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Takis PG, Vučković I, Kowalka AM, Tan T, Šuvakov M, Meloche R, Lanza IR, Macura S. Toward Absolute Quantification of Soluble Proteins via Proton Nuclear Magnetic Resonance Spectroscopy: Total Protein Concentration in Blood Plasma. Anal Chem 2024. [PMID: 39365892 DOI: 10.1021/acs.analchem.4c02711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2024]
Abstract
For absolute protein quantification using nuclear magnetic resonance (NMR) spectroscopy, we considered proteins as homopolymers and effective amino acid (AA) residues (AAREff) as monomer units. For diverse classes of proteins, we determined the AAREff molecular weight as 111.5 ± 3.2 Da and the number of hydrogens per AA as 7.8 ± 0.2. Their ratio of 14.3 ± 0.3 (g/LP)/(mol/LH) remains constant across various protein classes and is equivalent to Kjeldahl's nitrogen-to-protein conversion constant of 5.78 ± 0.29 gN/gP. By analogy to the Kjeldahl method, we suggest that the total integral of a 1H NMR solution protein spectrum could be used for total protein quantification. We synthesized low-resolution protein spectra from the weighted sums of individual AA spectra and compared them with experimental spectra. In the methyl region, the ratio of the protein mass to the total number of protons in the synthetic spectra (corrected for the chemical shift mismatch) was ∼1 (mg/mL)/mM, which agrees with an earlier reported experimental ratio for urine (1.05 ± 0.06 (mg/mL)/mM). For human blood plasma, in the methyl region, we found empirical ratios of 1.115 ± 0.006 (mg/mL)/mM (using 96 patient samples) and 1.121 ± 0.011 (mg/mL)/mM for the NIST plasma standard. This numerical agreement points to universal conversion constants, i.e., protein mixtures with unknown compositions could be quantified without the need for calibration standards by measuring the millimolar proton concentration within the methyl region of the NMR spectrum using the same conversion constant.
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Affiliation(s)
- Panteleimon G Takis
- Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion, and Reproduction, Imperial College London, London SW7 2AZ, U.K
- National Phenome Center, Department of Metabolism, Digestion, and Reproduction, Imperial College London, London W12 0NN, U.K
- Section of Analytical Chemistry, Department of Chemistry, University of Ioannina, Ioannina 45110, Greece
| | - Ivan Vučković
- Metabolomics Core, Mayo Clinic, Rochester, Minnesota 55905, United States
| | - Anna M Kowalka
- Section of Endocrinology and Investigative Medicine, Division of Diabetes, Endocrinology, and Metabolism, Department of Metabolism, Digestion, and Reproduction, Imperial College London, London SW7 2AZ, U.K
| | - Tricia Tan
- Section of Endocrinology and Investigative Medicine, Division of Diabetes, Endocrinology, and Metabolism, Department of Metabolism, Digestion, and Reproduction, Imperial College London, London SW7 2AZ, U.K
| | - Milovan Šuvakov
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, United States
| | - Ryan Meloche
- Metabolomics Core, Mayo Clinic, Rochester, Minnesota 55905, United States
| | - Ian R Lanza
- Metabolomics Core, Mayo Clinic, Rochester, Minnesota 55905, United States
- Division of Endocrinology and Metabolism, Mayo Clinic College of Medicine, Rochester, Minnesota 55905, United States
| | - Slobodan Macura
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905, United States
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2
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Byeon CH, Hansen KH, DePas W, Akbey Ü. High-resolution 2D solid-state NMR provides insights into nontuberculous mycobacteria. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2024; 134:101970. [PMID: 39312837 DOI: 10.1016/j.ssnmr.2024.101970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 09/05/2024] [Accepted: 09/09/2024] [Indexed: 09/25/2024]
Abstract
We present a high-resolution magic-angle spinning (MAS) solid-state NMR (ssNMR) study to characterize nontuberculous mycobacteria (NTM). We studied two different NTM strains, Mycobacterium smegmatis, a model, non-pathogenic strain, and Mycobacterium abscessus, an emerging and important human pathogen. Hydrated NTM samples were studied at natural abundance without isotope-labelling, as whole-cells versus cell envelope isolates, and native versus fixed sample preparations. We utilized 1D13C and 2D 1H-13C ssNMR spectra and peak deconvolution to identify NTM cell-wall chemical sites. More than ∼100 distinct 13C signals were identified in the ssNMR spectra. We provide tentative assignments for ∼30 polysaccharides by using well resolved 1H/13C chemical shifts from the 2D INEPT-based 1H-13C ssNMR spectrum. The signals originating from both the flexible and rigid fractions of the whole-cell bacteria samples were selectively analyzed by utilizing either CP or INEPT based 13C ssNMR spectra. CP buildup curves provide insights into the dynamical similarity of the cell-wall components for NTM strains. Signals from peptidoglycan, arabinogalactan and mycolic acid were identified. The majority of the 13C signals were not affected by fixation of the whole cell samples. The isolated cell envelope NMR spectrum overlap with the whole-cell spectrum to a large extent, where the latter has more signals. As an orthogonal way of characterizing these bacteria, electron microscopy (EM) was used to provide spatial information. ssNMR and EM data suggest that the M. abscessus cell-wall is composed of a smaller peptidoglycan layer which is more flexible compared to M. smegmatis, which may be related to its higher pathogenicity. Here in this work, we used high-resolution 2D ssNMR first time to characterize NTM strains and identify chemical sites. These results will aid the development of structure-based approaches to combat NTM infections.
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Affiliation(s)
| | | | - William DePas
- Department of Pediatrics, School of Medicine, University of Pittsburgh, Pittsburgh, 15261, United States
| | - Ümit Akbey
- Department of Structural Biology, United States.
