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Olea Ulloa C, Muñoz-Castro A. Infinitene as two fused helicoidal trails of fused rings: evaluation of the magnetic behavior of [12]infinitene and anionic species displaying global aromaticity and antiaromaticity. Phys Chem Chem Phys 2023; 25:8190-8197. [PMID: 36880673 DOI: 10.1039/d2cp06039f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
The unique formation of an infinity-shaped carbon backbone made exclusively from fused benzene rings has recently been achieved. The structure of [12]infinitene can be viewed as two fused [6]helicene structures with a central crossover section, depicting a global aromatic behavior along with the overall structure, with deshielding regions along both helicoidal axes. In addition, the 13C-NMR characteristics are discussed. The formation of a cumulative region involving the shielding regions from the aromatic rings is depicted along with the overall aesthetically pleasant structural backbone, which is enhanced at the crossover section. For the evaluated dianionic counterpart, the structure shows a deshielding region above the fused-ring trail and a helicoidal shielding region, ascribed to a global antiaromatic counterpart. The aromaticity is recovered and enhanced at the tetranionic state. Thus, the neutral and tetranionic states are able to build up a long-ranged shielding region, given by the global aromatic behavior, with an enhanced shielding region at the center of the crossover section displaying π-π stacked rings.
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Affiliation(s)
- Carolina Olea Ulloa
- Carrera de Química y Farmacia, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Pedro de Valdivia 425, Providencia, Santiago, Chile
| | - Alvaro Muñoz-Castro
- Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Bellavista 7, Santiago, 8420524, Chile.
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2
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Liang L, Ji Y, Chen K, Gao P, Zhao Z, Hou G. Solid-State NMR Dipolar and Chemical Shift Anisotropy Recoupling Techniques for Structural and Dynamical Studies in Biological Systems. Chem Rev 2022; 122:9880-9942. [PMID: 35006680 DOI: 10.1021/acs.chemrev.1c00779] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
With the development of NMR methodology and technology during the past decades, solid-state NMR (ssNMR) has become a particularly important tool for investigating structure and dynamics at atomic scale in biological systems, where the recoupling techniques play pivotal roles in modern high-resolution MAS NMR. In this review, following a brief introduction on the basic theory of recoupling in ssNMR, we highlight the recent advances in dipolar and chemical shift anisotropy recoupling methods, as well as their applications in structural determination and dynamical characterization at multiple time scales (i.e., fast-, intermediate-, and slow-motion). The performances of these prevalent recoupling techniques are compared and discussed in multiple aspects, together with the representative applications in biomolecules. Given the recent emerging advances in NMR technology, new challenges for recoupling methodology development and potential opportunities for biological systems are also discussed.
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Affiliation(s)
- Lixin Liang
- State Key Laboratory of Catalysis, 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, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Ji
- State Key Laboratory of Catalysis, 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, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kuizhi Chen
- State Key Laboratory of Catalysis, 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, Dalian 116023, China
| | - Pan Gao
- State Key Laboratory of Catalysis, 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, Dalian 116023, China
| | - Zhenchao Zhao
- State Key Laboratory of Catalysis, 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, Dalian 116023, China
| | - Guangjin Hou
- State Key Laboratory of Catalysis, 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, Dalian 116023, China
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3
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Identification of transmissible proteotoxic oligomer-like fibrils that expand conformational diversity of amyloid assemblies. Commun Biol 2021; 4:939. [PMID: 34354242 PMCID: PMC8342456 DOI: 10.1038/s42003-021-02466-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 07/19/2021] [Indexed: 11/08/2022] Open
Abstract
Protein misfolding and amyloid deposition are associated with numerous diseases. The detailed characterization of the proteospecies mediating cell death remains elusive owing to the (supra)structural polymorphism and transient nature of the assemblies populating the amyloid pathway. Here we describe the identification of toxic amyloid fibrils with oligomer-like characteristics, which were assembled from an islet amyloid polypeptide (IAPP) derivative containing an Asn-to-Gln substitution (N21Q). While N21Q filaments share structural properties with cytocompatible fibrils, including the 4.7 Å inter-strand distance and β-sheet-rich conformation, they concurrently display characteristics of oligomers, such as low thioflavin-T binding, high surface hydrophobicity and recognition by the A11 antibody, leading to high potency to disrupt membranes and cause cellular dysfunction. The toxic oligomer-like conformation of N21Q fibrils, which is preserved upon elongation, is transmissible to naïve IAPP. These stable fibrils expanding the conformational diversity of amyloid assemblies represent an opportunity to elucidate the structural basis of amyloid disorders. Nguyen et al identified cytotoxic amyloid fibrils with oligomer-like characteristics, which were assembled from an islet amyloid polypeptide (IAPP) derivative containing an Asn-to-Gln substitution (N21Q). They presented evidence to show that these stable fibrils expand the conformational diversity of amyloid assemblies, which represents an opportunity to elucidate the structural basis of amyloid disorders.
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4
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Hughes A, Liu M, Paul S, Cooper AI, Blanc F. Dynamics in Flexible Pillar[ n]arenes Probed by Solid-State NMR. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2021; 125:13370-13381. [PMID: 34239656 PMCID: PMC8237263 DOI: 10.1021/acs.jpcc.1c02046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 05/07/2021] [Indexed: 06/13/2023]
Abstract
Pillar[n]arenes are supramolecular assemblies that can perform a range of technologically important molecular separations which are enabled by their molecular flexibility. Here, we probe dynamical behavior by performing a range of variable-temperature solid-state NMR experiments on microcrystalline perethylated pillar[n]arene (n = 5, 6) and the corresponding three pillar[6]arene xylene adducts in the 100-350 K range. This was achieved either by measuring site-selective motional averaged 13C 1H heteronuclear dipolar couplings and subsequently accessing order parameters or by determining 1H and 13C spin-lattice relaxation times and extracting correlation times based on dipolar and/or chemical shift anisotropy relaxation mechanisms. We demonstrate fast motional regimes at room temperature and highlight a significant difference in dynamics between the core of the pillar[n]arenes, the protruding flexible ethoxy groups, and the adsorbed xylene guest. Additionally, unexpected and sizable 13C 1H heteronuclear dipolar couplings for a quaternary carbon were observed for p-xylene adsorbed in pillar[6]arene only, indicating a strong host-guest interaction and establishing the p-xylene location inside the host, confirming structural refinements.
