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Outcomes of novel pacing technologies with right ventricular pacing as a primary strategy for patient undergoing transvenous permanent pacing regardless of pacing indication. Eur Heart J 2021. [DOI: 10.1093/eurheartj/ehab724.0406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
Right ventricular pacing (RVP) may cause electrical and mechanical desynchrony leading to impaired left ventricular ejection fraction (LVEF). We investigated the outcomes of RVP with His bundle pacing (HBP) and left bundle branch pacing (LBBP) for patients requiring a de novo permeant pacemaker (PPM) irrespective of baseline pacing indication.
Methods and results
Systematic review of randomized clinical trials and observational studies comparing HBP or LBP with RVP for de novo PPM implantation between 01 January 2013 and 17 November 2020 using MEDLINE and Embase. Two independent reviewers extracted the data and assessed the risk of bias of included studies. Random and fixed effects meta-analyses of the effect of pacing technology on study outcomes (all-cause mortality, heart failure hospitalization (HFH), left ventricular ejection fraction, QRS duration, lead revision, atrial fibrillation and procedure and pacing metrics) were performed. Overall, 7 studies were included. HBP compared with RVP was associated with decreased mortality (risk ratio [RR] 0.76, 95% CI 0.59 to 0.98), preservation of LVEF (mean difference [MD] 1.2, 95% CI −1.37 to 3.8 vs. −5.22, 95% CI: −6.94 to −3.51), increased procedure duration (MD 15.17 min, 95% CI: 11.27 to 19.07) and more lead revisions (RR 6.30, 95% CI: 2.31 to 17.19). LBBP compared with RVP was associated with shorter paced QRS durations (MD 5.6 ms, 95% CI −6.4 to 17.6) vs. (51.0 ms, 95% CI 39.2 to 62.9) and increased procedure durations (MD 37.78 min, 95% CI: 20.04 to 55.51).
Conclusion
Of the limited studies published, this meta-analysis found that HBP and LBBP were superior to RVP in maintaining physiological ventricular activation as an initial pacing strategy. Well conducted comparative studies are required to understand the impact of such novel pacing strategies on clinical outcomes.
Funding Acknowledgement
Type of funding sources: None.
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Pluronic F127-Folate Coated Super Paramagenic Iron Oxide Nanoparticles as Contrast Agent for Cancer Diagnosis in Magnetic Resonance Imaging. Polymers (Basel) 2019; 11:polym11040743. [PMID: 31027171 PMCID: PMC6523503 DOI: 10.3390/polym11040743] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 04/09/2019] [Accepted: 04/13/2019] [Indexed: 11/17/2022] Open
Abstract
Contrast agents have been widely used in medicine to enhance contrast in magnetic resonance imaging (MRI). Among them, super paramagnetic iron oxide nanoparticles (SPION) have been reported to have low risk in clinical use. In our study, F127-Folate coated SPION was fabricated in order to efficiently target tumors and provide imaging contrast in MRI. SPION alone have an average core size of 15 nm. After stabilizing with Pluronic F127, the nanoparticles reached a hydrodynamic size of 180 nm and dispersed well in various kinds of media. The F127-Folate coated SPION were shown to specifically target folate receptor expressing cancer cells by flow cytometry analysis, confocal laser scanning microscope, as well as in vitro MRI. Furthermore, in vivo MRI images have shown the enhanced negative contrast from the F127-Folate coated SPION in tumor-bearing mice. In conclusion, our F127-Folate coated SPION have shown great potential as a contrast agent in MRI, as well as in the combination with drug delivery for cancer therapy.
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A unified heteronuclear decoupling picture in solid-state NMR under low radio-frequency amplitude and fast magic-angle-spinning frequency regime. J Chem Phys 2019; 150:144201. [PMID: 30981235 DOI: 10.1063/1.5082352] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Heteronuclear spin decoupling is a highly important component of solid-state NMR experiments to remove undesired coupling interactions between unlike spins for spectral resolution. Recently, experiments using a unification strategy of standard decoupling schemes were presented for high radio-frequency (RF) amplitudes and slow-intermediate magic-angle-spinning (MAS) frequencies, in the pursuit of deeper understanding of spin decoupling under phase-modulated RF irradiation [A. Equbal et al., J. Chem. Phys. 142, 184201 (2015)]. The approach, unified two-pulse heteronuclear decoupling (UTPD), incorporates the simultaneous time- and phase-modulation strategies, commonly used in solid-state NMR. Here, the UTPD based decoupling scheme is extended to the experimentally increasingly important regime of low RF amplitudes and fast MAS frequencies. The unified decoupling approach becomes increasingly effective in identifying the deleterious dipole-dipole and, in particular, J recoupling conditions which become critical for the low-amplitude RF regime. This is because J coupling is isotropic and therefore not averaged out by sample spinning unlike the anisotropic dipole-dipole coupling. Numerical simulations and analytic theory are used to understand the effects of various nuclear spin interactions on the decoupling performance of UTPD, in particular, the crucial difference between the low-phase and high-phase UTPD conditions with respect to J coupling. In the UTPD scheme, when the cycle-frequency of the pulse-sequence is comparable to the RF nutation frequency, the existence of a non-zero effective rotation in the basic two-pulse scheme becomes an essential feature for the efficient and robust averaging out of the scalar J coupling. This broad viewpoint is expected to bring different optimum low-power decoupling pulse schemes under a common footing.
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Cryogen-free dissolution dynamic nuclear polarization polarizer operating at 3.35 T, 6.70 T, and 10.1 T. Magn Reson Med 2018; 81:2184-2194. [PMID: 30357898 DOI: 10.1002/mrm.27537] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 08/26/2018] [Accepted: 08/27/2018] [Indexed: 12/27/2022]
Abstract
PURPOSE A novel dissolution dynamic nuclear polarization (dDNP) polarizer platform is presented. The polarizer meets a number of key requirements for in vitro, preclinical, and clinical applications. METHOD It uses no liquid cryogens, operates in continuous mode, accommodates a wide range of sample sizes up to and including those required for human studies, and is fully automated. RESULTS It offers a wide operational window both in terms of magnetic field, up to 10.1 T, and temperature, from room temperature down to 1.3 K. The polarizer delivers a 13 C liquid state polarization for [1-13 C]pyruvate of 70%. The build-up time constant in the solid state is approximately 1200 s (20 minutes), allowing a sample throughput of at least one sample per hour including sample loading and dissolution. CONCLUSION We confirm the previously reported strong field dependence in the range 3.35 to 6.7 T, but see no further increase in polarization when increasing the magnetic field strength to 10.1 T for [1-13 C]pyruvate and trityl. Using a custom dry magnet, cold head and recondensing, closed-cycle cooling system, combined with a modular DNP probe, and automation and fluid handling systems, we have designed a unique dDNP system with unrivalled flexibility and performance.
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Publisher's Note: "Parameter independent low-power heteronuclear decoupling for fast magic-angle spinning solid-state NMR" [J. Chem. Phys. 146, 084202 (2017)]. J Chem Phys 2017; 146:139901. [PMID: 28390378 DOI: 10.1063/1.4979997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Significance of symmetry in the nuclear spin Hamiltonian for efficient heteronuclear dipolar decoupling in solid-state NMR: A Floquet description of supercycled rCW schemes. J Chem Phys 2017; 146:104202. [PMID: 28298092 DOI: 10.1063/1.4977738] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Symmetry plays an important role in the retention or annihilation of a desired interaction Hamiltonian in NMR experiments. Here, we explore the role of symmetry in the radio-frequency interaction frame Hamiltonian of the refocused-continuous-wave (rCW) pulse scheme that leads to efficient 1H heteronuclear decoupling in solid-state NMR. It is demonstrated that anti-periodic symmetry of single-spin operators (Ix, Iy, Iz) in the interaction frame can lead to complete annihilation of the 1H-1H homonuclear dipolar coupling effects that induce line broadening in solid-state NMR experiments. This symmetry also plays a critical role in cancelling or minimizing the effect of 1H chemical-shift anisotropy in the effective Hamiltonian. An analytical description based on Floquet theory is presented here along with experimental evidences to understand the decoupling efficiency of supercycled (concatenated) rCW scheme.
