1
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Vugmeyster L, Ostrovsky D, Fu R. Carbon-detected deuterium solid-state NMR rotating frame relaxation measurements for protein methyl groups under magic angle spinning. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2024; 130:101922. [PMID: 38417233 PMCID: PMC11015826 DOI: 10.1016/j.ssnmr.2024.101922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 02/16/2024] [Accepted: 02/20/2024] [Indexed: 03/01/2024]
Abstract
Deuterium rotating frame solid-state NMR relaxation measurements (2H R1ρ) are important tools in quantitative studies of molecular dynamics. We demonstrate how 2H to 13C cross-polarization (CP) approaches under 10-40 kHz magic angle spinning rates can be combined with the 2H R1ρ blocks to allow for extension of deuterium rotating frame relaxation studies to methyl groups in biomolecules. This extension permits detection on the 13C nuclei and, hence, for the achievement of site-specific resolution. The measurements are demonstrated using a nine-residue low complexity peptide with the sequence GGKGMGFGL, in which a single selective -13CD3 label is placed at the methionine residue. Carbon-detected measurements are compared with the deuterium direct-detection results, which allows for fine-tuning of experimental approaches. In particular, we show how the adiabatic respiration CP scheme and the double adiabatic sweep on the 2H and 13C channels can be combined with the 2H R1ρ relaxation rates measurement. Off-resonance 2H R1ρ measurements are investigated in addition to the on-resonance condition, as they extent the range of effective spin-locking field.
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Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Colorado Denver, Denver, CO, 80204, USA.
| | - Dmitry Ostrovsky
- Department of Mathematics, University of Colorado Denver, Denver, CO, 80204, USA
| | - Riqiang Fu
- National High Field Magnetic Laboratory, Tallahassee, FL, 32310, USA
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2
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Hasanbasri Z, Tessmer MH, Stoll S, Saxena S. Modeling of Cu(II)-based protein spin labels using rotamer libraries. Phys Chem Chem Phys 2024; 26:6806-6816. [PMID: 38324256 PMCID: PMC10883468 DOI: 10.1039/d3cp05951k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
The bifunctional spin label double-histidine copper-(II) capped with nitrilotriacetate [dHis-Cu(II)-NTA], used in conjunction with electron paramagnetic resonance (EPR) methods can provide high-resolution distance data for investigating protein structure and backbone conformational diversity. Quantitative utilization of this data is limited due to a lack of rapid and accurate dHis-Cu(II)-NTA modeling methods that can be used to translate experimental data into modeling restraints. Here, we develop two dHis-Cu(II)-NTA rotamer libraries using a set of recently published molecular dynamics simulations and a semi-empirical meta-dynamics-based conformational ensemble sampling tool for use with the recently developed chiLife bifunctional spin label modeling method. The accuracy of both the libraries and the modeling method are tested by comparing model predictions to experimentally determined distance distributions. We show that this method is accurate with absolute deviation between the predicted and experimental modes between 0.0-1.2 Å with an average of 0.6 Å over the test data used. In doing so, we also validate the generality of the chiLife bifunctional label modeling method. Taken together, the increased structural resolution and modeling accuracy of dHis-Cu(II)-NTA over other spin labels promise improvements in the accuracy and resolution of protein models by EPR.
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Affiliation(s)
- Zikri Hasanbasri
- Department of Chemistry, University of Pittsburgh, PA, 15260, USA.
| | - Maxx H Tessmer
- Department of Chemistry, University of Washington, WA, 98195, USA.
| | - Stefan Stoll
- Department of Chemistry, University of Washington, WA, 98195, USA.
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, PA, 15260, USA.
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3
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Vugmeyster L, Ostrovsky D, Rodgers A, Gwin K, Smirnov SL, McKnight CJ, Fu R. Persistence of Methionine Side Chain Mobility at Low Temperatures in a Nine-Residue Low Complexity Peptide, as Probed by 2 H Solid-State NMR. Chemphyschem 2024; 25:e202300565. [PMID: 38175858 PMCID: PMC10922872 DOI: 10.1002/cphc.202300565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 12/01/2023] [Indexed: 01/06/2024]
Abstract
Methionine side chains are flexible entities which play important roles in defining hydrophobic interfaces. We utilize deuterium static solid-state NMR to assess rotameric inter-conversions and other dynamic modes of the methionine in the context of a nine-residue random-coil peptide (RC9) with the low-complexity sequence GGKGMGFGL. The measurements in the temperature range of 313 to 161 K demonstrate that the rotameric interconversions in the hydrated solid powder state persist to temperatures below 200 K. Removal of solvation significantly reduces the rate of the rotameric motions. We employed 2 H NMR line shape analysis, longitudinal and rotation frame relaxation, and chemical exchange saturation transfer methods and found that the combination of multiple techniques creates a significantly more refined model in comparison with a single technique. Further, we compare the most essential features of the dynamics in RC9 to two different methionine-containing systems, characterized previously. Namely, the M35 of hydrated amyloid-β1-40 in the three-fold symmetric polymorph as well as Fluorenylmethyloxycarbonyl (FMOC)-methionine amino acid with the bulky hydrophobic group. The comparison suggests that the driving force for the enhanced methionine side chain mobility in RC9 is the thermodynamic factor stemming from distributions of rotameric populations, rather than the increase in the rate constant.
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Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Colorado Denver, Denver CO USA 80204
| | - Dmitry Ostrovsky
- Department of Mathematics, University of Colorado Denver, Denver CO USA 80204
| | - Aryana Rodgers
- Department of Chemistry, University of Colorado Denver, Denver CO USA 80204
| | - Kirsten Gwin
- Department of Chemistry, University of Colorado Denver, Denver CO USA 80204
| | - Serge L. Smirnov
- Department of Chemistry, Western Washington University, Bellingham, WA 98225
| | - C. James McKnight
- Department of Pharmacology, Physiology and Biophysics, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, 02118
| | - Riqiang Fu
- National High Magnetic Field Laboratory, Tallahassee, FL USA 32310
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4
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Vugmeyster L, Au DF, Frazier B, Qiang W, Ostrovsky D. Rigidifying of the internal dynamics of amyloid-beta fibrils generated in the presence of synaptic plasma vesicles. Phys Chem Chem Phys 2024; 26:5466-5478. [PMID: 38277177 PMCID: PMC10956644 DOI: 10.1039/d3cp04824a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
We investigated the changes in internal flexibility of amyloid-β1-40 (Aβ) fibrils grown in the presence of rat synaptic plasma vesicles. The fibrils are produced using a modified seeded growth protocol, in which the Aβ concentration is progressively increased at the expense of the decreased lipid to protein ratio. The morphologies of each generation are carefully assessed at several fibrils' growth time points using transmission electron microscopy. The side-chain dynamics in the fibrils is investigated using deuterium solid-state NMR measurements, with techniques spanning line shapes analysis and several NMR relaxation rates measurements. The dynamics is probed in the site-specific fashion in the hydrophobic C-terminal domain and the disordered N-terminal domain. An overall strong rigidifying effect is observed in comparison with the wild-type fibrils generated in the absence of the membranes. In particular, the overall large-scale fluctuations of the N-terminal domain are significantly reduced, and the activation energies of rotameric inter-conversion in methyl-bearing side-chains of the core (L17, L34, M35, V36), as well as the ring-flipping motions of F19 are increased, indicating a restricted core environment. Membrane-induced flexibility changes in Aβ aggregates can be important for the re-alignment of protein aggregates within the membrane, which in turn would act as a disruption pathway of the bilayers' integrity.
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Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Colorado Denver, Denver, CO, USA, 80204.
| | - Dan Fai Au
- Department of Chemistry, University of Colorado Denver, Denver, CO, USA, 80204.
| | - Bailey Frazier
- Department of Chemistry, University of Colorado Denver, Denver, CO, USA, 80204.
| | - Wei Qiang
- Department of Chemistry, Binghamton University, Binghamton, New York, USA, 13902
| | - Dmitry Ostrovsky
- Department of Mathematics, University of Colorado Denver, Denver, CO, USA, 80204
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5
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Vugmeyster L, Rodgers A, Ostrovsky D, James McKnight C, Fu R. Deuteron off-resonance rotating frame relaxation for the characterization of slow motions in rotating and static solid-state proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 352:107493. [PMID: 37271094 PMCID: PMC10330767 DOI: 10.1016/j.jmr.2023.107493] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/24/2023] [Accepted: 05/25/2023] [Indexed: 06/06/2023]
Abstract
We demonstrate the feasibility of deuterium solid-state NMR off-resonance rotating frame relaxation measurements for studies of slow motions in biomolecular solids. The pulse sequence, which includes adiabatic pulses for magnetization alignment, is illustrated for static and magic-angle spinning conditions away from rotary resonances. We apply the measurements for three systems with selective deuterium labels at methyl groups: a) a model compound, Fluorenylmethyloxycarbonyl methionine-D3 amino acid, for which the principles of the measurements and corresponding motional modeling based on rotameric interconversions are demonstrated; b) amyloid-β1-40 fibrils labeled at a single alanine methyl group located in the disordered N-terminal domain. This system has been extensively studied in prior work and here serves as a test of the method for complex biological systems. The essential features of the dynamics consist of large-scale rearrangements of the disordered N-terminal domain and the conformational exchange between the free and bound forms of the domain, the latter one due to transient interactions with the structured core of the fibrils. and c) a 15-residue helical peptide which belongs to the predicted α-helical domain near the N-terminus of apolipoprotein B. The peptide is solvated with triolein and incorporates a selectively labeled leucine methyl groups. The method permits model refinement, indicating rotameric interconversions with a distribution of rate constants.