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Affiliation(s)
- Ashlea
R. Hughes
- Department
of Chemistry, University of Liverpool, Crown Street, Liverpool L69 7ZD, United
Kingdom
| | - Ming Liu
- Department
of Chemistry, University of Liverpool, Crown Street, Liverpool L69 7ZD, United
Kingdom
- Materials
Innovation Factory, University of Liverpool, 51 Oxford Street, Liverpool, L7 3NY, United Kingdom
| | - Subhradip Paul
- Nottingham
DNP MAS NMR Facility, Sir Peter Mansfield Imaging Centre, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Andrew I. Cooper
- Department
of Chemistry, University of Liverpool, Crown Street, Liverpool L69 7ZD, United
Kingdom
- Materials
Innovation Factory, University of Liverpool, 51 Oxford Street, Liverpool, L7 3NY, United Kingdom
| | - Frédéric Blanc
- Department
of Chemistry, University of Liverpool, Crown Street, Liverpool L69 7ZD, United
Kingdom
- Stephenson
Institute for Renewable Energy, University
of Liverpool, Crown Street, Liverpool L69 7ZD, United Kingdom
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5
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Xu J, Terskikh VV, Chu Y, Zheng A, Huang Y. 13 C chemical shift tensors in MOF α-Mg 3 (HCOO) 6 : Which component is more sensitive to host-guest interaction? MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:1082-1090. [PMID: 31659777 DOI: 10.1002/mrc.4944] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 08/23/2019] [Accepted: 09/16/2019] [Indexed: 06/10/2023]
Abstract
Metal-organic frameworks (MOFs) are a class of important porous materials with many current and potential applications. Their applications almost always involve the interaction between host framework and guest species. Therefore, understanding of host-guest interaction in MOF systems is fundamentally important. Solid-state NMR spectroscopy is an excellent technique for investigating host-guest interaction as it provides information complementary to that obtained from X-ray diffraction. In this work, using MOF α-Mg3 (HCOO)6 as an example, we demonstrated that 13 C chemical shift tensor of organic linker can be utilized to probe the host-guest interaction in MOFs. Obtaining 13 C chemical shift tensor components (δ11 , δ22 , and δ33 , where δ11 ≥ δ22 ≥ δ33 ) in this MOF is particularly challenging as there are six coordinatively equivalent but crystallographically non-equivalent carbons in the unit cell with very similar local coordination environment. Two-dimensional magic-angle-turning experiments were employed to measure the 13 C chemical shift tensors of each individual crystallographically non-equivalent carbon in three microporous α-Mg3 (HCOO)6 samples with different guest species. The results indicate that the δ22 component (with its direction approximately being co-planar with the formate anion and perpendicular to the C-H bond) is more sensitive to the adsorbate molecules inside the MOF channel due to the weak C-H···O hydrogen bonding or the ring current effect of benzene. The 13 C isotropic chemical shift, on the other hand, seems much less sensitive to the subtle changes in the local environment around formate linker induced by adsorption. The approach described in this study may be used in future studies on host-guest interaction within MOFs.
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Affiliation(s)
- Jun Xu
- Center for Rare Earth and Inorganic Functional Materials, Tianjin Key Lab for Rare Earth Materials and Applications, School of Materials Science and Engineering & National Institute for Advanced Materials, Nankai University, Tianjin, 300350, P.R. China
- Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada
| | - Victor V Terskikh
- Department of Chemistry, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Yueying Chu
- Chinese Academy of Sciences, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Wuhan, 430071, P.R. China
| | - Anmin Zheng
- Chinese Academy of Sciences, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Wuhan, 430071, P.R. China
| | - Yining Huang
- Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada
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6
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Abstract
The epididymal lumen contains a complex cystatin-rich nonpathological amyloid matrix with putative roles in sperm maturation and sperm protection. Given our growing understanding for the biological function of this and other functional amyloids, the problem still remains: how functional amyloids assemble including their initial transition to early oligomeric forms. To examine this, we developed a protocol for the purification of nondenatured mouse CRES, a component of the epididymal amyloid matrix, allowing us to examine its assembly to amyloid under conditions that may mimic those in vivo. Herein we use X-ray crystallography, solution-state NMR, and solid-state NMR to follow at the atomic level the assembly of the CRES amyloidogenic precursor as it progressed from monomeric folded protein to an advanced amyloid. We show the CRES monomer has a typical cystatin fold that assembles into highly branched amyloid matrices, comparable to those in vivo, by forming β-sheet assemblies that our data suggest occur via two distinct mechanisms: a unique conformational switch of a highly flexible disulfide-anchored loop to a rigid β-strand and by traditional cystatin domain swapping. Our results provide key insight into our understanding of functional amyloid assembly by revealing the earliest structural transitions from monomer to oligomer and by showing that some functional amyloid structures may be built by multiple and distinctive assembly mechanisms.
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7
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Ghosh M, Kango N, Dey KK. Investigation of the internal structure and dynamics of cellulose by 13C-NMR relaxometry and 2DPASS-MAS-NMR measurements. JOURNAL OF BIOMOLECULAR NMR 2019; 73:601-616. [PMID: 31414362 DOI: 10.1007/s10858-019-00272-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 07/15/2019] [Indexed: 06/10/2023]
Abstract
Internal structure and dynamics of commercial and natural cellulose were studied by measuring chemical shift anisotropy (CSA) parameters, and spin-lattice relaxation rate (1/T1) at each and every chemically different carbon nuclear site. CSA parameters were measured by 13C two-dimensional phase adjusted spinning sideband (2DPASS) cross-polarization magic angle spinning (CP-MAS) NMR experiment. Site specific spin-lattice relaxation time was measured by Torchia-CP method. Anisotropy parameters of C4 and C6 regions are higher than C1 and C235 regions and asymmetry of C4 line is lower than any other carbon site. The higher values of CSA parameters of C4 and C6 nuclei arise due to the rotation of O4-C4, C1-O4, O5-C5-C6-O6 and C4-C5-C6-O6 bonds at torsion angles ψ, Φ, χ and χ' respectively and the influence of interchain and intrachain hydrogen bondings. Two distinct peaks are also observed for C4 and C6 resonance line position-one peak arises primarily due to the nuclei in amorphous region and another one arises due to the same nuclei resides in paracrystalline region. The spin-lattice relaxation time and the CSA parameters are different at these two distinct peak positions of C4 and C6 line. Molecular correlation time of each and every chemically different carbon site was calculated with the help of CSA parameters and spin-lattice relaxation time. The molecular correlation time of the amorphous region is one order of magnitude less than the crystalline region. The distinction between amorphous and paracrystalline regions of cellulose is more vividly portrayed by determining spin-lattice relaxation time, CSA parameters, and molecular correlation time at each and every chemically different carbon site. This type of study correlating the structure and dynamics of cellulose will illuminate the path of inventing biomimetic materials.
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Affiliation(s)
- Manasi Ghosh
- Department of Physics, Dr. Harisingh Gour Central University, Sagar, MP, 470003, India
| | - Naveen Kango
- Department of Microbiology, Dr. Harisingh Gour Central University, Sagar, MP, 470003, India
| | - Krishna Kishor Dey
- Department of Physics, Dr. Harisingh Gour Central University, Sagar, MP, 470003, India.
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8
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Ghosh M, Prajapati BP, Kango N, Dey KK. A comprehensive and comparative study of the internal structure and dynamics of natural β-keratin and regeneratedβ-keratin by solid state NMR spectroscopy. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2019; 101:1-11. [PMID: 31055225 DOI: 10.1016/j.ssnmr.2019.04.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 04/21/2019] [Accepted: 04/23/2019] [Indexed: 06/09/2023]
Abstract
Structure and dynamics of natural and regenerated chicken feather β-keratin were investigated by 13C cross-polarization (CP) magic angle spinning (MAS) solid state nuclear magnetic resonance (SSNMR) spectral analysis, 13C and 1H spin-lattice relaxation time measurements, and 13C two dimensional phase adjusted spinning sidebands (2DPASS) MAS SSNMR measurements. Chemical shift anisotropy (CSA) parameters of both natural and regenerated chicken feather β-keratin were extracted by using 2DPASS MAS SSNMR experiment. The beauty of 2DPASS MAS SSNMR experiment is it can correlate the isotropic and anisotropic dimension with the help of shearing transformation and two dimensional Fourier Transformation. Molecular correlation time at each and every magnetically inequivalent carbon site of both natural and regenerated chicken feather β-keratin were also determined. The change in molecular dynamics of structural protein after pretreatment was monitored by 2DPASS MAS SSNMR and 13C relaxation measurement. This type of comprehensive study will provide the information about the interrelation between the structure and dynamics of structural protein and will also shed light in the way of developing methods for conversion of animal by-products to novel product.