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Reactive Center Loop Insertion in α-1-Antitrypsin Captured by Accelerated Molecular Dynamics Simulation. Biochemistry 2017; 56:634-646. [PMID: 27995800 DOI: 10.1021/acs.biochem.6b00839] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protease inhibition by metastable serine protease inhibitors (serpins) is mediated by one of the largest functional intradomain conformational changes known in biology. In this extensive structural rearrangement, protease-serpin complex formation triggers cleavage of the serpin reactive center loop (RCL), its subsequent insertion into central β-sheet A, and covalent trapping of the target protease. In this study, we present the first detailed accelerated molecular dynamics simulation of the insertion of the fully cleaved RCL in α-1-antitrypsin (α1AT), the archetypal member of the family of human serpins. Our results reveal internal water pathways that allow the initial incorporation of side chains of RCL residues into the protein interior. We observed structural plasticity of the helix F (hF) element that blocks the RCL path in the native state, which is in excellent agreement with previous experimental reports. Furthermore, the simulation suggested a novel role of hF and the connected turn (thFs3A) as chaperones that support the insertion process by reducing the conformational space available to the RCL. Transient electrostatic interactions of RCL residues potentially fine-tune the serpin inhibitory activity. On the basis of our simulation, we generated the α1AT mutants K168E, E346K, and K168E/E346K and analyzed their inhibitory activity along with their intrinsic stability and heat-induced polymerization. Remarkably, the E346K mutation exhibited enhanced inhibitory activity along with an increased rate of premature structural collapse (polymerization), suggesting a significant role of E346 in the gatekeeping of the strain in the metastable native state.
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Handling the influence of chemical shift in amplitude-modulated heteronuclear dipolar recoupling solid-state NMR. J Chem Phys 2016; 145:094202. [PMID: 27608995 DOI: 10.1063/1.4961736] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a theoretical analysis of the influence of chemical shifts on amplitude-modulated heteronuclear dipolar recoupling experiments in solid-state NMR spectroscopy. The method is demonstrated using the Rotor Echo Short Pulse IRrAdiaTION mediated Cross-Polarization ((RESPIRATION)CP) experiment as an example. By going into the pulse sequence rf interaction frame and employing a quintuple-mode operator-based Floquet approach, we describe how chemical shift offset and anisotropic chemical shift affect the efficiency of heteronuclear polarization transfer. In this description, it becomes transparent that the main attribute leading to non-ideal performance is a fictitious field along the rf field axis, which is generated from second-order cross terms arising mainly between chemical shift tensors and themselves. This insight is useful for the development of improved recoupling experiments. We discuss the validity of this approach and present quaternion calculations to determine the effective resonance conditions in a combined rf field and chemical shift offset interaction frame transformation. Based on this, we derive a broad-banded version of the (RESPIRATION)CP experiment. The new sequence is experimentally verified using SNNFGAILSS amyloid fibrils where simultaneous (15)N → (13)CO and (15)N → (13)Cα coherence transfer is demonstrated on high-field NMR instrumentation, requiring great offset stability.
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Improved transfer efficiencies in radio-frequency-driven recoupling solid-state NMR by adiabatic sweep through the dipolar recoupling condition. J Chem Phys 2016; 145:034201. [PMID: 27448878 DOI: 10.1063/1.4958318] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The homonuclear radio-frequency driven recoupling (RFDR) experiment is commonly used in solid-state NMR spectroscopy to gain insight into the structure of biological samples due to its ease of implementation, stability towards fluctuations/missetting of radio-frequency (rf) field strength, and in general low rf requirements. A theoretical operator-based Floquet description is presented to appreciate the effect of having a temporal displacement of the π-pulses in the RFDR experiment. From this description, we demonstrate improved transfer efficiency for the RFDR experiment by generating an adiabatic passage through the zero-quantum recoupling condition. We have compared the performances of RFDR and the improved sequence to mediate efficient (13)CO to (13)Cα polarization transfer for uniformly (13)C,(15)N-labeled glycine and for the fibril forming peptide SNNFGAILSS (one-letter amino acid codes) uniformly (13)C,(15)N-labeled at the FGAIL residues. Using numerically optimized sweeps, we get experimental gains of approximately 20% for glycine where numerical simulations predict an improvement of 25% relative to the standard implementation. For the fibril forming peptide, using the same sweep parameters as found for glycine, we have gains in the order of 10%-20% depending on the spectral regions of interest.
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Natural abundant (17) O NMR in a 1.5-T Halbach magnet. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2016; 54:510-512. [PMID: 25641664 DOI: 10.1002/mrc.4207] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 11/25/2014] [Accepted: 12/16/2014] [Indexed: 06/04/2023]
Abstract
We present mobile, low-field (17) O NMR as a means for monitoring oxygen in liquids. Whereas oxygen is one of the most important elements, oxygen NMR is limited by a poor sensitivity related to low natural abundance and gyro-magnetic ratio of the NMR active (17) O isotope. Here, we demonstrate (17) O NMR detection at a Larmor frequency of 8.74 MHz in a 1.5-T Halbach neodymium magnet with a home-built digital NMR instrument suitable for large-scale production and in-line monitoring applications. The proposed (17) O NMR sensor may be applied for direct, noninvasive measurements of water content in, for example, oil, manure, or food in automated quality or process control. Copyright © 2015 John Wiley & Sons, Ltd.
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Near-complete 1H, 13C, 15N resonance assignments of dimethylsulfoxide-denatured TGFBIp FAS1-4 A546T. BIOMOLECULAR NMR ASSIGNMENTS 2016; 10:25-29. [PMID: 26275916 DOI: 10.1007/s12104-015-9630-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 08/11/2015] [Indexed: 06/04/2023]
Abstract
The transforming growth factor beta induced protein (TGFBIp) is a major protein component of the human cornea. Mutations occurring in TGFBIp may cause corneal dystrophies, which ultimately lead to loss of vision. The majority of the disease-causing mutations are located in the C-terminal domain of TGFBIp, referred as the fourth fascilin-1 (FAS1-4) domain. In the present study the FAS1-4 Ala546Thr, a mutation that causes lattice corneal dystrophy, was investigated in dimethylsulfoxide using liquid-state NMR spectroscopy, to enable H/D exchange strategies for identification of the core formed in mature fibrils. Isotope-labeled fibrillated FAS1-4 A546T was dissolved in a ternary mixture 95/4/1 v/v/v% dimethylsulfoxide/water/trifluoroacetic acid, to obtain and assign a reference 2D (1)H-(15)N HSQC spectrum for the H/D exchange analysis. Here, we report the near-complete assignments of backbone and aliphatic side chain (1)H, (13)C and (15)N resonances for unfolded FAS1-4 A546T at 25 °C.