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3
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Peck Y, Pickering D, Mobli M, Liddell MJ, Wilson DT, Ruscher R, Ryan S, Buitrago G, McHugh C, Love NC, Pinlac T, Haertlein M, Kron MA, Loukas A, Daly NL. Solution structure of the N-terminal extension domain of a Schistosoma japonicum asparaginyl-tRNA synthetase. J Biomol Struct Dyn 2024; 42:7934-7944. [PMID: 37572327 DOI: 10.1080/07391102.2023.2241918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 07/24/2023] [Indexed: 08/14/2023]
Abstract
Several secreted proteins from helminths (parasitic worms) have been shown to have immunomodulatory activities. Asparaginyl-tRNA synthetases are abundantly secreted in the filarial nematode Brugia malayi (BmAsnRS) and the parasitic flatworm Schistosoma japonicum (SjAsnRS), indicating a possible immune function. The suggestion is supported by BmAsnRS alleviating disease symptoms in a T-cell transfer mouse model of colitis. This immunomodulatory function is potentially related to an N-terminal extension domain present in eukaryotic AsnRS proteins but few structure/function studies have been done on this domain. Here we have determined the three-dimensional solution structure of the N-terminal extension domain of SjAsnRS. A protein containing the 114 N-terminal amino acids of SjAsnRS was recombinantly expressed with isotopic labelling to allow structure determination using 3D NMR spectroscopy, and analysis of dynamics using NMR relaxation experiments. Structural comparisons of the N-terminal extension domain of SjAsnRS with filarial and human homologues highlight a high degree of variability in the β-hairpin region of these eukaryotic N-AsnRS proteins, but similarities in the disorder of the C-terminal regions. Limitations in PrDOS-based intrinsically disordered region (IDR) model predictions were also evident in this comparison. Empirical structural data such as that presented in our study for N-SjAsnRS will enhance the prediction of sequence-homology based structure modelling and prediction of IDRs in the future.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yoshimi Peck
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Darren Pickering
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Mehdi Mobli
- Centre for Advanced Imaging, The University of Queensland, St Lucia, QLD, Australia
| | - Michael J Liddell
- College of Science and Engineering, James Cook University, Cairns, QLD, Australia
| | - David T Wilson
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Roland Ruscher
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Stephanie Ryan
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Geraldine Buitrago
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Connor McHugh
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | | | - Theresa Pinlac
- Department of Biochemistry, University of the Philippines, Manila, Philippines
| | | | - Michael A Kron
- Department of Medicine, Division of Infectious Diseases, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Alex Loukas
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Norelle L Daly
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
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4
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Yu S, Qin R, Yuan W, Lin Z. 1H, 15N and 13C resonance assignments of eggcase silk protein 3. BIOMOLECULAR NMR ASSIGNMENTS 2024:10.1007/s12104-024-10192-4. [PMID: 39180712 DOI: 10.1007/s12104-024-10192-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 08/17/2024] [Indexed: 08/26/2024]
Abstract
Spider silk is a high-performance biomaterial known for its outstanding combination of strength and flexibility. Among the six distinct types of spider silk, eggcase silk stands out as it is exclusively produced from the tubuliform gland, playing a specialized role in offspring protection. In the spider species Latrodectus hesperus, eggcase silk is spun from a large spidroin complex, including the major silk component tubuliform spidroin 1 (TuSp1) and at least six different minor silk components. One of these minor components is eggcase protein 3 (ECP3), a small silk protein of 11.8 kDa that lacks the typical spidroin architecture. ECP3 shows very limited homology to all known spidroins. In this study, we report nearly complete backbone and side-chain resonance assignments of ECP3 as a basis for studying the structural mechanisms involved in eggcase silk formation.
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Affiliation(s)
- Shuixin Yu
- School of Life Sciences, Tianjin University, Tianjin, 300072, P.R. China
| | - Ruiqi Qin
- School of Life Sciences, Tianjin University, Tianjin, 300072, P.R. China
| | - Wensu Yuan
- School of Life Sciences, Tianjin University, Tianjin, 300072, P.R. China
| | - Zhi Lin
- School of Life Sciences, Tianjin University, Tianjin, 300072, P.R. China.
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Zhou BR, Feng H, Huang F, Zhu I, Portillo-Ledesma S, Shi D, Zaret KS, Schlick T, Landsman D, Wang Q, Bai Y. Structural insights into the cooperative nucleosome recognition and chromatin opening by FOXA1 and GATA4. Mol Cell 2024; 84:3061-3079.e10. [PMID: 39121853 PMCID: PMC11344660 DOI: 10.1016/j.molcel.2024.07.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 06/10/2024] [Accepted: 07/16/2024] [Indexed: 08/12/2024]
Abstract
Mouse FOXA1 and GATA4 are prototypes of pioneer factors, initiating liver cell development by binding to the N1 nucleosome in the enhancer of the ALB1 gene. Using cryoelectron microscopy (cryo-EM), we determined the structures of the free N1 nucleosome and its complexes with FOXA1 and GATA4, both individually and in combination. We found that the DNA-binding domains of FOXA1 and GATA4 mainly recognize the linker DNA and an internal site in the nucleosome, respectively, whereas their intrinsically disordered regions interact with the acidic patch on histone H2A-H2B. FOXA1 efficiently enhances GATA4 binding by repositioning the N1 nucleosome. In vivo DNA editing and bioinformatics analyses suggest that the co-binding mode of FOXA1 and GATA4 plays important roles in regulating genes involved in liver cell functions. Our results reveal the mechanism whereby FOXA1 and GATA4 cooperatively bind to the nucleosome through nucleosome repositioning, opening chromatin by bending linker DNA and obstructing nucleosome packing.
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Affiliation(s)
- Bing-Rui Zhou
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Hanqiao Feng
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Furong Huang
- Department of Pathology and Duke Cancer Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Iris Zhu
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stephanie Portillo-Ledesma
- Department of Chemistry, New York University, 100 Washington Square East, Silver Building, New York, NY 10003, USA; Simons Center for Computational Physical Chemistry, New York University, 24 Waverly Place, Silver Building, New York, NY 10003, USA
| | - Dan Shi
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Cell and Development Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Tamar Schlick
- Department of Chemistry, New York University, 100 Washington Square East, Silver Building, New York, NY 10003, USA; Simons Center for Computational Physical Chemistry, New York University, 24 Waverly Place, Silver Building, New York, NY 10003, USA; Courant Institute of Mathematical Sciences, New York University, 251 Mercer St., New York, NY 10012, USA; New York University-East China Normal University Center for Computational Chemistry, New York University Shanghai, Shanghai 200122, China
| | - David Landsman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
| | - Qianben Wang
- Department of Pathology and Duke Cancer Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Yawen Bai
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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6
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Smallwood TB, Krumpe LRH, Payne CD, Klein VG, O'Keefe BR, Clark RJ, Schroeder CI, Rosengren KJ. Picking the tyrosine-lock: chemical synthesis of the tyrosyl-DNA phosphodiesterase I inhibitor recifin A and analogues. Chem Sci 2024; 15:13227-13233. [PMID: 39183914 PMCID: PMC11339948 DOI: 10.1039/d4sc01976h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 06/11/2024] [Indexed: 08/27/2024] Open
Abstract
The peptide recifin A is the inaugural member of the structurally intriguing new fold referred to as a tyrosine-lock. Its central four stranded β-sheet is stabilized by a unique arrangement in which three disulfide bonds and their interconnecting backbone form a ring that wraps around one of the strands, resulting in a Tyr side chain being buried in the molecular core. Here we aimed to establish a synthetic route to this complex class of natural products. Full length recifin A was successfully generated through native chemical ligation chemistry joining two 21 amino acid residue fragments. Surprisingly, reduced linear recifin A readily adopts the correct, topologically-complex fold via random oxidation of the cysteines, suggesting it is highly energetically favored. Utilizing our synthetic strategy, we generated five recifin A analogues to investigate the structural role of the central Tyr residue and provide the first insights into the structure activity relationship of recifin A towards its cancer target tyrosyl-DNA phosphodiesterase I.