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Affiliation(s)
- Manasi Ghosh
- Department of Physics, Sagar, MP, 470003, India.
| | - Bhanu Pratap Prajapati
- Department of Microbiology, Dr. Hari Singh Gour Central University, Sagar, MP, 470003, India
| | - Naveen Kango
- Department of Microbiology, Dr. Hari Singh Gour Central University, Sagar, MP, 470003, India
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9
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Dabalos CL, Ohgo K, Kumashiro KK. Detection of Labile Conformations of Elastin’s Prolines by Solid-State Nuclear Magnetic Resonance and Fourier Transform Infrared Techniques. Biochemistry 2019; 58:3848-3860. [DOI: 10.1021/acs.biochem.9b00414] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Chester L. Dabalos
- Department of Chemistry, University of Hawaii, 2545 McCarthy Mall, Honolulu, Hawaii 96822, United States
| | - Kosuke Ohgo
- Department of Chemistry, University of Hawaii, 2545 McCarthy Mall, Honolulu, Hawaii 96822, United States
| | - Kristin K. Kumashiro
- Department of Chemistry, University of Hawaii, 2545 McCarthy Mall, Honolulu, Hawaii 96822, United States
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10
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Papkov D, Delpouve N, Delbreilh L, Araujo S, Stockdale T, Mamedov S, Maleckis K, Zou Y, Andalib MN, Dargent E, Dravid VP, Holt MV, Pellerin C, Dzenis YA. Quantifying Polymer Chain Orientation in Strong and Tough Nanofibers with Low Crystallinity: Toward Next Generation Nanostructured Superfibers. ACS NANO 2019; 13:4893-4927. [PMID: 31038925 DOI: 10.1021/acsnano.8b08725] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Advanced fibers revolutionized structural materials in the second half of the 20th century. However, all high-strength fibers developed to date are brittle. Recently, pioneering simultaneous ultrahigh strength and toughness were discovered in fine (<250 nm) individual electrospun polymer nanofibers (NFs). This highly desirable combination of properties was attributed to high macromolecular chain alignment coupled with low crystallinity. Quantitative analysis of the degree of preferred chain orientation will be crucial for control of NF mechanical properties. However, quantification of supramolecular nanoarchitecture in NFs with low crystallinity in the ultrafine diameter range is highly challenging. Here, we discuss the applicability of traditional as well as emerging methods for quantification of polymer chain orientation in nanoscale one-dimensional samples. Advantages and limitations of different techniques are critically evaluated on experimental examples. It is shown that straightforward application of some of the techniques to sub-wavelength-diameter NFs can lead to severe quantitative and even qualitative artifacts. Sources of such size-related artifacts, stemming from instrumental, materials, and geometric phenomena at the nanoscale, are analyzed on the example of polarized Raman method but are relevant to other spectroscopic techniques. A proposed modified, artifact-free method is demonstrated. Outstanding issues and their proposed solutions are discussed. The results provide guidance for accurate nanofiber characterization to improve fundamental understanding and accelerate development of nanofibers and related nanostructured materials produced by electrospinning or other methods. We expect that the discussion in this review will also be useful to studies of many biological systems that exhibit nanofilamentary architectures and combinations of high strength and toughness.
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Affiliation(s)
- Dimitry Papkov
- Department of Mechanical and Materials Engineering , University of Nebraska-Lincoln , Lincoln , Nebraska 68588-0526 , United States
- Nebraska Center for Materials and Nanoscience , University of Nebraska-Lincoln , Lincoln , Nebraska 68588-0298 , United States
| | - Nicolas Delpouve
- Département Systèmes Désordonnés et Polymères, Equipe Internationale de Recherche et de Caractérisation des Amorphes et des Polymères , Normandie Univ, UNIROUEN, INSA ROUEN, CNRS, GPM , 76000 Rouen , France
| | - Laurent Delbreilh
- Département Systèmes Désordonnés et Polymères, Equipe Internationale de Recherche et de Caractérisation des Amorphes et des Polymères , Normandie Univ, UNIROUEN, INSA ROUEN, CNRS, GPM , 76000 Rouen , France
| | - Steven Araujo
- Département Systèmes Désordonnés et Polymères, Equipe Internationale de Recherche et de Caractérisation des Amorphes et des Polymères , Normandie Univ, UNIROUEN, INSA ROUEN, CNRS, GPM , 76000 Rouen , France
| | - Taylor Stockdale
- Department of Mechanical and Materials Engineering , University of Nebraska-Lincoln , Lincoln , Nebraska 68588-0526 , United States
| | - Sergey Mamedov
- Division of HORIBA Instruments, Inc. , HORIBA Scientific , 20 Knightsbridge Road , Piscataway , New Jersey 08854 , United States
| | - Kaspars Maleckis
- Department of Mechanical and Materials Engineering , University of Nebraska-Lincoln , Lincoln , Nebraska 68588-0526 , United States
| | - Yan Zou
- Department of Mechanical and Materials Engineering , University of Nebraska-Lincoln , Lincoln , Nebraska 68588-0526 , United States
| | - Mohammad Nahid Andalib
- Department of Mechanical and Materials Engineering , University of Nebraska-Lincoln , Lincoln , Nebraska 68588-0526 , United States
| | - Eric Dargent
- Département Systèmes Désordonnés et Polymères, Equipe Internationale de Recherche et de Caractérisation des Amorphes et des Polymères , Normandie Univ, UNIROUEN, INSA ROUEN, CNRS, GPM , 76000 Rouen , France
| | - Vinayak P Dravid
- Department of Materials Science and Engineering , Northwestern University , Evanston , Illinois 60208 , United States
| | - Martin V Holt
- Center for Nanoscale Materials , Argonne National Laboratory , Argonne , Illinois 60439 , United States
| | - Christian Pellerin
- Département de chimie , Université de Montréal , Montréal , QC H3C 3J7 , Canada
| | - Yuris A Dzenis
- Department of Mechanical and Materials Engineering , University of Nebraska-Lincoln , Lincoln , Nebraska 68588-0526 , United States
- Nebraska Center for Materials and Nanoscience , University of Nebraska-Lincoln , Lincoln , Nebraska 68588-0298 , United States
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11
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Mukhopadhyay D, Gupta C, Theint T, Jaroniec CP. Peptide bond conformation in peptides and proteins probed by dipolar coupling-chemical shift tensor correlation solid-state NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 297:152-160. [PMID: 30396157 PMCID: PMC6289736 DOI: 10.1016/j.jmr.2018.10.015] [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: 09/29/2018] [Revised: 10/25/2018] [Accepted: 10/26/2018] [Indexed: 05/30/2023]
Abstract
Multidimensional magic-angle spinning solid-state NMR experiments are described that permit cis and trans peptide bonds in uniformly 13C,15N-labeled peptides and proteins to be unambiguously distinguished in residue-specific manner by determining the relative orientations of the amide 13C' CSA and 1H-15N dipolar coupling tensors. The experiments are demonstrated for model peptides glycylglycine and 2,5-diketopiperazine containing trans and cis peptide bonds, respectively. Subsequently, the measurements are extended to two representative proteins that contain exclusively trans peptide bonds, microcrystalline B3 immunoglobulin domain of protein G and Y145Stop human prion protein amyloid fibrils, to illustrate their applicability to a wide range of protein systems.
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Affiliation(s)
- Dwaipayan Mukhopadhyay
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, United States
| | - Chitrak Gupta
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, United States
| | - Theint Theint
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, United States
| | - Christopher P Jaroniec
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, United States.