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Three pulse recoupling and phase jump matching. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2016; 263:172-183. [PMID: 26777742 PMCID: PMC4959450 DOI: 10.1016/j.jmr.2015.11.012] [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: 09/12/2015] [Revised: 11/01/2015] [Accepted: 11/21/2015] [Indexed: 06/05/2023]
Abstract
The paper describes a family of novel recoupling pulse sequences, called three pulse recoupling. These pulse sequences can be employed for both homonuclear and heteronuclear recoupling experiments and are robust to dispersion in chemical shifts and rf-inhomogeneity. These recoupling pulse sequences can be used in design of two-dimensional solid state NMR experiments that use powdered dephased antiphase coherence (γ preparation) to encode chemical shifts in the indirect dimension. Both components of this chemical shift encoded gamma-prepared states can be refocused into inphase coherence by a recoupling element. This helps to achieve sensitivity enhancement in 2D NMR experiments by quadrature detection.
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Relative merits of rCW(A) and XiX heteronuclear spin decoupling in solid-state magic-angle-spinning NMR spectroscopy: A bimodal Floquet analysis. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2016; 263:55-64. [PMID: 26773527 DOI: 10.1016/j.jmr.2015.12.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 12/19/2015] [Accepted: 12/27/2015] [Indexed: 06/05/2023]
Abstract
We present a bimodal Floquet analysis of the recently introduced refocused continuous wave (rCW) solid-state NMR heteronuclear dipolar decoupling method and compare it with the similar looking X-inverse X (XiX) scheme. The description is formulated in the rf interaction frame and is valid for both finite and ideal π pulse rCW irradiation that forms the refocusing element in the rCW scheme. The effective heteronuclear dipolar coupling Hamiltonian up to first order is described. The analysis delineates the difference between the two sequences to different orders of their Hamiltonians for both diagonal and off-diagonal parts. All the resonance conditions observed in experiments and simulations have been characterised and their influence on residual line broadening is highlighted. The theoretical comparison substantiates the numerical simulations and experimental results to a large extent.
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Early Events in the Amyloid Formation of the A546T Mutant of Transforming Growth Factor β-Induced Protein in Corneal Dystrophies Compared to the Nonfibrillating R555W and R555Q Mutants. Biochemistry 2015; 54:5546-56. [PMID: 26305369 DOI: 10.1021/acs.biochem.5b00473] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The human transforming growth factor β-induced protein (TGFBIp) is involved in several types of corneal dystrophies where protein aggregation and amyloid fibril formation severely impair vision. Most disease-causing mutations are located in the last of four homologous fasciclin-1 (FAS1) domains of the protein, and it has been shown that when isolated, the fourth FAS1 domain (FAS1-4) mimics the behavior of full-length TGFBIp. In this study, we use molecular dynamics simulations and principal component analysis to study the wild-type FAS1-4 domain along with three disease-causing mutations (R555W, R555Q, and A546T) to decipher any internal difference in dynamical properties of the domains that may explain their varied stabilities and aggregation properties. In addition, we use a protein-protein docking method in combination with chemical cross-linking experiments and mass spectrometry of the cross-linked species to obtain information about interaction faces between identical FAS1-4 domains. The results show that the pathogenic mutations A546T and R555W affect the packing in the hydrophobic core of FAS1-4 in different directions. We further show that the FAS1-4 monomers associate using their β-rich regions, consistent with peptides observed to be part of the amyloid fibril core in lattice corneal dystrophy patients.
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Solid-state NMR methods for oriented membrane proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2015; 88-89:48-85. [PMID: 26282196 DOI: 10.1016/j.pnmrs.2015.05.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 04/27/2015] [Indexed: 06/04/2023]
Abstract
Oriented-sample solid-state NMR represents one of few experimental methods capable of characterising the membrane-bound conformation of proteins in the cell membrane. Since the technique was developed 25 years ago, the technique has been applied to study the structure of helix bundle membrane proteins and antimicrobial peptides, characterise protein-lipid interactions, and derive information on dynamics of the membrane anchoring of membrane proteins. We will review the major developments in various aspects of oriented-sample solid-state NMR, including sample-preparation methods, pulse sequences, theory required to interpret the experiments, perspectives for and guidelines to new experiments, and a number of representative applications.
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Optimized co-solute paramagnetic relaxation enhancement for the rapid NMR analysis of a highly fibrillogenic peptide. JOURNAL OF BIOMOLECULAR NMR 2015; 62:129-42. [PMID: 25820763 DOI: 10.1007/s10858-015-9925-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Accepted: 03/20/2015] [Indexed: 05/21/2023]
Abstract
Co-solute paramagnetic relaxation enhancement (PRE) is an attractive way to speed up data acquisition in NMR spectroscopy by shortening the T 1 relaxation time of the nucleus of interest and thus the necessary recycle delay. Here, we present the rationale to utilize high-spin iron(III) as the optimal transition metal for this purpose and characterize the properties of its neutral chelate form Fe(DO3A) as a suitable PRE agent. Fe(DO3A) effectively reduces the T 1 values across the entire sequence of the intrinsically disordered protein α-synuclein with negligible impact on line width. The agent is better suited than currently used alternatives, shows no specific interaction with the polypeptide chain and, due to its high relaxivity, is effective at low concentrations and in 'proton-less' NMR experiments. By using Fe(DO3A) we were able to complete the backbone resonance assignment of a highly fibrillogenic peptide from α1-antitrypsin by acquiring the necessary suite of multidimensional NMR datasets in 3 h.
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A unified heteronuclear decoupling strategy for magic-angle-spinning solid-state NMR spectroscopy. J Chem Phys 2015; 142:184201. [PMID: 25978884 DOI: 10.1063/1.4919634] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A unified strategy of two-pulse based heteronuclear decoupling for solid-state magic-angle spinning nuclear magnetic resonance is presented. The analysis presented here shows that different decoupling sequences like two-pulse phase-modulation (TPPM), X-inverse-X (XiX), and finite pulse refocused continuous wave (rCW(A)) are basically specific solutions of a more generalized decoupling scheme which incorporates the concept of time-modulation along with phase-modulation. A plethora of other good decoupling conditions apart from the standard, TPPM, XiX, and rCW(A) decoupling conditions are available from the unified decoupling approach. The importance of combined time- and phase-modulation in order to achieve the best decoupling conditions is delineated. The consequences of different indirect dipolar interactions arising from cross terms comprising of heteronuclear and homonuclear dipolar coupling terms and also those between heteronuclear dipolar coupling and chemical-shift anisotropy terms are presented in order to unfold the effects of anisotropic interactions under different decoupling conditions. Extensive numerical simulation results are corroborated with experiments on standard amino acids.
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Real-time 2D spatially selective MRI experiments: Comparative analysis of optimal control design methods. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 254:110-120. [PMID: 25863895 DOI: 10.1016/j.jmr.2015.03.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 03/12/2015] [Accepted: 03/13/2015] [Indexed: 06/04/2023]
Abstract
There is an increasing need for development of advanced radio-frequency (RF) pulse techniques in modern magnetic resonance imaging (MRI) systems driven by recent advancements in ultra-high magnetic field systems, new parallel transmit/receive coil designs, and accessible powerful computational facilities. 2D spatially selective RF pulses are an example of advanced pulses that have many applications of clinical relevance, e.g., reduced field of view imaging, and MR spectroscopy. The 2D spatially selective RF pulses are mostly generated and optimised with numerical methods that can handle vast controls and multiple constraints. With this study we aim at demonstrating that numerical, optimal control (OC) algorithms are efficient for the design of 2D spatially selective MRI experiments, when robustness towards e.g. field inhomogeneity is in focus. We have chosen three popular OC algorithms; two which are gradient-based, concurrent methods using first- and second-order derivatives, respectively; and a third that belongs to the sequential, monotonically convergent family. We used two experimental models: a water phantom, and an in vivo human head. Taking into consideration the challenging experimental setup, our analysis suggests the use of the sequential, monotonic approach and the second-order gradient-based approach as computational speed, experimental robustness, and image quality is key. All algorithms used in this work were implemented in the MATLAB environment and are freely available to the MRI community.
