1
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Ghosh S, Sepay N, Banerji B. Crystal to Hydrogel Transformation in S-Benzyl-L-Cysteine-Containing Cyclic Dipeptides - Nanostructure Elucidation and Applications. Chemistry 2024:e202401874. [PMID: 38853148 DOI: 10.1002/chem.202401874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 06/06/2024] [Accepted: 06/07/2024] [Indexed: 06/11/2024]
Abstract
Cyclic dipeptides (CDPs) are crucial building blocks for a range of functional nanomaterials due to their simple chemical structure and high molecular stability. In this investigation, we synthesized a set of S-benzyl-L-cysteine-based CDPs (designated as P1-P6) and thoroughly examined their self-assembly behavior in a methanol-water solvent to elucidate the relationship between their structure and gelation properties. The hydrophobicity of the amino acids within the CDPs was gradually increased. The present study employed a comprehensive array of analytical techniques, including NMR, FT-IR, AFM, thioflavin-T, congo-red CD, X-ray crystallography, and biophysical calculations like Hirshfield Surface analysis and DFT analysis. These methods revealed that in addition to hydrogen bonding, the hydrophobic nature of the amino acid side chain significantly influences the propensity of CDPs to form hydrogels. Each CDP yielded distinct nanofibrillar networks rich in β-sheet structures, showcasing unique morphological features. Moreover, we explored the practical application of these CDP-based hydrogels in water purification by utilizing them to remove harmful organic dyes from contaminated water. This application underscores the potential of CDPs in addressing environmental challenges, offering a promising avenue for the future development of these materials in water treatment technologies.
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Affiliation(s)
- Saswati Ghosh
- Organic & Medicinal Chemistry Division, Indian Institute of Chemical Biology (CSIR-IICB), 4-Raja S. C. Mullick Road, Kolkata, 700032, India
| | - Nayim Sepay
- Department of Chemistry, Lady Brabourne College, Suhrawardy Ave, Beniapukur, Kolkata, West Bengal, 700017, India
| | - Biswadip Banerji
- Organic & Medicinal Chemistry Division, Indian Institute of Chemical Biology (CSIR-IICB), 4-Raja S. C. Mullick Road, Kolkata, 700032, India
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2
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Rajan R, Matsumura K. Design of self-assembled glycopolymeric zwitterionic micelles as removable protein stabilizing agents. NANOSCALE ADVANCES 2023; 5:1767-1775. [PMID: 36926568 PMCID: PMC10012880 DOI: 10.1039/d3na00002h] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 02/20/2023] [Indexed: 06/15/2023]
Abstract
Developing stabilizers that protect proteins from denaturation under stress, and are easy to remove from solutions, is a challenge in protein therapeutics. In this study, micelles made of trehalose, a zwitterionic polymer (poly-sulfobetaine; poly-SPB), and polycaprolactone (PCL) were synthesized by a one-pot reversible addition-fragmentation chain-transfer (RAFT) polymerization reaction. The micelles protect lactate dehydrogenase (LDH) and human insulin from denaturation due to stresses like thermal incubation and freezing, and help them retain higher-order structures. Importantly, the protected proteins are readily isolated from the micelles by ultracentrifugation, with over 90% recovery, and almost all enzymatic activity is retained. This suggests the great potential of poly-SPB-based micelles for use in applications requiring protection and removal as required. The micelles may also be used to effectively stabilize protein-based vaccines and drugs.
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Affiliation(s)
- Robin Rajan
- School of Materials Science, Japan Advanced Institute of Science and Technology 1-1 Asahidai Nomi Ishikawa 923-1292 Japan
| | - Kazuaki Matsumura
- School of Materials Science, Japan Advanced Institute of Science and Technology 1-1 Asahidai Nomi Ishikawa 923-1292 Japan
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3
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Yanaka S, Yagi-Utsumi M, Kato K, Kuwajima K. The B domain of protein A retains residual structures in 6 M guanidinium chloride as revealed by hydrogen/deuterium-exchange NMR spectroscopy. Protein Sci 2023; 32:e4569. [PMID: 36659853 PMCID: PMC9926473 DOI: 10.1002/pro.4569] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 01/10/2023] [Accepted: 01/13/2023] [Indexed: 01/21/2023]
Abstract
The characterization of residual structures persistent in unfolded proteins is an important issue in studies of protein folding, because the residual structures present, if any, may form a folding initiation site and guide the subsequent folding reactions. Here, we studied the residual structures of the isolated B domain (BDPA) of staphylococcal protein A in 6 M guanidinium chloride. BDPA is a small three-helix-bundle protein, and until recently its folding/unfolding reaction has been treated as a simple two-state process between the native and the fully unfolded states. We employed a dimethylsulfoxide (DMSO)-quenched hydrogen/deuterium (H/D)-exchange 2D NMR techniques with the use of spin desalting columns, which allowed us to investigate the H/D-exchange behavior of individually identified peptide amide (NH) protons. We obtained H/D-exchange protection factors of the 21 NH protons that form an α-helical hydrogen bond in the native structure, and the majority of these NH protons were significantly protected with a protection factor of 2.0-5.2 in 6 M guanidinium chloride, strongly suggesting that these weakly protected NH protons form much stronger hydrogen bonds under native folding conditions. The results can be used to deduce the structure of an early folding intermediate, when such an intermediate is shown by other methods. Among three native helical regions, the third helix in the C-terminal side was highly protected and stabilized by side-chain salt bridges, probably acting as the folding initiation site of BDPA. The present results are discussed in relation to previous experimental and computational findings on the folding mechanisms of BDPA.
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Affiliation(s)
- Saeko Yanaka
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, Myodaiji, Okazaki, Aichi, Japan.,Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), Myodaiji, Okazaki, Aichi, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, Mizuho-ku, Nagoya, Aichi, Japan
| | - Maho Yagi-Utsumi
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, Myodaiji, Okazaki, Aichi, Japan.,Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), Myodaiji, Okazaki, Aichi, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, Mizuho-ku, Nagoya, Aichi, Japan
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, Myodaiji, Okazaki, Aichi, Japan.,Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), Myodaiji, Okazaki, Aichi, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, Mizuho-ku, Nagoya, Aichi, Japan
| | - Kunihiro Kuwajima
- Department of Physics, School of Science, University of Tokyo, Bunkyo-ku, Tokyo, Japan
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4
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Rajan R, Kumar N, Zhao D, Dai X, Kawamoto K, Matsumura K. Polyampholyte-Based Polymer Hydrogels for the Long-Term Storage, Protection and Delivery of Therapeutic Proteins. Adv Healthc Mater 2023:e2203253. [PMID: 36815203 DOI: 10.1002/adhm.202203253] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/20/2023] [Indexed: 02/24/2023]
Abstract
Protein storage and delivery are crucial for biomedical applications such as protein therapeutics and recombinant proteins. Lack of proper protocols results in the denaturation of proteins, rendering them inactive and manifesting undesired side effects. In this study, polyampholyte-based (succinylated ε-poly-l-lysine) hydrogels containing polyvinyl alcohol and polyethylene glycol polymer matrices to stabilize proteins are developed. These hydrogels facilitated the loading and release of therapeutic amounts of proteins and withstood thermal and freezing stress (15 freeze-thaw cycles and temperatures of -80 °C and 37 °C), without resulting in protein denaturation and aggregation. To the best of our knowledge, this strategy has not been applied to the design of hydrogels constituting polymers, (in particular, polyampholyte-based polymers) which have inherent efficiency to stabilize proteins and protect them from denaturation. Our findings can open up new avenues in protein biopharmaceutics for the design of materials that can store therapeutic proteins long-term under severe stress and safely deliver them.
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Affiliation(s)
- Robin Rajan
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi 923-1292, Ishikawa, Japan
| | - Nishant Kumar
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi 923-1292, Ishikawa, Japan
| | - Dandan Zhao
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi 923-1292, Ishikawa, Japan
| | - Xianda Dai
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi 923-1292, Ishikawa, Japan
| | - Keiko Kawamoto
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi 923-1292, Ishikawa, Japan
| | - Kazuaki Matsumura
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi 923-1292, Ishikawa, Japan
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5
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Lin P, W-M Fan T, Lane AN. NMR-based isotope editing, chemoselection and isotopomer distribution analysis in stable isotope resolved metabolomics. Methods 2022; 206:8-17. [PMID: 35908585 PMCID: PMC9539636 DOI: 10.1016/j.ymeth.2022.07.014] [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: 05/24/2022] [Revised: 07/18/2022] [Accepted: 07/25/2022] [Indexed: 11/20/2022] Open
Abstract
NMR is a very powerful tool for identifying and quantifying compounds within complex mixtures without the need for individual standards or chromatographic separation. Stable Isotope Resolved Metabolomics (or SIRM) is an approach to following the fate of individual atoms from precursors through metabolic transformation, producing an atom-resolved metabolic fate map. However, extracts of cells or tissue give rise to very complex NMR spectra. While multidimensional NMR experiments may partially overcome the spectral overlap problem, additional tools may be needed to determine site-specific isotopomer distributions. NMR is especially powerful by virtue of its isotope editing capabilities using NMR active nuclei such as 13C, 15N, 19F and 31P to select molecules containing just these atoms in a complex mixture, and provide direct information about which atoms are present in identified compounds and their relative abundances. The isotope-editing capability of NMR can also be employed to select for those compounds that have been selectively derivatized with an NMR-active stable isotope at particular functional groups, leading to considerable spectral simplification. Here we review isotope analysis by NMR, and methods of chemoselection both for spectral simplification, and for enhanced isotopomer analysis.
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Affiliation(s)
- Penghui Lin
- Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, KY 40536, USA
| | - Teresa W-M Fan
- Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, KY 40536, USA; Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA
| | - Andrew N Lane
- Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, KY 40536, USA; Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA.
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6
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Tarasca MV, Naser D, Schaefer A, Soule TG, Meiering EM. Quenched hydrogen-deuterium amide exchange optimization for high-resolution structural analysis of cellular protein aggregates. Anal Biochem 2022; 652:114675. [PMID: 35390328 DOI: 10.1016/j.ab.2022.114675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 12/17/2022]
Abstract
Inclusion bodies (IBs) are large, insoluble aggregates that often form during the overexpression of proteins in bacteria. These aggregates are of broad fundamental and practical significance, for recombinant protein preparation and due to their relevance to aggregation-related medical conditions and their recent emergence as promising functional nanomaterials. Despite their significance, high resolution knowledge of IB structure remains very limited. Such knowledge will advance understanding and control of IB formation and properties in myriad practical applications. Here, we report a detailed quenched hydrogen-deuterium amide exchange (qHDX) method with NMR readout to define the structure of IBs at the level of individual residues throughout the protein. Applying proper control of experimental conditions, such as sample pH, water content, temperature, and intrinsic rate of amide exchange, yields in depth results for these cellular protein aggregates. qHDX results illustrated for Cu, Zn superoxide dismutase 1 (SOD1) and Adnectins show their IBs include native-like structure and some but not all mutations alter IB structure.