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12
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Ohgo K, Dabalos CL, Kumashiro KK. Solid-State NMR Spectroscopy and Isotopic Labeling Target Abundant Dipeptide Sequences in Elastin’s Hydrophobic Domains. Macromolecules 2018. [DOI: 10.1021/acs.macromol.7b02616] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kosuke Ohgo
- Department of Chemistry, University of Hawaii, 2545 McCarthy Mall, Honolulu, Hawaii 96822, United States
| | - Chester L. Dabalos
- Department of Chemistry, University of Hawaii, 2545 McCarthy Mall, Honolulu, Hawaii 96822, United States
| | - Kristin K. Kumashiro
- Department of Chemistry, University of Hawaii, 2545 McCarthy Mall, Honolulu, Hawaii 96822, United States
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13
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Kamihara T, Mizuno T, Shoji A, Takegoshi K. Conformational Characterization of Left-Handed Helices in Poly(β-benzyl l-aspartate) by 13C Chemical Shift Anisotropy Using Solid-State NMR. Macromolecules 2015. [DOI: 10.1021/ma502165u] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Takayuki Kamihara
- Division of Chemistry,
Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | | | - Akira Shoji
- Department of Chemistry and Chemical Biology, Graduate School of
Engineering, Gunma University, Kiryu, Gunma 376-8515, Japan
| | - K. Takegoshi
- Division of Chemistry,
Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
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14
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Altheimer BD, Mehta MA. Effects of structural differences on the NMR chemical shifts in isostructural dipeptides. J Phys Chem A 2014; 118:2618-28. [PMID: 24654604 DOI: 10.1021/jp411220y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Porous crystalline dipeptides have gained recent attention for their potential as gas-storage materials. Within this large class is a group of dipeptides containing alanine, valine, and isoleucine with very similar crystal structures. We report the (13)C (carbonyl and Cα) and (15)N (amine and amide) solid-state NMR isotropic chemical shifts in a series of seven such isostructural porous dipeptides as well as shift tensor data for the carbonyl and amide sites. Using their known crystal structures and aided by ab initio quantum chemical calculations for the resonance assignments, we elucidate trends relating local structure, hydrogen-bonding patterns, and chemical shift. We find good correlation between the backbone dihedral angles and the Cα1 and Cα2 shifts. For the C1 shift tensor, the δ11 value shifts downfield as the hydrogen-bond distance increases, δ22 shifts upfield, and δ33 shows little variation. The C2 shift tensor shows no appreciable correlation with structural parameters. For the N2 tensor, δ11 shows little dependence on the hydrogen-bond length, whereas δ22 and δ33 both show a decrease in shielding as the hydrogen bond shortens. Our analysis teases apart some, but not all, structural contributors to the observed differences the solid-state NMR chemical shifts.
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Affiliation(s)
- Benjamin D Altheimer
- Department of Chemistry and Biochemistry, Oberlin College , 119 Woodland Street, Oberlin, Ohio 44074, United States
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15
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Zhang B, Spano J, Chen Y, Turner R, Wi S. Crystallinity and Motional Dynamics Study of a Series of Poly(arylene ether sulfone) Segmented Copolymer Analogues. J Phys Chem B 2012; 116:7970-80. [DOI: 10.1021/jp303606f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bin Zhang
- Department
of Chemistry, and ‡Macromolecules and Interfaces Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Justin Spano
- Department
of Chemistry, and ‡Macromolecules and Interfaces Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Ying Chen
- Department
of Chemistry, and ‡Macromolecules and Interfaces Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Richard Turner
- Department
of Chemistry, and ‡Macromolecules and Interfaces Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Sungsool Wi
- Department
of Chemistry, and ‡Macromolecules and Interfaces Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
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16
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Wang WD, Gao X, Strohmeier M, Wang W, Bai S, Dybowski C. Solid-State NMR Studies of Form I of Atorvastatin Calcium. J Phys Chem B 2012; 116:3641-9. [DOI: 10.1021/jp212074a] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wei David Wang
- State Key Laboratory of Applied
Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Xudong Gao
- State Key Laboratory of Applied
Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Mark Strohmeier
- Product Development, GlaxoSmithKline, Inc., 709 Swedeland Road, King of
Prussia, Pennsylvania 19406, United States
| | - Wei Wang
- State Key Laboratory of Applied
Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Shi Bai
- State Key Laboratory of Applied
Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, Gansu, 730000, China
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United
States
| | - Cecil Dybowski
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United
States
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17
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Veshtort M, Griffin RG. Proton-driven spin diffusion in rotating solids via reversible and irreversible quantum dynamics. J Chem Phys 2012; 135:134509. [PMID: 21992326 DOI: 10.1063/1.3635374] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Proton-driven spin diffusion (PDSD) experiments in rotating solids have received a great deal of attention as a potential source of distance constraints in large biomolecules. However, the quantitative relationship between the molecular structure and observed spin diffusion has remained obscure due to the lack of an accurate theoretical description of the spin dynamics in these experiments. We start with presenting a detailed relaxation theory of PDSD in rotating solids that provides such a description. The theory applies to both conventional and radio-frequency-assisted PDSD experiments and extends to the non-Markovian regime to include such phenomena as rotational resonance (R(2)). The basic kinetic equation of the theory in the non-Markovian regime has the form of a memory function equation, with the role of the memory function played by the correlation function. The key assumption used in the derivation of this equation expresses the intuitive notion of the irreversible dissipation of coherences in macroscopic systems. Accurate expressions for the correlation functions and for the spin diffusion constants are given. The theory predicts that the spin diffusion constants governing the multi-site PDSD can be approximated by the constants observed in the two-site diffusion. Direct numerical simulations of PDSD dynamics via reversible Liouville-von Neumann equation are presented to support and compliment the theory. Remarkably, an exponential decay of the difference magnetization can be observed in such simulations in systems consisting of only 12 spins. This is a unique example of a real physical system whose typically macroscopic and apparently irreversible behavior can be traced via reversible microscopic dynamics. An accurate value for the spin diffusion constant can be usually obtained through direct simulations of PDSD in systems consisting of two (13)C nuclei and about ten (1)H nuclei from their nearest environment. Spin diffusion constants computed by this method are in excellent agreement with the spin diffusion constants obtained through equations given by the relaxation theory of PDSD. The constants resulting from these two approaches were also in excellent agreement with the results of 2D rotary resonance recoupling proton-driven spin diffusion (R(3)-PDSD) experiments performed in three model compounds, where magnetization exchange occurred over distances up to 4.9 Å. With the methodology presented, highly accurate internuclear distances can be extracted from such data. Relayed transfer of magnetization between distant nuclei appears to be the main (and apparently resolvable) source of uncertainty in such measurements. The non-Markovian kinetic equation was applied to the analysis of the R(2) spin dynamics. The conventional semi-phenomenological treatment of relxation in R(2) has been shown to be equivalent to the assumption of the Lorentzian spectral density function in the relaxatoin theory of PDSD. As this assumption is a poor approximation in real physical systems, the conventional R(2) treatment is likely to carry a significant model error that has not been recognized previously. The relaxation theory of PDSD appears to provide an accurate, parameter-free alternative. Predictions of this theory agreed well with the full quantum mechanical simulations of the R(2) dynamics in the few simple model systems we considered.