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Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Colorado Denver, Denver, CO 80204, USA.
| | - Aryana Rodgers
- Department of Chemistry, University of Colorado Denver, Denver, CO 80204, USA
| | - Dmitry Ostrovsky
- Department of Mathematics, University of Colorado Denver, Denver, CO 80204, USA
| | - C James McKnight
- Department of Pharmacology, Physiology and Biophysics, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, United States
| | - Riqiang Fu
- National High Field Magnetic Laboratory, Tallahassee, FL 32310, USA
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6
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Shi X, Kannaian B, Prasanna C, Soman A, Nordenskiöld L. Structural and dynamical investigation of histone H2B in well-hydrated nucleosome core particles by solid-state NMR. Commun Biol 2023; 6:672. [PMID: 37355718 PMCID: PMC10290710 DOI: 10.1038/s42003-023-05050-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 06/16/2023] [Indexed: 06/26/2023] Open
Abstract
H2A-H2B dimer is a key component of nucleosomes and an important player in chromatin biology. Here, we characterized the structure and dynamics of H2B in precipitated nucleosome core particles (NCPs) with a physiologically relevant concentration using solid-state NMR. Our recent investigation of H3-H4 tetramer determined its unique dynamic properties and the present work provides a deeper understanding of the previously observed dynamic networks in NCP that is potentially functionally significant. Nearly complete 13C, 15N assignments were obtained for H2B R30-A121, which permit extracting unprecedented detailed structural and amino-acid site-specific dynamics. The derived structure of H2B in the well-hydrated NCP sample agrees well with that of X-ray crystals. Dynamics at different timescales were determined semi-quantitatively for H2B in a site-specific manner. Particularly, higher millisecond-microsecond dynamics are observed for H2B core regions including partial α1, L1, partial α2, and partial L3. The analysis of these regions in the context of the tertiary structure reveals the clustering of dynamical residues. Overall, this work fills a gap to a complete resonance assignment of all four histones in nucleosomes and delineates that the dynamic networks in NCP extend to H2B, which suggests a potential mechanism to couple histone core with distant DNA to modulate the DNA activities.
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Affiliation(s)
- Xiangyan Shi
- Department of Biology, Shenzhen MSU-BIT University, Shenzhen, Guangdong Province, China.
| | - Bhuvaneswari Kannaian
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Chinmayi Prasanna
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, USA
| | - Aghil Soman
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore.
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7
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Akbey Ü. Site-specific protein backbone deuterium 2H α quadrupolar patterns by proton-detected quadruple-resonance 3D 2H αc αNH MAS NMR spectroscopy. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2023; 125:101861. [PMID: 36989552 DOI: 10.1016/j.ssnmr.2023.101861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/23/2023] [Accepted: 03/06/2023] [Indexed: 06/11/2023]
Abstract
A novel deuterium-excited and proton-detected quadruple-resonance three-dimensional (3D) 2HαcαNH MAS nuclear magnetic resonance (NMR) method is presented to obtain site-specific 2Hα deuterium quadrupolar couplings from protein backbone, as an extension to the 2D version of the experiment reported earlier. Proton-detection results in high sensitivity compared to the heteronuclei detection methods. Utilizing four independent radiofrequency (RF) channels (quadruple-resonance), we managed to excite the 2Hα, then transfer deuterium polarization to its attached Cα, followed by polarization transfers to the neighboring backbone nitrogen and then to the amide proton for detection. This experiment results in an easy to interpret HSQC-like 2D 1H-15N fingerprint NMR spectrum, which contains site-specific deuterium quadrupolar patterns in the indirect third dimension. Provided that four-channel NMR probe technology is available, the setup of the 2HαcαNH experiment is relatively straightforward, by using low power deuterium excitation and polarization transfer schemes we have been developing. To our knowledge, this is the first demonstration of a quadruple-resonance MAS NMR experiment to link 2Hα quadrupolar couplings to proton-detection, extending our previous triple-resonance demonstrations. Distortion-free excitation and polarization transfer of ∼160-170 kHz 2Hα quadrupolar coupling were presented by using a deuterium RF strength of ∼20 kHz. From these 2Hα patterns, an average backbone order parameter of S = 0.92 was determined on a deuterated SH3 sample, with an average η = 0.22. These indicate that SH3 backbone represents sizable dynamics in the microsecond timescale where the 2Hα lineshape is sensitive. Moreover, site-specific 2Hα T1 relaxation times were obtained for a proof of concept. This 3D 2HαcαNH NMR experiment has the potential to determine structure and dynamics of perdeuterated proteins by utilizing deuterium as a novel reporter.
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Affiliation(s)
- Ümit Akbey
- Department of Structural Biology, School of Medicine, University of Pittsburgh, Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, 15261, United States.
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8
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Taware PP, Jain MG, Raran-Kurussi S, Agarwal V, Madhu PK, Mote KR. Measuring Dipolar Order Parameters in Nondeuterated Proteins Using Solid-State NMR at the Magic-Angle-Spinning Frequency of 100 kHz. J Phys Chem Lett 2023; 14:3627-3635. [PMID: 37026698 DOI: 10.1021/acs.jpclett.3c00492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Proteins are dynamic molecules, relying on conformational changes to carry out function. Measurement of these conformational changes can provide insight into how function is achieved. For proteins in the solid state, this can be done by measuring the decrease in the strength of anisotropic interactions due to motion-induced fluctuations. The measurement of one-bond heteronuclear dipole-dipole coupling at magic-angle-spinning (MAS) frequencies >60 kHz is ideal for this purpose. However, rotational-echo double resonance (REDOR), an otherwise gold-standard technique for the quantitative measurement of these couplings, is difficult to implement under these conditions, especially in nondeuterated samples. We present here a combination of strategies based on REDOR variants ϵ-REDOR and DEDOR (deferred REDOR) and simultaneously measure residue-specific 15N-1H and 13Cα-1Hα dipole-dipole couplings in nondeuterated systems at the MAS frequency of 100 kHz. These strategies open up avenues to access dipolar order parameters in a variety of systems at the increasingly fast MAS frequencies that are now available.
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Affiliation(s)
- Pravin P Taware
- Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad 500 046, Telangana, India
| | - Mukul G Jain
- Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad 500 046, Telangana, India
| | - Sreejith Raran-Kurussi
- Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad 500 046, Telangana, India
| | - Vipin Agarwal
- Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad 500 046, Telangana, India
| | - P K Madhu
- Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad 500 046, Telangana, India
| | - Kaustubh R Mote
- Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad 500 046, Telangana, India
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9
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Nishiyama Y, Hou G, Agarwal V, Su Y, Ramamoorthy A. Ultrafast Magic Angle Spinning Solid-State NMR Spectroscopy: Advances in Methodology and Applications. Chem Rev 2023; 123:918-988. [PMID: 36542732 PMCID: PMC10319395 DOI: 10.1021/acs.chemrev.2c00197] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Solid-state NMR spectroscopy is one of the most commonly used techniques to study the atomic-resolution structure and dynamics of various chemical, biological, material, and pharmaceutical systems spanning multiple forms, including crystalline, liquid crystalline, fibrous, and amorphous states. Despite the unique advantages of solid-state NMR spectroscopy, its poor spectral resolution and sensitivity have severely limited the scope of this technique. Fortunately, the recent developments in probe technology that mechanically rotate the sample fast (100 kHz and above) to obtain "solution-like" NMR spectra of solids with higher resolution and sensitivity have opened numerous avenues for the development of novel NMR techniques and their applications to study a plethora of solids including globular and membrane-associated proteins, self-assembled protein aggregates such as amyloid fibers, RNA, viral assemblies, polymorphic pharmaceuticals, metal-organic framework, bone materials, and inorganic materials. While the ultrafast-MAS continues to be developed, the minute sample quantity and radio frequency requirements, shorter recycle delays enabling fast data acquisition, the feasibility of employing proton detection, enhancement in proton spectral resolution and polarization transfer efficiency, and high sensitivity per unit sample are some of the remarkable benefits of the ultrafast-MAS technology as demonstrated by the reported studies in the literature. Although the very low sample volume and very high RF power could be limitations for some of the systems, the advantages have spurred solid-state NMR investigation into increasingly complex biological and material systems. As ultrafast-MAS NMR techniques are increasingly used in multidisciplinary research areas, further development of instrumentation, probes, and advanced methods are pursued in parallel to overcome the limitations and challenges for widespread applications. This review article is focused on providing timely comprehensive coverage of the major developments on instrumentation, theory, techniques, applications, limitations, and future scope of ultrafast-MAS technology.
