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Tomiyama R, So M, Yamaguchi K, Miyanoiri Y, Sakurai K. The residual structure of acid-denatured β 2 -microglobulin is relevant to an ordered fibril morphology. Protein Sci 2023; 32:e4487. [PMID: 36321362 PMCID: PMC9793977 DOI: 10.1002/pro.4487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/15/2022] [Accepted: 10/29/2022] [Indexed: 11/09/2022]
Abstract
β2 -Microglobulin (β2m) forms amyloid fibrils in vitro under acidic conditions. Under these conditions, the residual structure of acid-denatured β2m is relevant to seeding and fibril extension processes. Disulfide (SS) bond-oxidized β2m has been shown to form rigid, ordered fibrils, whereas SS bond-reduced β2m forms curvy, less-ordered fibrils. These findings suggest that the presence of an SS bond affects the residual structure of the monomer, which subsequently influences the fibril morphology. To clarify this process, we herein performed NMR experiments. The results obtained revealed that oxidized β2m contained a residual structure throughout the molecule, including the N- and C-termini, whereas the residual structure of the reduced form was localized and other regions had a random coil structure. The range of the residual structure in the oxidized form was wider than that of the fibril core. These results indicate that acid-denatured β2m has variable conformations. Most conformations in the ensemble cannot participate in fibril formation because their core residues are hidden by residual structures. However, when hydrophobic residues are exposed, polypeptides competently form an ordered fibril. This conformational selection phase may be needed for the ordered assembly of amyloid fibrils.
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Affiliation(s)
- Ryosuke Tomiyama
- Graduate School of Biology‐oriented Science and TechnologyKindai UniversityWakayamaJapan
| | - Masatomo So
- Institute for Protein ResearchOsaka UniversityOsakaJapan,Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsUK
| | - Keiichi Yamaguchi
- Global Center for Medical Engineering and InformaticsOsaka UniversitySuitaJapan
| | | | - Kazumasa Sakurai
- Graduate School of Biology‐oriented Science and TechnologyKindai UniversityWakayamaJapan,High Pressure Protein Research Center, Institute of Advanced TechnologyKindai UniversityWakayamaJapan
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2
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Hunashal Y, Percipalle M, Molnár T, Kardos J, Percipalle P, Esposito G. Approaching Protein Aggregation and Structural Dynamics by Equilibrium and Nonequilibrium Paramagnetic Perturbation. Anal Chem 2022; 94:10949-10958. [PMID: 35877130 DOI: 10.1021/acs.analchem.2c00751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
PENELOP (Paramagnetic Equilibrium vs Nonequilibrium magnetization Enhancement or LOss Perturbation) is the presented nuclear magnetic resonance (NMR) approach to identify at once the location of proteins' exposed surface, hindered accessibility, and exchange processes occurring on a μs-ms time scale. In addition to mapping the protein surface accessibility, the application of this method under specific conditions makes it possible to distinguish conformational mobility and chemical exchange processes, thereby providing an alternative to characterization by more demanding techniques (transverse relaxation dispersion, saturation transfer, and high-pressure NMR). Moreover, its high sensitivity enables studying samples at low, physiologically more relevant concentrations. Association, dynamics, and oligomerization are addressed by PENELOP for a component of SARS-CoV-2 replication transcription complex and an amyloidogenic protein.
