variant in both QTc and JTc duration adds to NOS1AP as evidence of involvement of the urea cycle and nitric oxide metabolism in cardiac repolarization in SCD. Larger replication studies are needed to confirm these findings and elucidate the underlying mechanisms.
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Affiliation(s)
- Mengna Zhang
- Department of Data Science, University of Mississippi Medical Center, Jackson, MS 39216, USA; Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - William B Hillegass
- Department of Data Science, University of Mississippi Medical Center, Jackson, MS 39216, USA; Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Xue Yu
- Department of Data Science, University of Mississippi Medical Center, Jackson, MS 39216, USA; Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Suvankar Majumdar
- Division of Hematology, Children's National Hospital, Washington, DC, USA
| | - J Daryl Pollard
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Erin Jackson
- Department of Pediatrics, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Jarrod Knudson
- Department of Pediatrics, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Douglas Wolfe
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Gregory J Kato
- Pittsburgh Heart, Lung and Blood Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Joseph F Maher
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA; Department of Internal Medicine/Cancer Genetics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14203, USA.
| | - Hao Mei
- Department of Data Science, University of Mississippi Medical Center, Jackson, MS 39216, USA; Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA.
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Öster C, Lange S, Hendriks K, Lange A. Detecting Bound Ions in Ion Channels by Solid-State NMR Experiments on 15N-Labelled Ammonium Ions. Methods Mol Biol 2024; 2796:23-34. [PMID: 38856893 DOI: 10.1007/978-1-0716-3818-7_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Solid-state NMR allows for the study of membrane proteins under physiological conditions. Here we describe a method for detection of bound ions in the selectivity filter of ion channels using solid-state NMR. This method employs standard 1H-detected solid-state NMR setup and experiment types, which is enabled by using 15N-labelled ammonium ions to mimic potassium ions.
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Affiliation(s)
- Carl Öster
- Research Unit Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany.
| | - Sascha Lange
- Research Unit Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Kitty Hendriks
- Research Unit Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Adam Lange
- Research Unit Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany.
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany.
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Yan Z, Zhang R. Multiple acquisitions in a single scan: exhausting abundant 1H polarization at fast MAS. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 346:107338. [PMID: 36463686 DOI: 10.1016/j.jmr.2022.107338] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 11/12/2022] [Accepted: 11/16/2022] [Indexed: 06/17/2023]
Abstract
Proton-detected solid-state NMR spectroscopy is emerging as a unique tool for atomic characterization of organic solids due to the boost of resolution and sensitivity afforded by the combined use of high magnetic field and ultrafast magic angle spinning (MAS). Here, we proposed a new set of proton-detected solid-state NMR sequences that hybrid multi-dimensional 1H-1H homonuclear chemical shift correlation (HOMCOR) and two-dimensional 1H-13C heteronuclear chemical shift correlation (HETCOR) sequences into a single experiment, enabling the simultaneous acquisition of multidimensional HOMCOR and HETCOR spectra and thus significant time savings. Based on the core idea of exhausting 1H polarization in each transient scan, we firstly demonstrated that 3D 1H multiple-quantum (MQ) HOMCOR sequence can be combined with 2D HETCOR sequence into a single experiment, leading to the simultaneous acquisition of a 3D 1H MQ HOMCOR and a 2D 1H-13C HETCOR spectrum. Besides, we also showed that 2D 1H/1H double-quantum/single-quantum (DQ/SQ) and single-quantum/single-quantum (SQ/SQ) HOMCOR sequence can be simultaneously combined with HETCOR sequence either, and thus three spectra can be simultaneously obtained from one experiment, including 2D 1H DQ/SQ, 2D 1H SQ/SQ and 2D 1H-13C HETCOR spectra. Since there is only one recycle delay in each experiment, experimental time is substantially reduced compared to separate acquisition of each multi-dimensional solid-state NMR spectrum. Furthermore, those new sequences can be implemented on any standard solid-state spectrometer with only one receiver. Thus, we foresee that these approaches can be valuable for the study of a broad range of molecular systems, including polymers, pharmaceuticals, covalent-organic frameworks (COF) and so on.
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Affiliation(s)
- Zhiwei Yan
- South China Advanced Institute for Soft Matter Science and Technology (AISMST), School of Emergent Soft Matter (SESM), South China University of Technology, Guangzhou 510640, PR China
| | - Rongchun Zhang
- South China Advanced Institute for Soft Matter Science and Technology (AISMST), School of Emergent Soft Matter (SESM), South China University of Technology, Guangzhou 510640, PR China; Guangdong Provincial Key Laboratory of Functional and Intelligent Hybrid Materials and Devices, South China University of Technology, Guangzhou 510640, PR China.
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Suzuki Y, Hirata K, Lisy JM, Ishiuchi SI, Fujii M. A bottom-up approach to the ion recognition mechanism of K + channels from laser spectroscopy of hydrated partial peptide-alkali metal ion complexes. Phys Chem Chem Phys 2022; 24:20803-20812. [PMID: 36000593 DOI: 10.1039/d2cp01667b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
K+ channels allow selective permeation of K+, but not physiologically abundant Na+, at almost diffusion limit rates. The conduction mechanism of K+ channels is still controversial, with experimental and computation studies supporting two distinct conduction mechanisms: either with or without water inside the channel. Here, we employ a bottom-up approach on hydrated alkali metal complexes of a model peptide of K+ channels, Ac-Tyr-NHMe, to characterize metal-peptide, metal-water, and water-peptide interactions that govern the selectivity of K+ channels at a molecular level. Both the extension to the series of alkali metal ions and to temperature-dependent studies (approaching physiological values) have revealed the clear difference between permeable and non-permeable ions in the spectral features of the ion complexes. Furthermore, the impact of hydration is discussed in relation to the K+ channels by comparisons of the non-hydrated and hydrated complexes.
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Affiliation(s)
- Yukina Suzuki
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan. .,School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8503, Japan
| | - Keisuke Hirata
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan. .,Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan.,Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovation Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan.
| | - James M Lisy
- Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovation Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan. .,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Shun-Ichi Ishiuchi
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan. .,Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan.,Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovation Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan.
| | - Masaaki Fujii
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan. .,School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8503, Japan.,Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovation Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan.
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