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A new RF tagging pulse based on the Frank poly-phase perfect sequence. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 247:50-53. [PMID: 25238576 DOI: 10.1016/j.jmr.2014.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Revised: 08/20/2014] [Accepted: 08/21/2014] [Indexed: 06/03/2023]
Abstract
Radio frequency (RF) spectrally selective multiband pulses or tagging pulses, are applicable in a broad range of magnetic resonance methods. We demonstrate through simulations and experiments a new phase-modulation-only RF pulse for RF tagging based on the Frank poly-phase perfect sequence. In addition, we introduce an extended version with a WURST modulation (Frank-WURST). The new pulses exhibit interesting and flexible spin tagging properties and are easily implemented in existing MR sequences, where they can substitute slice-selective pulses with no additional alterations.
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A hexameric peptide barrel as building block of amyloid-β protofibrils. Angew Chem Int Ed Engl 2014; 53:12756-60. [PMID: 25256598 DOI: 10.1002/anie.201406357] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 08/08/2014] [Indexed: 11/12/2022]
Abstract
Oligomeric and protofibrillar aggregates formed by the amyloid-β peptide (Aβ) are believed to be involved in the pathology of Alzheimer's disease. Central to Alzheimer pathology is also the fact that the longer Aβ42 peptide is more prone to aggregation than the more prevalent Aβ40 . Detailed structural studies of Aβ oligomers and protofibrils have been impeded by aggregate heterogeneity and instability. We previously engineered a variant of Aβ that forms stable protofibrils and here we use solid-state NMR spectroscopy and molecular modeling to derive a structural model of these. NMR data are consistent with packing of residues 16 to 42 of Aβ protomers into hexameric barrel-like oligomers within the protofibril. The core of the oligomers consists of all residues of the central and C-terminal hydrophobic regions of Aβ, and hairpin loops extend from the core. The model accounts for why Aβ42 forms oligomers and protofibrils more easily than Aβ40 .
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Efficient heteronuclear decoupling in MAS solid-state NMR using non-rotor-synchronized rCW irradiation. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 246:104-109. [PMID: 25123538 DOI: 10.1016/j.jmr.2014.07.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Revised: 06/30/2014] [Accepted: 07/09/2014] [Indexed: 06/03/2023]
Abstract
We present new non-rotor-synchronized variants of the recently introduced refocused continuous wave (rCW) heteronuclear decoupling method significantly improving the performance relative to the original rotor-synchronized variants. Under non-rotor-synchronized conditions the rCW decoupling sequences provide more efficient decoupling, are easier to setup, and prove more robust towards experimental parameters such as radio frequency (rf) field amplitude and spinning frequency. This is demonstrated through numerical simulations substantiated with experimental results under different sample spinning and rf field amplitude conditions for powder samples of U-(13)C-glycine and U-(13)C-L-histidine·HCl·H2O.
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Computer-intensive simulation of solid-state NMR experiments using SIMPSON. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 246:79-93. [PMID: 25093693 DOI: 10.1016/j.jmr.2014.07.002] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 07/08/2014] [Accepted: 07/13/2014] [Indexed: 06/03/2023]
Abstract
Conducting large-scale solid-state NMR simulations requires fast computer software potentially in combination with efficient computational resources to complete within a reasonable time frame. Such simulations may involve large spin systems, multiple-parameter fitting of experimental spectra, or multiple-pulse experiment design using parameter scan, non-linear optimization, or optimal control procedures. To efficiently accommodate such simulations, we here present an improved version of the widely distributed open-source SIMPSON NMR simulation software package adapted to contemporary high performance hardware setups. The software is optimized for fast performance on standard stand-alone computers, multi-core processors, and large clusters of identical nodes. We describe the novel features for fast computation including internal matrix manipulations, propagator setups and acquisition strategies. For efficient calculation of powder averages, we implemented interpolation method of Alderman, Solum, and Grant, as well as recently introduced fast Wigner transform interpolation technique. The potential of the optimal control toolbox is greatly enhanced by higher precision gradients in combination with the efficient optimization algorithm known as limited memory Broyden-Fletcher-Goldfarb-Shanno. In addition, advanced parallelization can be used in all types of calculations, providing significant time reductions. SIMPSON is thus reflecting current knowledge in the field of numerical simulations of solid-state NMR experiments. The efficiency and novel features are demonstrated on the representative simulations.
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VirtualSpectrum, a tool for simulating peak list for multi-dimensional NMR spectra. JOURNAL OF BIOMOLECULAR NMR 2014; 60:51-66. [PMID: 25119482 DOI: 10.1007/s10858-014-9851-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 08/01/2014] [Indexed: 06/03/2023]
Abstract
NMR spectroscopy is a widely used technique for characterizing the structure and dynamics of macromolecules. Often large amounts of NMR data are required to characterize the structure of proteins. To save valuable time and resources on data acquisition, simulated data is useful in the developmental phase, for data analysis, and for comparison with experimental data. However, existing tools for this purpose can be difficult to use, are sometimes specialized for certain types of molecules or spectra, or produce too idealized data. Here we present a fast, flexible and robust tool, VirtualSpectrum, for generating peak lists for most multi-dimensional NMR experiments for both liquid and solid state NMR. It is possible to tune the quality of the generated peak lists to include sources of artifacts from peak overlap, noise and missing signals. VirtualSpectrum uses an analytic expression to represent the spectrum and derive the peak positions, seamlessly handling overlap between signals. We demonstrate our tool by comparing simulated and experimental spectra for different multi-dimensional NMR spectra and analyzing systematically three cases where overlap between peaks is particularly relevant; solid state NMR data, liquid state NMR homonuclear (1)H and (15)N-edited spectra, and 2D/3D heteronuclear correlation spectra of unstructured proteins. We analyze the impact of protein size and secondary structure on peak overlap and on the accuracy of structure determination based on data of different qualities simulated by VirtualSpectrum.
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Efficient polarization transfer between spin-1/2 and ¹⁴N nuclei in solid-state MAS NMR spectroscopy. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 244:85-89. [PMID: 24880881 DOI: 10.1016/j.jmr.2014.04.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 04/15/2014] [Accepted: 04/21/2014] [Indexed: 06/03/2023]
Abstract
Polarization transfer between spin-1/2 nuclei and quadrupolar spin-1 nuclei such as (14)N in solid-state NMR is severely challenged by the typical presence of large quadrupole coupling interactions. This has effectively prevented the use of the abundant (14)N spin as a probe to structural information and its use as an element in multi-dimensional solid-state NMR correlation experiments for assignment and structural characterization. In turn, this has been a contributing factor to the extensive use of isotope labeling in biological solid-state NMR, where (14)N is replaced with (15)N. The alternative strategy of using the abundant (14)N spins calls for methods enabling efficient polarization transfer between (14)N and its binding partners. This work demonstrates that the recently introduced (RESPIRATION)CP transfer method can be optimized to achieve efficient (1)H ↔(14)N polarization transfer under magic angle spinning conditions. The method is demonstrated numerically and experimentally on powder samples of NH4NO3 and L-alanine.
