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Sergeyev IV, Fritzsching K, Rogawski R, McDermott A. Resolution in cryogenic solid state NMR: Challenges and solutions. Protein Sci 2024; 33:e4803. [PMID: 37847566 PMCID: PMC11184935 DOI: 10.1002/pro.4803] [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: 01/20/2023] [Revised: 09/30/2023] [Accepted: 10/03/2023] [Indexed: 10/18/2023]
Abstract
NMR at cryogenic temperatures has the potential to provide rich site-specific details regarding biopolymer structure, function, and mechanistic intermediates. Broad spectral lines compared with room temperature NMR can sometimes present practical challenges. A number of hypotheses regarding the origins of line broadening are explored. One frequently considered explanation is the presence of inhomogeneous conformational distributions. Possibly these arise when the facile characteristic motions that occur near room temperature become dramatically slower or "frozen out" at temperatures below the solvent phase change. Recent studies of low temperature spectra harness the distributions in properties in these low temperature spectra to uncover information regarding the conformational ensembles that drive biological function.
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Affiliation(s)
| | | | - Rivkah Rogawski
- Columbia University, Department of ChemistryNew YorkNew YorkUSA
| | - Ann McDermott
- Columbia University, Department of ChemistryNew YorkNew YorkUSA
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2
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Burakova E, Vasa SK, Linser R. Characterization of conformational heterogeneity via higher-dimensionality, proton-detected solid-state NMR. JOURNAL OF BIOMOLECULAR NMR 2022; 76:197-212. [PMID: 36149571 PMCID: PMC9712413 DOI: 10.1007/s10858-022-00405-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 09/07/2022] [Indexed: 06/16/2023]
Abstract
Site-specific heterogeneity of solid protein samples can be exploited as valuable information to answer biological questions ranging from thermodynamic properties determining fibril formation to protein folding and conformational stability upon stress. In particular, for proteins of increasing molecular weight, however, site-resolved assessment without residue-specific labeling is challenging using established methodology, which tends to rely on carbon-detected 2D correlations. Here we develop purely chemical-shift-based approaches for assessment of relative conformational heterogeneity that allows identification of each residue via four chemical-shift dimensions. High dimensionality diminishes the probability of peak overlap in the presence of multiple, heterogeneously broadened resonances. Utilizing backbone dihedral-angle reconstruction from individual contributions to the peak shape either via suitably adapted prediction routines or direct association with a relational database, the methods may in future studies afford assessment of site-specific heterogeneity of proteins without site-specific labeling.
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Affiliation(s)
- Ekaterina Burakova
- Department of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
- Department of Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Suresh K Vasa
- Department of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
- Department of Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Rasmus Linser
- Department of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany.
- Department of Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany.
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3
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Cerofolini L, Parigi G, Ravera E, Fragai M, Luchinat C. Solid-state NMR methods for the characterization of bioconjugations and protein-material interactions. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2022; 122:101828. [PMID: 36240720 DOI: 10.1016/j.ssnmr.2022.101828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/26/2022] [Accepted: 09/07/2022] [Indexed: 06/16/2023]
Abstract
Protein solid-state NMR has evolved dramatically over the last two decades, with the development of new hardware and sample preparation methodologies. This technique is now ripe for complex applications, among which one can count bioconjugation, protein chemistry and functional biomaterials. In this review, we provide our account on this aspect of protein solid-state NMR.
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Affiliation(s)
- Linda Cerofolini
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Giacomo Parigi
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Magnetic Resonance Center (CERM), Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Enrico Ravera
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Magnetic Resonance Center (CERM), Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy; Florence Data Science, Università degli Studi di Firenze, Italy.
| | - Marco Fragai
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Magnetic Resonance Center (CERM), Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy.
| | - Claudio Luchinat
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Magnetic Resonance Center (CERM), Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy.