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Affiliation(s)
- Yamanappa Hunashal
- Chemistry Program, Science Division, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates.,Dipartimento di Area Medica, Universita' di Udine, P.le Kolbe 4, 33100 Udine, Italy
| | - Mathias Percipalle
- Chemistry Program, Science Division, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates.,Department of Chemistry and Magnetic Resonance Center, University of Florence, 50019 Florence, Italy
| | - Tamás Molnár
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest 1117, Hungary
| | - Jòzsef Kardos
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest 1117, Hungary
| | - Piergiorgio Percipalle
- Biology Program, Science Division, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates.,Department of Molecular Bioscience, The Wenner Gren Institute Stockholm University, Stockholm SE-106 91, Sweden
| | - Gennaro Esposito
- Chemistry Program, Science Division, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates.,INBB, Viale Medaglie d'Oro 305, Roma 00136, Italy
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3
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Fernando LD, Dickwella Widanage MC, Penfield J, Lipton AS, Washton N, Latgé JP, Wang P, Zhang L, Wang T. Structural Polymorphism of Chitin and Chitosan in Fungal Cell Walls From Solid-State NMR and Principal Component Analysis. Front Mol Biosci 2021; 8:727053. [PMID: 34513930 PMCID: PMC8423923 DOI: 10.3389/fmolb.2021.727053] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 08/10/2021] [Indexed: 12/15/2022] Open
Abstract
Chitin is a major carbohydrate component of the fungal cell wall and a promising target for novel antifungal agents. However, it is technically challenging to characterize the structure of this polymer in native cell walls. Here, we recorded and compared 13C chemical shifts of chitin using isotopically enriched cells of six Aspergillus, Rhizopus, and Candida strains, with data interpretation assisted by principal component analysis (PCA) and linear discriminant analysis (LDA) methods. The structure of chitin is found to be intrinsically heterogeneous, with peak multiplicity detected in each sample and distinct fingerprints observed across fungal species. Fungal chitin exhibits partial similarity to the model structures of α- and γ-allomorphs; therefore, chitin structure is not significantly affected by interactions with other cell wall components. Addition of antifungal drugs and salts did not significantly perturb the chemical shifts, revealing the structural resistance of chitin to external stress. In addition, the structure of the deacetylated form, chitosan, was found to resemble a relaxed two-fold helix conformation. This study provides high-resolution information on the structure of chitin and chitosan in their cellular contexts. The method is applicable to the analysis of other complex carbohydrates and polymer composites.
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Affiliation(s)
- Liyanage D Fernando
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, United States
| | | | - Jackson Penfield
- Department of Chemical Engineering, Tennessee Technological University, Cookeville, TN, United States
| | - Andrew S Lipton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Nancy Washton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Jean-Paul Latgé
- Unité des Aspergillus, Département de Mycologie, Institut Pasteur, Paris, France
| | - Ping Wang
- Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Liqun Zhang
- Department of Chemical Engineering, Tennessee Technological University, Cookeville, TN, United States
| | - Tuo Wang
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, United States
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4
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NMR-Guided Repositioning of Non-Steroidal Anti-Inflammatory Drugs into Tight Junction Modulators. Int J Mol Sci 2021; 22:ijms22052583. [PMID: 33806674 PMCID: PMC7961873 DOI: 10.3390/ijms22052583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 02/26/2021] [Accepted: 02/27/2021] [Indexed: 12/24/2022] Open
Abstract
Bioavailability is a major bottleneck in the clinical application of medium molecular weight therapeutics, including protein and peptide drugs. Paracellular transport of these molecules is hampered by intercellular tight junction (TJ) complexes. Therefore, safe chemical regulators for TJ loosening are desired. Here, we showed a potential application of select non-steroidal anti-inflammatory drugs (NSAIDs) as TJ modulators. Based on our previous observation that diclofenac and flufenamic acid directly bound various PDZ domains with a broad specificity, we applied solution nuclear magnetic resonance techniques to examine the interaction of other NSAIDs and the first PDZ domain (PDZ1) of zonula occludens (ZO)-1, ZO-1(PDZ1). Inhibition of ZO-1(PDZ1) is expected to provide loosening of the epithelial barrier function because the domain plays a crucial role in maintaining TJ integrity. Accordingly, diclofenac and indomethacin were found to decrease the subcellular localization of claudin (CLD)-2 but not occludin and ZO-1 at the apicolateral intercellular compartment of Madin–Darby canine kidney (MDCK) II cells. These NSAIDs exhibited 125–155% improved paracellular efflux of fluorescein isothiocyanate insulin for the Caco-2 cell monolayer. We propose that these NSAIDs can be repurposed as drug absorption enhancers for peptide drugs.