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Affiliation(s)
- Taylor B Smallwood
- The University of Queensland, School of Biomedical Sciences Brisbane QLD 4072 Australia
| | - Lauren R H Krumpe
- Molecular Targets Program, Centre for Cancer Research, National Cancer Institute, National Institute of Health Frederick MD 21702 USA
| | - Colton D Payne
- The University of Queensland, School of Biomedical Sciences Brisbane QLD 4072 Australia
| | - Victoria G Klein
- Chemical Biology Laboratory, Centre for Cancer Research, National Cancer Institute, National Institute of Health Frederick MD 21702 USA
| | - Barry R O'Keefe
- Molecular Targets Program, Centre for Cancer Research, National Cancer Institute, National Institute of Health Frederick MD 21702 USA
- Natural Products Branch, Centre for Cancer Research, National Cancer Institute, National Institute of Health Frederick MD 21702 USA
| | - Richard J Clark
- The University of Queensland, School of Biomedical Sciences Brisbane QLD 4072 Australia
| | - Christina I Schroeder
- Chemical Biology Laboratory, Centre for Cancer Research, National Cancer Institute, National Institute of Health Frederick MD 21702 USA
- Peptide Therapeutics, Genentech Inc 1 DNA Way South San Francisco CA 94080 USA
| | - K Johan Rosengren
- The University of Queensland, School of Biomedical Sciences Brisbane QLD 4072 Australia
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7
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Ghosh M, Gupta PK, Behera LM, Rana S. Structure of Designer Antibody-like Peptides Binding to the Human C5a with Potential to Modulate the C5a Receptor Signaling. J Med Chem 2024; 67:14110-14124. [PMID: 39051153 DOI: 10.1021/acs.jmedchem.4c00961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
C5a is an integral glycoprotein of the complement system that plays an important role in inflammation and immunity. The physiological concentration of C5a is observed to be elevated under various immunoinflammatory pathophysiological conditions in humans. The pathophysiology of C5a is linked to the "two-site" protein-protein interactions (PPIs) with two genomically related receptors, such as C5aR1 and C5aR2. Therefore, pharmacophores that can potentially block the PPIs between C5a-C5aR1 and C5a-C5aR2 have tremendous potential for development as future therapeutics. Notably, the FDA has already approved antibodies that target the precursors of C5a (Eculizumab, 148 kDa) and C5a (Vilobelimab, 149 kDa) for marketing as complement-targeted therapeutics. In this context, the current study reports the structural characterization of a pair of synthetic designer antibody-like peptides (DePA and DePA1; ≤3.8 kDa) that bind to hotspot regions on C5a and also demonstrates potential traits to neutralize the function of C5a under pathophysiological conditions.
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Affiliation(s)
- Manaswini Ghosh
- Chemical Biology Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, Odisha 752050, India
| | - Pulkit Kr Gupta
- Chemical Biology Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, Odisha 752050, India
| | - Lalita Mohan Behera
- Chemical Biology Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, Odisha 752050, India
| | - Soumendra Rana
- Chemical Biology Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, Odisha 752050, India
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8
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Tehrani MJ, Matsuda I, Yamagata A, Kodama Y, Matsunaga T, Sato M, Toyooka K, McElheny D, Kobayashi N, Shirouzu M, Ishii Y. E22G Aβ40 fibril structure and kinetics illuminate how Aβ40 rather than Aβ42 triggers familial Alzheimer's. Nat Commun 2024; 15:7045. [PMID: 39147751 PMCID: PMC11327332 DOI: 10.1038/s41467-024-51294-w] [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: 12/22/2023] [Accepted: 08/05/2024] [Indexed: 08/17/2024] Open
Abstract
Arctic (E22G) mutation in amyloid-β (Aβ enhances Aβ40 fibril accumulation in Alzheimer's disease (AD). Unlike sporadic AD, familial AD (FAD) patients with the mutation exhibit more Aβ40 in the plaque core. However, structural details of E22G Aβ40 fibrils remain elusive, hindering therapeutic progress. Here, we determine a distinctive W-shaped parallel β-sheet structure through co-analysis by cryo-electron microscopy (cryoEM) and solid-state nuclear magnetic resonance (SSNMR) of in-vitro-prepared E22G Aβ40 fibrils. The E22G Aβ40 fibrils displays typical amyloid features in cotton-wool plaques in the FAD, such as low thioflavin-T fluorescence and a less compact unbundled morphology. Furthermore, kinetic and MD studies reveal previously unidentified in-vitro evidence that E22G Aβ40, rather than Aβ42, may trigger Aβ misfolding in the FAD, and prompt subsequent misfolding of wild-type (WT) Aβ40/Aβ42 via cross-seeding. The results provide insight into how the Arctic mutation promotes AD via Aβ40 accumulation and cross-propagation.
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Affiliation(s)
- Mohammad Jafar Tehrani
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8503, Japan
| | - Isamu Matsuda
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8503, Japan
| | - Atsushi Yamagata
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Yu Kodama
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8503, Japan
| | - Tatsuya Matsunaga
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8503, Japan
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Mayuko Sato
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Kiminori Toyooka
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Dan McElheny
- Department of Chemistry, University of Illinois at Chicago, 845 W Taylor St, Chicago, IL, 60607, USA
| | - Naohiro Kobayashi
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Mikako Shirouzu
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Yoshitaka Ishii
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8503, Japan.