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r TPPM: towards improving solid-state NMR two-pulse phase-modulation heteronuclear dipolar decoupling sequence by refocusing. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 244:68-73. [PMID: 24879300 DOI: 10.1016/j.jmr.2014.04.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 03/31/2014] [Accepted: 04/07/2014] [Indexed: 06/03/2023]
Abstract
We present here a simple refocused modification, r TPPM, of the Two-Pulse Phase-Modulation (TPPM) heteronuclear decoupling method, which improves decoupling and makes the sequence much more robust with respect to essential experimental parameters. The modified sequence is compared with the established TPPM sequence and a variety of other decoupling sequences at low to moderate magic-angle spinning frequencies. Simulations are shown to compare TPPM and r TPPM with respect to various experimental parameters. The observations from simulations are corroborated with experimental findings at two spinning frequencies on U-(13)C-glycine and U-(13)C-L-histidine.HCl.H2O.
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Automated robust and accurate assignment of protein resonances for solid state NMR. JOURNAL OF BIOMOLECULAR NMR 2014; 59:119-34. [PMID: 24817190 DOI: 10.1007/s10858-014-9835-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 04/29/2014] [Indexed: 05/26/2023]
Abstract
The process of resonance assignment represents a time-consuming and potentially error-prone bottleneck in structural studies of proteins by solid-state NMR (ssNMR). Software for the automation of this process is therefore of high interest. Procedures developed through the last decades for solution-state NMR are not directly applicable for ssNMR due to the inherently lower data quality caused by lower sensitivity and broader lines, leading to overlap between peaks. Recently, the first efforts towards procedures specifically aimed for ssNMR have been realized (Schmidt et al. in J Biomol NMR 56(3):243-254, 2013). Here we present a robust automatic method, which can accurately assign protein resonances using peak lists from a small set of simple 2D and 3D ssNMR experiments, applicable in cases with low sensitivity. The method is demonstrated on three uniformly (13)C, (15)N labeled biomolecules with different challenges on the assignments. In particular, for the immunoglobulin binding domain B1 of streptococcal protein G automatic assignment shows 100% accuracy for the backbone resonances and 91.8% when including all side chain carbons. It is demonstrated, by using a procedure for generating artificial spectra with increasing line widths, that our method, GAMES_ASSIGN can handle a significant amount of overlapping peaks in the assignment. The impact of including different ssNMR experiments is evaluated as well.
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Quadruple-resonance magic-angle spinning NMR spectroscopy of deuterated solid proteins. Angew Chem Int Ed Engl 2014; 53:2438-42. [PMID: 24474388 DOI: 10.1002/anie.201308927] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2013] [Revised: 12/03/2013] [Indexed: 11/12/2022]
Abstract
(1)H-detected magic-angle spinning NMR experiments facilitate structural biology of solid proteins, which requires using deuterated proteins. However, often amide protons cannot be back-exchanged sufficiently, because of a possible lack of solvent exposure. For such systems, using (2)H excitation instead of (1)H excitation can be beneficial because of the larger abundance and shorter longitudinal relaxation time, T1, of deuterium. A new structure determination approach, "quadruple-resonance NMR spectroscopy", is presented which relies on an efficient (2)H-excitation and (2)H-(13)C cross-polarization (CP) step, combined with (1)H detection. We show that by using (2)H-excited experiments better sensitivity is possible on an SH3 sample recrystallized from 30 % H2O. For a membrane protein, the ABC transporter ArtMP in native lipid bilayers, different sets of signals can be observed from different initial polarization pathways, which can be evaluated further to extract structural properties.
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Magic-angle spinning solid-state multinuclear NMR on low-field instrumentation. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 238:20-25. [PMID: 24291330 DOI: 10.1016/j.jmr.2013.10.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Revised: 10/18/2013] [Accepted: 10/24/2013] [Indexed: 06/02/2023]
Abstract
Mobile and cost-effective NMR spectroscopy exploiting low-field permanent magnets is a field of tremendous development with obvious applications for arrayed large scale analysis, field work, and industrial screening. So far such demonstrations have concentrated on relaxation measurements and lately high-resolution liquid-state NMR applications. With high-resolution solid-state NMR spectroscopy being increasingly important in a broad variety of applications, we here introduce low-field magic-angle spinning (MAS) solid-state multinuclear NMR based on a commercial ACT 0.45 T 62 mm bore Halbach magnet along with a homebuilt FPGA digital NMR console, amplifiers, and a modified standard 45 mm wide MAS probe for 7 mm rotors. To illustrate the performance of the instrument and address cases where the low magnetic field may offer complementarity to high-field NMR experiments, we demonstrate applications for (23)Na MAS NMR with enhanced second-order quadrupolar coupling effects and (31)P MAS NMR where reduced influence from chemical shift anisotropy at low field may facilitate determination of heteronuclear dipole-dipole couplings.
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Accumulation of nano-sized particles in a murine model of angiogenesis. Biochem Biophys Res Commun 2013; 443:470-6. [PMID: 24321551 DOI: 10.1016/j.bbrc.2013.11.127] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 11/27/2013] [Indexed: 01/09/2023]
Abstract
PURPOSE To evaluate the ability of nm-scaled iron oxide particles conjugated with Azure A, a classic histological dye, to accumulate in areas of angiogenesis in a recently developed murine angiogenesis model. MATERIALS AND METHODS We characterised the Azure A particles with regard to their hydrodynamic size, zeta potential, and blood circulation half-life. The particles were then investigated by Magnetic Resonance Imaging (MRI) in a recently developed murine angiogenesis model along with reference particles (Ferumoxtran-10) and saline injections. RESULTS The Azure A particles had a mean hydrodynamic diameter of 51.8 ± 43.2 nm, a zeta potential of -17.2 ± 2.8 mV, and a blood circulation half-life of 127.8 ± 74.7 min. Comparison of MR images taken pre- and 24-h post-injection revealed a significant increase in R2(*) relaxation rates for both Azure A and Ferumoxtran-10 particles. No significant difference was found for the saline injections. The relative increase was calculated for the three groups, and showed a significant difference between the saline group and the Azure A group, and between the saline group and the Ferumoxtran-10 group. However, no significant difference was found between the two particle groups. CONCLUSION Ultrahigh-field MRI revealed localisation of both types of iron oxide particles to areas of neovasculature. However, the Azure A particles did not show any enhanced accumulation relative to Ferumoxtran-10, suggesting the accumulation in both cases to be passive.
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Adiabatic Rotor-Echo-Short-Pulse-Irradiation mediated cross-polarization. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2013; 237:147-151. [PMID: 24220613 DOI: 10.1016/j.jmr.2013.09.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 08/25/2013] [Accepted: 09/05/2013] [Indexed: 05/14/2023]
Abstract
We present a new dipolar recoupling method for efficient and robust heteronuclear polarization transfer in solid-state NMR under magic-angle-spinning (MAS) conditions. The method combines the recent (RESPIRATION)CP method with a modulation of the amplitude of the rotor-synchronized pulses at one of the involved rf channels through the recoupling condition. In this manner, it is possible to achieve high transfer efficiencies while maintaining robustness towards rf-field inhomogeneities and resonance offsets. The performance of the so-called adiabatic-(RESPIRATION)CP experiment is demonstrated numerically and experimentally using uniformly (13)C,(15)N-labeled samples of alanine and ubiquitin. In particular for cases with relatively high rf inhomogeneity, the scheme offers advantages over the commonly used dipolar recoupling pulse sequences.