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Affiliation(s)
- Mikhail Veshtort
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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18
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Pawlak T, Trzeciak-Karlikowska K, Czernek J, Ciesielski W, Potrzebowski MJ. Computed and Experimental Chemical Shift Parameters for Rigid and Flexible YAF Peptides in the Solid State. J Phys Chem B 2012; 116:1974-83. [DOI: 10.1021/jp2111567] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tomasz Pawlak
- Centre of Molecular
and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, PL-90-363 Lodz, Poland
| | | | - Jiri Czernek
- Institute of Macromolecular
Chemistry, Academy of Sciences of the Czech Republic, Heyrovsky Square 2, CZ-16206 Praha 6, Czech
Republic
| | - Wlodzimierz Ciesielski
- Centre of Molecular
and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, PL-90-363 Lodz, Poland
| | - Marek J. Potrzebowski
- Centre of Molecular
and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, PL-90-363 Lodz, Poland
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19
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Ośmiałowski B, Kolehmainen E, Ikonen S, Ahonen K, Löfman M. NMR crystallography of 2-acylamino-6-[1H]-pyridones: Solid-state NMR, GIPAW computational, and single crystal X-ray diffraction studies. J Mol Struct 2011. [DOI: 10.1016/j.molstruc.2011.10.034] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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20
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Tang S, Case DA. Calculation of chemical shift anisotropy in proteins. JOURNAL OF BIOMOLECULAR NMR 2011; 51:303-12. [PMID: 21866436 PMCID: PMC3196061 DOI: 10.1007/s10858-011-9556-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Accepted: 08/03/2011] [Indexed: 05/24/2023]
Abstract
Individual peptide groups in proteins must exhibit some variation in the chemical shift anisotropy (CSA) of their constituent atoms, but not much is known about the extent or origins of this dispersion. Direct spectroscopic measurement of CSA remains technically challenging, and theoretical methods can help to overcome these limitations by estimating shielding tensors for arbitrary structures. Here we use an automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) approach to compute (15)N, (13)C' and (1)H chemical shift tensors for human ubiquitin and the GB1 and GB3 fragments of staphylococcal protein G. The average and range of variation of the anisotropies is in good agreement with experimental estimates from solid-state NMR, and the variation among residues is somewhat smaller than that estimated from solution-state measurements. Hydrogen-bond effects account for much of the variation, both between helix and sheet regions, and within elements of secondary structure, but other effects (including variations in torsion angles) may play a role as well.
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Affiliation(s)
- Sishi Tang
- Department of Chemistry and Chemical Biology, BioMaPS Institute, Rutgers University, Piscataway, NJ 08854, USA
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21
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Trzeciak-Karlikowska K, Bujacz A, Ciesielski W, Bujacz GD, Potrzebowski MJ. The Influence of the Stereochemistry of Alanine Residue on the Solid State Conformation and Crystal Packing of Opioid Peptides Containing d-Ala or l-Ala in Message Domain – XRD and NMR Study. J Phys Chem B 2011; 115:9910-9. [DOI: 10.1021/jp205570y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Anna Bujacz
- Institute of Technical Biochemistry, Technical University of Lodz, Stefanowskiego 4/10, 90-924 Lodz, Poland
| | - Włodzimierz Ciesielski
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Grzegorz D. Bujacz
- Institute of Technical Biochemistry, Technical University of Lodz, Stefanowskiego 4/10, 90-924 Lodz, Poland
| | - Marek J. Potrzebowski
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
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22
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Structural characterization of polyglutamine fibrils by solid-state NMR spectroscopy. J Mol Biol 2011; 412:121-36. [PMID: 21763317 DOI: 10.1016/j.jmb.2011.06.045] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Revised: 06/21/2011] [Accepted: 06/27/2011] [Indexed: 01/21/2023]
Abstract
Protein aggregation via polyglutamine stretches occurs in a number of severe neurodegenerative diseases such as Huntington's disease. We have investigated fibrillar aggregates of polyglutamine peptides below, at, and above the toxicity limit of around 37 glutamine residues using solid-state NMR and electron microscopy. Experimental data are consistent with a dry fibril core of at least 70-80 Å in width for all constructs. Solid-state NMR dipolar correlation experiments reveal a largely β-strand character of all samples and point to tight interdigitation of hydrogen-bonded glutamine side chains from different sheets. Two approximately equally frequent populations of glutamine residues with distinct sets of chemical shifts are found, consistent with local backbone dihedral angles compensating for β-strand twist or with two distinct sets of side-chain conformations. Peptides comprising 15 glutamine residues are present as single extended β-strands. Data obtained for longer constructs are most compatible with a superpleated arrangement with individual molecules contributing β-strands to more than one sheet and an antiparallel assembly of strands within β-sheets.
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23
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Sani MA, Separovic F, Gehman J. Disentanglement of heterogeneous dynamics in mixed lipid systems. Biophys J 2011; 100:L40-2. [PMID: 21504719 PMCID: PMC3077697 DOI: 10.1016/j.bpj.2011.03.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Revised: 02/25/2011] [Accepted: 03/02/2011] [Indexed: 10/18/2022] Open
Abstract
Static phosphorous NMR has been a powerful technique for the study of model supramolecular phospholipid structures. Application to natural lipid bilayers with complex compositions, however, has been severely limited by the difficulty in deconvoluting overlapping broad lineshapes. We demonstrate a solution to this problem, using a global fit to a few slow magic-angle spinning spectra, in combination with an adaptation of Boltzmann statistics maximum entropy. The method provides a model-free means to characterize a heterogeneous mix of lipid dynamics via a distribution of (31)P chemical shift anisotropies. It is used here to identify clear changes in membrane dynamics of a phosphatidylethanolamine and phosphatidylglycerol mixture, mimicking an Escherichia coli membrane upon addition of just 2% of the antimicrobial peptide maculatin 1.1. This illustration opens the prospect for investigation of arbitrarily complex natural lipid systems, important in many areas of biophysical chemistry and biomedicine.
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Affiliation(s)
| | | | - John D. Gehman
- School of Chemistry and Bio21 Institute, The University of Melbourne, Melbourne, Victoria, Australia
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24
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Gowda CM, Vasconcelos F, Schwartz E, van Eck ERH, Marsman M, Cornelissen JJLM, Rowan AE, de Wijs GA, Kentgens APM. Hydrogen bonding and chemical shift assignments in carbazole functionalized isocyanides from solid-state NMR and first-principles calculations. Phys Chem Chem Phys 2011; 13:13082-95. [DOI: 10.1039/c1cp20304e] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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25
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Nowicka K, Bujacz A, Paluch P, Sobczuk A, Jeziorna A, Ciesielski W, Bujacz GD, Jurczak J, Potrzebowski MJ. Study of host–guest interactions in benzodiazacoronands by means of solid state NMR spectroscopy, X-ray diffraction and quantum mechanical computations. Phys Chem Chem Phys 2011; 13:6423-33. [DOI: 10.1039/c0cp02401e] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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26
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Yao L, Grishaev A, Cornilescu G, Bax A. The impact of hydrogen bonding on amide 1H chemical shift anisotropy studied by cross-correlated relaxation and liquid crystal NMR spectroscopy. J Am Chem Soc 2010; 132:10866-75. [PMID: 20681720 PMCID: PMC2915638 DOI: 10.1021/ja103629e] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Site-specific 1H chemical shift anisotropy (CSA) tensors have been derived for the well-ordered backbone amide moieties in the B3 domain of protein G (GB3). Experimental input data include residual chemical shift anisotropy (RCSA), measured in six mutants that align differently relative to the static magnetic field when dissolved in a liquid crystalline Pf1 suspension, and cross-correlated relaxation rates between the 1HN CSA tensor and either the 1H−15N, the 1H−13C′, or the 1H−13Cα dipolar interactions. Analyses with the assumption that the 1HN CSA tensor is symmetric with respect to the peptide plane (three-parameter fit) or without this premise (five-parameter fit) yield very similar results, confirming the robustness of the experimental input data, and that, to a good approximation, one of the principal components orients orthogonal to the peptide plane. 1HN CSA tensors are found to deviate strongly from axial symmetry, with the most shielded tensor component roughly parallel to the N−H vector, and the least shielded component orthogonal to the peptide plane. DFT calculations on pairs of N-methyl acetamide and acetamide in H-bonded geometries taken from the GB3 X-ray structure correlate with experimental data and indicate that H-bonding effects dominate variations in the 1HN CSA. Using experimentally derived 1HN CSA tensors, the optimal relaxation interference effect needed for narrowest 1HN TROSY line widths is found at ∼1200 MHz.