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
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9
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Hansen KH, Byeon CH, Liu Q, Drace T, Boesen T, Conway JF, Andreasen M, Akbey Ü. Structure of biofilm-forming functional amyloid PSMα1 from Staphylococcus aureus. Proc Natl Acad Sci U S A 2024; 121:e2406775121. [PMID: 39116134 PMCID: PMC11331129 DOI: 10.1073/pnas.2406775121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 06/25/2024] [Indexed: 08/10/2024] Open
Abstract
Biofilm-protected pathogenic Staphylococcus aureus causes chronic infections that are difficult to treat. An essential building block of these biofilms are functional amyloid fibrils that assemble from phenol-soluble modulins (PSMs). PSMα1 cross-seeds other PSMs into cross-β amyloid folds and is therefore a key element in initiating biofilm formation. However, the paucity of high-resolution structures hinders efforts to prevent amyloid assembly and biofilm formation. Here, we present a 3.5 Å resolution density map of the major PSMα1 fibril form revealing a left-handed cross-β fibril composed of two C2-symmetric U-shaped protofilaments whose subunits are unusually tilted out-of-plane. Monomeric α-helical PSMα1 is extremely cytotoxic to cells, despite the moderate toxicity of the cross-β fibril. We suggest mechanistic insights into the PSM functional amyloid formation and conformation transformation on the path from monomer-to-fibril formation. Details of PSMα1 assembly and fibril polymorphism suggest how S. aureus utilizes functional amyloids to form biofilms and establish a framework for developing therapeutics against infection and antimicrobial resistance.
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Affiliation(s)
- Kasper Holst Hansen
- Department of Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA15261
- Department of Biomedicine, Aarhus University, Aarhus8000, Denmark
| | - Chang Hyeock Byeon
- Department of Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA15261
| | - Qian Liu
- Department of Biomedicine, Aarhus University, Aarhus8000, Denmark
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus8000, Denmark
| | - Taner Drace
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus8000, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus8000, Denmark
| | - Thomas Boesen
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus8000, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus8000, Denmark
| | - James F. Conway
- Department of Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA15261
| | - Maria Andreasen
- Department of Biomedicine, Aarhus University, Aarhus8000, Denmark
| | - Ümit Akbey
- Department of Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA15261
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10
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Fiorucci L, Schiavina M, Felli IC, Pierattelli R, Ravera E. Are Protein Conformational Ensembles in Agreement with Experimental Data? A Geometrical Interpretation of the Problem. J Chem Inf Model 2024; 64:5392-5401. [PMID: 38959217 DOI: 10.1021/acs.jcim.4c00582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
The conformational variability of biological macromolecules can play an important role in their biological function. Therefore, understanding conformational variability is expected to be key for predicting the behavior of a particular molecule in the context of organism-wide studies. Several experimental methods have been developed and deployed for accessing this information, and computational methods are continuously updated for the profitable integration of different experimental sources. The outcome of this endeavor is conformational ensembles, which may vary significantly in properties and composition when different ensemble reconstruction methods are used, and this raises the issue of comparing the predicted ensembles against experimental data. In this article, we discuss a geometrical formulation to provide a framework for understanding the agreement of an ensemble prediction to the experimental observations.
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Affiliation(s)
- Letizia Fiorucci
- Department of Chemistry "Ugo Schiff" and Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Marco Schiavina
- Department of Chemistry "Ugo Schiff" and Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Isabella C Felli
- Department of Chemistry "Ugo Schiff" and Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Roberta Pierattelli
- Department of Chemistry "Ugo Schiff" and Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Enrico Ravera
- Department of Chemistry "Ugo Schiff" and Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Florence Data Science, University of Florence, Viale G.B. Morgagni 59, 50134 Florence, Italy
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11
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Jiang Z, Huang YH, Kaas Q, Craik DJ, Wang CK. Structure and Activity of Reconstructed Pseudo-Ancestral Cyclotides. ChemMedChem 2024; 19:e202400124. [PMID: 38632079 DOI: 10.1002/cmdc.202400124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 04/17/2024] [Accepted: 04/17/2024] [Indexed: 04/19/2024]
Abstract
Cyclotides are cyclic peptides that are promising scaffolds for the design of drug candidates and chemical tools. However, despite there being hundreds of reported cyclotides, drug design studies have commonly focussed on a select few prototypic examples. Here, we explored whether ancestral sequence reconstruction could be used to generate new cyclotides for further optimization. We show that the reconstructed 'pseudo-ancestral' sequences, named Ancy-m (for the ancestral cyclotide of the Möbius sub-family) and Ancy-b (for the bracelet sub-family), have well-defined structures like their extant members, comprising the core structural feature of a cyclic cystine knot. This motif underpins efforts to re-engineer cyclotides for agrochemical and therapeutic applications. We further show that the reconstructed sequences are resistant to temperatures approaching boiling, bind to phosphatidyl-ethanolamine lipid bilayers at micromolar affinity, and inhibit the growth of insect cells at inhibitory concentrations in the micromolar range. Interestingly, the Ancy-b cyclotide had a higher oxidative folding yield than its comparator cyclotide cyO2, which belongs to the bracelet cyclotide subfamily known to be notoriously difficult to fold. Overall, this study provides new cyclotide sequences not yet found naturally that could be valuable starting points for the understanding of cyclotide evolution and for further optimization as drug leads.
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Affiliation(s)
- Zhihao Jiang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Yen-Hua Huang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Quentin Kaas
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Conan K Wang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Qld, 4072, Australia
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12
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Xu Q, Yang M, Ji J, Weng J, Wang W, Xu X. Impact of Nonnative Interactions on the Binding Kinetics of Intrinsically Disordered p53 with MDM2: Insights from All-Atom Simulation and Markov State Model Analysis. J Chem Inf Model 2024; 64:5219-5231. [PMID: 38916177 DOI: 10.1021/acs.jcim.3c01833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Intrinsically disordered proteins (IDPs) lack a well-defined tertiary structure but are essential players in various biological processes. Their ability to undergo a disorder-to-order transition upon binding to their partners, known as the folding-upon-binding process, is crucial for their function. One classical example is the intrinsically disordered transactivation domain (TAD) of the tumor suppressor protein p53, which quickly forms a structured α-helix after binding to its partner MDM2, with clinical significance for cancer treatment. However, the contribution of nonnative interactions between the IDP and its partner to the rapid binding kinetics, as well as their interplay with native interactions, is not well understood at the atomic level. Here, we used molecular dynamics simulation and Markov state model (MSM) analysis to study the folding-upon-binding mechanism between p53-TAD and MDM2. Our results suggest that the system progresses from the nascent encounter complex to the well-structured encounter complex and finally reaches the native complex, following an induced-fit mechanism. We found that nonnative hydrophobic and hydrogen bond interactions, combined with native interactions, effectively stabilize the nascent and well-structured encounter complexes. Among the nonnative interactions, Leu25p53-Leu54MDM2 and Leu25p53-Phe55MDM2 are particularly noteworthy, as their interaction strength is close to the optimum. Evidently, strengthening or weakening these interactions could both adversely affect the binding kinetics. Overall, our findings suggest that nonnative interactions are evolutionarily optimized to accelerate the binding kinetics of IDPs in conjunction with native interactions.