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Ivanova MI, Lin Y, Lee YH, Zheng J, Ramamoorthy A. Biophysical processes underlying cross-seeding in amyloid aggregation and implications in amyloid pathology. Biophys Chem 2021; 269:106507. [PMID: 33254009 PMCID: PMC10317075 DOI: 10.1016/j.bpc.2020.106507] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/13/2020] [Accepted: 11/13/2020] [Indexed: 12/18/2022]
Abstract
Abnormal aggregation of proteins into filamentous aggregates commonly associates with many diseases, such as Alzheimer's disease, Parkinson's disease and type-2 diabetes. These filamentous aggregates, also known as amyloids, can propagate their abnormal structures to either the same precursor molecules (seeding) or other protein monomers (cross-seeding). Cross-seeding has been implicated in the abnormal protein aggregation and has been found to facilitate the formation of physiological amyloids. It has risen to be an exciting area of research with a high volume of published reports. In this review article, we focus on the biophysical processes underlying the cross-seeding for some of the most commonly studied amyloid proteins. Here we will discuss the relevant literature related to cross-seeded polymerization of amyloid-beta, human islet amyloid polypeptide (hIAPP, or also known as amylin) and alpha-synuclein. SEVI (semen-derived enhancer of viral infection) amyloid formation by the cross-seeding between the bacterial curli protein and PAP248-286 is also briefly discussed.
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Affiliation(s)
- Magdalena I Ivanova
- Neurology, University of Michigan, Ann Arbor, MI 48109, USA; Biophysics, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Yuxi Lin
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Ochang, Chungbuk 28119, South Korea
| | - Young-Ho Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Ochang, Chungbuk 28119, South Korea; Bio-Analytical Science, University of Science and Technology, Daejeon 34113, South Korea; Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 34134, South Korea; Research headquarters, Korea Brain Research Institute, Daegu 41068, South Korea
| | - Jie Zheng
- Department of Chemical and Biomolecular Engineering, The University of Akron, Ohio, USA
| | - Ayyalusamy Ramamoorthy
- Biophysics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA; Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI 48109, USA; Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA.
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6
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Iwaya N, Goda N, Matsuzaki M, Narita A, Shigemitsu Y, Tenno T, Abe Y, Hoshi M, Hiroaki H. Principal component analysis of data from NMR titration experiment of uniformly 15N labeled amyloid beta (1-42) peptide with osmolytes and phenolic compounds. Arch Biochem Biophys 2020; 690:108446. [PMID: 32593678 DOI: 10.1016/j.abb.2020.108446] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 05/11/2020] [Accepted: 06/01/2020] [Indexed: 10/24/2022]
Abstract
A simple NMR method to analyze the data obtained by NMR titration experiment of amyloid formation inhibitors against uniformly 15N-labeled amyloid-β 1-42 peptide (Aβ(1-42)) was described. By using solution nuclear magnetic resonance (NMR) measurement, the simplest method for monitoring the effects of Aβ fibrilization inhibitors is the NMR chemical shift perturbation (CSP) experiment using 15N-labeled Aβ(1-42). However, the flexible and dynamic nature of Aβ(1-42) monomer may hamper the interpretation of CSP data. Here we introduced principal component analysis (PCA) for visualizing and analyzing NMR data of Aβ(1-42) in the presence of amyloid inhibitors including high concentration osmolytes. We measured 1H-15N 2D spectra of Aβ(1-42) at various temperatures as well as of Aβ(1-42) with several inhibitors, and subjected all the data to PCA (PCA-HSQC). The PCA diagram succeeded in differentiating the various amyloid inhibitors, including epigallocatechin gallate (EGCg), rosmarinic acid (RA) and curcumin (CUR) from high concentration osmolytes. We hypothesized that the CSPs reflected the conformational equilibrium of intrinsically disordered Aβ(1-42) induced by weak inhibitor binding rather than the specific molecular interactions.