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Affiliation(s)
| | - Dalia Naser
- Department of Chemistry, University of Waterloo, Waterloo, Canada
| | - Anna Schaefer
- Department of Chemistry, University of Waterloo, Waterloo, Canada
| | - Tyler Gb Soule
- Department of Chemistry, University of Waterloo, Waterloo, Canada
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7
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Schaefer A, Naser D, Siebeneichler B, Tarasca MV, Meiering EM. Methodological advances and strategies for high resolution structure determination of cellular protein aggregates. J Biol Chem 2022; 298:102197. [PMID: 35760099 PMCID: PMC9396402 DOI: 10.1016/j.jbc.2022.102197] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 01/14/2023] Open
Abstract
Aggregation of proteins is at the nexus of molecular processes crucial to aging, disease, and employing proteins for biotechnology and medical applications. There has been much recent progress in determining the structural features of protein aggregates that form in cells; yet, owing to prevalent heterogeneity in aggregation, many aspects remain obscure and often experimentally intractable to define. Here, we review recent results of structural studies for cell-derived aggregates of normally globular proteins, with a focus on high-resolution methods for their analysis and prediction. Complementary results obtained by solid-state NMR spectroscopy, FTIR spectroscopy and microspectroscopy, cryo-EM, and amide hydrogen/deuterium exchange measured by NMR and mass spectrometry, applied to bacterial inclusion bodies and disease inclusions, are uncovering novel information on in-cell aggregation patterns as well as great diversity in the structural features of useful and aberrant protein aggregates. Using these advances as a guide, this review aims to advise the reader on which combination of approaches may be the most appropriate to apply to their unique system.
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Affiliation(s)
- Anna Schaefer
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, Canada
| | - Dalia Naser
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, Canada
| | | | - Michael V Tarasca
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, Canada
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8
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Kuwajima K, Yagi-Utsumi M, Yanaka S, Kato K. DMSO-Quenched H/D-Exchange 2D NMR Spectroscopy and Its Applications in Protein Science. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123748. [PMID: 35744871 PMCID: PMC9230524 DOI: 10.3390/molecules27123748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 11/16/2022]
Abstract
Hydrogen/deuterium (H/D) exchange combined with two-dimensional (2D) NMR spectroscopy has been widely used for studying the structure, stability, and dynamics of proteins. When we apply the H/D-exchange method to investigate non-native states of proteins such as equilibrium and kinetic folding intermediates, H/D-exchange quenching techniques are indispensable, because the exchange reaction is usually too fast to follow by 2D NMR. In this article, we will describe the dimethylsulfoxide (DMSO)-quenched H/D-exchange method and its applications in protein science. In this method, the H/D-exchange buffer is replaced by an aprotic DMSO solution, which quenches the exchange reaction. We have improved the DMSO-quenched method by using spin desalting columns, which are used for medium exchange from the H/D-exchange buffer to the DMSO solution. This improvement has allowed us to monitor the H/D exchange of proteins at a high concentration of salts or denaturants. We describe methodological details of the improved DMSO-quenched method and present a case study using the improved method on the H/D-exchange behavior of unfolded human ubiquitin in 6 M guanidinium chloride.
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Affiliation(s)
- Kunihiro Kuwajima
- Department of Physics, School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Correspondence: (K.K.); (K.K.)
| | - Maho Yagi-Utsumi
- Exploratory Research Center on Life and Living Systems and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Aichi, Japan; (M.Y.-U.); (S.Y.)
- Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Aichi, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Aichi, Japan
| | - Saeko Yanaka
- Exploratory Research Center on Life and Living Systems and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Aichi, Japan; (M.Y.-U.); (S.Y.)
- Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Aichi, Japan
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Aichi, Japan; (M.Y.-U.); (S.Y.)
- Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Aichi, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Aichi, Japan
- Correspondence: (K.K.); (K.K.)
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9
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Ghosh S, Nag S, Saha KD, Banerji B. S-Benzyl Cysteine Based Cyclic Dipeptide Super Hydrogelator: Enhancing Efficacy of an Anticancer Drug via Sustainable Release. J Pept Sci 2022; 28:e3403. [PMID: 35001443 DOI: 10.1002/psc.3403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 12/23/2021] [Accepted: 12/30/2021] [Indexed: 11/09/2022]
Abstract
Peptide based low molecular weight supramolecular hydrogels hold promising aspects in various fields of application especially in biomaterial and biomedical sciences such as drug delivery, wound healing, tissue engineering, cell proliferation, etc due to their extreme biocompatibility. Unlike linear peptides, cyclic peptides have more structural rigidity and tolerance to enzymatic degradation and high environmental stability which make them even better candidates for the above said applications. Herein, a new small cyclic dipeptide (CDP) cyclo-(Leu-S-Bzl-Cys) (P1) consisting of L-leucine and S-benzyl protected L-cysteine was reported which formed hydrogel at physiological conditions (at 37o C and pH=7.46). The hydrogel formed from the cyclic dipeptide P1 showed very good tolerance towards environmental parameters such as pH, temperature and was seen to be stable for more than a year without any deformation. The hydrogel was thermoreversible and stable in the pH range 6-12. Mechanical strength of P1 hydrogel was measured by rheology experiment. AFM and FE-SEM images revealed that in aqueous solvents P1 self-assembled into a highly cross-linked nanofibrillar network which immobilized water molecules inside the cages and formed the hydrogel. The self-assembled cyclic dipeptide acquired antiparallel β-sheet secondary structure which was evident from CD and FT-IR studies. The β-sheet arrangement and formation of amyloid fibrils were further established by ThT binding assay. Furthermore, P1 was able to form hydrogel in presence of anticancer drug 5-fluorouracil (5FU) and sustainable release of the drug from the hydrogel was measured in-vitro. The hydrogelator P1 showed almost no cytotoxicity towards human colorectal cancer cell line HCT116 up to a considerable high concentration and showed potential application in sustainable drug delivery. The co-assembly of 5FU and P1 hydrogel exhibited much better anticancer activity towards HCT116 cancer cell line than 5-fluorouracil alone and decreased the IC50 dose of 5-fluorouracil to a much lower value.
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Affiliation(s)
- Saswati Ghosh
- Organic & Medicinal Chemistry Division, Indian Institute of Chemical Biology (CSIR-IICB), Kolkata, India
| | - Sayoni Nag
- Cancer Biology & Inflammatory Disorder, Indian Institute of Chemical Biology (CSIR-IICB), Kolkata, India
| | - Krishna Das Saha
- Cancer Biology & Inflammatory Disorder, Indian Institute of Chemical Biology (CSIR-IICB), Kolkata, India
| | - Biswadip Banerji
- Organic & Medicinal Chemistry Division, Indian Institute of Chemical Biology (CSIR-IICB), Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), Indian Institute of Chemical Biology (CSIR-IICB), Kolkata, India
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10
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Cohn PG, Qavi S, Cubuk J, Jani M, Megdad ML, Shah D, Cattafi C, Baul P, Rajaraman S, Foudazi R. Getting control of hydrogel networks with cross-linkable monomers. J Mater Chem B 2021; 9:9497-9504. [PMID: 34553741 DOI: 10.1039/d1tb00482d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The structure of a hydrogel network determines its ability to dissipate stress upon deformation, as well as its ability to swell in water. By designing systems with cross-linkable thiol groups in the monomers, radical thiol-ene chemistry was used to form controlled networks for acrylamide monomers. The use of radical thiol-ene chemistry effectively suppressed homo-polymerization of the bis(acrylamide) monomer and resulted in networks of alternating thiol and acrylamide monomers. Additionally, if the stoichiometry between the monomers is controlled, the network should approach that of ideality. In the case of bis(acrylamide) monomers, the incorporation of hydrogen-bond donors into the network creates a single network hydrogel with the benefits of high strength and ductility from the simultaneous incorporation of chemical and physical cross-links. Additionally, this strategy suppresses the formation of homo-polymerization in the acrylamide monomer to achieve an alternating network, which is supported with NMR characterization of base-digested fragments. For three different monomer compositions, the resulting gels had high compressive strength (up to 40 MPa) and tunable mechanical properties. The high mechanical strength of the 1 : 1, thiol : ene gel composition is due to the uniform distribution of cross-links, which creates defect-free networks for efficient stress transfer. The present one-pot synthetic strategy toward controlled gel networks affords monomer versatility and synthetic ease, as well as the potential for mechanically robust materials.
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Affiliation(s)
- Pamela G Cohn
- Chemistry Program, Stockton University, Galloway, NJ 08205, USA.
| | - Sahar Qavi
- Department of Chemical and Materials Engineering, New Mexico State University, Las Cruces, NM 88003, USA
| | - Jasmine Cubuk
- Chemistry Program, Stockton University, Galloway, NJ 08205, USA.
| | - Mihir Jani
- Chemistry Program, Stockton University, Galloway, NJ 08205, USA.
| | | | - Dhvani Shah
- Chemistry Program, Stockton University, Galloway, NJ 08205, USA.
| | - Cara Cattafi
- Chemistry Program, Stockton University, Galloway, NJ 08205, USA.
| | - Panchatapa Baul
- Chemistry Program, Stockton University, Galloway, NJ 08205, USA.
| | | | - Reza Foudazi
- Department of Chemical and Materials Engineering, New Mexico State University, Las Cruces, NM 88003, USA.,School of Chemical, Biological and Materials Engineering, University of Oklahoma, Norman, OK 73019, USA.