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4
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Xu C, Kandel N, Qiao X, Khan MI, Pratakshya P, Tolouei NE, Chen B, Gorodetsky AA. Long-Range Proton Transport in Films from a Reflectin-Derived Polypeptide. ACS APPLIED MATERIALS & INTERFACES 2021; 13:20938-20946. [PMID: 33938723 DOI: 10.1021/acsami.0c18929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Protein- and peptide-based proton conductors have been extensively studied because of their important roles in biological processes and established potential for bioelectronic device applications. However, despite much progress, the demonstration of long-range proton transport for such materials has remained relatively rare. Herein, we fabricate, electrically interrogate, and physically characterize films from a reflectin-derived polypeptide. The electrical measurements indicate that device-integrated films exhibit proton conductivities with values of ∼0.4 mS/cm and sustain proton transport over distances of ∼1 mm. The accompanying physical characterization indicates that the polypeptide possesses characteristics analogous to those of the parent protein class and furnishes insight into the relationship between the polypeptide's electrical functionality and structure in the solid state. When considered together, our findings hold significance for the continued development and engineering of not only reflectin-based materials but also other bioinspired proton conductors.
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Affiliation(s)
- Chengyi Xu
- Department of Materials Science and Engineering, University of California, Irvine, Irvine, California 92697, United States
| | - Nabin Kandel
- Department of Physics, University of Central Florida, Orlando, Florida 32816, United States
| | - Xin Qiao
- Department of Physics, University of Central Florida, Orlando, Florida 32816, United States
| | - Md Imran Khan
- Department of Physics, University of Central Florida, Orlando, Florida 32816, United States
| | - Preeta Pratakshya
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Nadia E Tolouei
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697, United States
| | - Bo Chen
- Department of Physics, University of Central Florida, Orlando, Florida 32816, United States
| | - Alon A Gorodetsky
- Department of Materials Science and Engineering, University of California, Irvine, Irvine, California 92697, United States
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697, United States
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5
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Ghosh R, Kragelj J, Xiao Y, Frederick KK. Cryogenic Sample Loading into a Magic Angle Spinning Nuclear Magnetic Resonance Spectrometer that Preserves Cellular Viability. J Vis Exp 2020:10.3791/61733. [PMID: 32955491 PMCID: PMC7797162 DOI: 10.3791/61733] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Dynamic nuclear polarization (DNP) can dramatically increase the sensitivity of magic angle spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy. These sensitivity gains increase as temperatures decrease and are large enough to enable the study of molecules at very low concentrations at the operating temperatures (~100 K) of most commercial DNP-equipped NMR spectrometers. This leads to the possibility of in-cell structural biology on cryopreserved cells for macromolecules at their endogenous levels in their native environments. However, the freezing rates required for cellular cryopreservation are exceeded during typical sample handling for DNP MAS NMR and this results in loss of cellular integrity and viability. This article describes a detailed protocol for the preparation and cryogenic transfer of a frozen sample of mammalian cells into a MAS NMR spectrometer.
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Affiliation(s)
- Rupam Ghosh
- Department of Biophysics, University of Texas Southwestern Medical Center
| | - Jaka Kragelj
- Department of Biophysics, University of Texas Southwestern Medical Center
| | - Yiling Xiao
- Department of Biophysics, University of Texas Southwestern Medical Center
| | - Kendra K Frederick
- Department of Biophysics, University of Texas Southwestern Medical Center; Center for Alzheimer's and Neurodegenerative Disease and Center for Systems Biology, University of Texas Southwestern Medical Center;
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Damman R, Schütz S, Luo Y, Weingarth M, Sprangers R, Baldus M. Atomic-level insight into mRNA processing bodies by combining solid and solution-state NMR spectroscopy. Nat Commun 2019; 10:4536. [PMID: 31586050 PMCID: PMC6778109 DOI: 10.1038/s41467-019-12402-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 09/09/2019] [Indexed: 01/07/2023] Open
Abstract
Liquid-liquid phase separation is increasingly recognized as a process involved in cellular organization. Thus far, a detailed structural characterization of this intrinsically heterogeneous process has been challenging. Here we combine solid- and solution-state NMR spectroscopy to obtain atomic-level insights into the assembly and maturation of cytoplasmic processing bodies that contain mRNA as well as enzymes involved in mRNA degradation. In detail, we have studied the enhancer of decapping 3 (Edc3) protein that is a central hub for processing body formation in yeast. Our results reveal that Edc3 domains exhibit diverse levels of structural organization and dynamics after liquid-liquid phase separation. In addition, we find that interactions between the different Edc3 domains and between Edc3 and RNA in solution are largely preserved in the condensed protein state, allowing processing bodies to rapidly form and dissociate upon small alterations in the cellular environment.