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Affiliation(s)
- Yusuke Nishiyama
- JEOL Ltd., Akishima, Tokyo196-8558, Japan
- RIKEN-JEOL Collaboration Center, Yokohama, Kanagawa230-0045, Japan
| | - Guangjin Hou
- State Key Laboratory of Catalysis, Dalian National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian116023, China
| | - Vipin Agarwal
- Tata Institute of Fundamental Research, Sy. No. 36/P, Gopanpally, Hyderabad500 046, India
| | - Yongchao Su
- Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey07065, United States
| | - Ayyalusamy Ramamoorthy
- Biophysics, Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, Michigan Neuroscience Institute, University of Michigan, Ann Arbor, Michigan41809-1055, United States
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10
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Ahlawat S, Mopidevi SMV, Taware PP, Raran-Kurussi S, Mote KR, Agarwal V. Assignment of aromatic side-chain spins and characterization of their distance restraints at fast MAS. J Struct Biol X 2022; 7:100082. [PMID: 36618437 PMCID: PMC9817166 DOI: 10.1016/j.yjsbx.2022.100082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 11/18/2022] [Accepted: 12/27/2022] [Indexed: 12/30/2022] Open
Abstract
The assignment of aromatic side-chain spins has always been more challenging than assigning backbone and aliphatic spins. Selective labeling combined with mutagenesis has been the approach for assigning aromatic spins. This manuscript reports a method for assigning aromatic spins in a fully protonated protein by connecting them to the backbone atoms using a low-power TOBSY sequence. The pulse sequence employs residual polarization and sequential acquisitions techniques to record HN- and HC-detected spectra in a single experiment. The unambiguous assignment of aromatic spins also enables the characterization of 1H-1H distance restraints involving aromatic spins. Broadband (RFDR) and selective (BASS-SD) recoupling sequences were used to generate HN-ΗC, HC-HN and HC-HC restraints involving the side-chain proton spins of aromatic residues. This approach has been demonstrated on a fully protonated U-[13C,15N] labeled GB1 sample at 95-100 kHz MAS.
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11
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How does it really move? Recent progress in the investigation of protein nanosecond dynamics by NMR and simulation. Curr Opin Struct Biol 2022; 77:102459. [PMID: 36148743 DOI: 10.1016/j.sbi.2022.102459] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 07/29/2022] [Accepted: 08/05/2022] [Indexed: 12/14/2022]
Abstract
Nuclear magnetic resonance (NMR) spin relaxation experiments currently probe molecular motions on timescales from picoseconds to nanoseconds. The detailed interpretation of these motions in atomic detail benefits from complementarity with the results from molecular dynamics (MD) simulations. In this mini-review, we describe the recent developments in experimental techniques to study the backbone dynamics from 15N relaxation and side-chain dynamics from 13C relaxation, discuss the different analysis approaches from model-free to dynamics detectors, and highlight the many ways that NMR relaxation experiments and MD simulations can be used together to improve the interpretation and gain insights into protein dynamics.
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12
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Duan P, Dregni AJ, Hong M. Solid-State NMR 19F- 1H- 15N Correlation Experiments for Resonance Assignment and Distance Measurements of Multifluorinated Proteins. J Phys Chem A 2022; 126:7021-7032. [PMID: 36150071 PMCID: PMC10867861 DOI: 10.1021/acs.jpca.2c05154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Several solid-state NMR techniques have been introduced recently to measure nanometer distances involving 19F, whose high gyromagnetic ratio makes it a potent nuclear spin for structural investigation. These solid-state NMR techniques either use 19F correlation with 1H or 13C to obtain qualitative interatomic contacts or use the rotational-echo double-resonance (REDOR) pulse sequence to measure quantitative distances. However, no NMR technique is yet available for disambiguating 1H-19F distances in multiply fluorinated proteins and protein-ligand complexes. Here, we introduce a three-dimensional (3D) 19F-15N-1H correlation experiment that resolves the distances of multiple fluorines to their adjacent amide protons. We show that optimal polarization transfer between 1H and 19F spins is achieved using an out-and-back 1H-19F REDOR sequence. We demonstrate this 3D correlation experiment on the model protein GB1 and apply it to the multidrug-resistance transporter, EmrE, complexed to a tetrafluorinated substrate. This technique should be useful for resolving and assigning distance constraints in multiply fluorinated proteins, leading to significant savings of time and precious samples compared to producing several singly fluorinated samples. Moreover, the method enables structural determination of protein-ligand complexes for ligands that contain multiple fluorines.
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Affiliation(s)
- Pu Duan
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
| | - Aurelio J. Dregni
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
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13
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Singewald K, Wilkinson JA, Hasanbasri Z, Saxena S. Beyond structure: Deciphering site-specific dynamics in proteins from double histidine-based EPR measurements. Protein Sci 2022; 31:e4359. [PMID: 35762707 DOI: 10.1002/pro.4359] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/16/2022] [Accepted: 05/20/2022] [Indexed: 12/27/2022]
Abstract
Site-specific dynamics in proteins are at the heart of protein function. While electron paramagnetic resonance (EPR) has potential to measure dynamics in large protein complexes, the reliance on flexible nitroxide labels is limitating especially for the accurate measurement of site-specific β-sheet dynamics. Here, we employed EPR spectroscopy to measure site-specific dynamics across the surface of a protein, GB1. Through the use of the double Histidine (dHis) motif, which enables labeling with a Cu(II) - nitrilotriacetic acid (NTA) complex, dynamics information was obtained for both α-helical and β-sheet sites. Spectral simulations of the resulting CW-EPR report unique site-specific fluctuations across the surface of GB1. Additionally, we performed molecular dynamics (MD) simulations to complement the EPR data. The dynamics observed from MD agree with the EPR results. Furthermore, we observe small changes in gǁ values for different sites, which may be due to small differences in coordination geometry and/or local electrostatics of the site. Taken together, this work expands the utility of Cu(II)NTA-based EPR measurements to probe information beyond distance constraints.
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Affiliation(s)
- Kevin Singewald
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - James A Wilkinson
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Zikri Hasanbasri
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
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14
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Borcik C, Eason IR, Vanderloop B, Wylie BJ. 2H, 13C-Cholesterol for Dynamics and Structural Studies of Biological Membranes. ACS OMEGA 2022; 7:17151-17160. [PMID: 35647452 PMCID: PMC9134247 DOI: 10.1021/acsomega.2c00796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/08/2022] [Indexed: 05/19/2023]
Abstract
We present a cost-effective means of 2H and 13C enrichment of cholesterol. This method exploits the metabolism of 2H,13C-acetate into acetyl-CoA, the first substrate in the mevalonate pathway. We show that growing the cholesterol producing strain RH6827 of Saccharomyces cerevisiae in 2H,13C-acetate-enriched minimal media produces a skip-labeled pattern of deuteration. We characterize this cholesterol labeling pattern by mass spectrometry and solid-state nuclear magnetic resonance spectroscopy. It is confirmed that most 2H nuclei retain their original 2H-13C bonds from acetate throughout the biosynthetic pathway. We then quantify the changes in 13C chemical shifts brought by deuteration and the impact upon 13C-13C spin diffusion. Finally, using adiabatic rotor echo short pulse irradiation cross-polarization (RESPIRATIONCP), we acquire the 2H-13C correlation spectra to site specifically quantify cholesterol dynamics in two model membranes as a function of temperature. These measurements show that cholesterol acyl chains at physiological temperatures in mixtures of 1-palmitoyl-2-oleoylphosphatidylcholine (POPC), sphingomyelin, and cholesterol are more dynamic than cholesterol in POPC. However, this overall change in motion is not uniform across the cholesterol molecule. This result establishes that this cholesterol labeling pattern will have great utility in reporting on cholesterol dynamics and orientation in a variety of environments and with different membrane bilayer components, as well as monitoring the mevalonate pathway product interactions within the bilayer. Finally, the flexibility and universality of acetate labeling will allow this technique to be widely applied to a large range of lipids and other natural products.
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15
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Shi X, Zhai Z, Chen Y, Li J, Nordenskiöld L. Recent Advances in Investigating Functional Dynamics of Chromatin. Front Genet 2022; 13:870640. [PMID: 35450211 PMCID: PMC9017861 DOI: 10.3389/fgene.2022.870640] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/11/2022] [Indexed: 11/26/2022] Open
Abstract
Dynamics spanning the picosecond-minute time domain and the atomic-subcellular spatial window have been observed for chromatin in vitro and in vivo. The condensed organization of chromatin in eukaryotic cells prevents regulatory factors from accessing genomic DNA, which requires dynamic stabilization and destabilization of structure to initiate downstream DNA activities. Those processes are achieved through altering conformational and dynamic properties of nucleosomes and nucleosome–protein complexes, of which delineating the atomistic pictures is essential to understand the mechanisms of chromatin regulation. In this review, we summarize recent progress in determining chromatin dynamics and their modulations by a number of factors including post-translational modifications (PTMs), incorporation of histone variants, and binding of effector proteins. We focus on experimental observations obtained using high-resolution techniques, primarily including nuclear magnetic resonance (NMR) spectroscopy, Förster (or fluorescence) resonance energy transfer (FRET) microscopy, and molecular dynamics (MD) simulations, and discuss the elucidated dynamics in the context of functional response and relevance.