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11
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Peacock RB, Komives EA. Hydrogen/Deuterium Exchange and Nuclear Magnetic Resonance Spectroscopy Reveal Dynamic Allostery on Multiple Time Scales in the Serine Protease Thrombin. Biochemistry 2021; 60:3441-3448. [PMID: 34159782 DOI: 10.1021/acs.biochem.1c00277] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A deeper understanding of how hydrogen/deuterium exchange mass spectrometry (HDX-MS) reveals allostery is important because HDX-MS can reveal allostery in systems that are not amenable to nuclear magnetic resonance (NMR) spectroscopy. We were able to study thrombin and its complex with thrombomodulin, an allosteric regulator, by both HDX-MS and NMR. In this Perspective, we compare and contrast the results from both experiments and from molecular dynamics simulations. NMR detects changes in the chemical environment around the protein backbone N-H bond vectors, providing residue-level information about the conformational exchange between distinct states. HDX-MS detects changes in amide proton solvent accessibility and H-bonding. Taking advantage of NMR relaxation dispersion measurements of the time scale of motions, we draw conclusions about the motions reflected in HDX-MS experiments. Both experiments detect allostery, but they reveal different components of the allosteric transition. The insights gained from integrating NMR and HDX-MS into thrombin dynamics enable a clearer interpretation of the evidence for allostery revealed by HDX-MS in larger protein complexes and assemblies that are not amenable to NMR.
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Affiliation(s)
- Riley B Peacock
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0378, United States
| | - Elizabeth A Komives
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0378, United States
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12
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Ghorbani-Choghamarani A, Taherinia Z, Heidarnezhad Z, Moradi Z. Application of Nanofibers Based on Natural Materials as Catalyst in Organic Reactions. J IND ENG CHEM 2021. [DOI: 10.1016/j.jiec.2020.10.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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13
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Yagi-Utsumi M, Chandak MS, Yanaka S, Hiranyakorn M, Nakamura T, Kato K, Kuwajima K. Residual Structure of Unfolded Ubiquitin as Revealed by Hydrogen/Deuterium-Exchange 2D NMR. Biophys J 2020; 119:2029-2038. [PMID: 33142107 DOI: 10.1016/j.bpj.2020.10.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/10/2020] [Accepted: 10/07/2020] [Indexed: 12/01/2022] Open
Abstract
The characterization of residual structures persistent in unfolded proteins in concentrated denaturant solution is currently an important issue in studies of protein folding because the residual structure present, if any, in the unfolded state may form a folding initiation site and guide the subsequent folding reactions. Here, we studied the hydrogen/deuterium (H/D)-exchange behavior of unfolded human ubiquitin in 6 M guanidinium chloride. We employed a dimethylsulfoxide (DMSO)-quenched H/D-exchange NMR technique with the use of spin desalting columns, which allowed us to perform a quick medium exchange from 6 M guanidinium chloride to a quenching DMSO solution. Based on the backbone resonance assignment of ubiquitin in the DMSO solution, we successfully investigated the H/D-exchange kinetics of 60 identified peptide amide groups in the ubiquitin sequence. Although a majority of these amide groups were not protected, certain amide groups involved in a middle helix (residues 23-34) and an N-terminal β-hairpin (residues 2-16) were significantly protected with a protection factor of 2.1-4.2, indicating that there were residual structures in unfolded ubiquitin and that these amide groups were more than 52% hydrogen bonded in the residual structures. We show that the hydrogen-bonded residual structures in the α-helix and the β-hairpin are formed even in 6 M guanidinium chloride, suggesting that these residual structures may function as a folding initiation site to guide the subsequent folding reactions of ubiquitin.
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Affiliation(s)
- Maho Yagi-Utsumi
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi, Japan; Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, Japan; Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), Okazaki, Aichi, Japan
| | - Mahesh S Chandak
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, Japan; Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), Okazaki, Aichi, Japan
| | - Saeko Yanaka
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi, Japan; Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, Japan; Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), Okazaki, Aichi, Japan
| | - Methanee Hiranyakorn
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi, Japan; Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, Japan; Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), Okazaki, Aichi, Japan
| | - Takashi Nakamura
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi, Japan; Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, Japan; Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), Okazaki, Aichi, Japan.
| | - Kunihiro Kuwajima
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, Japan; Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), Okazaki, Aichi, Japan; Department of Physics, Graduate School of Science, the University of Tokyo, Tokyo, Japan; School of Computational Sciences, Korea Institute for Advanced Study, Seoul, Korea.
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14
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Majumder L, Chatterjee M, Bera K, Maiti NC, Banerji B. Solvent-Assisted Tyrosine-Based Dipeptide Forms Low-Molecular Weight Gel: Preparation and Its Potential Use in Dye Removal and Oil Spillage Separation from Water. ACS OMEGA 2019; 4:14411-14419. [PMID: 31528794 PMCID: PMC6739715 DOI: 10.1021/acsomega.9b01301] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 06/27/2019] [Indexed: 06/10/2023]
Abstract
Low-molecular weight gelators (supramolecular, or simply molecular gels) are highly important molecular frameworks because of their potential application in drug delivery, catalysis, pollutant removal, sensing materials, and so forth. Herein, a small dipeptide composed of N-(tert-butoxycarbonyl)pentafluoro-l-phenylalanine and O-benzyl-l-tyrosine methyl ester was synthesized, and its gelation ability was investigated in different solvent systems. It was found that the dipeptide was unable to form gel with a single solvent, but a mixture of solvent systems was found to be suitable for the gelation of this dipeptide. Interestingly, water was found to be essential for gelation with the polar protic solvent, and long-chain hydrocarbon units such as, petroleum ether, kerosene, and diesel, were important for gelation with aromatic solvents. The structural insights of these gels were characterized by field-emission scanning electronic microscopy, atomic force microscopy, Fourier transform infrared analysis, and X-ray diffraction studies, and their mechanical strengths were characterized by rheological experiments. Both of the gels obtained from these two solvent systems were thermoreversible in nature, and these translucent gels had potential application for the treatment of waste water. The gel obtained from dipeptides with methanol-water was used to remove toxic dyes (crystal violet, Eriochrome Black T, and rhodamine B) from water. Furthermore, the gel obtained from dipeptide with assistance from toluene-petroleum ether was used as a phase-selective gelator for oil-spill recovery.
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Affiliation(s)
- Leena Majumder
- Organic
and Medicinal Chemistry Division, Academy of Science and Industrial
Research, and Structural Biology and Bioinformatics Division, CSIR—Indian Institute of Chemical Biology, Jadavpur, Kolkata 700032, India
| | - Moumita Chatterjee
- Organic
and Medicinal Chemistry Division, Academy of Science and Industrial
Research, and Structural Biology and Bioinformatics Division, CSIR—Indian Institute of Chemical Biology, Jadavpur, Kolkata 700032, India
| | - Kaushik Bera
- Organic
and Medicinal Chemistry Division, Academy of Science and Industrial
Research, and Structural Biology and Bioinformatics Division, CSIR—Indian Institute of Chemical Biology, Jadavpur, Kolkata 700032, India
| | - Nakul Chandra Maiti
- Organic
and Medicinal Chemistry Division, Academy of Science and Industrial
Research, and Structural Biology and Bioinformatics Division, CSIR—Indian Institute of Chemical Biology, Jadavpur, Kolkata 700032, India
| | - Biswadip Banerji
- Organic
and Medicinal Chemistry Division, Academy of Science and Industrial
Research, and Structural Biology and Bioinformatics Division, CSIR—Indian Institute of Chemical Biology, Jadavpur, Kolkata 700032, India
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15
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Rennella E, Morgan GJ, Yan N, Kelly JW, Kay LE. The Role of Protein Thermodynamics and Primary Structure in Fibrillogenesis of Variable Domains from Immunoglobulin Light Chains. J Am Chem Soc 2019; 141:13562-13571. [PMID: 31364359 DOI: 10.1021/jacs.9b05499] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Immunoglobulin light-chain amyloidosis is a protein aggregation disease that leads to proteinaceous deposits in a variety of organs in the body and, if untreated, ultimately results in death. The mechanisms by which light-chain aggregation occurs are not well understood. Here we have used solution NMR spectroscopy and biophysical studies to probe immunoglobulin variable domain λV6-57 VL aggregation, a process that appears to drive the degenerative phenotypes in amyloidosis patients. Our results establish that aggregation proceeds via the unfolded state. We identify, through NMR relaxation experiments recorded on the unfolded domain ensemble, a series of hotspots that could be involved in the initial phases of aggregate formation. Mutational analysis of these hotspots reveals that the region that includes K16-R24 is particularly aggregation prone. Notably, this region includes the site of the R24G substitution, a mutation that is found in variable domains of λ light-chain deposits in 25% of patients. The R24G λV6-57 VL domain aggregates more rapidly than would be expected on the basis of thermodynamic stability alone, while substitutions in many of the aggregation-prone regions significantly slow down fibril formation.
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Affiliation(s)
- Enrico Rennella
- Departments of Molecular Genetics, Biochemistry and Chemistry , The University of Toronto , Toronto , Ontario , Canada M5S1A8
| | - Gareth J Morgan
- Departments of Molecular Medicine and Chemistry , The Scripps Research Institute , La Jolla , California 92037 , United States.,Department of Medicine , Boston University School of Medicine , Boston , Massachusetts 02118 , United States
| | - Nicholas Yan
- Departments of Molecular Medicine and Chemistry , The Scripps Research Institute , La Jolla , California 92037 , United States
| | - Jeffery W Kelly
- Departments of Molecular Medicine and Chemistry , The Scripps Research Institute , La Jolla , California 92037 , United States
| | - Lewis E Kay
- Departments of Molecular Genetics, Biochemistry and Chemistry , The University of Toronto , Toronto , Ontario , Canada M5S1A8.,The Hospital for Sick Children , Program in Molecular Medicine , 555 University Avenue , Toronto , Ontario , Canada M5G1X8
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16
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Nastasa V, Stavarache C, Hanganu A, Coroaba A, Nicolescu A, Deleanu C, Sadet A, Vasos PR. Hyperpolarised NMR to follow water proton transport through membrane channels via exchange with biomolecules. Faraday Discuss 2019; 209:67-82. [PMID: 29989626 DOI: 10.1039/c8fd00021b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Water uptake in vesicles and the subsequent exchange between water protons and amide -NH protons in amino acids can be followed by a new, highly sensitive, type of magnetic resonance spectroscopy: dynamic nuclear polarisation (DNP)-enhanced NMR in the liquid state. Water hydrogen atoms are detected prior to and after their transfer to molecular sites in peptides and proteins featuring highly-accessible proton-exchangeable groups, as is the case for the -NH groups of intrinsically disordered proteins. The detected rates for amide proton-water proton exchange can be modulated by membrane-crossing rates, when a membrane channel is interposed. We hyperpolarised water proton spins via dynamic nuclear polarisation followed by sample dissolution (d-DNP) and transferred the created polarisation to -NH groups with high solvent accessibility in an intrinsically disordered protein domain. This domain is the membrane anchor of c-Src kinase, whose activity controls cell proliferation. The hindrance of effective water proton transfer rate constants observed in free solvent when a membrane-crossing step is involved is discussed. This study aims to assess the feasibility of recently-introduced hyperpolarised (DNP-enhanced) NMR to assess water membrane crossing dynamics.