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Affiliation(s)
- Naoko Iwaya
- Research Fellowship for Young Scientists, Japan Society for the Promotion of Science, Japan; Laboratory of Structural Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Furocho, Chikusa-ku, Nagoya, 464-8601, Japan.
| | - Natsuko Goda
- Laboratory of Structural Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Furocho, Chikusa-ku, Nagoya, 464-8601, Japan.
| | - Mizuki Matsuzaki
- Structural Biology Research Center and Division of Biological Sciences, Graduate School of Science, Nagoya University, Furocho, Chikusa-ku, Nagoya, 464-8601, Japan.
| | - Akihiro Narita
- Structural Biology Research Center and Division of Biological Sciences, Graduate School of Science, Nagoya University, Furocho, Chikusa-ku, Nagoya, 464-8601, Japan.
| | - Yoshiki Shigemitsu
- Laboratory of Structural Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Furocho, Chikusa-ku, Nagoya, 464-8601, Japan; School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuda, 4259, Midori-ku, Yokohama, Kanagawa, 226-8503, Japan.
| | - Takeshi Tenno
- Laboratory of Structural Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Furocho, Chikusa-ku, Nagoya, 464-8601, Japan; Structural Biology Research Center and Division of Biological Sciences, Graduate School of Science, Nagoya University, Furocho, Chikusa-ku, Nagoya, 464-8601, Japan.
| | - Yoshito Abe
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan.
| | - Minako Hoshi
- Institute of Biomedical Research and Innovation, Kobe, 650-0047, Japan.
| | - Hidekazu Hiroaki
- Laboratory of Structural Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Furocho, Chikusa-ku, Nagoya, 464-8601, Japan; Structural Biology Research Center and Division of Biological Sciences, Graduate School of Science, Nagoya University, Furocho, Chikusa-ku, Nagoya, 464-8601, Japan.
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Loosening of Side-Chain Packing Associated with Perturbations in Peripheral Dynamics Induced by the D76N Mutation of β 2-Microglobulin Revealed by Pressure-NMR and Molecular Dynamic Simulations. Biomolecules 2019; 9:biom9090491. [PMID: 31527472 PMCID: PMC6769805 DOI: 10.3390/biom9090491] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 09/09/2019] [Accepted: 09/11/2019] [Indexed: 01/24/2023] Open
Abstract
β2-Microglobulin (β2m) is the causative protein of dialysis-related amyloidosis, and its D76N variant is less stable and more prone to aggregation. Since their crystal structures are indistinguishable from each other, enhanced amyloidogenicity induced by the mutation may be attributed to changes in the structural dynamics of the molecule. We examined pressure and mutation effects on the β2m molecule by NMR and MD simulations, and found that the mutation induced the loosening of the inter-sheet packing of β2m, which is relevant to destabilization and subsequent amyloidogenicity. On the other hand, this loosening was coupled with perturbed dynamics at some peripheral regions. The key result for this conclusion was that both the mutation and pressure induced similar reductions in the mobility of these residues, suggesting that there is a common mechanism underlying the suppression of inherent fluctuations in the β2m molecule. Analyses of data obtained under high pressure conditions suggested that the network of dynamically correlated residues included not only the mutation site, but also distal residues, such as those of the C- and D-strands. Reductions in these local dynamics correlated with the loosening of inter-sheet packing.
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Kumar N, Marx D. How do ribozymes accommodate additional water molecules upon hydrostatic compression deep into the kilobar pressure regime? Biophys Chem 2019; 252:106192. [DOI: 10.1016/j.bpc.2019.106192] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/23/2019] [Accepted: 05/23/2019] [Indexed: 12/19/2022]
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