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Affiliation(s)
- Qianjun Xu
- Department of Chemistry, Institute of Biomedical Sciences and Multiscale Research Institute of Complex Systems, Fudan University, Shanghai 200438, China
| | - Maohua Yang
- Department of Chemistry, Institute of Biomedical Sciences and Multiscale Research Institute of Complex Systems, Fudan University, Shanghai 200438, China
| | - Jie Ji
- Department of Chemistry, Institute of Biomedical Sciences and Multiscale Research Institute of Complex Systems, Fudan University, Shanghai 200438, China
| | - Jingwei Weng
- Department of Chemistry, Institute of Biomedical Sciences and Multiscale Research Institute of Complex Systems, Fudan University, Shanghai 200438, China
| | - Wenning Wang
- Department of Chemistry, Institute of Biomedical Sciences and Multiscale Research Institute of Complex Systems, Fudan University, Shanghai 200438, China
| | - Xin Xu
- Department of Chemistry, Institute of Biomedical Sciences and Multiscale Research Institute of Complex Systems, Fudan University, Shanghai 200438, China
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13
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Berner F, Kovermann M. Including the Ensemble of Unstructured Conformations in the Analysis of Protein's Native State by High-Pressure NMR Spectroscopy. Angew Chem Int Ed Engl 2024; 63:e202401343. [PMID: 38656763 DOI: 10.1002/anie.202401343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/11/2024] [Accepted: 04/12/2024] [Indexed: 04/26/2024]
Abstract
The analysis of pressure induced changes in the chemical shift of proteins allows statements on structural fluctuations proteins exhibit at ambient pressure. The inherent issue of separating general pressure effects from structural related effects on the pressure dependence of chemical shifts has so far been addressed by considering the characteristics of random coil peptides on increasing pressure. In this work, chemically and pressure denatured states of the cold shock protein B from Bacillus subtilis (BsCspB) have been assigned in 2D 1H-15N HSQC NMR spectra and their dependence on increasing hydrostatic pressure has been evaluated. The pressure denatured polypeptide chain has been used to separate general from structural related effects on 1H and 15N chemical shifts of native BsCspB and the implications on the interpretation of pressure induced changes in the chemical shift regarding the structure of BsCspB are discussed. It has been found that the ensemble of unstructured conformations of BsCspB shows different responses to increasing pressure than random coil peptides do. Thus, the approach used for considering the general effects that arise when hydrostatic pressure increases changes the structural conclusions that are drawn from high pressure NMR spectroscopic experiments that rely on the analysis of chemical shifts.
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Affiliation(s)
- Frederic Berner
- Department of Chemistry, University of Konstanz, Universitätsstrasse 10, 78464, Konstanz, Germany
| | - Michael Kovermann
- Department of Chemistry, University of Konstanz, Universitätsstrasse 10, 78464, Konstanz, Germany
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14
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Miao J, Ghosh AP, Ho MN, Li C, Huang X, Pentelute BL, Baleja JD, Lin YS. Assessing the Performance of Peptide Force Fields for Modeling the Solution Structural Ensembles of Cyclic Peptides. J Phys Chem B 2024; 128:5281-5292. [PMID: 38785765 PMCID: PMC11163431 DOI: 10.1021/acs.jpcb.4c00157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 05/02/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024]
Abstract
Molecular dynamics simulation is a powerful tool for characterizing the solution structural ensembles of cyclic peptides. However, the ability of simulation to recapitulate experimental results and make accurate predictions largely depends on the force fields used. In our work here, we evaluate the performance of seven state-of-the-art force fields in recapitulating the experimental NMR results in water of 12 benchmark cyclic peptides, consisting of 6 cyclic pentapeptides, 4 cyclic hexapeptides, and 2 cyclic heptapeptides. The results show that RSFF2+TIP3P, RSFF2C+TIP3P, and Amber14SB+TIP3P exhibit similar and the best performance, all recapitulating the NMR-derived structure information on 10 cyclic peptides. Amber19SB+OPC successfully recapitulates the NMR-derived structure information on 8 cyclic peptides. In contrast, OPLS-AA/M+TIP4P, Amber03+TIP3P, and Amber14SBonlysc+GB-neck2 could only recapitulate the NMR-derived structure information on 5 cyclic peptides, the majority of which are not well-structured.
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Affiliation(s)
- Jiayuan Miao
- Department
of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Arghya Pratim Ghosh
- Department
of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Minh Ngoc Ho
- Department
of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Chengxi Li
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
- College
of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang 310030, China
- Engineering
Research Center of Functional Materials Intelligent Manufacturing
of Zhejiang Province, ZJU-Hangzhou Global
Scientific and Technological Innovation Center, Hangzhou, Zhejiang 311215, China
| | - Xuejian Huang
- Graduate
Program in Pharmacology and Experimental Therapeutics, Graduate School
of Biomedical Sciences, Tufts University, Boston, Massachusetts 02111, United States
| | - Bradley L. Pentelute
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
| | - James D. Baleja
- Graduate
Program in Pharmacology and Experimental Therapeutics, Graduate School
of Biomedical Sciences, Tufts University, Boston, Massachusetts 02111, United States
| | - Yu-Shan Lin
- Department
of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
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15
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Cotten ML, Starich MR, He Y, Yin J, Yuan Q, Tjandra N. NMR chemical shift assignment of Drosophila odorant binding protein 44a in complex with 8(Z)-eicosenoic acid. BIOMOLECULAR NMR ASSIGNMENTS 2024:10.1007/s12104-024-10178-2. [PMID: 38822991 DOI: 10.1007/s12104-024-10178-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 05/09/2024] [Indexed: 06/03/2024]
Abstract
The odorant binding protein, OBP44a is one of the most abundant proteins expressed in the brain of the developing fruit fly Drosophila melanogaster. Its cellular function has not yet been determined. The OBP family of proteins is well established to recognize hydrophobic molecules. In this study, NMR is employed to structurally characterize OBP44a. NMR chemical shift perturbation measurements confirm that OBP44a binds to fatty acids. Complete assignments of the backbone chemical shifts and secondary chemical shift analysis demonstrate that the apo state of OBP44a is comprised of six α-helices. Upon binding 8(Z)-eicosenoic acid (8(Z)-C20:1), the OBP44a C-terminal region undergoes a conformational change, from unstructured to α-helical. In addition to C-terminal restructuring upon ligand binding, some hydrophobic residues show dramatic chemical shift changes. Surprisingly, several charged residues are also strongly affected by lipid binding. Some of these residues could represent key structural features that OBP44a relies on to perform its cellular function. The NMR chemical shift assignment is the first step towards characterizing the structure of OBP44a and how specific residues might play a role in lipid binding and release. This information will be important in deciphering the biological function of OBP44a during fly brain development.