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Affiliation(s)
- Reinier Damman
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Stefan Schütz
- Department of Biophysics I, University of Regensburg, 93053, Regensburg, Germany
| | - Yanzhang Luo
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Markus Weingarth
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Remco Sprangers
- Department of Biophysics I, University of Regensburg, 93053, Regensburg, Germany.
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
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7
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Structural analysis of the Aβ(11-42) amyloid fibril based on hydrophobicity distribution. J Comput Aided Mol Des 2019; 33:665-675. [PMID: 31292794 PMCID: PMC6687686 DOI: 10.1007/s10822-019-00209-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 05/31/2019] [Indexed: 01/11/2023]
Abstract
The structure of the Aβ(11–42) amyloid available in PDB makes possible the molecular analysis of the specificity of amyloid formation. This molecule (PDB ID 2MVX) is the object of analysis. This work presents the outcome of in silico experiments involving various alternative conformations of the Aβ(11–42) sequence, providing clues as to the amylodogenecity of its constituent fragments. The reference structure (PDB) has been compared with folds generated using I-Tasser and Robetta—the strongest contenders in the CASP challenge. Additionally, a polypeptide which matches the Aβ(11–42) sequence has been subjected to folding simulations based on the fuzzy oil drop model, which favors the production of a monocentric hydrophobic core. Computer simulations yielded 15 distinct structural forma (five per software package), which, when compared to the experimentally determined structure, allow us to study the role of structural elements which cause an otherwise globular protein to transform into an amyloid. The unusual positions of hydrophilic residues disrupting the expected hydrophobic core and propagating linearly along the long axis of fibril is recognized as the seed for amyloidogenic transformation in this polypeptide. This paper discusses the structure of the Aβ(11–42) amyloid fibril, listed in PDB under ID 2MXU (fragment od Aβ(1–42) amyloid).
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8
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König A, Schölzel D, Uluca B, Viennet T, Akbey Ü, Heise H. Hyperpolarized MAS NMR of unfolded and misfolded proteins. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2019; 98:1-11. [PMID: 30641444 DOI: 10.1016/j.ssnmr.2018.12.003] [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: 09/28/2018] [Revised: 12/28/2018] [Accepted: 12/30/2018] [Indexed: 05/09/2023]
Abstract
In this article we give an overview over the use of DNP-enhanced solid-state NMR spectroscopy for the investigation of unfolded, disordered and misfolded proteins. We first provide an overview over studies in which DNP spectroscopy has successfully been applied for the structural investigation of well-folded amyloid fibrils formed by short peptides as well as full-length proteins. Sample cooling to cryogenic temperatures often leads to severe line broadening of resonance signals and thus a loss in resolution. However, inhomogeneous line broadening at low temperatures provides valuable information about residual dynamics and flexibility in proteins, and, in combination with appropriate selective isotope labeling techniques, inhomogeneous linewidths in disordered proteins or protein regions may be exploited for evaluation of conformational ensembles. In the last paragraph we highlight some recent studies where DNP-enhanced MAS-NMR-spectroscopy was applied to the study of disordered proteins/protein regions and inhomogeneous sample preparations.
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Affiliation(s)
- Anna König
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Research Center Jülich, 52425, Jülich, Germany; Institute of Physical Biology, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Daniel Schölzel
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Research Center Jülich, 52425, Jülich, Germany; Institute of Physical Biology, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Boran Uluca
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Research Center Jülich, 52425, Jülich, Germany; Institute of Physical Biology, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Thibault Viennet
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Research Center Jülich, 52425, Jülich, Germany; Institute of Physical Biology, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Ümit Akbey
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Research Center Jülich, 52425, Jülich, Germany; Institute of Physical Biology, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Henrike Heise
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Research Center Jülich, 52425, Jülich, Germany; Institute of Physical Biology, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany.