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Affiliation(s)
- Xiangyan Shi
- Department of Biology, Shenzhen MSU-BIT University, Shenzhen, China
| | - Ziwei Zhai
- Department of Biology, Shenzhen MSU-BIT University, Shenzhen, China
| | - Yinglu Chen
- Department of Biology, Shenzhen MSU-BIT University, Shenzhen, China
| | - Jindi Li
- Department of Biology, Shenzhen MSU-BIT University, Shenzhen, China
| | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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16
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Ahlawat S, Mote KR, Lakomek NA, Agarwal V. Solid-State NMR: Methods for Biological Solids. Chem Rev 2022; 122:9643-9737. [PMID: 35238547 DOI: 10.1021/acs.chemrev.1c00852] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In the last two decades, solid-state nuclear magnetic resonance (ssNMR) spectroscopy has transformed from a spectroscopic technique investigating small molecules and industrial polymers to a potent tool decrypting structure and underlying dynamics of complex biological systems, such as membrane proteins, fibrils, and assemblies, in near-physiological environments and temperatures. This transformation can be ascribed to improvements in hardware design, sample preparation, pulsed methods, isotope labeling strategies, resolution, and sensitivity. The fundamental engagement between nuclear spins and radio-frequency pulses in the presence of a strong static magnetic field is identical between solution and ssNMR, but the experimental procedures vastly differ because of the absence of molecular tumbling in solids. This review discusses routinely employed state-of-the-art static and MAS pulsed NMR methods relevant for biological samples with rotational correlation times exceeding 100's of nanoseconds. Recent developments in signal filtering approaches, proton methodologies, and multiple acquisition techniques to boost sensitivity and speed up data acquisition at fast MAS are also discussed. Several examples of protein structures (globular, membrane, fibrils, and assemblies) solved with ssNMR spectroscopy have been considered. We also discuss integrated approaches to structurally characterize challenging biological systems and some newly emanating subdisciplines in ssNMR spectroscopy.
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Affiliation(s)
- Sahil Ahlawat
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Kaustubh R Mote
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Nils-Alexander Lakomek
- University of Düsseldorf, Institute for Physical Biology, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Vipin Agarwal
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
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17
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Reif B. Deuteration for High-Resolution Detection of Protons in Protein Magic Angle Spinning (MAS) Solid-State NMR. Chem Rev 2021; 122:10019-10035. [PMID: 34870415 DOI: 10.1021/acs.chemrev.1c00681] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proton detection developed in the last 20 years as the method of choice to study biomolecules in the solid state. In perdeuterated proteins, proton dipolar interactions are strongly attenuated, which allows yielding of high-resolution proton spectra. Perdeuteration and backsubstitution of exchangeable protons is essential if samples are rotated with MAS rotation frequencies below 60 kHz. Protonated samples can be investigated directly without spin dilution using proton detection methods in case the MAS frequency exceeds 110 kHz. This review summarizes labeling strategies and the spectroscopic methods to perform experiments that yield assignments, quantitative information on structure, and dynamics using perdeuterated samples. Techniques for solvent suppression, H/D exchange, and deuterium spectroscopy are discussed. Finally, experimental and theoretical results that allow estimation of the sensitivity of proton detected experiments as a function of the MAS frequency and the external B0 field in a perdeuterated environment are compiled.
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Affiliation(s)
- Bernd Reif
- Bayerisches NMR Zentrum (BNMRZ) at the Department of Chemistry, Technische Universität München (TUM), Lichtenbergstr. 4, 85747 Garching, Germany.,Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Institute of Structural Biology (STB), Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
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18
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Gelenter MD, Chen KJ, Hong M. Off-resonance 13C- 2H REDOR NMR for site-resolved studies of molecular motion. JOURNAL OF BIOMOLECULAR NMR 2021; 75:335-345. [PMID: 34342847 PMCID: PMC8830769 DOI: 10.1007/s10858-021-00377-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/19/2021] [Indexed: 06/06/2023]
Abstract
We introduce a 13C-2H Rotational Echo DOuble Resonance (REDOR) technique that uses the difference between on-resonance and off-resonance 2H irradiation to detect dynamic segments in deuterated molecules. By selectively inverting specific regions of the 2H magic-angle spinning (MAS) sideband manifold to recouple some of the deuterons to nearby carbons, we distinguish dynamic and rigid residues in 1D and 2D 13C spectra. We demonstrate this approach on deuterated GB1, H/D exchanged GB1, and perdeuterated bacterial cellulose. Numerical simulations reproduce the measured mixing-time and 2H carrier-frequency dependence of the REDOR dephasing of bacterial cellulose. Combining numerical simulations with experiments thus allow the extraction of motionally averaged quadrupolar couplings from REDOR dephasing values.
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Affiliation(s)
- Martin D Gelenter
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, MA, 02139, Cambridge, USA
| | - Kelly J Chen
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, MA, 02139, Cambridge, USA
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, MA, 02139, Cambridge, USA.
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19
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Akbey Ü. Dynamics of uniformly labelled solid proteins between 100 and 300 K: A 2D 2H- 13C MAS NMR approach. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2021; 327:106974. [PMID: 33823335 DOI: 10.1016/j.jmr.2021.106974] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 03/20/2021] [Accepted: 03/20/2021] [Indexed: 06/12/2023]
Abstract
We describe a 2H based MAS nuclear magnetic resonance (NMR) method to obtain site-specific molecular dynamics of biomolecules. The method utilizes the use of deuterium nucleus as a spin label that is proven to be very useful in dynamics studies of solid biological and functional materials. The aim is to understand overall characteristics of protein backbone and side-chain motions for CD3, CD2 and CD groups, in terms of timescale, type and activation energy of the underlying processes. Variable temperature two-dimensional (2D) 2H-13C correlation MAS NMR spectra were recorded for the uniformly 2H,13C,15N labelled Alanine and microcrystalline SH3 at a broad temperature range, from 320 K down to 100 K. First, the deuterium quadrupolar-coupling constant from specific D-C sites is obtained with the 2D experiment by utilizing carbon chemical shifts. Second, the static quadrupolar patterns are obtained at 100 K. Third, variable temperature approach enabled the observation of quadrupolar pattern over different motional regimes; slow, intermediate and fast. And finally, the apparent activation energies for C-D sites are determined and compared, by evaluating the temperature induced signal intensities. This information led to the determination of the dynamic processes for different D-C sites at a broad range of temperature and motional timescales. This is a first representation of 2D 2H-13C MAS NMR approach applied to fully isotope labelled deuterated protein covering 220 K temperature range.
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Affiliation(s)
- Ümit Akbey
- Weizmann Institute of Science, Department of Chemical and Biological Physics, Perlman Chemical Sciences Building, P.O. Box 26, Rehovot 76100, Israel.
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20
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Bonaccorsi M, Le Marchand T, Pintacuda G. Protein structural dynamics by Magic-Angle Spinning NMR. Curr Opin Struct Biol 2021; 70:34-43. [PMID: 33915352 DOI: 10.1016/j.sbi.2021.02.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 02/20/2021] [Indexed: 02/07/2023]
Abstract
Magic-Angle Spinning (MAS) Nuclear Magnetic Resonance (NMR) is a fast-developing technique, capable of complementing solution NMR, X-ray crystallography, and electron microscopy for the biophysical characterization of microcrystalline, poorly crystalline or disordered protein samples, such as enzymes, biomolecular assemblies, membrane-embedded systems or fibrils. Beyond structures, MAS NMR is an ideal tool for the investigation of dynamics, since it is unique in its ability to distinguish static and dynamic disorder, and to characterize not only amplitudes but also timescales of motion. Building on seminal work on model proteins, the technique is now ripe for widespread application in structural biology. This review briefly summarizes the recent evolutions in biomolecular MAS NMR and accounts for the growing number of systems where this spectroscopy has provided a description of conformational dynamics over the very last few years.
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Affiliation(s)
- Marta Bonaccorsi
- Université de Lyon, Centre de RMN à Très hauts Champs, UMR 5280 (CNRS / Ecole Normale Supérieure de Lyon / Université Claude Bernard Lyon 1), 5 rue de la Doua, F-69100, Villeurbanne, France
| | - Tanguy Le Marchand
- Université de Lyon, Centre de RMN à Très hauts Champs, UMR 5280 (CNRS / Ecole Normale Supérieure de Lyon / Université Claude Bernard Lyon 1), 5 rue de la Doua, F-69100, Villeurbanne, France
| | - Guido Pintacuda
- Université de Lyon, Centre de RMN à Très hauts Champs, UMR 5280 (CNRS / Ecole Normale Supérieure de Lyon / Université Claude Bernard Lyon 1), 5 rue de la Doua, F-69100, Villeurbanne, France.