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Affiliation(s)
- Myriam L Cotten
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, 97331, USA
| | - Mary R Starich
- Laboratory of Molecular Biophysics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yi He
- Fermentation Facility, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jun Yin
- Dendrite Morphogenesis and Plasticity Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Quan Yuan
- Dendrite Morphogenesis and Plasticity Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Nico Tjandra
- Laboratory of Molecular Biophysics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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16
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Franco Machado J, Sá M, Pires I, da Silva MT, Marques F, Coelho JAS, Mendes F, Piedade MFM, Machuqueiro M, Jiménez MA, Garcia MH, Correia JDG, Morais TS. Dual FGFR-targeting and pH-activatable ruthenium-peptide conjugates for targeted therapy of breast cancer. Dalton Trans 2024; 53:7682-7693. [PMID: 38573236 DOI: 10.1039/d4dt00497c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Dysregulation of Fibroblast Growth Factor Receptors (FGFRs) signaling has been associated with breast cancer, yet employing FGFR-targeted delivery systems to improve the efficacy of cytotoxic agents is still sparsely exploited. Herein, we report four new bi-functional ruthenium-peptide conjugates (RuPCs) with FGFR-targeting and pH-dependent releasing abilities, envisioning the selective delivery of cytotoxic Ru complexes to FGFR(+)-breast cancer cells, and controlled activation at the acidic tumoral microenvironment. The antiproliferative potential of the RuPCs and free Ru complexes was evaluated in four breast cancer cell lines with different FGFR expression levels (SKBR-3, MDA-MB-134-VI, MCF-7, and MDA-MB-231) and in human dermal fibroblasts (HDF), at pH 6.8 and pH 7.4 aimed at mimicking the tumor microenvironment and normal tissues/bloodstream pHs, respectively. The RuPCs showed higher cytotoxicity in cells with higher level of FGFR expression at acidic pH. Additionally, RuPCs showed up to 6-fold higher activity in the FGFR(+) breast cancer lines compared to the normal cell line. The release profile of Ru complexes from RuPCs corroborates the antiproliferative effects observed. Remarkably, the cytotoxicity and releasing ability of RuPCs were shown to be strongly dependent on the conjugation of the peptide position in the Ru complex. Complementary molecular dynamic simulations and computational calculations were performed to help interpret these findings at the molecular level. In summary, we identified a lead bi-functional RuPC that holds strong potential as a FGFR-targeted chemotherapeutic agent.
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Affiliation(s)
- João Franco Machado
- Centro de Química Estrutural, Institute of Molecular Sciences, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal.
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10 (km 139, 7), 2695-066 Bobadela LRS, Portugal.
| | - Marco Sá
- Centro de Química Estrutural, Institute of Molecular Sciences, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal.
| | - Inês Pires
- BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Miguel Tarita da Silva
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10 (km 139, 7), 2695-066 Bobadela LRS, Portugal.
| | - Fernanda Marques
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10 (km 139, 7), 2695-066 Bobadela LRS, Portugal.
- Departamento de Engenharia e Ciências Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10 (km 139, 7), 2695-066 Bobadela LRS, Portugal
| | - Jaime A S Coelho
- Centro de Química Estrutural, Institute of Molecular Sciences, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal.
| | - Filipa Mendes
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10 (km 139, 7), 2695-066 Bobadela LRS, Portugal.
- Departamento de Engenharia e Ciências Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10 (km 139, 7), 2695-066 Bobadela LRS, Portugal
| | - M Fátima M Piedade
- Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
- Centro de Química Estrutural, Institute of Molecular Sciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Miguel Machuqueiro
- BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
- Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - María Angeles Jiménez
- Institute of Physical Chemistry Blas Cabreras (IQF-CSIC), Serrano 119, E-28006 Madrid, Spain
| | - Maria Helena Garcia
- Centro de Química Estrutural, Institute of Molecular Sciences, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal.
- Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - João D G Correia
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10 (km 139, 7), 2695-066 Bobadela LRS, Portugal.
- Departamento de Engenharia e Ciências Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10 (km 139, 7), 2695-066 Bobadela LRS, Portugal
| | - Tânia S Morais
- Centro de Química Estrutural, Institute of Molecular Sciences, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal.
- Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
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17
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Byeon CH, Hansen KH, Jeffrey J, Saricayir H, Andreasen M, Akbey Ü. Intrinsically disordered Pseudomonas chaperone FapA slows down the fibrillation of major biofilm-forming functional amyloid FapC. FEBS J 2024; 291:1925-1943. [PMID: 38349812 DOI: 10.1111/febs.17084] [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: 10/23/2023] [Revised: 12/29/2023] [Accepted: 01/29/2024] [Indexed: 02/15/2024]
Abstract
Functional bacterial amyloids play a crucial role in the formation of biofilms, which mediate chronic infections and contribute to antimicrobial resistance. This study focuses on the FapC amyloid fibrillar protein from Pseudomonas, a major contributor to biofilm formation. We investigate the initial steps of FapC amyloid formation and the impact of the chaperone-like protein FapA on this process. Using solution nuclear magnetic resonance (NMR), we recently showed that both FapC and FapA are intrinsically disordered proteins (IDPs). Here, the secondary structure propensities (SSPs) are compared to alphafold (DeepMind, protein structure prediction tool/algorithm: https://alphafold.ebi.ac.uk/) models. We further demonstrate that the FapA chaperone interacts with FapC and significantly slows down the formation of FapC fibrils. Our NMR titrations reveal ~ 18% of the resonances show FapA-induced chemical shift perturbations (CSPs), which has not been previously observed, the largest being for A82, N201, C237, C240, A241, and G245. These sites may suggest a specific interaction site and/or hotspots of fibrillation inhibition/control interface at the repeat-1 (R1)/loop-2 (L2) and L2/R3 transition areas and at the C-terminus of FapC. Remarkably, ~ 90% of FapA NMR signals exhibit substantial CSPs upon titration with FapC, the largest being for S63, A69, A80, and I92. A temperature-dependent effect of FapA was observed on FapC by thioflavin T (ThT) and NMR experiments. This study provides a detailed understanding of the interaction between the FapA and FapC, shedding light on the regulation and slowing down of amyloid formation, and has important implications for the development of therapeutic strategies targeting biofilms and associated infections.