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9
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Ghosh S, Salama F, Dines M, Lahav A, Adir N. Biophysical and structural characterization of the small heat shock protein HspA from Thermosynechococcus vulcanus in 2 M urea. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:442-452. [PMID: 30711645 DOI: 10.1016/j.bbapap.2018.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 11/29/2018] [Accepted: 12/11/2018] [Indexed: 10/27/2022]
Abstract
Small heat shock proteins (sHSPs) belong to the superfamily of molecular chaperones. They prevent aggregation of partially unfolded or misfolded client proteins, providing protection to organisms under stress conditions. Here, we report the biophysical and structural characterization of a small heat shock protein (HspA) from a thermophilic cyanobacterium Thermosynechococcus vulcanus in the presence of 2 M urea. HspA has been shown to be important for the protection of Photosystem II and the Phycobilisome antenna complex at elevated temperatures. Heterologously expressed HspA requires the presence of 1-2 M urea to maintain its solubility at concentrations required for most characterization methods. Spectroscopic studies reveal the presence of the β-sheet structure and intactness of the tertiary fold in HspA. In vitro assays show that the HspA maintains chaperone-like activity in protecting soluble proteins from thermal aggregation. Chromatography and electron microscopy show that the HspA exists as a mixture of oligomeric forms in the presence of 2 M urea. HspA was successfully crystallized only in the presence of 2 M urea. The crystal structure of HspA shows urea-induced loss of about 30% of the secondary structure without major alteration in the tertiary structure of the protein. The electron density maps reveal changes in the hydrogen bonding network which we attribute to the presence of urea. The crystal structure of HspA demonstrates a mixture of both direct interactions between urea and protein functionalities and interactions between urea and the surrounding solvent that indirectly affect the protein, which are in accordance with previously published studies.
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Affiliation(s)
- Sudeshna Ghosh
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Technion City, Haifa 32000, Israel
| | - Faris Salama
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Technion City, Haifa 32000, Israel
| | - Monica Dines
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Technion City, Haifa 32000, Israel
| | - Avital Lahav
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Technion City, Haifa 32000, Israel
| | - Noam Adir
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Technion City, Haifa 32000, Israel.
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10
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de sa Peixoto P, Roiland C, Thomas D, Briard-Bion V, Le Guellec R, Parayre S, Deutsch SM, Jan G, Guyomarc'h F. Recrystallized S-layer protein of a probiotic Propionibacterium: structural and nanomechanical changes upon temperature or pH shifts probed by solid-state NMR and AFM. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 31:199-208. [PMID: 25479375 DOI: 10.1021/la503735z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Surface protein layers (S layers) are common constituents of the bacterial cell wall and originate from the assembly of strain-dependent surface layer proteins (Slps). These proteins are thought to play important roles in the bacteria's biology and to have very promising technological applications as biomaterials or as part of cell-host cross-talk in probiotic mechanism. The SlpA from Propionibacterium freudenreichii PFCIRM 118 strain was isolated and recrystallized to investigate organization and assembly of the protein using atomic force microscopy and solid-state (1)H and (13)C-nuclear magnetic resonance. SlpA was found to form hexagonal p1 monolayer lattices where the protein exhibited high proportions of disordered regions and of bound water. The lattice structure was maintained, but softened, upon mild heating or acidification, probably in relation with the increasing mobilities of the disordered protein regions. These results gave structural insights on the mobile protein regions exposed by S layer films, upon physiologically relevant changes of their environmental conditions.