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Affiliation(s)
- Lishan Yao
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266061, China
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27
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Liu W, Wang WD, Wang W, Bai S, Dybowski C. Influence of Structure on the Spectroscopic Properties of the Polymorphs of Piroxicam. J Phys Chem B 2010; 114:16641-9. [DOI: 10.1021/jp1084444] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Wei Liu
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou, Gansu, 730000, China, and Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Wei David Wang
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou, Gansu, 730000, China, and Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Wei Wang
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou, Gansu, 730000, China, and Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Shi Bai
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou, Gansu, 730000, China, and Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Cecil Dybowski
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou, Gansu, 730000, China, and Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
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28
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Saitô H, Ando I, Ramamoorthy A. Chemical shift tensor - the heart of NMR: Insights into biological aspects of proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2010; 57:181-228. [PMID: 20633363 PMCID: PMC2905606 DOI: 10.1016/j.pnmrs.2010.04.005] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2010] [Accepted: 04/26/2010] [Indexed: 05/19/2023]
Affiliation(s)
- Hazime Saitô
- Department of Life Science, Himeji Institute of Technology, University of Hyogo, Kamigori, Hyog, 678-1297, Japan
| | - Isao Ando
- Department of Chemistry and Materials Science, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo, 152-0033, Japan
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109-1055, USA
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29
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Vugmeyster L, Ostrovsky D, Li Y. Comparison of fast backbone dynamics at amide nitrogen and carbonyl sites in dematin headpiece C-terminal domain and its S74E mutant. JOURNAL OF BIOMOLECULAR NMR 2010; 47:155-162. [PMID: 20396930 DOI: 10.1007/s10858-010-9417-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2010] [Accepted: 03/29/2010] [Indexed: 05/29/2023]
Abstract
We perform a detailed comparison of fast backbone dynamics probed at amide nitrogen versus carbonyl carbon sites for dematin headpiece C-terminal domain (DHP) and its S74E mutant (DHPS74E). Carbonyl dynamics is probed via auto-correlated longitudinal rates and transverse C'/C'-C(alpha) CSA/dipolar and C'/C'-N CSA/dipolar cross-correlated rates, while (15)N data are taken from a previous study. Resulting values of effective order parameters and internal correlation times support the conclusion that C' relaxation reports on a different subset of fast motions compared to those probed at N-H bond vectors in the same peptide planes. (13)C' order parameters are on the average 0.08 lower than (15)N order parameters with the exception of the flexible loop region in DHP. The reduction of mobility in the loop region upon the S74E mutation can be seen from the (15)N order parameters but not from the (13)C order parameters. Internal correlation times at (13)C' sites are on the average an order of magnitude longer than those at (15)N sites for the well-structured C-terminal subdomains, while the more flexible N-terminal subdomains have more comparable average internal correlation times.
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Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry and Environment and Natural Resources Institute, University of Alaska at Anchorage, 3211 Providence Drive, Anchorage, AK 99508, USA.
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30
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SOUMA H, KUROSU H, SHOJI A. Precise Structural Analysis of Polypeptides by Quantum Chemical Calculation. KOBUNSHI RONBUNSHU 2010. [DOI: 10.1295/koron.67.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Hiroyuki SOUMA
- Department of Chemistry and Chemical Biology, Graduate School of Engineering, Gunma University
| | - Hiromichi KUROSU
- Graduate School of Humanities and Sciences, Nara Women's University
| | - Akira SHOJI
- Department of Chemistry and Chemical Biology, Graduate School of Engineering, Gunma University
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31
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Rougier L, Milon A, Réat V, Jolibois F. Modelling the influence of hydrogen bond network on chemical shielding tensors description. GIAO-DFT study of WALP23 transmembrane α-helix as a test case. Phys Chem Chem Phys 2010; 12:6999-7008. [DOI: 10.1039/b923883b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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32
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33
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Tulip P, Bates S. First principles determination of structural, electronic and lattice dynamical properties of a model dipeptide molecular crystal. Mol Phys 2009. [DOI: 10.1080/00268970903224955] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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34
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Bhate MP, Woodard JC, Mehta MA. Solvation and Hydrogen Bonding in Alanine- and Glycine-Containing Dipeptides Probed Using Solution- and Solid-State NMR Spectroscopy. J Am Chem Soc 2009; 131:9579-89. [DOI: 10.1021/ja902917s] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Manasi P. Bhate
- Department of Chemistry and Biochemistry, Oberlin College, Oberlin, Ohio 44074
| | - Jaie C. Woodard
- Department of Chemistry and Biochemistry, Oberlin College, Oberlin, Ohio 44074
| | - Manish A. Mehta
- Department of Chemistry and Biochemistry, Oberlin College, Oberlin, Ohio 44074
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35
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Zheng A, Liu SB, Deng F. 13C shielding tensors of crystalline amino acids and peptides: Theoretical predictions based on periodic structure models. J Comput Chem 2009; 30:222-35. [DOI: 10.1002/jcc.21118] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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36
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Precise structural analysis of α-helical copolypeptide H-(Ala-Gly)9-OH by quantum chemical calculation and high-resolution solid-state NMR measurement. J Mol Struct 2008. [DOI: 10.1016/j.molstruc.2008.03.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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37
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Shoji A, Souma H, Ozaki T, Kurosu H, Ando I, Berger S. Precise structural analysis of α-helical poly(l-alanine) by quantum chemical calculation. J Mol Struct 2008. [DOI: 10.1016/j.molstruc.2008.01.031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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38
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Yao S, Zhang MM, Yoshikami D, Azam L, Olivera BM, Bulaj G, Norton RS. Structure, dynamics, and selectivity of the sodium channel blocker mu-conotoxin SIIIA. Biochemistry 2008; 47:10940-9. [PMID: 18798648 DOI: 10.1021/bi801010u] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
mu-SIIIA, a novel mu-conotoxin from Conus striatus, appeared to be a selective blocker of tetrodotoxin-resistant sodium channels in frog preparations. It also exhibited potent analgesic activity in mice, although its selectivity profile against mammalian sodium channels remains unknown. We have determined the structure of mu-SIIIA in aqueous solution and characterized its backbone dynamics by NMR and its functional properties electrophysiologically. Consistent with the absence of hydroxyprolines, mu-SIIIA adopts a single conformation with all peptide bonds in the trans conformation. The C-terminal region contains a well-defined helix encompassing residues 11-16, while residues 3-5 in the N-terminal region form a helix-like turn resembling 3 10-helix. The Trp12 and His16 side chains are close together, as in the related conotoxin mu-SmIIIA, but Asn2 is more distant. Dynamics measurements show that the N-terminus and Ser9 have larger-magnitude motions on the subnanosecond time scale, while the C-terminus is more rigid. Cys4, Trp12, and Cys13 undergo significant conformational exchange on microsecond to millisecond time scales. mu-SIIIA is a potent, nearly irreversible blocker of Na V1.2 but also blocks Na V1.4 and Na V1.6 with submicromolar potency. The selectivity profile of mu-SIIIA, including poor activity against the cardiac sodium channel, Na V1.5, is similar to that of the closely related mu-KIIIA, suggesting that the C-terminal regions of both are critical for blocking neuronal Na V1.2. The structural and functional characterization described in this paper of an analgesic mu-conotoxin that targets neuronal subtypes of mammalian sodium channels provides a basis for the design of novel analogues with an improved selectivity profile.