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Affiliation(s)
- Viorel Nastasa
- Extreme Light Infrastructure - Nuclear Physics (ELI-NP), Horia Hulubei Institute for Nuclear Physics (IFIN-HH), Reactorului Str., 30, Magurele Campus, Bucharest, Romania.
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17
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Wang R, Chen P, Shen Z, Lin G, Xiao G, Dai Z, Zhang B, Chen Y, Lai L, Zong X, Li Y, Tang Y, Wu R. Brain Amide Proton Transfer Imaging of Rat With Alzheimer's Disease Using Saturation With Frequency Alternating RF Irradiation Method. Front Aging Neurosci 2019; 11:217. [PMID: 31507405 PMCID: PMC6713910 DOI: 10.3389/fnagi.2019.00217] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 08/02/2019] [Indexed: 02/05/2023] Open
Abstract
Amyloid-β (Aβ) deposits and some proteins play essential roles in the pathogenesis of Alzheimer's disease (AD). Amide proton transfer (APT) imaging, as an imaging modality to detect tissue protein, has shown promising features for the diagnosis of AD disease. In this study, we chose 10 AD model rats as the experimental group and 10 sham-operated rats as the control group. All the rats underwent a Y-maze test before APT image acquisition, using saturation with frequency alternating RF irradiation (APTSAFARI) method on a 7.0 T animal MRI scanner. Compared with the control group, APT (3.5 ppm) values of brain were significantly reduced in AD models (p < 0.002). The APTSAFARI imaging is more significant than APT imaging (p < 0.0001). AD model mice showed spatial learning and memory loss in the Y-maze experiment. In addition, there was significant neuronal loss in the hippocampal CA1 region and cortex compared with sham-operated rats. In conclusion, we demonstrated that APT imaging could potentially provide molecular biomarkers for the non-invasive diagnosis of AD. APTSAFARI MRI could be used as an effective tool to improve the accuracy of diagnosis of AD compared with conventional APT imaging.
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Affiliation(s)
- Runrun Wang
- Department of Medical Imaging, The Second Affiliated Hospital, Shantou University Medical College, Shantou, China
| | - Peidong Chen
- Department of Medical Imaging, The Second Affiliated Hospital, Shantou University Medical College, Shantou, China
| | - Zhiwei Shen
- Department of Medical Imaging, The Second Affiliated Hospital, Shantou University Medical College, Shantou, China
- Philips Healthcare, Shantou, China
| | - Guisen Lin
- Department of Medical Imaging, The Second Affiliated Hospital, Shantou University Medical College, Shantou, China
| | - Gang Xiao
- Department of Mathematics and Statistics, Hanshan Normal University, Chaozhou, China
| | - Zhuozhi Dai
- Department of Medical Imaging, The Second Affiliated Hospital, Shantou University Medical College, Shantou, China
| | - Bingna Zhang
- Translational Medicine, The Second Affiliated Hospital, Shantou University Medical College, Shantou, China
| | - Yuanfeng Chen
- Department of Medical Imaging, The Second Affiliated Hospital, Shantou University Medical College, Shantou, China
| | - Lihua Lai
- Department of Medical Imaging, The Second Affiliated Hospital, Shantou University Medical College, Shantou, China
| | - Xiaodan Zong
- Department of Medical Imaging, The Second Affiliated Hospital, Shantou University Medical College, Shantou, China
| | - Yan Li
- Department of Medical Imaging, The Second Affiliated Hospital, Shantou University Medical College, Shantou, China
| | - Yanyan Tang
- Department of Medical Imaging, The Second Affiliated Hospital, Shantou University Medical College, Shantou, China
| | - Renhua Wu
- Department of Medical Imaging, The Second Affiliated Hospital, Shantou University Medical College, Shantou, China
- *Correspondence: Renhua Wu,
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18
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Banerji B, Chatterjee M, Pal U, Maiti NC. Formation of Annular Protofibrillar Assembly by Cysteine Tripeptide: Unraveling the Interactions with NMR, FTIR, and Molecular Dynamics. J Phys Chem B 2017; 121:6367-6379. [DOI: 10.1021/acs.jpcb.7b04373] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Biswadip Banerji
- Organic
and Medicinal Chemistry and ‡Structural Biology and Bio-Informatics
Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C.
Mullick Road, Kolkata, West
Bengal 700032, India
| | - Moumita Chatterjee
- Organic
and Medicinal Chemistry and ‡Structural Biology and Bio-Informatics
Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C.
Mullick Road, Kolkata, West
Bengal 700032, India
| | - Uttam Pal
- Organic
and Medicinal Chemistry and ‡Structural Biology and Bio-Informatics
Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C.
Mullick Road, Kolkata, West
Bengal 700032, India
| | - Nakul C. Maiti
- Organic
and Medicinal Chemistry and ‡Structural Biology and Bio-Informatics
Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C.
Mullick Road, Kolkata, West
Bengal 700032, India
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19
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A 31-residue peptide induces aggregation of tau's microtubule-binding region in cells. Nat Chem 2017; 9:874-881. [PMID: 28837163 DOI: 10.1038/nchem.2754] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 02/23/2017] [Indexed: 12/22/2022]
Abstract
The self-propagation of misfolded conformations of tau underlies neurodegenerative diseases, including Alzheimer's. There is considerable interest in discovering the minimal sequence and active conformational nucleus that defines this self-propagating event. The microtubule-binding region, spanning residues 244-372, reproduces much of the aggregation behaviour of tau in cells and animal models. Further dissection of the amyloid-forming region to a hexapeptide from the third microtubule-binding repeat resulted in a peptide that rapidly forms fibrils in vitro. We show that this peptide lacks the ability to seed aggregation of tau244-372 in cells. However, as the hexapeptide is gradually extended to 31 residues, the peptides aggregate more slowly and gain potent activity to induce aggregation of tau244-372 in cells. X-ray fibre diffraction, hydrogen-deuterium exchange and solid-state NMR studies map the beta-forming region to a 25-residue sequence. Thus, the nucleus for self-propagating aggregation of tau244-372 in cells is packaged in a remarkably small peptide.
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20
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Abstract
Although each type of protein fold and in some cases individual proteins within a fold classification can have very different mechanisms of folding, the underlying biophysical and biochemical principles that operate to cause a linear polypeptide chain to fold into a globular structure must be the same. In an aqueous solution, the protein takes up the thermodynamically most stable structure, but the pathway along which the polypeptide proceeds in order to reach that structure is a function of the amino acid sequence, which must be the final determining factor, not only in shaping the final folded structure, but in dictating the folding pathway. A number of groups have focused on a single protein or group of proteins, to determine in detail the factors that influence the rate and mechanism of folding in a defined system, with the hope that hypothesis-driven experiments can elucidate the underlying principles governing the folding process. Our research group has focused on the folding of the globin family of proteins, and in particular on the monomeric protein apomyoglobin. Apomyoglobin (apoMb) folds relatively slowly (∼2 s) via an ensemble of obligatory intermediates that form rapidly after the initiation of folding. The folding pathway can be dissected using rapid-mixing techniques, which can probe processes in the millisecond time range. Stopped-flow measurements detected by circular dichroism (CD) or fluorescence spectroscopy give information on the rates of folding events. Quench-flow experiments utilize the differential rates of hydrogen-deuterium exchange of amide protons protected in parts of the structure that are folded early; protection of amides can be detected by mass spectrometry or proton nuclear magnetic resonance spectroscopy (NMR). In addition, apoMb forms an intermediate at equilibrium at pH ∼ 4, which is sufficiently stable for it to be structurally characterized by solution methods such as CD, fluorescence and NMR spectroscopies, and the conformational ensembles formed in the presence of denaturing agents and low pH can be characterized as models for the unfolded states of the protein. Newer NMR techniques such as measurement of residual dipolar couplings in the various partly folded states, and relaxation dispersion measurements to probe invisible states present at low concentrations, have contributed to providing a detailed picture of the apomyoglobin folding pathway. The research summarized in this Account was aimed at characterizing and comparing the equilibrium and kinetic intermediates both structurally and dynamically, as well as delineating the complete folding pathway at a residue-specific level, in order to answer the question: "What is it about the amino acid sequence that causes each molecule in the unfolded protein ensemble to start folding, and, once started, to proceed towards the formation of the correctly folded three-dimensional structure?"
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Affiliation(s)
- H Jane Dyson
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla California 92037, United States
| | - Peter E Wright
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla California 92037, United States
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21
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NISHIMURA C. Folding of apomyoglobin: Analysis of transient intermediate structure during refolding using quick hydrogen deuterium exchange and NMR. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2017; 93:10-27. [PMID: 28077807 PMCID: PMC5406622 DOI: 10.2183/pjab.93.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 10/31/2016] [Indexed: 05/27/2023]
Abstract
The structures of apomyoglobin folding intermediates have been widely analyzed using physical chemistry methods including fluorescence, circular dichroism, small angle X-ray scattering, NMR, mass spectrometry, and rapid mixing. So far, at least two intermediates (on sub-millisecond- and millisecond-scales) have been demonstrated for apomyoglobin folding. The combination of pH-pulse labeling and NMR is a useful tool for analyzing the kinetic intermediates at the atomic level. Its use has revealed that the latter-phase kinetic intermediate of apomyoglobin (6 ms) was composed of helices A, B, G and H, whereas the equilibrium intermediate, called the pH 4 molten-globule intermediate, was composed mainly of helices A, G and H. The improved strategy for the analysis of the kinetic intermediate was developed to include (1) the dimethyl sulfoxide method, (2) data processing with the various labeling times, and (3) a new in-house mixer. Particularly, the rapid mixing revealed that helices A and G were significantly more protected at the earlier stage (400 µs) of the intermediate (former-phase intermediate) than the other helices. Mutation studies, where each hydrophobic residue was replaced with an alanine in helices A, B, E, F, G and H, indicated that both non-native and native-like structures exist in the latter-phase folding intermediate. The N-terminal part of helix B is a weak point in the intermediate, and the docking of helix E residues to the core of the A, B, G and H helices was interrupted by a premature helix B, resulting in the accumulation of the intermediate composed of helices A, B, G and H. The prediction-based protein engineering produced important mutants: Helix F in a P88K/A90L/S92K/A94L mutant folded in the latter-phase intermediate, although helix F in the wild type does not fold even at the native state. Furthermore, in the L11G/W14G/A70L/G73W mutant, helix A did not fold but helix E did, which is similar to what was observed in the kinetic intermediate of apoleghemoglobin. Thus, this protein engineering resulted in a changed structure for the apomyoglobin folding intermediate.