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21
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Reif B, Ashbrook SE, Emsley L, Hong M. Solid-state NMR spectroscopy. NATURE REVIEWS. METHODS PRIMERS 2021; 1:2. [PMID: 34368784 PMCID: PMC8341432 DOI: 10.1038/s43586-020-00002-1] [Citation(s) in RCA: 165] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/29/2020] [Indexed: 12/18/2022]
Abstract
Solid-state nuclear magnetic resonance (NMR) spectroscopy is an atomic-level method used to determine the chemical structure, three-dimensional structure, and dynamics of solids and semi-solids. This Primer summarizes the basic principles of NMR as applied to the wide range of solid systems. The fundamental nuclear spin interactions and the effects of magnetic fields and radiofrequency pulses on nuclear spins are the same as in liquid-state NMR. However, because of the anisotropy of the interactions in the solid state, the majority of high-resolution solid-state NMR spectra is measured under magic-angle spinning (MAS), which has profound effects on the types of radiofrequency pulse sequences required to extract structural and dynamical information. We describe the most common MAS NMR experiments and data analysis approaches for investigating biological macromolecules, organic materials, and inorganic solids. Continuing development of sensitivity-enhancement approaches, including 1H-detected fast MAS experiments, dynamic nuclear polarization, and experiments tailored to ultrahigh magnetic fields, is described. We highlight recent applications of solid-state NMR to biological and materials chemistry. The Primer ends with a discussion of current limitations of NMR to study solids, and points to future avenues of development to further enhance the capabilities of this sophisticated spectroscopy for new applications.
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Affiliation(s)
- Bernd Reif
- Technische Universität München, Department Chemie, Lichtenbergstr. 4, D-85747 Garching, Germany
| | - Sharon E. Ashbrook
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Lyndon Emsley
- École Polytechnique Fédérale de Lausanne (EPFL), Institut des sciences et ingénierie chimiques, CH-1015 Lausanne, Switzerland
| | - Mei Hong
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
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22
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Dynamic networks observed in the nucleosome core particles couple the histone globular domains with DNA. Commun Biol 2020; 3:639. [PMID: 33128005 PMCID: PMC7599221 DOI: 10.1038/s42003-020-01369-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 10/09/2020] [Indexed: 12/12/2022] Open
Abstract
The dynamics of eukaryotic nucleosomes are essential in gene activity and well regulated by various factors. Here, we elucidated the internal dynamics at multiple timescales for the human histones hH3 and hH4 in the Widom 601 nucleosome core particles (NCP), suggesting that four dynamic networks are formed by the residues exhibiting larger-scale μs-ms motions that extend from the NCP core to the histone tails and DNA. Furthermore, despite possessing highly conserved structural features, histones in the telomeric NCP exhibit enhanced μs-ms dynamics in the globular sites residing at the identified dynamic networks and in a neighboring region. In addition, higher mobility was observed for the N-terminal tails of hH3 and hH4 in the telomeric NCP. The results demonstrate the existence of dynamic networks in nucleosomes, through which the center of the core regions could interactively communicate with histone tails and DNA to potentially propagate epigenetic changes. Shi et al. use solid-state nuclear magnetic resonance spectroscopy to reveal the internal dynamics of human histones hH3 and hH4 in the Widom 601 and the telomeric nucleosome core particles. This work has implications for the propagation of epigenetic changes via the center of the nucleosome core communicating with histone tails and DNA.
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23
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Nimerovsky E, Soutar CP. A modification of γ-encoded RN symmetry pulses for increasing the scaling factor and more accurate measurements of the strong heteronuclear dipolar couplings. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2020; 319:106827. [PMID: 32950918 DOI: 10.1016/j.jmr.2020.106827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 09/02/2020] [Accepted: 09/03/2020] [Indexed: 06/11/2023]
Abstract
Symmetry based γ-encoded RNnν elements are broadly used in magic-angle spinning solid-state NMR experiments to achieve selective recoupling of the heteronuclear dipolar interactions. The recoupled dipolar couplings in such experiments are scaled by a factor, Ksc, which theoretically depends on the chosen symmetry numbers N, n, and ν. However, the maximum theoretical value of Ksc for γ-encoded RNnν pulses is limited to ~0.25, resulting in long RNnν experiment times. Also, the dependence of Ksc on the experimental parameters can result in systematic errors in the experimental determination of the dipolar couplings, especially at low and moderate MAS rates. In this manuscript, we investigate the use of MODifiEd RNnν symmetry (MODERNnν(ϕM)) pulses that increase the dipolar scaling factor by at least 1.45 fold compared to γ-encoded RNnν. The second advantage of MODERNnν(ϕM) pulses with respect to traditional RNnν pulses is the reduced influence of experimental parameters on Ksc, which allows for more accurate measurement of short-range distances. The robustness of MODERNnν(ϕM) is compared with γ-encoded R1423 symmetry pulses. The enhanced performance is demonstrated on two uniformly-13C-enriched samples, N-acetyl valine and the microcrystalline protein GB1, at a 31.111 kHz MAS rate.
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Affiliation(s)
- Evgeny Nimerovsky
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Corinne P Soutar
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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24
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Anderson JS, Hernández G, LeMaster DM. 13C NMR Relaxation Analysis of Protein GB3 for the Assessment of Side Chain Dynamics Predictions by Current AMBER and CHARMM Force Fields. J Chem Theory Comput 2020; 16:2896-2913. [PMID: 32268062 DOI: 10.1021/acs.jctc.0c00050] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Molecular simulations with seven current AMBER- and CHARMM-based force fields yield markedly differing internal bond vector autocorrelation function predictions for many of the 223 methine and methylene H-C bonds of the 56-residue protein GB3. To enable quantification of accuracy, 13C R1, R2, and heteronuclear NOE relaxation rates have been determined for the methine and stereochemically assigned methylene Cα and Cβ positions. With only three experimental relaxation values for each bond vector, central to this analysis is the accuracy with which MD-derived autocorrelation curves can be represented by a 3-parameter equation which, in turn, maps onto the NMR relaxation values. In contrast to the more widely used extended Lipari-Szabo order parameter representation, 95% of these MD-derived internal autocorrelation curves for GB3 can be fitted to within 1.0% rmsd over the time frame from 30 ps to 4 ns by a biexponential Larmor frequency-selective representation (LF-S2). Applying the LF-S2 representation to the experimental relaxation rates and uncertainties serves to determine the boundary range for the autocorrelation function of each bond vector consistent with the experimental data. Not surprisingly, all seven force fields predict the autocorrelation functions for the more motionally restricted 1Hα-13Cα and 1Hβ-13Cβ bond vectors with reasonable accuracy. However, for the 1Hβ-13Cβ bond vectors exhibiting aggregate order parameter S2 values less than 0.85, only 1% of the MD-derived predictions lie with 1 σ of the experimentally determined autocorrelation functions and only 7% within 2 σ. On the other hand, substantial residue type-specific improvements in predictive performance were observed among the recent AMBER force fields. This analysis indicates considerable potential for the use of 13C relaxation measurements in guiding the optimization of the side chain dynamics characteristics of protein molecular simulations.
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Affiliation(s)
- Janet S Anderson
- Department of Chemistry, Union College, Schenectady, New York 12308, United States
| | - Griselda Hernández
- Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, New York 12201, United States
| | - David M LeMaster
- Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, New York 12201, United States
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25
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Shi X, Prasanna C, Pervushin K, Nordenskiöld L. Solid-state NMR 13C, 15N assignments of human histone H3 in the nucleosome core particle. BIOMOLECULAR NMR ASSIGNMENTS 2020; 14:99-104. [PMID: 31907727 DOI: 10.1007/s12104-020-09927-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 01/02/2020] [Indexed: 06/10/2023]
Abstract
Nucleosome core particle (NCP), the basic unit of chromatin in eukaryotic cells, consists of ~ 147 bp DNA wrapped around a histone octamer (HO) formed by two H2A-H2B dimers and one (H3-H4)2 tetramer. Histones undergo various post-translational modifications (PTMs), which regulates genomic activities in different cellular phases. High-resolution structures have been solved for many nucleosomes primarily including NCPs. However, the atomic-resolution structures of nucleosome arrays and chromatin fiber, as well as the dynamics of nucleosomes remain poorly understood. Solid-state NMR (SSNMR) is one of the premier techniques to answer these questions. In this study, we present the 13C and 15N chemical shifts assignments for the globular domain of human histone H3 (hH3) using multidimensional SSNMR experiments. The obtained spectra are of outstanding resolution and the assignments are nearly 100% complete for the backbone 13C and 15N spins of R42-G132 and ~ 80% when taking into account the side chains. The secondary structure derived from the chemical shifts agrees with the previously reported X-ray crystal structure. The reported chemical shifts can be carried over to future SSNMR studies of structure and dynamics of hH3 in NCPs, nucleosome array, chromatin fibers and nucleosome-protein complexes.
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Affiliation(s)
- Xiangyan Shi
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore.
| | - Chinmayi Prasanna
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Konstantin Pervushin
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.