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Affiliation(s)
- Shenggen Yao
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3050, Australia
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39
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The photoisomerization of a peptidic derivative of azobenzene: A nonadiabatic dynamics simulation of a supramolecular system. Chem Phys 2008. [DOI: 10.1016/j.chemphys.2008.01.030] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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40
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Blanc F, Basset JM, Copéret C, Sinha A, Tonzetich ZJ, Schrock RR, Solans-Monfort X, Clot E, Eisenstein O, Lesage A, Emsley L. Dynamics of Silica-Supported Catalysts Determined by Combining Solid-State NMR Spectroscopy and DFT Calculations. J Am Chem Soc 2008; 130:5886-900. [DOI: 10.1021/ja077749v] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Frédéric Blanc
- Laboratoire de Chimie, Catalyse, Polymères et Procédés (UMR 5265), Chimie Organométallique de Surface, ESCPE Lyon, Université de Lyon, 43 Bd du 11 Novembre 1918, F-69616 Villeurbanne, France, Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain, Institut Charles Gerhardt Montpellier (UMR 5253, CNRS, UM2, UM1, ENSCM), Université Montpellier 2, cc 1501, Place E. Bataillon, F-34095
| | - Jean-Marie Basset
- Laboratoire de Chimie, Catalyse, Polymères et Procédés (UMR 5265), Chimie Organométallique de Surface, ESCPE Lyon, Université de Lyon, 43 Bd du 11 Novembre 1918, F-69616 Villeurbanne, France, Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain, Institut Charles Gerhardt Montpellier (UMR 5253, CNRS, UM2, UM1, ENSCM), Université Montpellier 2, cc 1501, Place E. Bataillon, F-34095
| | - Christophe Copéret
- Laboratoire de Chimie, Catalyse, Polymères et Procédés (UMR 5265), Chimie Organométallique de Surface, ESCPE Lyon, Université de Lyon, 43 Bd du 11 Novembre 1918, F-69616 Villeurbanne, France, Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain, Institut Charles Gerhardt Montpellier (UMR 5253, CNRS, UM2, UM1, ENSCM), Université Montpellier 2, cc 1501, Place E. Bataillon, F-34095
| | - Amritanshu Sinha
- Laboratoire de Chimie, Catalyse, Polymères et Procédés (UMR 5265), Chimie Organométallique de Surface, ESCPE Lyon, Université de Lyon, 43 Bd du 11 Novembre 1918, F-69616 Villeurbanne, France, Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain, Institut Charles Gerhardt Montpellier (UMR 5253, CNRS, UM2, UM1, ENSCM), Université Montpellier 2, cc 1501, Place E. Bataillon, F-34095
| | - Zachary J. Tonzetich
- Laboratoire de Chimie, Catalyse, Polymères et Procédés (UMR 5265), Chimie Organométallique de Surface, ESCPE Lyon, Université de Lyon, 43 Bd du 11 Novembre 1918, F-69616 Villeurbanne, France, Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain, Institut Charles Gerhardt Montpellier (UMR 5253, CNRS, UM2, UM1, ENSCM), Université Montpellier 2, cc 1501, Place E. Bataillon, F-34095
| | - Richard R. Schrock
- Laboratoire de Chimie, Catalyse, Polymères et Procédés (UMR 5265), Chimie Organométallique de Surface, ESCPE Lyon, Université de Lyon, 43 Bd du 11 Novembre 1918, F-69616 Villeurbanne, France, Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain, Institut Charles Gerhardt Montpellier (UMR 5253, CNRS, UM2, UM1, ENSCM), Université Montpellier 2, cc 1501, Place E. Bataillon, F-34095
| | - Xavier Solans-Monfort
- Laboratoire de Chimie, Catalyse, Polymères et Procédés (UMR 5265), Chimie Organométallique de Surface, ESCPE Lyon, Université de Lyon, 43 Bd du 11 Novembre 1918, F-69616 Villeurbanne, France, Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain, Institut Charles Gerhardt Montpellier (UMR 5253, CNRS, UM2, UM1, ENSCM), Université Montpellier 2, cc 1501, Place E. Bataillon, F-34095
| | - Eric Clot
- Laboratoire de Chimie, Catalyse, Polymères et Procédés (UMR 5265), Chimie Organométallique de Surface, ESCPE Lyon, Université de Lyon, 43 Bd du 11 Novembre 1918, F-69616 Villeurbanne, France, Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain, Institut Charles Gerhardt Montpellier (UMR 5253, CNRS, UM2, UM1, ENSCM), Université Montpellier 2, cc 1501, Place E. Bataillon, F-34095
| | - Odile Eisenstein
- Laboratoire de Chimie, Catalyse, Polymères et Procédés (UMR 5265), Chimie Organométallique de Surface, ESCPE Lyon, Université de Lyon, 43 Bd du 11 Novembre 1918, F-69616 Villeurbanne, France, Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain, Institut Charles Gerhardt Montpellier (UMR 5253, CNRS, UM2, UM1, ENSCM), Université Montpellier 2, cc 1501, Place E. Bataillon, F-34095
| | - Anne Lesage
- Laboratoire de Chimie, Catalyse, Polymères et Procédés (UMR 5265), Chimie Organométallique de Surface, ESCPE Lyon, Université de Lyon, 43 Bd du 11 Novembre 1918, F-69616 Villeurbanne, France, Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain, Institut Charles Gerhardt Montpellier (UMR 5253, CNRS, UM2, UM1, ENSCM), Université Montpellier 2, cc 1501, Place E. Bataillon, F-34095
| | - Lyndon Emsley
- Laboratoire de Chimie, Catalyse, Polymères et Procédés (UMR 5265), Chimie Organométallique de Surface, ESCPE Lyon, Université de Lyon, 43 Bd du 11 Novembre 1918, F-69616 Villeurbanne, France, Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain, Institut Charles Gerhardt Montpellier (UMR 5253, CNRS, UM2, UM1, ENSCM), Université Montpellier 2, cc 1501, Place E. Bataillon, F-34095
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41
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Wylie BJ, Rienstra CM. Multidimensional solid state NMR of anisotropic interactions in peptides and proteins. J Chem Phys 2008; 128:052207. [PMID: 18266412 DOI: 10.1063/1.2834735] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Accurate determinations of chemical shift anisotropy (CSA) tensors are valuable for NMR of biological systems. In this review we describe recent developments in CSA measurement techniques and applications, particularly in the context of peptides and proteins. These techniques include goniometeric measurements of single crystals, slow magic-angle spinning studies of powder samples, and CSA recoupling under moderate to fast MAS. Experimental CSA data can be analyzed by comparison with ab initio calculations for structure determination and refinement. This approach has particularly high potential for aliphatic (13)C analysis, especially Calpha tensors which are directly related to structure. Carbonyl and (15)N CSA tensors demonstrate a more complex dependence upon hydrogen bonding and electrostatics, in addition to conformational dependence. The improved understanding of these tensors and the ability to measure them quantitatively provide additional opportunities for structure determination, as well as insights into dynamics.