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Mutation in transforming growth factor beta induced protein associated with granular corneal dystrophy type 1 reduces the proteolytic susceptibility through local structural stabilization. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:2812-22. [PMID: 24129074 DOI: 10.1016/j.bbapap.2013.10.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 09/30/2013] [Accepted: 10/06/2013] [Indexed: 10/26/2022]
Abstract
Hereditary mutations in the transforming growth factor beta induced (TGFBI) gene cause phenotypically distinct corneal dystrophies characterized by protein deposition in cornea. We show here that the Arg555Trp mutant of the fourth fasciclin 1 (FAS1-4) domain of the protein (TGFBIp/keratoepithelin/βig-h3), associated with granular corneal dystrophy type 1, is significantly less susceptible to proteolysis by thermolysin and trypsin than the WT domain. High-resolution liquid-state NMR of the WT and Arg555Trp mutant FAS1-4 domains revealed very similar structures except for the region around position 555. The Arg555Trp substitution causes Trp555 to be buried in an otherwise empty hydrophobic cavity of the FAS1-4 domain. The first thermolysin cleavage in the core of the FAS1-4 domain occurs on the N-terminal side of Leu558 adjacent to the Arg555 mutation. MD simulations indicated that the C-terminal end of helix α3' containing this cleavage site is less flexible in the mutant domain, explaining the observed proteolytic resistance. This structural change also alters the electrostatic properties, which may explain increased propensity of the mutant to aggregate in vitro with 2,2,2-trifluoroethanol. Based on our results we propose that the Arg555Trp mutation disrupts the normal degradation/turnover of corneal TGFBIp, leading to accumulation and increased propensity to aggregate through electrostatic interactions.
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Abstract
BACKGROUND Currently, radiation treatments are being optimised based on in vivo imaging of radioresistant, hypoxic tumour areas. This study aimed at detecting nicotinamide's reduction of acute hypoxia in a mouse tumour model by two clinically relevant magnetic resonance imaging (MRI) methods at ultra-high magnetic field strength. MATERIAL AND METHODS The C3H mammary carcinoma was grown to 200 mm(3) in the right rear foot of CDF1 mice. The mice were anaesthetised with ketamine and xylazine prior to imaging. A treatment group received nicotinamide intraperitoneally (i.p.) at the dose 1000 mg/kg, and a control group received saline. MRI was performed at 16.4 T with a spatial resolution of 0.156 × 0.156 × 0.5 mm(3). The imaging protocol included BOLD imaging and two DCE-MRI scans. Initial area under the curve (IAUC) and the parameters from the extended Toft's model were estimated from the DCE-MRI data. Tumour median values of 1) T2* mean, 2) T2* standard deviation, 3) DCE-MRI parameters, and 4) DCE-MRI parameter differences between scans were compared between the treatment groups using Student's t-test (significance level p < 0.05). RESULTS Parametric maps showed intra- and inter-tumour heterogeneity. Blood volume was significantly larger in the nicotinamide-treated group, and also the blood volume difference between the two DCE-MRI scans was significantly larger in the treatment group. CONCLUSION Higher blood volume and blood volume variation was observed by DCE-MRI in the treatment group. Other DCE-MRI parameters showed no significant differences, and the higher blood volume was not detected by BOLD MRI. The higher blood volume variation seen with DCE-MRI may be influenced by the drug effect reducing over time, and furthermore the anaesthesia may play an important role.
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Targeting of peptide conjugated magnetic nanoparticles to urokinase plasminogen activator receptor (uPAR) expressing cells. NANOSCALE 2013; 5:8192-8201. [PMID: 23835641 DOI: 10.1039/c3nr32922d] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Ultrasmall superparamagnetic iron oxide (USPIO) nanoparticles are currently being used as a magnetic resonance imaging (MRI) contrast agent in vivo, mainly by their passive accumulation in tissues of interest. However, a higher specificity can ideally be achieved when the nanoparticles are targeted towards cell specific receptors and this may also facilitate specific drug delivery by an enhanced target-mediated endocytosis. We report efficient peptide-mediated targeting of magnetic nanoparticles to cells expressing the urokinase plasminogen activator receptor (uPAR), a surface biomarker for poor patient prognosis shared by several cancers including breast, colorectal, and gastric cancers. Conjugation of a uPAR specific targeting peptide onto polyethylene glycol (PEG) coated USPIO nanoparticles by click chemistry resulted in a five times higher uptake in vitro in a uPAR positive cell line compared to nanoparticles carrying a non-binding control peptide. In accordance with specific receptor-mediated recognition, a low uptake was observed in the presence of an excess of ATF, a natural ligand for uPAR. The uPAR specific magnetic nanoparticles can potentially provide a useful supplement for tumor patient management when combined with MRI and drug delivery.
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Dynamic nuclear polarization and optimal control spatial-selective 13C MRI and MRS. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2013; 227:57-61. [PMID: 23298857 DOI: 10.1016/j.jmr.2012.12.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2012] [Revised: 11/04/2012] [Accepted: 12/04/2012] [Indexed: 06/01/2023]
Abstract
Aimed at (13)C metabolic magnetic resonance imaging (MRI) and spectroscopy (MRS) applications, we demonstrate that dynamic nuclear polarization (DNP) may be combined with optimal control 2D spatial selection to simultaneously obtain high sensitivity and well-defined spatial restriction. This is achieved through the development of spatial-selective single-shot spiral-readout MRI and MRS experiments combined with dynamic nuclear polarization hyperpolarized [1-(13)C]pyruvate on a 4.7 T pre-clinical MR scanner. The method stands out from related techniques by facilitating anatomic shaped region-of-interest (ROI) single metabolite signals available for higher image resolution or single-peak spectra. The 2D spatial-selective rf pulses were designed using a novel Krotov-based optimal control approach capable of iteratively fast providing successful pulse sequences in the absence of qualified initial guesses. The technique may be important for early detection of abnormal metabolism, monitoring disease progression, and drug research.
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Robust and efficient 19F heteronuclear dipolar decoupling using refocused continuous-wave rf irradiation. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2013; 226:88-92. [PMID: 23220184 DOI: 10.1016/j.jmr.2012.11.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2012] [Revised: 11/04/2012] [Accepted: 11/07/2012] [Indexed: 06/01/2023]
Abstract
Refocused continuous wave (rCW) decoupling is presented as an efficient and robust means to obtain well-resolved magic-angle-spinning solid-state NMR spectra of low-γ spins, such as (13)C dipolar coupled to fluorine. The rCW decoupling sequences, recently introduced for (1)H decoupling, are very robust towards large isotropic and anisotropic shift ranges as often encountered for (19)F spins. In rCW decoupling, the so-called refocusing pulses inserted into the CW irradiation eliminate critical residual second- and third-order dipolar coupling and dipolar-coupling against chemical shielding anisotropy cross-terms in the effective Hamiltonian through time-reversal (i.e. refocusing). As important additional assets, the rCW decoupling sequences are robust towards variations in rf amplitudes, operational at low to high spinning speeds, and easy to set-up for optimal performance experimentally. These aspects are demonstrated analytically/numerically and experimentally in comparison to state-of-the-art decoupling sequences such as TPPM, SPINAL-64, and frequency-swept variants of these.