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Affiliation(s)
- Chiaki NISHIMURA
- Faculty of Pharmaceutical Sciences, Teikyo Heisei University, Nakano-ku, Tokyo, Japan
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22
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Hiew SH, Guerette PA, Zvarec OJ, Phillips M, Zhou F, Su H, Pervushin K, Orner BP, Miserez A. Modular peptides from the thermoplastic squid sucker ring teeth form amyloid-like cross-β supramolecular networks. Acta Biomater 2016; 46:41-54. [PMID: 27693688 DOI: 10.1016/j.actbio.2016.09.040] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 09/23/2016] [Accepted: 09/28/2016] [Indexed: 12/22/2022]
Abstract
The hard sucker ring teeth (SRT) from decapodiforme cephalopods, which are located inside the sucker cups lining the arms and tentacles of these species, have recently emerged as a unique model structure for biomimetic structural biopolymers. SRT are entirely composed of modular, block co-polymer-like proteins that self-assemble into a large supramolecular network. In order to unveil the molecular principles behind SRT's self-assembly and robustness, we describe a combinatorial screening assay that maps the molecular-scale interactions between the most abundant modular peptide blocks of suckerin proteins. By selecting prominent interaction hotspots from this assay, we identified four peptides that exhibited the strongest homo-peptidic interactions, and conducted further in-depth biophysical characterizations complemented by molecular dynamic (MD) simulations to investigate the nature of these interactions. Circular Dichroism (CD) revealed conformations that transitioned from semi-extended poly-proline II (PII) towards β-sheet structure. The peptides spontaneously self-assembled into microfibers enriched with cross β-structures, as evidenced by Fourier-Transform Infrared Spectroscopy (FTIR) and Congo red staining. Nuclear Magnetic Resonance (NMR) experiments identified the residues involved in the hydrogen-bonded network and demonstrated that these self-assembled β-sheet-based fibers exhibit high protection factors that bear resemblance to amyloids. The high stability of the β-sheet network and an amyloid-like model of fibril assembly were supported by MD simulations. The work sheds light on how Nature has evolved modular sequence design for the self-assembly of mechanically robust functional materials, and expands our biomolecular toolkit to prepare load-bearing biomaterials from protein-based block co-polymers and self-assembled peptides. STATEMENT OF SIGNIFICANCE The sucker ring teeth (SRT) located on the arms and tentacles of cephalopods represent as a very promising protein-based biopolymer with the potential to rival silk in biomedical and engineering applications. SRT are made of modular, block co-polymer like proteins (suckerins), which assemble into a semicrystalline polymer reinforced by nano-confined β-sheets, resulting in a supramolecular network with mechanical properties that match those of the strongest engineering polymers. In this study, we aimed to understand the molecular mechanisms behind SRT's self-assembly and robustness. The most abundant modular peptidic blocks of suckerin proteins were studied by various spectroscopic methods, which demonstrate that SRT peptides form amyloid-like cross-β structures.
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23
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Ubiquitin utilizes an acidic surface patch to alter chromatin structure. Nat Chem Biol 2016; 13:105-110. [PMID: 27870837 PMCID: PMC5161692 DOI: 10.1038/nchembio.2235] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 09/07/2016] [Indexed: 02/06/2023]
Abstract
Ubiquitylation of histone H2B, associated with gene activation, leads to chromatin decompaction through an unknown mechanism. We used a hydrogen-deuterium exchange strategy coupled with nuclear magnetic resonance spectroscopy to map the ubiquitin surface responsible for its structural effects on chromatin. Our studies revealed that a previously uncharacterized acidic patch on ubiquitin comprising residues Glu16 and Glu18 is essential for decompaction. These residues mediate promiscuous electrostatic interactions with the basic histone proteins, potentially positioning the ubiquitin moiety as a dynamic “wedge” that prevents the intimate association of neighboring nucleosomes. Using two independent cross-linking strategies and an oligomerization assay, we also showed that ubiquitin-ubiquitin contacts occur in the chromatin environment and are important for the solubilization of the chromatin polymers. Our work highlights a novel, chromatin-related aspect of the “ubiquitin code”, and sheds light on how the information rich ubiquitin modification can orchestrate different biochemical outcomes using different surface features.
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24
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Abstract
Amyloid fibrils are associated with a number of human diseases. These aggregatively misfolded intermolecular β-sheet assemblies constitute some of the most challenging targets in structural biology because to their complexity, size, and insolubility. Here, protocols and controls are described for experiments designed to study hydrogen-bonding in amyloid fibrils indirectly, by transferring information about amide proton occupancy in the fibrils to the dimethyl sulfoxide-denatured state. Since the denatured state is amenable to solution NMR spectroscopy, the method can provide residue-level-resolution data on hydrogen exchange for the monomers that make up the fibrils.
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Affiliation(s)
- Andrei T Alexandrescu
- Department of Molecular and Cell Biology, University of Connecticut, Unit 3125, BSP 209, 91 N. Eagleville Rd., Storrs, CT, 06269-3125, USA.
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25
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Mao Y, Zlatic CO, Griffin MDW, Howlett GJ, Todorova N, Yarovsky I, Gooley PR. Hydrogen/Deuterium Exchange and Molecular Dynamics Analysis of Amyloid Fibrils Formed by a D69K Charge-Pair Mutant of Human Apolipoprotein C-II. Biochemistry 2015. [DOI: 10.1021/acs.biochem.5b00535] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yu Mao
- Department of Biochemistry and
Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Courtney O. Zlatic
- Department of Biochemistry and
Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Michael D. W. Griffin
- Department of Biochemistry and
Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Geoffrey J. Howlett
- Department of Biochemistry and
Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Nevena Todorova
- Health Innovations
Research Institute, RMIT University, GPO
Box 2476, Melbourne, Victoria 3001, Australia
| | - Irene Yarovsky
- Health Innovations
Research Institute, RMIT University, GPO
Box 2476, Melbourne, Victoria 3001, Australia
| | - Paul R. Gooley
- Department of Biochemistry and
Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
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26
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Engen JR, Wales TE. Analytical Aspects of Hydrogen Exchange Mass Spectrometry. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2015; 8:127-48. [PMID: 26048552 PMCID: PMC4989240 DOI: 10.1146/annurev-anchem-062011-143113] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
This article reviews the analytical aspects of measuring hydrogen exchange by mass spectrometry (HX MS). We describe the nature of analytical selectivity in hydrogen exchange, then review the analytical tools required to accomplish fragmentation, separation, and the mass spectrometry measurements under restrictive exchange quench conditions. In contrast to analytical quantitation that relies on measurements of peak intensity or area, quantitation in HX MS depends on measuring a mass change with respect to an undeuterated or deuterated control, resulting in a value between zero and the maximum amount of deuterium that can be incorporated. Reliable quantitation is a function of experimental fidelity and to achieve high measurement reproducibility, a large number of experimental variables must be controlled during sample preparation and analysis. The method also reports on important qualitative aspects of the sample, including conformational heterogeneity and population dynamics.
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Affiliation(s)
- John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115;
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27
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Wu RH, Nguyen TP, Marquart GW, Miesen TJ, Mau T, Mackiewicz MR. A facile route to tailoring peptide-stabilized gold nanoparticles using glutathione as a synthon. Molecules 2014; 19:6754-75. [PMID: 24858266 PMCID: PMC6271629 DOI: 10.3390/molecules19056754] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 05/20/2014] [Accepted: 05/21/2014] [Indexed: 12/13/2022] Open
Abstract
The preparation of gold nanoparticles (AuNPs) of high purity and stability remains a major challenge for biological applications. This paper reports a simple synthetic strategy to prepare water-soluble peptide-stabilized AuNPs. Reduced glutathione, a natural tripeptide, was used as a synthon for the growth of two peptide chains directly on the AuNP surface. Both nonpolar (tryptophan and methionine) and polar basic (histidine and dansylated arginine) amino acids were conjugated to the GSH-capped AuNPs. Ultracentrifugation concentrators with polyethersulfone (PES) membranes were used to purify precursor materials in each stage of the multi-step synthesis to minimize side reactions. Thin layer chromatography, transmission electron microscopy, UV-Visible, 1H-NMR, and fluorescence spectroscopies demonstrated that ultracentrifugation produces high purity AuNPs, with narrow polydispersity, and minimal aggregation. More importantly, it allows for more control over the composition of the final ligand structure. Studies under conditions of varying pH and ionic strength revealed that peptide length, charge, and hydrophobicity influence the stability as well as solubility of the peptide-capped AuNPs. The synthetic and purification strategies used provide a facile route for developing a library of tailored biocompatible peptide-stabilized AuNPs for biomedical applications.