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26
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Chen Q, Xu S, Lu X, Boeri MV, Pepelyayeva Y, Diaz EL, Soni SD, Allaire M, Forstner MB, Bahnson BJ, Rozovsky S. 77Se NMR Probes the Protein Environment of Selenomethionine. J Phys Chem B 2020; 124:601-616. [PMID: 31846581 DOI: 10.1021/acs.jpcb.9b07466] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Sulfur is critical for the correct structure and proper function of proteins. Yet, lacking a sensitive enough isotope, nuclear magnetic resonance (NMR) experiments are unable to deliver for sulfur in proteins the usual wealth of chemical, dynamic, and structural information. This limitation can be circumvented by substituting sulfur with selenium, which has similar physicochemical properties and minimal impact on protein structures but possesses an NMR compatible isotope (77Se). Here we exploit the sensitivity of 77Se NMR to the nucleus' chemical milieu and use selenomethionine as a probe for its proteinaceous environment. However, such selenium NMR spectra of proteins currently resist a reliable interpretation because systematic connections between variations of system variables and changes in 77Se NMR parameters are still lacking. To start narrowing this knowledge gap, we report here on a biological 77Se magnetic resonance data bank based on a systematically designed library of GB1 variants in which a single selenomethionine was introduced at different locations within the protein. We recorded the resulting isotropic 77Se chemical shifts and relaxation times for six GB1 variants by solution-state 77Se NMR. For four of the GB1 variants we were also able to determine the chemical shift anisotropy tensor of SeM by solid-state 77Se NMR. To enable interpretation of the NMR data, the structures of five of the GB1 variants were solved by X-ray crystallography to a resolution of 1.2 Å, allowing us to unambiguously determine the conformation of the selenomethionine. Finally, we combine our solution- and solid-state NMR data with the structural information to arrive at general insights regarding the execution and interpretation of 77Se NMR experiments that exploit selenomethionine to probe proteins.
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Affiliation(s)
- Qingqing Chen
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Shiping Xu
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Xingyu Lu
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States.,Instrumentation and Service Center for Physical Sciences , Westlake University , Hangzhou , Zhejiang 310024 , China
| | - Michael V Boeri
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States.,Neuroscience Department, Medical Toxicology Research Division , U.S. Army Medical Research Institute of Chemical Defense , 8350 Ricketts Point Road , Gunpowder , Maryland 21010 , United States
| | - Yuliya Pepelyayeva
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States.,Department of Microbiology & Molecular Genetics, College of Osteopathic Medicine , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Elizabeth L Diaz
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Sunil-Datta Soni
- Neuroscience Department, Medical Toxicology Research Division , U.S. Army Medical Research Institute of Chemical Defense , 8350 Ricketts Point Road , Gunpowder , Maryland 21010 , United States
| | - Marc Allaire
- Berkeley Center for Structural Biology, Molecular Biophysics & Integrated Bioimaging , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Martin B Forstner
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Brian J Bahnson
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Sharon Rozovsky
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
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27
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Khudozhitkov AE, Neumann J, Niemann T, Zaitsau D, Stange P, Paschek D, Stepanov AG, Kolokolov DI, Ludwig R. Hydrogen Bonding Between Ions of Like Charge in Ionic Liquids Characterized by NMR Deuteron Quadrupole Coupling Constants-Comparison with Salt Bridges and Molecular Systems. Angew Chem Int Ed Engl 2019; 58:17863-17871. [PMID: 31588622 PMCID: PMC6899581 DOI: 10.1002/anie.201912476] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Indexed: 11/23/2022]
Abstract
We present deuteron quadrupole coupling constants (DQCC) for hydroxyl-functionalized ionic liquids (ILs) in the crystalline or glassy states characterizing two types of hydrogen bonding: The regular Coulomb-enhanced hydrogen bonds between cation and anion (c-a), and the unusual hydrogen bonds between cation and cation (c-c), which are present despite repulsive Coulomb forces. We measure these sensitive probes of hydrogen bonding by means of solid-state NMR spectroscopy. The DQCCs of (c-a) ion pairs and (c-c) H-bonds are compared to those of salt bridges in supramolecular complexes and those present in molecular liquids. At low temperatures, the (c-c) species successfully compete with the (c-a) ion pairs and dominate the cluster populations. Equilibrium constants obtained from molecular-dynamics (MD) simulations show van't Hoff behavior with small transition enthalpies between the differently H-bonded species. We show that cationic-cluster formation prevents these ILs from crystallizing. With cooling, the (c-c) hydrogen bonds persist, resulting in supercooling and glass formation.
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Affiliation(s)
- Alexander E. Khudozhitkov
- Boreskov Institute of CatalysisSiberian Branch of Russian Academy of SciencesProspekt Akademika Lavrentieva 5Novosibirsk630090Russia
- Novosibirsk State UniversityPirogova Street 2Novosibirsk630090Russia
| | - Jan Neumann
- Universität RostockInstitut für ChemieAbteilung für Physikalische ChemieDr.-Lorenz-Weg 218059RostockGermany
| | - Thomas Niemann
- Universität RostockInstitut für ChemieAbteilung für Physikalische ChemieDr.-Lorenz-Weg 218059RostockGermany
| | - Dzmitry Zaitsau
- Department LL&MUniversity of RostockAlbert-Einstein-Str. 2518059RostockGermany
| | - Peter Stange
- Universität RostockInstitut für ChemieAbteilung für Physikalische ChemieDr.-Lorenz-Weg 218059RostockGermany
| | - Dietmar Paschek
- Universität RostockInstitut für ChemieAbteilung für Physikalische ChemieDr.-Lorenz-Weg 218059RostockGermany
| | - Alexander G. Stepanov
- Boreskov Institute of CatalysisSiberian Branch of Russian Academy of SciencesProspekt Akademika Lavrentieva 5Novosibirsk630090Russia
- Novosibirsk State UniversityPirogova Street 2Novosibirsk630090Russia
| | - Daniil I. Kolokolov
- Boreskov Institute of CatalysisSiberian Branch of Russian Academy of SciencesProspekt Akademika Lavrentieva 5Novosibirsk630090Russia
- Novosibirsk State UniversityPirogova Street 2Novosibirsk630090Russia
| | - Ralf Ludwig
- Universität RostockInstitut für ChemieAbteilung für Physikalische ChemieDr.-Lorenz-Weg 218059RostockGermany
- Department LL&MUniversity of RostockAlbert-Einstein-Str. 2518059RostockGermany
- Leibniz-Institut für Katalyse an der Universität Rostock e.V.Albert-Einstein-Str. 29a18059RostockGermany
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Khudozhitkov AE, Neumann J, Niemann T, Zaitsau D, Stange P, Paschek D, Stepanov AG, Kolokolov DI, Ludwig R. Hydrogen Bonding Between Ions of Like Charge in Ionic Liquids Characterized by NMR Deuteron Quadrupole Coupling Constants—Comparison with Salt Bridges and Molecular Systems. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201912476] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Alexander E. Khudozhitkov
- Boreskov Institute of CatalysisSiberian Branch of Russian Academy of Sciences Prospekt Akademika Lavrentieva 5 Novosibirsk 630090 Russia
- Novosibirsk State University Pirogova Street 2 Novosibirsk 630090 Russia
| | - Jan Neumann
- Universität RostockInstitut für ChemieAbteilung für Physikalische Chemie Dr.-Lorenz-Weg 2 18059 Rostock Germany
| | - Thomas Niemann
- Universität RostockInstitut für ChemieAbteilung für Physikalische Chemie Dr.-Lorenz-Weg 2 18059 Rostock Germany
| | - Dzmitry Zaitsau
- Department LL&MUniversity of Rostock Albert-Einstein-Str. 25 18059 Rostock Germany
| | - Peter Stange
- Universität RostockInstitut für ChemieAbteilung für Physikalische Chemie Dr.-Lorenz-Weg 2 18059 Rostock Germany
| | - Dietmar Paschek
- Universität RostockInstitut für ChemieAbteilung für Physikalische Chemie Dr.-Lorenz-Weg 2 18059 Rostock Germany
| | - Alexander G. Stepanov
- Boreskov Institute of CatalysisSiberian Branch of Russian Academy of Sciences Prospekt Akademika Lavrentieva 5 Novosibirsk 630090 Russia
- Novosibirsk State University Pirogova Street 2 Novosibirsk 630090 Russia
| | - Daniil I. Kolokolov
- Boreskov Institute of CatalysisSiberian Branch of Russian Academy of Sciences Prospekt Akademika Lavrentieva 5 Novosibirsk 630090 Russia
- Novosibirsk State University Pirogova Street 2 Novosibirsk 630090 Russia
| | - Ralf Ludwig
- Universität RostockInstitut für ChemieAbteilung für Physikalische Chemie Dr.-Lorenz-Weg 2 18059 Rostock Germany
- Department LL&MUniversity of Rostock Albert-Einstein-Str. 25 18059 Rostock Germany
- Leibniz-Institut für Katalyse an der Universität Rostock e.V. Albert-Einstein-Str. 29a 18059 Rostock Germany
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29
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Meirovitch E, Freed JH. Local ordering and dynamics in anisotropic media by magnetic resonance: from liquid crystals to proteins. LIQUID CRYSTALS 2019; 47:1926-1954. [PMID: 32435078 PMCID: PMC7239324 DOI: 10.1080/02678292.2019.1622158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Indexed: 06/11/2023]
Abstract
Magnetic resonance methods have been used extensively for over 50 years to elucidate molecular structure and dynamics of liquid crystals (LCs), providing information quite unique in its rigour and extent. The ESR- or NMR-active probe is often a solute molecule reporting on characteristics associated with the surrounding (LC) medium, which exerts the spatial restrictions on the probe. The theoretical approaches developed for LCs are applicable to anisotropic media in general. Of particular interest is the interior space of a globular protein labelled, e.g. with a nitroxide moiety or a 15N-1H bond. The ESR or NMR label plays the role of the probe and the internal protein surroundings the role of the anisotropic medium. A general feature of the restricted motions is the local ordering, i.e. the nature, magnitude and symmetry of the spatial restraints exerted at the site of the moving probe. This property is the main theme of the present review article. We outline its treatment in our work from both the theoretical and the experimental points of view, highlighting the new physical insights gained. Our illustrations include studies on thermotropic (nematic and smectic) and lyotropic liquid crystals formed by phospholipids, in addition to studies of proteins.