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Fast numerical design of spatial-selective rf pulses in MRI using Krotov and quasi-Newton based optimal control methods. J Chem Phys 2012; 137:054203. [PMID: 22894341 DOI: 10.1063/1.4739755] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The use of increasingly strong magnetic fields in magnetic resonance imaging (MRI) improves sensitivity, susceptibility contrast, and spatial or spectral resolution for functional and localized spectroscopic imaging applications. However, along with these benefits come the challenges of increasing static field (B(0)) and rf field (B(1)) inhomogeneities induced by radial field susceptibility differences and poorer dielectric properties of objects in the scanner. Increasing fields also impose the need for rf irradiation at higher frequencies which may lead to elevated patient energy absorption, eventually posing a safety risk. These reasons have motivated the use of multidimensional rf pulses and parallel rf transmission, and their combination with tailoring of rf pulses for fast and low-power rf performance. For the latter application, analytical and approximate solutions are well-established in linear regimes, however, with increasing nonlinearities and constraints on the rf pulses, numerical iterative methods become attractive. Among such procedures, optimal control methods have recently demonstrated great potential. Here, we present a Krotov-based optimal control approach which as compared to earlier approaches provides very fast, monotonic convergence even without educated initial guesses. This is essential for in vivo MRI applications. The method is compared to a second-order gradient ascent method relying on the Broyden-Fletcher-Goldfarb-Shanno (BFGS) quasi-Newton method, and a hybrid scheme Krotov-BFGS is also introduced in this study. These optimal control approaches are demonstrated by the design of a 2D spatial selective rf pulse exciting the letters "JCP" in a water phantom.
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Scanning tunneling microscopy reveals single-molecule insights into the self-assembly of amyloid fibrils. ACS NANO 2012; 6:6882-6889. [PMID: 22779709 DOI: 10.1021/nn301708d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Many severe diseases are associated with amyloid fibril deposits in the body caused by protein misfolding. Structural information on amyloid fibrils is accumulating rapidly, but little is known about the assembly of peptides into fibrils at the level of individual molecules. Here we investigate self-assembly of the fibril-forming tetrapeptides KFFE and KVVE on a gold surface under ultraclean vacuum conditions using scanning tunneling microscopy. Combined with restrained molecular dynamics modeling, we identify peptide arrangements with interesting similarities to fibril structures. By resolving individual peptide residues and revealing conformational heterogeneities and dynamics, we demonstrate how conformational correlations may be involved in cooperative fibril growth. Most interestingly, intermolecular interactions prevail over intramolecular interactions, and assembly of the phenyl-rich KFFE peptide appears not to be dominated by π-π interactions. This study offers interesting perspectives for obtaining fundamental single-molecule insights into fibril formation using a surface science approach to study idealized model systems.
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Polymorphic fibrillation of the destabilized fourth fasciclin-1 domain mutant A546T of the Transforming growth factor-β-induced protein (TGFBIp) occurs through multiple pathways with different oligomeric intermediates. J Biol Chem 2012; 287:34730-42. [PMID: 22893702 DOI: 10.1074/jbc.m112.379552] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mutations in the transforming growth factor β-induced protein (TGFBIp) are linked to the development of corneal dystrophies in which abnormal protein deposition in the cornea leads to a loss of corneal transparency and ultimately blindness. Different mutations give rise to phenotypically distinct corneal dystrophies. Most mutations are located in the fourth fasciclin-1 domain (FAS1-4). The amino acid substitution A546T in the FAS1-4 domain is linked to the development of lattice corneal dystrophy with amyloid deposits in the superficial and deep stroma, classifying it as an amyloid disease. Here we provide a detailed description of the fibrillation of the isolated FAS1-4 domain carrying the A546T substitution. The A546T substitution leads to a significant destabilization of FAS1-4 and induces a partially folded structure with increased surface exposure of hydrophobic patches. The mutation also leads to two distinct fibril morphologies. Long straight fibrils composed of pure β-sheet structure are formed at lower concentrations, whereas short and curly fibrils containing a mixture of α-helical and β-sheet structures are formed at higher concentrations. The formation of short and curly fibrils is preceded by the formation of a small number of oligomeric species with high membrane permeabilization potential and rapid fibril formation. The long straight fibrils are formed more slowly and through progressively bigger oligomers that lose their membrane permeabilization potential as fibrillation proceeds beyond the lag phase. These different fibril classes and associated biochemical differences may lead to different clinical symptoms associated with the mutation.
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Cyclodextrin-scaffolded alamethicin with remarkably efficient membrane permeabilizing properties and membrane current conductance. J Phys Chem B 2012; 116:7652-9. [PMID: 22676384 DOI: 10.1021/jp2098679] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Bacterial resistance to classical antibiotics is a serious medical problem, which continues to grow. Small antimicrobial peptides represent a potential solution and are increasingly being developed as novel therapeutic agents. Many of these peptides owe their antibacterial activity to the formation of trans-membrane ion-channels resulting in cell lysis. However, to further develop the field of peptide antibiotics, a thorough understanding of their mechanism of action is needed. Alamethicin belongs to a class of peptides called peptaibols and represents one of these antimicrobial peptides. To examine the dynamics of assembly and to facilitate a thorough structural evaluation of the alamethicin ion-channels, we have applied click chemistry for the synthesis of templated alamethicin multimers covalently attached to cyclodextrin-scaffolds. Using oriented circular dichroism, calcein release assays, and single-channel current measurements, the α-helices of the templated multimers were demonstrated to insert into lipid bilayers forming highly efficient and remarkably stable ion-channels.
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In situ solid-state NMR spectroscopy of protein in heterogeneous membranes: the baseplate antenna complex of Chlorobaculum tepidum. Angew Chem Int Ed Engl 2012; 51:6891-5. [PMID: 22685072 DOI: 10.1002/anie.201201160] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2012] [Revised: 05/16/2012] [Indexed: 11/06/2022]
Abstract
A clever combination: an in situ solid-state NMR analysis of CsmA proteins in the heterogeneous environment of the photoreceptor of Chlorobaculum tepidum is reported. Using different combinations of 2D and 3D solid-state NMR spectra, 90 % of the CsmA resonances are assigned and provide on the basis of chemical shift data information about the structure and conformation of CsmA in the CsmA-bacteriochlorophyll a complex.
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Isotope-labeling of the fibril binding compound FSB via a Pd-catalyzed double alkoxycarbonylation. J Org Chem 2012; 77:5357-63. [PMID: 22612598 DOI: 10.1021/jo300746x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
We have synthesized two isotopically labeled variants of the β-amyloid binding compound FSB possessing (13)C-labels on the two terminal aryl carboxylic acid moieties. One of these was also fully deuterated on the olefinic spacers. The (13)C-isotope labeling was achieved applying a Pd-catalyzed methoxycarbonylation of the corresponding aryl chlorides with externally (ex situ) generated (13)C-labeled CO. Application of the Shirakawa-Hayashi protocol for the Pd-catalyzed reduction of a dialkyne intermediate using D(2)O allowed for the selective deuterium labeling of the two trans-C,C double bonds of FSB.
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Accumulation of magnetic iron oxide nanoparticles coated with variably sized polyethylene glycol in murine tumors. NANOSCALE 2012; 4:2352-2361. [PMID: 22395568 DOI: 10.1039/c2nr11554a] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Iron oxide nanoparticles have found widespread applications in different areas including cell separation, drug delivery and as contrast agents. Due to water insolubility and stability issues, nanoparticles utilized for biological applications require coatings such as the commonly employed polyethylene glycol (PEG). Despite its frequent use, the influence of PEG coatings on the physicochemical and biological properties of iron nanoparticles has hitherto not been studied in detail. To address this, we studied the effect of 333-20,000 Da PEG coatings that resulted in larger hydrodynamic size, lower surface charge, longer circulation half-life, and lower uptake in macrophage cells when the particles were coated with high molecular weight (M(w)) PEG molecules. By use of magnetic resonance imaging, we show coating-dependent in vivo uptake in murine tumors with an optimal coating M(w) of 10,000 Da.