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Affiliation(s)
- Rosina Ho Wu
- Department of Chemistry, Portland State University, Portland, OR 97201, USA
| | - Tan P Nguyen
- Department of Chemistry, Portland State University, Portland, OR 97201, USA
| | - Grant W Marquart
- Department of Chemistry, Portland State University, Portland, OR 97201, USA
| | - Thomas J Miesen
- Department of Chemistry, Portland State University, Portland, OR 97201, USA
| | - Theresa Mau
- Department of Chemistry, Portland State University, Portland, OR 97201, USA
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Palmieri M, Russo L, Malgieri G, Esposito S, Baglivo I, Rivellino A, Farina B, de Paola I, Zaccaro L, Milardi D, Isernia C, Pedone PV, Fattorusso R. Deciphering the zinc coordination properties of the prokaryotic zinc finger domain: The solution structure characterization of Ros87 H42A functional mutant. J Inorg Biochem 2014; 131:30-6. [DOI: 10.1016/j.jinorgbio.2013.10.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 10/17/2013] [Accepted: 10/19/2013] [Indexed: 11/26/2022]
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29
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Foti MC, Rocco C. Unveiling the chemistry behind bromination of quercetin: the ‘violet chromogen’. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.01.081] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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30
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Xiao Y, Stone T, Moya W, Killian P, Herget T. Confocal Raman Characterization of Different Protein Desorption Behaviors from Chromatographic Particles. Anal Chem 2014; 86:1007-15. [DOI: 10.1021/ac401081s] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yuewu Xiao
- EMD Millipore, 80 Ashby Road, Bedford, Massachusetts 01730, United States
| | - Thomas Stone
- EMD Millipore, 80 Ashby Road, Bedford, Massachusetts 01730, United States
| | - Wilson Moya
- EMD Millipore, 80 Ashby Road, Bedford, Massachusetts 01730, United States
| | - Paul Killian
- EMD Millipore, 80 Ashby Road, Bedford, Massachusetts 01730, United States
| | - Thomas Herget
- Merck Millipore, Frankfurter
Strasse 250, D 64293 Darmstadt, Germany
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31
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Heffern MC, Kurutz JW, Meade TJ. Spectroscopic elucidation of the inhibitory mechanism of Cys2His2 zinc finger transcription factors by cobalt(III) Schiff base complexes. Chemistry 2013; 19:17043-53. [PMID: 24203451 DOI: 10.1002/chem.201301659] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 10/05/2013] [Indexed: 01/22/2023]
Abstract
Transcription factors are key regulators in both normal and pathological cell processes. Affecting the activity of these proteins is a promising strategy for understanding gene regulation and developing effective therapeutics. Co(III) Schiff base complexes ([Co(acacen)(L)2](+) where L=labile axial ligands) have been shown to be potent inhibitors of a number of zinc metalloproteins including Cys2His2 zinc finger transcription factors. Inhibition by [Co(acacen)(L)2](+) of the target protein is believed to occur through a dissociative exchange of the labile axial ligands for histidine (His) residues essential for function. Here, we report a series of spectroscopic investigations with model peptides of zinc fingers that elucidate the interaction between [Co(acacen)(L)2](+) complexes and zinc finger transcription factors. Observed changes in NMR chemical shifts and 2D (1)H-(1)H NOESY NMR spectra demonstrate the preference of [Co(acacen)(L)2](+) complexes to coordinate His residues over other amino acids. The conformation of [Co(acacen)(L)2](+) upon His coordination was characterized by (1)H NMR spectroscopy, near-UV CD, and electronic absorption. These studies reveal that the resulting His-coordinated [Co(acacen)(L)2](+) complex possesses an octahedral structure. The effects of [Co(acacen)(L)2](+) complexes on the zinc-finger structure were assessed by the degree of hydrogen bonding (probed by 2D NMR spectroscopy) and secondary-structure profiles measured by far-UV CD. These structural studies demonstrate the ability of [Co(acacen)(L)2](+) complexes to disrupt the ββα structure of zinc fingers, resulting in primarily random-coil conformations. A mechanism is described wherein [Co(acacen)(L)2](+) complexes inhibit zinc finger transcription factor activity through selectively coordinating His residues in the zinc finger by dissociative ligand exchange and disrupting the ββα structural motif required for gene regulation.
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Affiliation(s)
- Marie C Heffern
- Department of Chemistry, Molecular Biosciences, Neurobiology, Biomedical Engineering, and Radiology, Northwestern University, Evanston, Illinois 60208-3113 (USA)
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32
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The transcriptional repressor domain of Gli3 is intrinsically disordered. PLoS One 2013; 8:e76972. [PMID: 24146948 PMCID: PMC3798401 DOI: 10.1371/journal.pone.0076972] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 08/26/2013] [Indexed: 01/03/2023] Open
Abstract
The transcription factor Gli3 is acting mainly as a transcriptional repressor in the Sonic hedgehog signal transduction pathway. Gli3 contains a repressor domain in its N-terminus from residue G106 to E236. In this study we have characterized the intracellular structure of the Gli3 repressor domain using a combined bioinformatics and experimental approach. According to our findings the Gli3 repressor domain while being intrinsically disordered contains predicted anchor sites for partner interactions. The obvious interaction partners to test were Ski and DNA; however, with both of these the structure of Gli3 repressor domain remained disordered. To locate residues important for the repressor function we mutated several residues within the Gli3 repressor domain. Two of these, H141A and H157N, targeting predicted helical regions, significantly decreased transcriptional repression and thus identify important functional parts of the domain.
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Chandak MS, Nakamura T, Makabe K, Takenaka T, Mukaiyama A, Chaudhuri TK, Kato K, Kuwajima K. The H/D-exchange kinetics of the Escherichia coli co-chaperonin GroES studied by 2D NMR and DMSO-quenched exchange methods. J Mol Biol 2013; 425:2541-60. [PMID: 23583779 DOI: 10.1016/j.jmb.2013.04.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 03/29/2013] [Accepted: 04/05/2013] [Indexed: 11/18/2022]
Abstract
We studied hydrogen/deuterium-exchange reactions of peptide amide protons of GroES using two different techniques: (1) two-dimensional (1)H-(15)N transverse-optimized NMR spectroscopy and (2) the dimethylsulfoxide-quenched hydrogen-exchange method combined with conventional (1)H-(15)N heteronuclear single quantum coherence spectroscopy. By using these techniques together with direct heteronuclear single quantum coherence experiments, we quantitatively evaluated the exchange rates for 33 out of the 94 peptide amide protons of GroES and their protection factors, and for the remaining 61 residues, we obtained the lower limits of the exchange rates. The protection factors of the most highly protected amide protons were on the order of 10(6)-10(7), and the values were comparable in magnitude to those observed in typical small globular proteins, but the number of the highly protected amide protons with a protection factor larger than 10(6) was only 10, significantly smaller than the numbers reported for the small globular proteins, indicating that significant portions of free heptameric GroES are flexible and natively unfolded. The highly protected amino acid residues with a protection factor larger than 10(5) were mainly located in three β-strands that form the hydrophobic core of GroES, while the residues in a mobile loop (residues 17-34) were not highly protected. The protection factors of the most highly protected amide protons were orders of magnitude larger than the value expected from the equilibrium unfolding parameters previously reported, strongly suggesting that the equilibrium unfolding of GroES is more complicated than a simple two-state or three-state mechanism and may involve more than a single intermediate.
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Affiliation(s)
- Mahesh S Chandak
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
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34
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Palmieri M, Malgieri G, Russo L, Baglivo I, Esposito S, Netti F, Del Gatto A, de Paola I, Zaccaro L, Pedone PV, Isernia C, Milardi D, Fattorusso R. Structural Zn(II) Implies a Switch from Fully Cooperative to Partly Downhill Folding in Highly Homologous Proteins. J Am Chem Soc 2013; 135:5220-8. [DOI: 10.1021/ja4009562] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Maddalena Palmieri
- Department of Environmental,
Biological and Pharmaceutical Science and Technology, Second University of Naples, Via Vivaldi 43, 81100
Caserta, Italy
| | - Gaetano Malgieri
- Department of Environmental,
Biological and Pharmaceutical Science and Technology, Second University of Naples, Via Vivaldi 43, 81100
Caserta, Italy
| | - Luigi Russo
- Department of Environmental,
Biological and Pharmaceutical Science and Technology, Second University of Naples, Via Vivaldi 43, 81100
Caserta, Italy
| | - Ilaria Baglivo
- Department of Environmental,
Biological and Pharmaceutical Science and Technology, Second University of Naples, Via Vivaldi 43, 81100
Caserta, Italy
| | - Sabrina Esposito
- Department of Environmental,
Biological and Pharmaceutical Science and Technology, Second University of Naples, Via Vivaldi 43, 81100
Caserta, Italy
| | - Fortuna Netti
- Department of Environmental,
Biological and Pharmaceutical Science and Technology, Second University of Naples, Via Vivaldi 43, 81100
Caserta, Italy
| | - Annarita Del Gatto
- Institute of Biostructures and Bioimaging-CNR (Naples), Via Mezzocannone 16, 80134
Naples, Italy
| | - Ivan de Paola
- Institute of Biostructures and Bioimaging-CNR (Naples), Via Mezzocannone 16, 80134
Naples, Italy
| | - Laura Zaccaro
- Institute of Biostructures and Bioimaging-CNR (Naples), Via Mezzocannone 16, 80134
Naples, Italy
| | - Paolo V. Pedone
- Department of Environmental,
Biological and Pharmaceutical Science and Technology, Second University of Naples, Via Vivaldi 43, 81100
Caserta, Italy
| | - Carla Isernia
- Department of Environmental,
Biological and Pharmaceutical Science and Technology, Second University of Naples, Via Vivaldi 43, 81100
Caserta, Italy
| | - Danilo Milardi
- Institute of Biostructures and Bioimaging-CNR (Catania), Viale A. Doria 6, 95125
Catania, Italy
| | - Roberto Fattorusso
- Department of Environmental,
Biological and Pharmaceutical Science and Technology, Second University of Naples, Via Vivaldi 43, 81100
Caserta, Italy
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35
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Kim S, Wu KP, Baum J. Fast hydrogen exchange affects ¹⁵N relaxation measurements in intrinsically disordered proteins. JOURNAL OF BIOMOLECULAR NMR 2013; 55:249-256. [PMID: 23314729 PMCID: PMC3615062 DOI: 10.1007/s10858-013-9706-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2012] [Accepted: 01/05/2013] [Indexed: 05/31/2023]
Abstract
Unprotected amide protons can undergo fast hydrogen exchange (HX) with protons from the solvent. Generally, NMR experiments using the out-and-back coherence transfer with amide proton detection are affected by fast HX and result in reduced signal intensity. When one of these experiments, (1)H-(15)N HSQC, is used to measure the (15)N transverse relaxation rate (R2), the measured R2 rate is convoluted with the HX rate (kHX) and has higher apparent R2 values. Since the (15)N R2 measurement is important for analyzing protein backbone dynamics, the HX effect on the R2 measurement is investigated and described here by multi-exponential signal decay. We demonstrate these effects by performing (15)N R 2 (CPMG) experiments on α-synuclein, an intrinsically disordered protein, in which the amide protons are exposed to solvent. We show that the HX effect on R 2 (CPMG) can be extracted by the derived equation. In conclusion, the HX effect may be pulse sequence specific and results from various sources including the J coupling evolution, the change of steady state water proton magnetization, and the D2O content in the sample. To avoid the HX effect on the analysis of relaxation data of unprotected amides, it is suggested that NMR experimental conditions insensitive to the HX should be considered or that intrinsic R 2 (CPMG) values be obtained by methods described herein.