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Affiliation(s)
- Chang-Hyeock Byeon
- Department of Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kasper Holst Hansen
- Department of Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Jasper Jeffrey
- Department of Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Hakan Saricayir
- Department of Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Maria Andreasen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Ümit Akbey
- Department of Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
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18
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Tian S, de Veer SJ, Durek T, Wang CK, Craik DJ. Nucleation of a key beta-turn promotes cyclotide oxidative folding. J Biol Chem 2024; 300:107125. [PMID: 38432638 PMCID: PMC10999817 DOI: 10.1016/j.jbc.2024.107125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 02/05/2024] [Accepted: 02/19/2024] [Indexed: 03/05/2024] Open
Abstract
Cyclotides are plant-derived peptides characterized by a head-to-tail cyclic backbone and a cystine knot motif comprised of three disulfide bonds. Formation of this motif via in vitro oxidative folding can be challenging and can result in misfolded isomers with nonnative disulfide connectivities. Here, we investigated the effect of β-turn nucleation on cyclotide oxidative folding. Two types of β-turn mimics were grafted into kalata B1, individually replacing each of the four β-turns in the folded cyclotide. Insertion of d-Pro-Gly into loop 5 was beneficial to the folding of both cyclic kB1 and a linear form of the peptide. The linear grafted analog folded four-times faster in aqueous conditions than cyclic kB1 in optimized conditions. Additionally, the cyclic analogue folded without the need for redox agents by transitioning through a native-like intermediate that was on-pathway to product formation. Kalata B1 is from the Möbius subfamily of cyclotides. Grafting d-Pro-Gly into loop 5 of cyclotides from two other subfamilies also had a beneficial effect on folding. Our findings demonstrate the importance of a β-turn nucleation site for cyclotide oxidative folding, which could be adopted as a chemical strategy to improve the in vitro folding of diverse cystine-rich peptides.
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Affiliation(s)
- Sixin Tian
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Simon J de Veer
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Thomas Durek
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Conan K Wang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia.
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19
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Raffaelli T, Wilson DT, Dutertre S, Giribaldi J, Vetter I, Robinson SD, Thapa A, Widi A, Loukas A, Daly NL. Structural analysis of a U-superfamily conotoxin containing a mini-granulin fold: Insights into key features that distinguish between the ICK and granulin folds. J Biol Chem 2024; 300:107203. [PMID: 38508311 PMCID: PMC11035057 DOI: 10.1016/j.jbc.2024.107203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 02/28/2024] [Accepted: 03/14/2024] [Indexed: 03/22/2024] Open
Abstract
We are entering an exciting time in structural biology where artificial intelligence can be used to predict protein structures with greater accuracy than ever before. Extending this level of accuracy to the predictions of disulfide-rich peptide structures is likely to be more challenging, at least in the short term, given the tight packing of cysteine residues and the numerous ways that the disulfide bonds can potentially be linked. It has been previously shown in many cases that several disulfide bond connectivities can be accommodated by a single set of NMR-derived structural data without significant violations. Disulfide-rich peptides are prevalent throughout nature, and arguably the most well-known are those present in venoms from organisms such as cone snails. Here, we have determined the first three-dimensional structure and disulfide connectivity of a U-superfamily cone snail venom peptide, TxVIIB. TxVIIB has a VI/VII cysteine framework that is generally associated with an inhibitor cystine knot (ICK) fold; however, AlphaFold predicted that the peptide adopts a mini-granulin fold with a granulin disulfide connectivity. Our experimental studies using NMR spectroscopy and orthogonal protection of cysteine residues indicate that TxVIIB indeed adopts a mini-granulin fold but with the ICK disulfide connectivity. Our findings provide structural insight into the underlying features that govern formation of the mini-granulin fold rather than the ICK fold and will provide fundamental information for prediction algorithms, as the subtle complexity of disulfide isomers may be not adequately addressed by the current prediction algorithms.
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Affiliation(s)
- Tiziano Raffaelli
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Australia
| | - David T Wilson
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Australia
| | | | | | - Irina Vetter
- Institute for Molecular Bioscience, The University of Queensland, Queensland, Australia; School of Pharmacy, The University of Queensland, Queensland, Australia
| | - Samuel D Robinson
- Institute for Molecular Bioscience, The University of Queensland, Queensland, Australia
| | - Ashvriya Thapa
- Institute for Molecular Bioscience, The University of Queensland, Queensland, Australia; School of Pharmacy, The University of Queensland, Queensland, Australia
| | - Antin Widi
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Australia
| | - Alex Loukas
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Australia
| | - Norelle L Daly
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Australia.
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20
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Robang A, Roy A, Dodd-o JB, He D, Le JV, McShan AC, Hu Y, Kumar VA, Paravastu AK. Structural Consequences of Introducing Bioactive Domains to Designer β-Sheet Peptide Self-Assemblies. Biomacromolecules 2024; 25:1429-1438. [PMID: 38408372 PMCID: PMC10934295 DOI: 10.1021/acs.biomac.3c00962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 02/09/2024] [Accepted: 02/12/2024] [Indexed: 02/28/2024]
Abstract
We applied solid- and solution-state nuclear magnetic resonance spectroscopy to examine the structure of multidomain peptides composed of self-assembling β-sheet domains linked to bioactive domains. Bioactive domains can be selected to stimulate specific biological responses (e.g., via receptor binding), while the β-sheets provide the desirable nanoscale properties. Although previous work has established the efficacy of multidomain peptides, molecular-level characterization is lacking. The bioactive domains are intended to remain solvent-accessible without being incorporated into the β-sheet structure. We tested for three possible anticipated molecular-level consequences of introducing bioactive domains to β-sheet-forming peptides: (1) the bioactive domain has no effect on the self-assembling peptide structure; (2) the bioactive domain is incorporated into the β-sheet nanofiber; and (3) the bioactive domain interferes with self-assembly such that nanofibers are not formed. The peptides involved in this study incorporated self-assembling domains based on the (SL)6 motif and bioactive domains including a VEGF-A mimic (QK), an IGF-mimic (IGF-1c), and a de novo SARS-CoV-2 binding peptide (SBP3). We observed all three of the anticipated outcomes from our examination of peptides, illustrating the unintended structural effects that could adversely affect the desired biofunctionality and biomaterial properties of the resulting peptide hydrogel. This work is the first attempt to evaluate the structural effects of incorporating bioactive domains into a set of peptides unified by a similar self-assembling peptide domain. These structural insights reveal unmet challenges in the design of highly tunable bioactive self-assembling peptide hydrogels.