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Affiliation(s)
- Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Jack H Freed
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
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30
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Makrinich M, Goldbourt A. 1H-Detected quadrupolar spin-lattice relaxation measurements under magic-angle spinning solid-state NMR. Chem Commun (Camb) 2019; 55:5643-5646. [PMID: 31026003 DOI: 10.1039/c9cc01176e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Proton detection and phase-modulated pulse saturation enable the measurement of spin-lattice relaxation times of "invisible" quadrupolar nuclei with extensively large quadrupolar couplings. For nitrogen-14, efficient cross-polarization is obtained with a long-duration preparation pulse. The experiment paves the way to the characterization of a large variety of materials containing halogens, metals and more.
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Affiliation(s)
- Maria Makrinich
- School of Chemistry, Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 6997801, Tel Aviv, Israel.
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31
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Aharoni T, Goldbourt A. Rapid automated determination of chemical shift anisotropy values in the carbonyl and carboxyl groups of fd-y21m bacteriophage using solid state NMR. JOURNAL OF BIOMOLECULAR NMR 2018; 72:55-67. [PMID: 30141148 DOI: 10.1007/s10858-018-0206-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 08/17/2018] [Indexed: 06/08/2023]
Abstract
Determination of chemical shift anisotropy (CSA) in immobilized proteins and protein assemblies is one of several tools to determine protein dynamics on the timescales of microseconds and faster. The large CSA values of C=O groups in the rigid limit makes them in particular attractive for measurements of large amplitude motions, or their absence. In this study, we implement a 3D R-symmetry-based sequence that recouples the second spatial component of the 13C CSA with the corresponding isotropic 13C'-13C cross-peaks in order to probe backbone and sidechain dynamics in an intact fd-y21m filamentous phage viral capsid. The assignment of the isotropic cross-peaks and the analysis were conducted automatically using a new software named 'Raven'. The software can be utilized to auto-assign any 2D 13C-13C or 15N-13C spectrum given a previously-determined assignment table and generates simultaneously all intensity curves acquired in the third dimension. Here, all CSA spectra were automatically generated, and subsequently matched against a simulated set of CSA curves to yield their values. For the multi-copy, 50-residue-long protein capsid of fd-y21m, the backbone of the helical region is rigid, with reduced CSA values of ~ 12.5 kHz (~ 83 ppm). The N-terminus shows motionally-averaged CSA lineshapes and the carboxylic sidechain groups of four residues indicate large amplitude motions for D4, D5, D12 and E20. The current results further strengthen our previous studies of 15N CSA values and are in agreement with qualitative analysis of 13C-13C dipolar build-up curves, which were automatically obtained using our software. Our automated analysis technique is general and can be applied to study protein structure and dynamics, with data resulting from experiments that probe different variables such as relaxation rates and scaled anisotropic interactions.
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Affiliation(s)
- Tom Aharoni
- School of Chemistry, The Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv, 6997801, Tel Aviv, Israel
| | - Amir Goldbourt
- School of Chemistry, The Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv, 6997801, Tel Aviv, Israel.
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32
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Martin RW, Kelly JE, Kelz JI. Advances in instrumentation and methodology for solid-state NMR of biological assemblies. J Struct Biol 2018; 206:73-89. [PMID: 30205196 DOI: 10.1016/j.jsb.2018.09.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 07/08/2018] [Accepted: 09/06/2018] [Indexed: 01/11/2023]
Abstract
Many advances in instrumentation and methodology have furthered the use of solid-state NMR as a technique for determining the structures and studying the dynamics of molecules involved in complex biological assemblies. Solid-state NMR does not require large crystals, has no inherent size limit, and with appropriate isotopic labeling schemes, supports solving one component of a complex assembly at a time. It is complementary to cryo-EM, in that it provides local, atomic-level detail that can be modeled into larger-scale structures. This review focuses on the development of high-field MAS instrumentation and methodology; including probe design, benchmarking strategies, labeling schemes, and experiments that enable the use of quadrupolar nuclei in biomolecular NMR. Current challenges facing solid-state NMR of biological assemblies and new directions in this dynamic research area are also discussed.
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Affiliation(s)
- Rachel W Martin
- Department of Chemistry, University of California, Irvine 92697-2025, United States; Department of Molecular Biology and Biochemistry, University of California, Irvine 92697-3900, United States.
| | - John E Kelly
- Department of Chemistry, University of California, Irvine 92697-2025, United States
| | - Jessica I Kelz
- Department of Chemistry, University of California, Irvine 92697-2025, United States
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33
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Shi X, Prasanna C, Nagashima T, Yamazaki T, Pervushin K, Nordenskiöld L. Structure and Dynamics in the Nucleosome Revealed by Solid-State NMR. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804707] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Xiangyan Shi
- School of Physical and Mathematical Sciences; Nanyang Technological University; 21 Nanyang Link Singapore 637371 Singapore
| | - Chinmayi Prasanna
- School of Biological Sciences; Nanyang Technological University; 60 Nanyang Drive Singapore 637551 Singapore
| | - Toshio Nagashima
- RIKEN Center for Life Science Technologies; Yokohama City Kanagawa 230-0045 Japan
| | - Toshio Yamazaki
- RIKEN Center for Life Science Technologies; Yokohama City Kanagawa 230-0045 Japan
| | - Konstantin Pervushin
- School of Biological Sciences; Nanyang Technological University; 60 Nanyang Drive Singapore 637551 Singapore
| | - Lars Nordenskiöld
- School of Biological Sciences; Nanyang Technological University; 60 Nanyang Drive Singapore 637551 Singapore
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34
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Shi X, Prasanna C, Nagashima T, Yamazaki T, Pervushin K, Nordenskiöld L. Structure and Dynamics in the Nucleosome Revealed by Solid-State NMR. Angew Chem Int Ed Engl 2018; 57:9734-9738. [DOI: 10.1002/anie.201804707] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 05/23/2018] [Indexed: 02/01/2023]
Affiliation(s)
- Xiangyan Shi
- School of Physical and Mathematical Sciences; Nanyang Technological University; 21 Nanyang Link Singapore 637371 Singapore
| | - Chinmayi Prasanna
- School of Biological Sciences; Nanyang Technological University; 60 Nanyang Drive Singapore 637551 Singapore
| | - Toshio Nagashima
- RIKEN Center for Life Science Technologies; Yokohama City Kanagawa 230-0045 Japan
| | - Toshio Yamazaki
- RIKEN Center for Life Science Technologies; Yokohama City Kanagawa 230-0045 Japan
| | - Konstantin Pervushin
- School of Biological Sciences; Nanyang Technological University; 60 Nanyang Drive Singapore 637551 Singapore
| | - Lars Nordenskiöld
- School of Biological Sciences; Nanyang Technological University; 60 Nanyang Drive Singapore 637551 Singapore
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35
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Matlahov I, van der Wel PCA. Hidden motions and motion-induced invisibility: Dynamics-based spectral editing in solid-state NMR. Methods 2018; 148:123-135. [PMID: 29702226 DOI: 10.1016/j.ymeth.2018.04.015] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 04/05/2018] [Accepted: 04/16/2018] [Indexed: 10/17/2022] Open
Abstract
Solid-state nuclear magnetic resonance (ssNMR) spectroscopy enables the structural characterization of a diverse array of biological assemblies that include amyloid fibrils, non-amyloid aggregates, membrane-associated proteins and viral capsids. Such biological samples feature functionally relevant molecular dynamics, which often affect different parts of the sample in different ways. Solid-state NMR experiments' sensitivity to dynamics represents a double-edged sword. On the one hand, it offers a chance to measure dynamics in great detail. On the other hand, certain types of motion lead to signal loss and experimental inefficiencies that at first glance interfere with the application of ssNMR to overly dynamic proteins. Dynamics-based spectral editing (DYSE) ssNMR methods leverage motion-dependent signal losses to simplify spectra and enable the study of sub-structures with particular motional properties.