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Affiliation(s)
- Seho Kim
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, 08854
| | - Kuen-Phon Wu
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, 08854
| | - Jean Baum
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, 08854
- BioMaPS Institute for Quantitative Biology, Rutgers University, Piscataway, New Jersey, 08854
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36
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Alexandrescu AT. Amide proton solvent protection in amylin fibrils probed by quenched hydrogen exchange NMR. PLoS One 2013; 8:e56467. [PMID: 23457571 PMCID: PMC3574092 DOI: 10.1371/journal.pone.0056467] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2012] [Accepted: 01/11/2013] [Indexed: 11/24/2022] Open
Abstract
Amylin is an endocrine hormone that accumulates in amyloid plaques in patients with advanced type 2 diabetes. The amyloid plaques have been implicated in the destruction of pancreatic β-cells, which synthesize amylin and insulin. To better characterize the secondary structure of amylin in amyloid fibrils we assigned the NMR spectrum of the unfolded state in 95% DMSO and used a quenched hydrogen-deuterium exchange technique to look at amide proton solvent protection in the fibrils. In this technique, partially exchanged fibrils are dissolved in 95% DMSO and information about amide proton occupancy in the fibrils is determined from DMSO-denatured monomers. Hydrogen exchange lifetimes at pH 7.6 and 37°C vary between ∼5 h for the unstructured N-terminus to 600 h for amide protons in the two β-strands that form inter-molecular hydrogen bonds between amylin monomers along the length of the fibril. Based on the protection data we conclude that residues A8-H18 and I26-Y37 comprise the two β-strands in amylin fibrils. There is variation in protection within the β-strands, particularly for strand β1 where only residues F15-H18 are strongly protected. Differences in protection appear to be due to restrictions on backbone dynamics imposed by the packing of two-layers of C2-symmetry-related β-hairpins in the protofilament structure, with strand β1 positioned on the surface and β2 in the interior.
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Affiliation(s)
- Andrei T Alexandrescu
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America.
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37
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Chandak MS, Nakamura T, Takenaka T, Chaudhuri TK, Yagi-Utsumi M, Chen J, Kato K, Kuwajima K. The use of spin desalting columns in DMSO-quenched H/D-exchange NMR experiments. Protein Sci 2013; 22:486-91. [PMID: 23339068 DOI: 10.1002/pro.2221] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 01/10/2013] [Accepted: 01/12/2012] [Indexed: 01/22/2023]
Abstract
Dimethylsulfoxide (DMSO)-quenched hydrogen/deuterium (H/D)-exchange is a powerful method to characterize the H/D-exchange behaviors of proteins and protein assemblies, and it is potentially useful for investigating non-protected fast-exchanging amide protons in the unfolded state. However, the method has not been used for studies on fully unfolded proteins in a concentrated denaturant or protein solutions at high salt concentrations. In all of the current DMSO-quenched H/D-exchange studies of proteins so far reported, lyophilization was used to remove D2 O from the protein solution, and the lyophilized protein was dissolved in the DMSO solution to quench the H/D exchange reactions and to measure the amide proton signals by two-dimensional nuclear magnetic resonance (2D NMR) spectra. The denaturants or salts remaining after lyophilization thus prevent the measurement of good NMR spectra. In this article, we report that the use of spin desalting columns is a very effective alternative to lyophilization for the medium exchange from the D2 O buffer to the DMSO solution. We show that the medium exchange by a spin desalting column takes only about 10 min in contrast to an overnight length of time required for lyophilization, and that the use of spin desalting columns has made it possible to monitor the H/D-exchange behavior of a fully unfolded protein in a concentrated denaturant. We report the results of unfolded ubiquitin in 6.0M guanidinium chloride.
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Affiliation(s)
- Mahesh S Chandak
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
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38
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Nieuwland M, Ruizendaal L, Brinkmann A, Kroon-Batenburg L, van Hest JCM, Löwik DWPM. A structural study of the self-assembly of a palmitoyl peptide amphiphile. Faraday Discuss 2013; 166:360-79. [DOI: 10.1039/c3fd00055a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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39
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Noda Y, Narama K, Kasai K, Tachibana H, Segawa SI. Glycerol-enhanced detection of a preferential structure latent in unstructured 1SS-variants of lysozyme. Biopolymers 2012; 97:539-49. [DOI: 10.1002/bip.22037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Accepted: 02/10/2012] [Indexed: 02/01/2023]
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40
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Vilar M, Wang L, Riek R. Structural studies of amyloids by quenched hydrogen-deuterium exchange by NMR. Methods Mol Biol 2012; 849:185-198. [PMID: 22528091 DOI: 10.1007/978-1-61779-551-0_13] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The elucidation of the structure of amyloid fibrils and related aggregates is an important step towards understanding the pathogenesis of diseases such as Alzheimer's and Parkinson's, which feature protein misfolding and/or aggregation. However, the large size and poor solubility of amyloid-like fibrils make them resistant to high-resolution structure determination. Here, we describe the use of hydrogen-deuterium exchange coupled with NMR as an indirect strategy to determine the folding regions of amyloid-forming proteins at residue level resolution.
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Affiliation(s)
- Marçal Vilar
- Neurodegeneration Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain.
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41
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Li J, Hoop CL, Kodali R, Sivanandam VN, van der Wel PCA. Amyloid-like fibrils from a domain-swapping protein feature a parallel, in-register conformation without native-like interactions. J Biol Chem 2011; 286:28988-28995. [PMID: 21715337 PMCID: PMC3190706 DOI: 10.1074/jbc.m111.261750] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Revised: 06/21/2011] [Indexed: 11/06/2022] Open
Abstract
The formation of amyloid-like fibrils is characteristic of various diseases, but the underlying mechanism and the factors that determine whether, when, and how proteins form amyloid, remain uncertain. Certain mechanisms have been proposed based on the three-dimensional or runaway domain swapping, inspired by the fact that some proteins show an apparent correlation between the ability to form domain-swapped dimers and a tendency to form fibrillar aggregates. Intramolecular β-sheet contacts present in the monomeric state could constitute intermolecular β-sheets in the dimeric and fibrillar states. One example is an amyloid-forming mutant of the immunoglobulin binding domain B1 of streptococcal protein G, which in its native conformation consists of a four-stranded β-sheet and one α-helix. Under native conditions this mutant adopts a domain-swapped dimer, and it also forms amyloid-like fibrils, seemingly in correlation to its domain-swapping ability. We employ magic angle spinning solid-state NMR and other methods to examine key structural features of these fibrils. Our results reveal a highly rigid fibril structure that lacks mobile domains and indicate a parallel in-register β-sheet structure and a general loss of native conformation within the mature fibrils. This observation contrasts with predictions that native structure, and in particular intermolecular β-strand interactions seen in the dimeric state, may be preserved in "domain-swapping" fibrils. We discuss these observations in light of recent work on related amyloid-forming proteins that have been argued to follow similar mechanisms and how this may have implications for the role of domain-swapping propensities for amyloid formation.
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Affiliation(s)
- Jun Li
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260
| | - Cody L Hoop
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260
| | - Ravindra Kodali
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260
| | - V N Sivanandam
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260
| | - Patrick C A van der Wel
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260.
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42
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Damo SM, Phillips AH, Young AL, Li S, Woods VL, Wemmer DE. Probing the conformation of a prion protein fibril with hydrogen exchange. J Biol Chem 2010; 285:32303-11. [PMID: 20679344 DOI: 10.1074/jbc.m110.114504] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
A fragment of the prion protein, PrP(89-143, P101L), bearing a mutation implicated in familial prion disease, forms fibrils that have been shown to induce prion disease when injected intracerebrally into transgenic mice expressing full-length PrP containing the P101L mutation. In this study, we utilize amide hydrogen exchange measurements to probe the organization of the peptide in its fibrillar form. We determined the extent of hydrogen exchange first by tandem proteolysis, liquid chromatography, and mass spectrometry (HXMS) and then by exchange-quenched NMR. Although single amide resolution is afforded by NMR measurements, HXMS is well suited to the study of natural prions because it does not require labeling with NMR active isotopes. Thus, natural prions obtained from infected animals can be compared with model systems such as PrP(89-143, P101L) studied here. In our study, we find two segments of sequence that display a high level of protection from exchange, residues 102-109 and 117-136. In addition, there is a region that displays exchange behavior consistent with the presence of a conformationally heterogeneous turn. We discuss our data with respect to several structural models proposed for infectious PrP aggregates and highlight HXMS as one of the few techniques well suited to studying natural prions.
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Affiliation(s)
- Steven M Damo
- Department of Chemistry, University of California, Berkeley, California 94720, USA
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43
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Enantiodifferent proton exchange in alanine and asparagine in the presence of H(2)(17)O. J Mol Evol 2010; 71:23-33. [PMID: 20593168 DOI: 10.1007/s00239-010-9361-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2009] [Accepted: 05/26/2010] [Indexed: 10/19/2022]
Abstract
Using Time Domain (1)H Nuclear Magnetic Resonance with H (2) (17) O (H (2) (17) O-TD-(1)HNMR), we found [H (2) (17) O]- and pH-controlled chiral differences in proton exchange properties in alanine (Ala) and asparagine (Asn). To minimize and equalize chemical impurities, Asn enantiomers were purified by crystallization from racemic solution. At <0.1 M H (2) (17) O, a shift in isoelectric pH (pI) occurred, approximately 1.14 kJ mol(-1) L: -D: -Asn DeltaDeltaG (o)' in the 5.91-6.42 pH range. One potential source for this asymmetry is the enantio-different magnetic moments (L: mu upward arrow not equal D: mu downward arrow) produced by neutral ring currents in the chiral center, leading to enantio-different nuclear spin organization and charge distribution in the amino group. At >or=pI, dissimilar interactions may occur in the hydration of the amino group with H (2) (17) O (NH(2)/H (2) (17) O not equal NH(2)/H (2) (16) O; NH(3) (+)/H (2) (17) O not equal NH(2)/H (2) (17) O; L: -*C-NH(2)/H (2) (17) O not equal D: -*C-NH(2)/H (2) (17) O). As L: mu upward arrow not equal D: mu downward arrow, the L: -*C-amino and the D: -*C-amino groups are diastereo spin-isomers. The nuclear spin of (17)O may be parallel or antiparallel with the ortho-(1)H(1)H pair; hence two ortho-H (2) (17) O molecules exist, also diastereo spin-isomers. As the pK of H (2) (17) O is different from H (2) (16) O, dissimilarities between L: -*C- and D: -*C-amino groups are converted into proton exchange differences. During H (2) (17) O-TD-(1)HNMR, the H (2) (17) O molecule is a "probe" of the state of the amino group. Regarding prebiotic evolution: prebiotic chirality may not require stochastic symmetry breaking or preexisting chiral conditions; chemical chiral effects due to L: mu upward arrow not equal D: mu downward arrow are small and need chiral amplification to generate an enantiomeric excess significant for prebiotic evolution; and prebiotic symmetry breaking was homochiral because the effect of L: mu upward arrow and D: mu downward arrow on the amino group should be similar in all alpha amino acids.