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Affiliation(s)
- Paulo de sa Peixoto
- INRA-AGROCAMPUS OUEST UMR 1253 Science et Technologie du Lait et de l'Œuf, 35042 Rennes, France
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11
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Iyer LK, Moorthy BS, Topp EM. Photolytic labeling to probe molecular interactions in lyophilized powders. Mol Pharm 2013; 10:4629-39. [PMID: 24125175 DOI: 10.1021/mp4004332] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Local side-chain interactions in lyophilized protein formulations were mapped using solid-state photolytic labeling-mass spectrometry (ssPL-MS). Photoactive amino acid analogues (PAAs) were used as probes and either added to the lyophilized matrix or incorporated within the amino acid sequence of a peptide. In the first approach, apomyoglobin was lyophilized with sucrose and varying concentrations of photoleucine (L-2-amino-4,4'-azipentanoic acid; pLeu). The lyophilized solid was irradiated at 365 nm to initiate photolabeling. The rate and extent of labeling were measured using electrospray ionization/high-performance liquid chromatography/mass spectrometry (ESI-HPLC-MS), with labeling reaching a plateau at ~30 min, forming up to six labeled populations. Bottom-up MS/MS analysis was able to provide peptide-level resolution of the location of pLeu. ssPL-MS was also able to detect differences in side-chain environment between sucrose and guanidine hydrochloride formulations. In the second approach, peptide GCG (1-8)* containing p-benzoyl-L-phenylalanine (pBpA) in the amino acid sequence was lyophilized with various excipients and irradiated. Peptide-peptide and peptide-excipient adducts were detected using MS. Top-down MS/MS on the peptide dimer provided amino acid-level resolution regarding interactions and the cross-linking partner for pBpA in the solid state. The results show that ssPL-MS can provide high-resolution information about protein interactions in the lyophilized environment.
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Affiliation(s)
- Lavanya K Iyer
- Department of Industrial and Physical Pharmacy, Purdue University , West Lafayette, Indiana 47901, United States
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12
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Kotecha M, Klatt D, Magin RL. Monitoring cartilage tissue engineering using magnetic resonance spectroscopy, imaging, and elastography. TISSUE ENGINEERING PART B-REVIEWS 2013; 19:470-84. [PMID: 23574498 DOI: 10.1089/ten.teb.2012.0755] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A key technical challenge in cartilage tissue engineering is the development of a noninvasive method for monitoring the composition, structure, and function of the tissue at different growth stages. Due to its noninvasive, three-dimensional imaging capabilities and the breadth of available contrast mechanisms, magnetic resonance imaging (MRI) techniques can be expected to play a leading role in assessing engineered cartilage. In this review, we describe the new MR-based tools (spectroscopy, imaging, and elastography) that can provide quantitative biomarkers for cartilage tissue development both in vitro and in vivo. Magnetic resonance spectroscopy can identify the changing molecular structure and alternations in the conformation of major macromolecules (collagen and proteoglycans) using parameters such as chemical shift, relaxation rates, and magnetic spin couplings. MRI provides high-resolution images whose contrast reflects developing tissue microstructure and porosity through changes in local relaxation times and the apparent diffusion coefficient. Magnetic resonance elastography uses low-frequency mechanical vibrations in conjunction with MRI to measure soft tissue mechanical properties (shear modulus and viscosity). When combined, these three techniques provide a noninvasive, multiscale window for characterizing cartilage tissue growth at all stages of tissue development, from the initial cell seeding of scaffolds to the development of the extracellular matrix during construct incubation, and finally, to the postimplantation assessment of tissue integration in animals and patients.
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Affiliation(s)
- Mrignayani Kotecha
- Department of Bioengineering, University of Illinois at Chicago , Chicago, Illinois
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13
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Shaghaghi H, Ebrahimi HP, Bahrami Panah N, Tafazzoli M. Layer selection effect on solid state 13C and 15N chemical shifts calculation using ONIOM approach. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2013; 51-52:31-36. [PMID: 23414630 DOI: 10.1016/j.ssnmr.2013.01.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 01/15/2013] [Accepted: 01/21/2013] [Indexed: 06/01/2023]
Abstract
Solid state (13)C and (15)N chemical shifts of uracil and imidazole have been calculated using a 2-layer ONIOM approach at 32 levels of theory. The effect of electron correlation between two layers has been investigated by choosing two different kinds of layer selection. Factorial design has been applied as a multivariate technique to analyze the effect of wave function and layer selection on solid state (13)C and (15)N chemical shifts calculations. PBEPBE/6-311+G(d,p) was recommended as an optimally selected level of theory for high layer in both models. It is illustrated that considering the electron correlation of two layers of ONIOM models is important factor to calculate solid state (15)N chemical shifts. The agreement between the calculated and experimental values of solid state (13)C and (15)N chemical shifts using ONIOM (PBEPBE/6-311+G(d,p):AM1) for both uracil and imidazole confirmed the reliability of the selected wave functions and layer selection.