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Affiliation(s)
- Irina Matlahov
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15213, USA
| | - Patrick C A van der Wel
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15213, USA; Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
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36
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Meirovitch E, Liang Z, Freed JH. Protein dynamics in the solid-state from 2H NMR lineshape analysis. III. MOMD in the presence of Magic Angle Spinning. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2018; 89:35-44. [PMID: 29208317 PMCID: PMC5772661 DOI: 10.1016/j.ssnmr.2017.11.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 11/11/2017] [Accepted: 11/13/2017] [Indexed: 06/07/2023]
Abstract
We report on a new approach to the analysis of dynamic NMR lineshapes from polycrystalline (i.e., macroscopically disordered) samples in the presence of Magic Angle Spinning (MAS). This is an application of the Stochastic Liouville Equation developed by Freed and co-workers for treating restricted (i.e., microscopically ordered) motions. The 2H nucleus in an internally-mobile C-CD3 moiety serves as a prototype probe. The acronym is 2H/MOMD/MAS, where MOMD stands for "microscopic-order-macroscopic-disorder." The key elements describing internal motions - their type, the local spatial restrictions, and related features of local geometry - are treated in MOMD generally, within their rigorous three-dimensional tensorial requirements. Based on this representation a single physically well-defined model of local motion has the capability of reproducing experimental spectra. There exist other methods for analyzing dynamic 2H/MAS spectra which advocate simple motional modes. Yet, to reproduce satisfactorily the experimental lineshapes, one has either to use unusual parameter values, or combine several simple motional modes. The multi-simple-mode reasoning assumes independence of the constituent modes, features ambiguity as different simple modes may be used, renders inter-system comparison difficult as the overall models differ, and makes possible model-improvement only by adding yet another simple mode, i.e., changing the overall model. 2H/MOMD/MAS is free of such limitations and inherently provides a clear physical interpretation. These features are illustrated. The advantage of 2H/MOMD/MAS in dealing with sensitive but hardly investigated slow-motional lineshapes is demonstrated by applying it to actual experimental data. The results differ from those obtained previously with a two-site exchange scheme that yielded unusual parameters.
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Affiliation(s)
- Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel.
| | - Zhichun Liang
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA
| | - Jack H Freed
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA
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37
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Collier KA, Sengupta S, Espinosa CA, Kelly JE, Kelz JI, Martin RW. Design and construction of a quadruple-resonance MAS NMR probe for investigation of extensively deuterated biomolecules. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2017; 285:8-17. [PMID: 29059553 PMCID: PMC6317732 DOI: 10.1016/j.jmr.2017.10.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 10/03/2017] [Accepted: 10/06/2017] [Indexed: 05/22/2023]
Abstract
Extensive deuteration is frequently used in solid-state NMR studies of biomolecules because it dramatically reduces both homonuclear (1H-1H) and heteronuclear (1H-13C and 1H-15N) dipolar interactions. This approach greatly improves resolution, enables low-power rf decoupling, and facilitates 1H-detected experiments even in rigid solids at moderate MAS rates. However, the resolution enhancement is obtained at some cost due the reduced abundance of protons available for polarization transfer. Although deuterium is a useful spin-1 NMR nucleus, in typical experiments the deuterons are not directly utilized because the available probes are usually triple-tuned to 1H,13C and 15N. Here we describe a 1H/13C/2H/15N MAS ssNMR probe designed for solid-state NMR of extensively deuterated biomolecules. The probe utilizes coaxial coils, with a modified Alderman-Grant resonator for the 1H channel, and a multiply resonant solenoid for 13C/2H/15N. A coaxial tuning-tube design is used for all four channels in order to efficiently utilize the constrained physical space available inside the magnet bore. Isolation among the channels is likewise achieved using short, adjustable transmission line elements. We present benchmarks illustrating the tuning of each channel and isolation among them and the magnetic field profiles at each frequency of interest. Finally, representative NMR data are shown demonstrating the performance of both the detection and decoupling circuits.
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Affiliation(s)
- Kelsey A Collier
- Department of Physics & Astronomy, UC Irvine, Irvine, CA 92697-4575, United States
| | - Suvrajit Sengupta
- Department of Chemistry, UC Irvine, Irvine, CA 92697-2025, United States
| | | | - John E Kelly
- Department of Chemistry, UC Irvine, Irvine, CA 92697-2025, United States
| | - Jessica I Kelz
- Department of Chemistry, UC Irvine, Irvine, CA 92697-2025, United States
| | - Rachel W Martin
- Department of Chemistry, UC Irvine, Irvine, CA 92697-2025, United States; Department of Molecular Biology & Biochemistry, UC Irvine, Irvine, CA 92697-3900, United States.
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38
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Abstract
Rotational echo double resonance (REDOR) is a highly successful method for heteronuclear distance determination in biological solid-state NMR, and 1H detection methods have emerged in recent years as a powerful approach to improving sensitivity and resolution for small sample quantities by utilizing fast magic-angle spinning (>30 kHz) and deuteration strategies. In theory, involving 1H as one of the spins for measuring REDOR effects can greatly increase the distance measurement range, but few experiments of this type have been reported. Here we introduce a pulse sequence that combines frequency-selective REDOR (FSR) with 1H detection. We demonstrate this method with applications to samples of uniformly 13C,15N,2H-labeled alanine and uniformly 13C,2H,15N-labeled GB1 protein, back-exchanged with 30% H2O and 70% D2O, employing a variety of frequency-selective 13C pulses to highlight unique spectral features. The resulting, robust REDOR effects provide (1) tools for resonance assignment, (2) restraints of secondary structure, (3) probes of tertiary structure, and (4) approaches to determine the preferred orientation of aromatic rings in the protein core.
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Affiliation(s)
- Manali Ghosh
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Chad M. Rienstra
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
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39
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Gelenter MD, Wang T, Liao SY, O'Neill H, Hong M. 2H- 13C correlation solid-state NMR for investigating dynamics and water accessibilities of proteins and carbohydrates. JOURNAL OF BIOMOLECULAR NMR 2017; 68:257-270. [PMID: 28674916 PMCID: PMC6908442 DOI: 10.1007/s10858-017-0124-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 06/29/2017] [Indexed: 05/29/2023]
Abstract
Site-specific determination of molecular motion and water accessibility by indirect detection of 2H NMR spectra has advantages over dipolar-coupling based techniques due to the large quadrupolar couplings and the ensuing high angular resolution. Recently, a Rotor Echo Short Pulse IRrAdiaTION mediated cross polarization (RESPIRATIONCP) technique was developed, which allowed efficient transfer of 2H magnetization to 13C at moderate 2H radiofrequency field strengths available on most commercial MAS probes. In this work, we investigate the 2H-13C magnetization transfer characteristics of one-bond perdeuterated CD n spin systems and two-bond H/D exchanged C-(O)-D and C-(N)-D spin systems in carbohydrates and proteins. Our results show that multi-bond, broadband 2H-13C polarization transfer can be achieved using 2H radiofrequency fields of ~50 kHz, relatively short contact times of 1.3-1.7 ms, and with sufficiently high sensitivity to enable 2D 2H-13C correlation experiments with undistorted 2H spectra in the indirect dimension. To demonstrate the utility of this 2H-13C technique for studying molecular motion, we show 2H-13C correlation spectra of perdeuterated bacterial cellulose, whose surface glucan chains exhibit a motionally averaged C6 2H quadrupolar coupling that indicates fast trans-gauche isomerization about the C5-C6 bond. In comparison, the interior chains in the microfibril core are fully immobilized. Application of the 2H-13C correlation experiment to H/D exchanged Arabidopsis primary cell walls show that the O-D quadrupolar spectra of the highest polysaccharide peaks can be fit to a two-component model, in which 74% of the spectral intensity, assigned to cellulose, has a near-rigid-limit coupling, while 26% of the intensity, assigned to matrix polysaccharides, has a weakened coupling of 50 kHz. The latter O-D quadrupolar order parameter of 0.22 is significantly smaller than previously reported C-D dipolar order parameters of 0.46-0.55 for pectins, suggesting that additional motions exist at the C-O bonds in the wall polysaccharides. 2H-13C polarization transfer profiles are also compared between statistically deuterated and H/D exchanged GB1.
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Affiliation(s)
- Martin D Gelenter
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Tuo Wang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Shu-Yu Liao
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Hugh O'Neill
- Center for Structural Molecular Biology, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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40
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Bärenwald R, Achilles A, Lange F, Ferreira TM, Saalwächter K. Applications of Solid-State NMR Spectroscopy for the Study of Lipid Membranes with Polyphilic Guest (Macro)Molecules. Polymers (Basel) 2016; 8:E439. [PMID: 30974716 PMCID: PMC6432237 DOI: 10.3390/polym8120439] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 12/01/2016] [Accepted: 12/08/2016] [Indexed: 11/16/2022] Open
Abstract
The incorporation of polymers or smaller complex molecules into lipid membranes allows for property modifications or the introduction of new functional elements. The corresponding molecular-scale details, such as changes in dynamics or features of potential supramolecular structures, can be studied by a variety of solid-state NMR techniques. Here, we review various approaches to characterizing the structure and dynamics of the guest molecules as well as the lipid phase structure and dynamics by different high-resolution magic-angle spinning proton and 13C NMR experiments as well as static 31P NMR experiments. Special emphasis is placed upon the incorporation of novel synthetic polyphilic molecules such as shape-persistent T- and X-shaped molecules as well as di- and tri-block copolymers. Most of the systems studied feature dynamic heterogeneities, for instance those arising from the coexistence of different phases; possibilities for a quantitative assessment are of particular concern.
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Affiliation(s)
- Ruth Bärenwald
- Institut für Physik-NMR, Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle, Germany
| | - Anja Achilles
- Institut für Physik-NMR, Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle, Germany
| | - Frank Lange
- Institut für Physik-NMR, Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle, Germany
| | - Tiago Mendes Ferreira
- Institut für Physik-NMR, Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle, Germany
| | - Kay Saalwächter
- Institut für Physik-NMR, Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle, Germany.
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