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Affiliation(s)
- Benjamin J Wylie
- Department of Chemistry, Department of Biochemistry and Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
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42
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Tafazzoli M, Amini SK. Theoretical 13C chemical shift, 14N, and 2H quadrupole coupling- constant studies of hydrogen bonding in L-alanylglycine dipeptide. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2008; 46:370-376. [PMID: 18273875 DOI: 10.1002/mrc.2185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
(13)C chemical shieldings and (14)N and (2)H electric field gradient (EFG) tensors of L-alanylglycine (L-alagly) dipeptide were calculated at RHF/6-31 + + G** and B3LYP/6-31 + + G** levels of theory respectively. For these calculations a crystal structure of this dipeptide obtained from X-ray crystallography was used. Atomic coordinates of different clusters containing several L-alagly molecules were used as input files for calculations. These clusters consist of central and surrounding L-alagly molecules, the latter forming short, strong, hydrogen bonds with the central molecule. Since the calculations did not converge for these clusters, the surrounding L-alagly molecules were replaced by glycine molecules. In order to improve the accuracy of calculated chemical shifts and nuclear quadrupole coupling constants (NQCCs), different geometry-optimization strategies were applied for hydrogen nuclei. Agreement between calculated and experimental data confirms that our optimized coordinates for hydrogen nuclei are more accurate than those obtained by X-ray diffraction.
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Affiliation(s)
- M Tafazzoli
- Department of Chemistry, Sharif University of Technology, Tehran, Iran.
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43
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Duma L, Abergel D, Tekely P, Bodenhausen G. Proton chemical shift anisotropy measurements of hydrogen-bonded functional groups by fast magic-angle spinning solid-state NMR spectroscopy. Chem Commun (Camb) 2008:2361-3. [PMID: 18473070 DOI: 10.1039/b801154k] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The suitability of fast MAS solid-state NMR spectroscopy for probing (1)H chemical shift anisotropy of hydrogen-bonded species has been demonstrated.
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Affiliation(s)
- Luminita Duma
- Département de Chimie, associé au CNRS, Ecole Normale Supérieure, 75231, Paris, Cedex 05, France
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44
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Olejniczak S, Mikuła-Pacholczyk J, Hughes CE, Potrzebowski MJ. 15N and 13C High-Resolution Solid-State NMR Study of the Polymorphism of the l-Enantiomer of N-Benzoylphenylalanine. J Phys Chem B 2008; 112:1586-93. [DOI: 10.1021/jp073428u] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sebastian Olejniczak
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland, and School of Chemistry, Cardiff University, Cardiff, CF10 3AT, United Kingdom
| | - Justyna Mikuła-Pacholczyk
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland, and School of Chemistry, Cardiff University, Cardiff, CF10 3AT, United Kingdom
| | - Colan E. Hughes
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland, and School of Chemistry, Cardiff University, Cardiff, CF10 3AT, United Kingdom
| | - Marek J. Potrzebowski
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland, and School of Chemistry, Cardiff University, Cardiff, CF10 3AT, United Kingdom
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45
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Chierotti MR, Gobetto R. Solid-state NMR studies of weak interactions in supramolecular systems. Chem Commun (Camb) 2008:1621-34. [PMID: 18368147 DOI: 10.1039/b711551b] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The field of application of solid-state NMR to the study of supramolecular systems is growing rapidly, with many research groups involved in the development of techniques for the study of crystalline and amorphous phases. This Feature Article aims to provide an overview of the recent contributions of our research group to this field, paying particular attention to the study of the weak interactions such as hydrogen bonds in supramolecular systems through solid-state NMR investigations. The structure and dynamic behaviour of selected host-guest systems will be also discussed.
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Affiliation(s)
- Michele R Chierotti
- Università degli Studi di Torino, Dipartimento di Chimica I.F.M, Via P. Giuria 7, 10125 Torino, Italy
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46
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A high resolution structure of the putative hinge region in M2 channel-lining segments of the nicotinic acetylcholine receptor. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:2961-70. [DOI: 10.1016/j.bbamem.2007.10.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2007] [Revised: 10/12/2007] [Accepted: 10/15/2007] [Indexed: 02/07/2023]
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47
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Theoretical calculations of hypersurfaces of the 13C chemical shift anisotropy in the CO⋯HN hydrogen bond and the benefit for the ab initio structure determination. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.theochem.2007.08.029] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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48
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Dürr UH, Waskell L, Ramamoorthy A. The cytochromes P450 and b5 and their reductases—Promising targets for structural studies by advanced solid-state NMR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:3235-59. [DOI: 10.1016/j.bbamem.2007.08.007] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2007] [Accepted: 08/08/2007] [Indexed: 02/02/2023]
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49
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Gardiennet-Doucet C, Assfeld X, Henry B, Tekely P. Revealing successive steps of deprotonation of L- phosphoserine through 13C and 31P chemical shielding tensor fingerprints. J Phys Chem A 2007; 110:9137-44. [PMID: 16854026 DOI: 10.1021/jp062184v] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The effects of deprotonation on the (13)C and (31)P chemical shielding tensors of L-O-phosphoserine are revealed by using solid-state NMR spectroscopy and ab initio calculations. The characteristic changes in some principal elements of the (13)C and (31)P chemical shift tensors have been detected during successive steps of deprotonation of carboxyl, phosphate, and amide functional groups. The calculations carried out in a polarizable continuum taking into account the effects of the surroundings have shown their ability to reproduce correctly the changes of the principal values induced by deprotonation and to provide precious information, which is very difficult to obtain experimentally, about the concurrent changes in the orientation of chemical shielding tensors in the molecular frame. The experimentally observed subtle effects related to the deprotonation-induced modifications of intermolecular contacts involving hydrogen bonding as well as the influence of counterions on the (13)C and (31)P principal elements of the chemical shift tensors are also discussed.
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Affiliation(s)
- Carole Gardiennet-Doucet
- Méthodologie RMN, UMR CNRS 7565, Université Henri Poincaré, Nancy 1, 54506 Vandoeuvre-lès-Nancy, France
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50
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Matsuki Y, Akutsu H, Fujiwara T. Spectral fitting for signal assignment and structural analysis of uniformly 13C-labeled solid proteins by simulated annealing based on chemical shifts and spin dynamics. JOURNAL OF BIOMOLECULAR NMR 2007; 38:325-39. [PMID: 17612797 DOI: 10.1007/s10858-007-9170-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2007] [Accepted: 05/24/2007] [Indexed: 05/16/2023]
Abstract
We describe an approach for the signal assignment and structural analysis with a suite of two-dimensional (13)C-(13)C magic-angle-spinning solid-state NMR spectra of uniformly (13)C-labeled peptides and proteins. We directly fit the calculated spectra to experimental ones by simulated annealing in restrained molecular dynamics program CNS as a function of atomic coordinates. The spectra are calculated from the conformation dependent chemical shift obtained with SHIFTX and the cross-peak intensities computed for recoupled dipolar interactions. This method was applied to a membrane-bound 14-residue peptide, mastoparan-X. The obtained C', C(alpha) and C(beta) chemical shifts agreed with those reported previously at the precisions of 0.2, 0.7 and 0.4 ppm, respectively. This spectral fitting program also provides backbone dihedral angles with a precision of about 50 degrees from the spectra even with resonance overlaps. The restraints on the angles were improved by applying protein database program TALOS to the obtained chemical shifts. The peptide structure provided by these restraints was consistent with the reported structure at the backbone RMSD of about 1 A.
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Affiliation(s)
- Yoh Matsuki
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871, Japan
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