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Simultaneous acquisition of PAR and PAIN spectra. JOURNAL OF BIOMOLECULAR NMR 2012; 52:283-288. [PMID: 22371268 DOI: 10.1007/s10858-012-9616-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2011] [Accepted: 02/07/2012] [Indexed: 05/31/2023]
Abstract
We present a scheme that allows the simultaneous detection of PAR and PAIN correlation spectra in a single two-dimensional experiment. For both spectra, we obtain almost the same signal-to-noise ratio as if a PAR or PAIN spectrum is recorded separately, which in turn implies that one of the spectra may be considered additional information for free. The experiment is based on the observation that in a PAIN experiment, the PAR condition is always also fulfilled. The performance is demonstrated experimentally using uniformly (13)C,(15)N-labeled samples of N-f-MLF-OH and ubiquitin.
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Efficient and Robust Heteronuclear Cross-Polarization for High-Speed-Spinning Biological Solid-State NMR Spectroscopy. J Phys Chem Lett 2012; 3:703-708. [PMID: 26286276 DOI: 10.1021/jz3000905] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We present a new and highly efficient approach for heteronuclear coherence transfer in solid-state NMR spectroscopy under high-speed spinning conditions. The so-called (RESPIRATION)CP experiment exploits phase-alternated recoupling on only one of the two rf channels intertwined in a synchronized train of short rf pulses on both channels. The method provides significantly higher efficiencies than state-of-the art techniques including ramped and adiabatic cross-polarization experiments with long durations of intense rf irradiation. At the same time, it is easier to setup experimentally and significantly more robust toward imperfections such as rf inhomogeneity, misadjustments, and sample-induced variations in the rf tuning. The method is described analytically, numerically, and experimentally for biological solids. We demonstrate sensitivity gains of factors of 1.3 and 1.8 for typical (1)H→(15)N and (15)N→(13)C transfers and a combined gain of a factor of 2-4 for a typical NCA experiment for biological solid-state NMR.
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Cold tolerance and freeze-induced glucose accumulation in three terrestrial slugs. Comp Biochem Physiol A Mol Integr Physiol 2012; 161:443-9. [PMID: 22248916 DOI: 10.1016/j.cbpa.2012.01.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 12/21/2011] [Accepted: 01/03/2012] [Indexed: 11/28/2022]
Abstract
Cold tolerance and metabolic responses to freezing of three slug species common in Scandinavia (Arion ater, Arion rufus and Arion lusitanicus) are reported. Autumn collected slugs were cold acclimated in the laboratory and subjected to freezing conditions simulating likely winter temperatures in their habitat. Slugs spontaneously froze at about -4 °C when cooled under dry conditions, but freezing of body fluids was readily induced at -1 °C when in contact with external ice crystals. All three species survived freezing for 2 days at -1 °C, and some A. rufus and A. lusitanicus also survived freezing at -2 °C. (1)H NMR spectroscopy revealed that freezing of body fluids resulted in accumulation of lactate, succinate and glucose. Accumulation of lactate and succinate indicates that ATP production occurred via fermentative pathways, which is likely a result of oxygen depletion in frozen tissues. Glucose increased from about 6 to 22 μg/mg dry tissue upon freezing in A. rufus, but less so in A. ater and A. lusitanicus. Glucose may thus act as a cryoprotectant in these slugs, although the concentrations are not as high as reported for other freeze tolerant invertebrates.
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A comparison of NCO and NCA transfer methods for biological solid-state NMR spectroscopy. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2012; 214:81-90. [PMID: 22116035 PMCID: PMC3257381 DOI: 10.1016/j.jmr.2011.10.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2011] [Revised: 09/24/2011] [Accepted: 10/17/2011] [Indexed: 05/09/2023]
Abstract
Three different techniques (adiabatic passage Hartman-Hahn cross-polarization, optimal control designed pulses, and EXPORT) are compared for transferring (15)N magnetization to (13)C in solid-state NMR experiments under magic-angle-spinning conditions. We demonstrate that, in comparison to adiabatic passage Hartman-Hahn cross-polarization, optimal control transfer pulses achieve similar or better transfer efficiencies for uniformly-(13)C,(15)N labeled samples and are generally superior for samples with non-uniform labeling schemes (such as 1,3- and 2-(13)C glycerol labeling). In addition, the optimal control pulses typically use substantially lower average RF field strengths and are more robust with respect to experimental variation and RF inhomogeneity. Consequently, they are better suited for demanding samples.
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Rapid solid-state NMR of deuterated proteins by interleaved cross-polarization from ¹H and ²H nuclei. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2012; 214:324-328. [PMID: 22130517 DOI: 10.1016/j.jmr.2011.10.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Revised: 10/27/2011] [Accepted: 10/29/2011] [Indexed: 05/31/2023]
Abstract
We present a novel sampling strategy, interleaving acquisition of multiple NMR spectra by exploiting initial polarization subsequently from (1)H and (2)H spins, taking advantage of their different T(1) relaxation times. Different (1)H- and (2)H-polarization based spectra are in this way simultaneously recorded improving either information content or sensitivity by adding spectra. The so-called Relaxation-optimized Acquisition of Proton Interleaved with Deuterium (RAPID) (1)H→(13)C/(2)H→(13)C CP/MAS multiple-acquisition method is demonstrated by 1D and 2D experiments using a uniformly (2)H, (15)N,(13)C-labeled α-spectrin SH3 domain sample with all or 30% back-exchanged labile (2)H to (1)H. It is demonstrated how 1D (13)C CP/MAS or 2D (13)C-(13)C correlation spectra initialized with polarization from either (1)H or (2)H may be recorded simultaneously with flexibility to be added or used individually for spectral editing. It is also shown how 2D (13)C-(13)C correlation spectra may be recorded interleaved with (2)H-(13)C correlation spectra to obtain (13)C-(13)C correlations along with information about dynamics from (2)H sideband patterns.
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SIMPSON: a general simulation program for solid-state NMR spectroscopy. 2000. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2011; 213:366-400. [PMID: 22152357 DOI: 10.1016/j.jmr.2011.09.008] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
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SIMPSON - an important driver for numerical simulations in solid-state NMR spectroscopy. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2011; 213:401-403. [PMID: 21903437 DOI: 10.1016/j.jmr.2011.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We present a historical recollection on the development of the software package SIMPSON (SIMulation Package for SOlid-state Nmr). This covers a brief description of the underlying ideas and events leading to creation of SIMPSON and numerous auxiliary programs as well as comments on its impact on the development and application of solid-state NMR in research laboratories world-wide.
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Optimal (2)H rf Pulses and (2)H-(13)C Cross-Polarization Methods for Solid-State (2)H MAS NMR of Perdeuterated Proteins. J Phys Chem Lett 2011; 2:1289-94. [PMID: 26295423 DOI: 10.1021/jz200511b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
We present a novel concept for rf pulses and optimal control designed cross-polarization experiments for quadrupolar nuclei. The methods are demonstrated for (2)H CP-MAS and (2)H multiple-pulse NMR of perdeuterated proteins, for which sensitivity enhancements up to an order of magnitude are presented relative to commonly used approaches. The so-called RESPIRATION rf pulses combines the concept of short broad-band pulses with generation of pulses with large flip angles through distribution of the rf pulse over several rotor echoes. This lead to close-to-ideal rf pulses, facilitating implementation of experiments relying on the ability to realize high-performance 90 and 180° pulses, as, for example, in refocused INEPT and double-to-single quantum coherence experiments, or just pulses that provide a true representation of the quadrupolar powder pattern to extract information about the structure or dynamics. The optimal control (2)H → (13)C CP-MAS method demonstrates transfer efficiencies up to around 85% while being extremely robust toward rf inhomogeneity and resonance offsets.
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