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Affiliation(s)
- Hoora Shaghaghi
- Department of Chemistry, Sharif University of Technology, Tehran, Iran
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14
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Comellas G, Lemkau LR, Zhou DH, George JM, Rienstra CM. Structural intermediates during α-synuclein fibrillogenesis on phospholipid vesicles. J Am Chem Soc 2012; 134:5090-9. [PMID: 22352310 PMCID: PMC3331674 DOI: 10.1021/ja209019s] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
α-Synuclein (AS) fibrils are the main protein component of Lewy bodies, the pathological hallmark of Parkinson's disease and other related disorders. AS forms helices that bind phospholipid membranes with high affinity, but no atomic level data for AS aggregation in the presence of lipids is yet available. Here, we present direct evidence of a conversion from α-helical conformation to β-sheet fibrils in the presence of anionic phospholipid vesicles and direct conversion to β-sheet fibrils in their absence. We have trapped intermediate states throughout the fibril formation pathways to examine the structural changes using solid-state NMR spectroscopy and electron microscopy. The comparison between mature AS fibrils formed in aqueous buffer and those derived in the presence of anionic phospholipids demonstrates no major changes in the overall fibril fold. However, a site-specific comparison of these fibrillar states demonstrates major perturbations in the N-terminal domain with a partial disruption of the long β-strand located in the 40s and small perturbations in residues located in the "non-β amyloid component" (NAC) domain. Combining all these results, we propose a model for AS fibrillogenesis in the presence of phospholipid vesicles.
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Affiliation(s)
- Gemma Comellas
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Luisel R. Lemkau
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Donghua H. Zhou
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Julia M. George
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Chad M. Rienstra
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
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15
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Su Y, Hong M. Conformational disorder of membrane peptides investigated from solid-state NMR line widths and line shapes. J Phys Chem B 2011; 115:10758-67. [PMID: 21806038 PMCID: PMC3222302 DOI: 10.1021/jp205002n] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A challenge in the application of solid-state NMR spectroscopy to membrane peptides and proteins is the relatively broad line widths compared to those for solution NMR spectra. To understand the linewidth contributions to membrane protein NMR spectra, we have measured the inhomogeneous and homogeneous line widths of several well-studied membrane peptides under immobilized conditions. (13)C T(2) relaxation times of uniformly (13)C-labeled residues show that the homogeneous line widths of the peptides are comparable to those of crystalline model compounds under identical (1)H decoupling and magic angle spinning conditions, indicating that the homogeneous line widths are determined by conformation-independent factors, including residual dipolar coupling, J-coupling, and intrinsic T(2) relaxation. However, the membrane peptides exhibit larger apparent line widths than the crystalline compounds, indicating conformational disorder. A cationic cell-penetrating peptide, the human immunodeficiency virus TAT, exhibits the largest apparent line widths, which are about five-fold larger than the homogeneous line widths, while the transmembrane helix of the influenza M2 peptide and the β-hairpin antimicrobial peptide PG-1 show moderately larger apparent line widths than the crystalline compounds. These results are consistent with the random coil nature of the TAT peptide, which contrasts with the intramolecularly hydrogen bonded M2 and PG-1. Cross peak line shapes of 2D double-quantum correlation spectra show that the conformational disorder can occur at the residue level and can result from three origins, lipid-peptide interaction, intrinsic conformational disorder encoded in the amino acid sequence, and side-chain rotameric averaging. A particularly important lipid-peptide interaction for cationic membrane peptides is guanidinium-phosphate ion pair interaction. Thus, NMR line widths and line shapes are useful for understanding the conformational disorder of membrane peptides and proteins.