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Kato H, Gruschus J, Ghirlando R, Tjandra N, Bai Y. Characterization of the N-terminal tail domain of histone H3 in condensed nucleosome arrays by hydrogen exchange and NMR. J Am Chem Soc 2009; 131:15104-5. [PMID: 19795894 PMCID: PMC3523682 DOI: 10.1021/ja9070078] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The N-terminal tail domains (NTDs) of histones play important roles in the formation of higher-order structures of chromatin and the regulation of gene functions. Although the structure of the nucleosome core particle has been determined by X-ray crystallography at near-atomic resolution, the histone tails are not observed in this structure. Here, we demonstrate that large quantities of nucleosome arrays with well-defined DNA positioning can be reconstituted using specific DNA sequences and recombinant isotope-labeled histones, allowing for the investigation of NTD conformations by amide hydrogen exchange and multidimensional nuclear magnetic resonance (NMR) methods. We examined the NTD of Drosophila melanogaster histones H3 in condensed nucleosome arrays. The results reveal that the majority of the amide protons in the NTD of H3 are protected from exchange, consistent with the NTDs having formed folded structures. Our study demonstrates hydrogen exchange coupled with NMR can provide residue-by-residue characterization of NTDs of histones in condensed nucleosome arrays, a technique that may be used to study NTDs of other histones and those with post-translational modifications.
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Affiliation(s)
- Hidenori Kato
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892
| | - James Gruschus
- Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892
| | - Nico Tjandra
- Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892
| | - Yawen Bai
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892
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Sakamoto K, Hirai KI, Kitamura Y, Yamazaki K, Yusa M, Tokunaga N, Doi G, Noda Y, Tachibana H, Segawa SI. Glycerol-induced folding of unstructured disulfide-deficient lysozyme into a native-like conformation. Biopolymers 2009; 91:665-75. [PMID: 19353641 DOI: 10.1002/bip.21198] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
2SS[6-127,64-80] variant of lysozyme which has two disulfide bridges, Cys6-Cys127 and Cys64-Cys80, and lacks the other two disulfide bridges, Cys30-Cys115 and Cys76-Cys94, was quite unstructured in water, but a part of the polypeptide chain was gradually frozen into a native-like conformation with increasing glycerol concentration. It was monitored from the protection factors of amide hydrogens against H/D exchange. In solution containing various concentrations of glycerol, H/D exchange reactions were carried out at pH* 3.0 and 4 degrees C. Then, (1)H-(15)N-HSQC spectra of partially deuterated protein were measured in a quenching buffer for H/D exchange (95% DMSO/5% D(2)O mixture at pH* 5.5 adjusted with dichloroacetate). In a solution of 10% glycerol, the protection factors were nearly equal to 10 at most of residues. With increasing glycerol concentration, some selected regions were further protected, and their protection factors reached about a 1000 in 30% glycerol solution. The highly protected residues were included in A-, B-, and C-helices and beta3-strand, and especially centered on Ile 55 and Leu 56. In 2SS[6-127,64-80], long-range interactions were recovered due to the preferential hydration by glycerol in the hydrophobic box of the alpha-domain. Glycerol-induced recovering of the native-like structure is discussed from the viewpoint of molten globules growing with the protein folding. (c) 2009 Wiley Periodicals, Inc. Biopolymers 91: 665-675, 2009.This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com.
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Affiliation(s)
- Keiko Sakamoto
- School of Science and Technology, Kwansei Gakuin University, Sanda, 669-1337, Japan
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Ye T, Mo H, Shanaiah N, Nagana Gowda GA, Zhang S, Raftery D. Chemoselective 15N tag for sensitive and high-resolution nuclear magnetic resonance profiling of the carboxyl-containing metabolome. Anal Chem 2009; 81:4882-8. [PMID: 19518144 PMCID: PMC2861042 DOI: 10.1021/ac900539y] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metabolic profiling has received increasing recognition as an indispensable complement to genomics and proteomics for probing biological systems and for clinical applications. (1)H nuclear magnetic resonance (NMR) is widely used in the field but is challenged by spectral complexity and overlap. Improved and simple methods that quantitatively profile a large number of metabolites are sought to make further progress. Here, we demonstrate a simple isotope tagging strategy, in which metabolites with carboxyl groups are chemically tagged with (15)N-ethanolamine and detected using a 2D heteronuclear correlation NMR experiment. This method is capable of detecting over 100 metabolites at concentrations as low as a few micromolar in biological samples, both quantitatively and reproducibly. Carboxyl-containing compounds are found in almost all metabolic pathways, and thus this new approach should find a variety of applications.
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Affiliation(s)
- Tao Ye
- Department of Chemistry, Purdue University, West Lafayette, IN 47907
| | - Huaping Mo
- Purdue Inter-Departmental NMR Facility, Purdue University, West Lafayette, IN 47907
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907
| | | | | | - Shucha Zhang
- Department of Chemistry, Purdue University, West Lafayette, IN 47907
| | - Daniel Raftery
- Department of Chemistry, Purdue University, West Lafayette, IN 47907
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Svane ASP, Jahn K, Deva T, Malmendal A, Otzen DE, Dittmer J, Nielsen NC. Early stages of amyloid fibril formation studied by liquid-state NMR: the peptide hormone glucagon. Biophys J 2008; 95:366-77. [PMID: 18339765 PMCID: PMC2426625 DOI: 10.1529/biophysj.107.122895] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2007] [Accepted: 02/21/2008] [Indexed: 11/18/2022] Open
Abstract
The 29-residue peptide hormone glucagon forms amyloid fibrils within a few hours at low pH. In this study, we use glucagon as a model system to investigate fibril formation by liquid-state (1)H-NMR spectroscopy One-dimensional, correlation, and diffusion experiments monitoring the fibril formation process provide insight into the early stages of the pathway on which the molecules aggregate to fibrils. In conjunction with these techniques, exchange experiments give information about the end-state conformation. Within the limits of detection, there are no signs of larger oligomeric intermediates in the course of the fibril formation process. Kinetic information is extracted from the time course of the residual free glucagon signal decay. This suggests that glucagon amyloids form by a nucleated growth mechanism in which trimers (rather than monomers) of glucagon interact directly with the growing fibrils rather than with each other. The results of proton/deuterium exchange experiments on mature fibrils with subsequent dissolution show that the N-terminal of glucagon is the least amenable to exchange, which indicates that this part is strongly involved in the intermolecular bonds of the fibrils.
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Affiliation(s)
- Anna Sigrid Pii Svane
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, Denmark
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The His–His sequence of the antimicrobial peptide demegen P-113 makes it very attractive ligand for Cu2+. J Inorg Biochem 2008; 102:960-72. [DOI: 10.1016/j.jinorgbio.2007.12.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2007] [Revised: 11/09/2007] [Accepted: 12/22/2007] [Indexed: 11/24/2022]
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Morgan GJ, Giannini S, Hounslow AM, Craven CJ, Zerovnik E, Turk V, Waltho JP, Staniforth RA. Exclusion of the native alpha-helix from the amyloid fibrils of a mixed alpha/beta protein. J Mol Biol 2008; 375:487-98. [PMID: 18021806 DOI: 10.1016/j.jmb.2007.10.033] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2007] [Revised: 10/08/2007] [Accepted: 10/13/2007] [Indexed: 11/17/2022]
Abstract
Members of the cystatin superfamily are involved in an inherited form of cerebral amyloid angiopathy and readily form amyloid fibrils in vitro. We have determined the structured core of human stefin B (cystatin B) amyloid fibrils using quenched hydrogen exchange and NMR. The core contains residues from four of the five strands of the native beta-sheet, delimited by unprotected loop regions analogous to those of the native monomeric structure. However, non-native features are also apparent, the most striking of which is the exclusion of the native alpha-helix. Before forming amyloid in vitro, cystatins dimerise via 3D domain swapping, and assemble into tetramers with trans to cis isomerism of a conserved proline. In the fibril, the hinge loop that forms an extended beta-structure in the dimer remains protected, consistent with the domain-swapping interface being maintained. However, the fibril data are not compatible with a simple 3D domain-swapping model for amyloid formation, and the displacement of the helix points to alternative packing arrangements of native-like beta-structure, in which proline isomerism is important in preventing steric clashing.
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Affiliation(s)
- Gareth J Morgan
- Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
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Scorei RI, Cimpoiaşu VM, Popa R. TD-1HNMR measurements show enantioselective dissociation of ribose and glucose in the presence of H2(17)O. ASTROBIOLOGY 2007; 7:733-744. [PMID: 17963473 DOI: 10.1089/ast.2006.0076] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We used Time Domain (1)H Nuclear Magnetic Resonance (NMR) to characterize changes in proton exchange between water and sugar enantiomers at different concentrations of H(2)(17)O (approximately 15-450 mM) and found that dissociation of the (-)-enantiomers of glucose and ribose occurs at significantly higher rates at higher concentrations of H(2)(17)O. The mechanism behind this enantioselective effect is unclear. The hypothesis we propose is that the large magnetic field (B(o) approximately 0.6T) applied during NMR measurements induces electric moments opposite in sign for the D and L-isomers. Because (17)O has a nuclear electric quadrupole moment not = 0, asymmetrically hydrated complexes may form between the B(o)-polarized enantiomers and H(2)(17)O. Either H(2)(17)O is more often hydrating the (+) than the (-)-enantiomers--and consequently pK differences between H(2)(16)O and H(2)(17)O lead to differences in proton exchange between enantiomers and water--or the orientation of H(2)(17)O relative to the B(o)-polarized enantiomers is different, in total or in part, which leads to hydrated complexes with different spatial geometries and different proton exchange properties. This effect is significant for Magneto-Chiral Stereo-Chemistry (MCSC) and astrobiology, and it may help us better understand specific instances of mass independent isotopic fractionation and aid in the development of new technologies for chiral and isotopic separation.
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