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Affiliation(s)
- Yongchao Su
- Department of Chemistry, Iowa State University, Ames, IA 50011
| | - Mei Hong
- Department of Chemistry, Iowa State University, Ames, IA 50011
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16
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Xu J, Smith PES, Soong R, Ramamoorthy A. A proton spin diffusion based solid-state NMR approach for structural studies on aligned samples. J Phys Chem B 2011; 115:4863-71. [PMID: 21466219 PMCID: PMC3085961 DOI: 10.1021/jp201501q] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Rapidly expanding research on nonsoluble and noncrystalline chemical and biological materials necessitates sophisticated techniques to image these materials at atomic-level resolution. Although their study poses a formidable challenge, solid-state NMR is a powerful tool that has demonstrated application to the investigation of their molecular architecture and functioning. In particular, 2D separated-local-field (SLF) spectroscopy is increasingly applied to obtain high-resolution molecular images of these materials. However, despite the common use of SLF experiments in the structural studies of a variety of aligned molecules, the lack of a resonance assignment approach has been a major disadvantage. As a result, solid-state NMR studies have mostly been limited to aligned systems that are labeled with an isotope at a single site. Here, we demonstrate an approach for resonance assignment through a controlled reintroduction of proton spin diffusion in the 2D proton-evolved-local-field (PELF) pulse sequence. Experimental results and simulations suggest that the use of spin diffusion also enables the measurement of long-range heteronuclear dipolar couplings that can be used as additional constraints in the structural and dynamical studies of aligned molecules. The new method is used to determine the de novo atomic-level resolution structure of a liquid crystalline material, N-(4-methoxybenzylidene)-4-butylaniline, and its use on magnetically aligned bicelles is also demonstrated. We expect this technique to also be valuable in the structural studies of functional molecules like columnar liquid crystals and other biomaterials.
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Affiliation(s)
- Jiadi Xu
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055
| | - Pieter E. S. Smith
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055
| | - Ronald Soong
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055
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17
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Chen J, Rempel DL, Gross ML. Temperature jump and fast photochemical oxidation probe submillisecond protein folding. J Am Chem Soc 2011; 132:15502-4. [PMID: 20958033 DOI: 10.1021/ja106518d] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report a new mass-spectrometry-based approach for studying protein-folding dynamics on the submillisecond time scale. The strategy couples a temperature jump with fast photochemical oxidation of proteins (FPOP), whereby folding/unfolding is followed by changes in oxidative modifications by OH radical reactions. Using a flow system containing the protein barstar as a model, we altered the protein's equilibrium conformation by applying the temperature jump and demonstrated that its reactivity with OH free radicals serves as a reporter of the conformational change. Furthermore, we found that the time-dependent increase in mass resulting from free-radical oxidation is a measure of the rate constant for the transition from the unfolded to the first intermediate state. This advance offers the promise that, when extended with mass-spectrometry-based proteomic analysis, the sites and kinetics of folding/unfolding can also be followed on the submillisecond time scale.
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Affiliation(s)
- Jiawei Chen
- Department of Chemistry, Washington University, One Brookings Drive, Saint Louis, Missouri 63130, United States
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18
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Etzkorn M, Böckmann A, Baldus M. Kinetic analysis of protein aggregation monitored by real-time 2D solid-state NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2011; 49:121-129. [PMID: 21253842 PMCID: PMC3042102 DOI: 10.1007/s10858-011-9468-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Accepted: 01/01/2011] [Indexed: 05/30/2023]
Abstract
It is shown that real-time 2D solid-state NMR can be used to obtain kinetic and structural information about the process of protein aggregation. In addition to the incorporation of kinetic information involving intermediate states, this approach can offer atom-specific resolution for all detectable species. The analysis was carried out using experimental data obtained during aggregation of the 10.4 kDa Crh protein, which has been shown to involve a partially unfolded intermediate state prior to aggregation. Based on a single real-time 2D (13)C-(13)C transition spectrum, kinetic information about the refolding and aggregation step could be extracted. In addition, structural rearrangements associated with refolding are estimated and several different aggregation scenarios were compared to the experimental data.
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Affiliation(s)
- Manuel Etzkorn
- Department of NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
- Present Address: Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Ave, Boston, MA 02115 USA
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS-UCBL, Université de Lyon, 7, passage du Vercors, 69367 Lyon, France
| | - Marc Baldus
- Department of NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 Utrecht, The Netherlands
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19
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Koch K, Afonin S, Ieronimo M, Berditsch M, Ulrich AS. Solid-State 19F-NMR of Peptides in Native Membranes. Top Curr Chem (Cham) 2011; 306:89-118. [DOI: 10.1007/128_2011_162] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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