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Affiliation(s)
- Alicia
S. Robang
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Abhishek Roy
- Department
of Biomedical Engineering, New Jersey Institute
of Technology, Newark, New Jersey 07102, United States
| | - Joseph B. Dodd-o
- Department
of Biomedical Engineering, New Jersey Institute
of Technology, Newark, New Jersey 07102, United States
| | - Dongjing He
- George
W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Justin V. Le
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Andrew C. McShan
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
| | - Yuhang Hu
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- George
W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- Parker
H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Vivek A. Kumar
- Department
of Biomedical Engineering, New Jersey Institute
of Technology, Newark, New Jersey 07102, United States
- Department
of Chemicals and Materials Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
- Department
of Biology, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Anant K. Paravastu
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- Parker
H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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21
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Cherniavskyi YK, Oliva R, Stellato M, Del Vecchio P, Galdiero S, Falanga A, Dames SA, Tieleman DP. Structural characterization of the antimicrobial peptides myxinidin and WMR in bacterial membrane mimetic micelles and bicelles. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184272. [PMID: 38211645 DOI: 10.1016/j.bbamem.2024.184272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 01/03/2024] [Accepted: 01/04/2024] [Indexed: 01/13/2024]
Abstract
Antimicrobial peptides are a promising class of potential antibiotics that interact selectively with negatively charged lipid bilayers. This paper presents the structural characterization of the antimicrobial peptides myxinidin and WMR associated with bacterial membrane mimetic micelles and bicelles by NMR, CD spectroscopy, and molecular dynamics simulations. Both peptides adopt a different conformation in the lipidic environment than in aqueous solution. The location of the peptides in micelles and bicelles has been studied by paramagnetic relaxation enhancement experiments with paramagnetic tagged 5- and 16-doxyl stearic acid (5-/16-SASL). Molecular dynamics simulations of multiple copies of the peptides were used to obtain an atomic level of detail on membrane-peptide and peptide-peptide interactions. Our results highlight an essential role of the negatively charged membrane mimetic in the structural stability of both myxinidin and WMR. The peptides localize predominantly in the membrane's headgroup region and have a noticeable membrane thinning effect on the overall bilayer structure. Myxinidin and WMR show a different tendency to self-aggregate, which is also influenced by the membrane composition (DOPE/DOPG versus DOPE/DOPG/CL) and can be related to the previously observed difference in the ability of the peptides to disrupt different types of model membranes.
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Affiliation(s)
- Yevhen K Cherniavskyi
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Rosario Oliva
- Department of Chemical Sciences, University of Naples "Federico II", via Cintia, 80126 Naples, Italy
| | - Marco Stellato
- Department of Chemical Sciences, University of Naples "Federico II", via Cintia, 80126 Naples, Italy
| | - Pompea Del Vecchio
- Department of Chemical Sciences, University of Naples "Federico II", via Cintia, 80126 Naples, Italy
| | - Stefania Galdiero
- Department of Pharmacy, University of Naples 'Federico II', Via Domenico Montesano 49, 80131 Naples, Italy
| | - Annarita Falanga
- Department of Agricultural Science, University of Naples 'Federico II', Via dell' Università 100, 80055 Portici, Naples, Italy
| | - Sonja A Dames
- Chair of Biomolecular NMR Spectroscopy, Department of Chemistry, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany; Hausdorff Center for Mathematics, University of Bonn, Endenicher Allee 62, 53115 Bonn, Germany; Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany.
| | - D Peter Tieleman
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada.
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22
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Thurber KR, Yau WM, Tycko R. Structure of Amyloid Peptide Ribbons Characterized by Electron Microscopy, Atomic Force Microscopy, and Solid-State Nuclear Magnetic Resonance. J Phys Chem B 2024; 128:1711-1723. [PMID: 38348474 PMCID: PMC11423861 DOI: 10.1021/acs.jpcb.3c07867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Polypeptides often self-assemble to form amyloid fibrils, which contain cross-β structural motifs and are typically 5-15 nm in width and micrometers in length. In many cases, short segments of longer amyloid-forming protein or peptide sequences also form cross-β assemblies but with distinctive ribbon-like morphologies that are characterized by a well-defined thickness (on the order of 5 nm) in one lateral dimension and a variable width (typically 10-100 nm) in the other. Here, we use a novel combination of data from solid-state nuclear magnetic resonance (ssNMR), dark-field transmission electron microscopy (TEM), atomic force microscopy (AFM), and cryogenic electron microscopy (cryoEM) to investigate the structures within amyloid ribbons formed by residues 14-23 and residues 11-25 of the Alzheimer's disease-associated amyloid-β peptide (Aβ14-23 and Aβ11-25). The ssNMR data indicate antiparallel β-sheets with specific registries of intermolecular hydrogen bonds. Mass-per-area values are derived from dark-field TEM data. The ribbon thickness is determined from AFM images. For Aβ14-23 ribbons, averaged cryoEM images show a periodic spacing of β-sheets. The combined data support structures in which the amyloid ribbon growth direction is the direction of intermolecular hydrogen bonds between β-strands, the ribbon thickness corresponds to the width of one β-sheet (i.e., approximately the length of one molecule), and the variable ribbon width is a variable multiple of the thickness of one β-sheet (i.e., a multiple of the repeat distance in a stack of β-sheets). This architecture for a cross-β assembly may generally exist within amyloid ribbons.
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Affiliation(s)
- Kent R Thurber
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - Wai-Ming Yau
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
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23
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Menke AJ, Jacobus ZP, Claton LE, Annunziata O, Capelli R, Pavan GM, Simanek EE. Proton Affinity and Conformational Integrity of a 24-Atom Triazine Macrocycle across Physiologically Relevant pH. J Org Chem 2024; 89:2467-2473. [PMID: 38299798 DOI: 10.1021/acs.joc.3c02495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
For 24-atom triazine macrocycles, protonation of the heterocycle leads to a rigid, folded structure presenting a network of hydrogen bonds. These molecules derive from dynamic covalent chemistry wherein triazine monomers bearing a protected hydrazine group and acetal tethered by the amino acid dimerize quantitatively in an acidic solution. Here, lysine is used, and the product is a tetracation. The primary amines of the lysine side chains do not interfere with quantitative yields of the desired bis(hydrazone) at concentrations of 5-125 mg/mL. Mathematical modeling of data derived from titration experiments of the macrocycle reveals that the pKa values of the protonated triazines are 5.6 and 6.7. Changes in chemical shifts of resonances in the 1H NMR spectra corroborate these values and further support assignment of the protonation sites. The pKa values of the lysine side chains are consistent with expectation. Upon deprotonation, the macrocycle enjoys greater conformational freedom as evident from the broadening of resonances in the 1H and 13C NMR spectra indicative of dynamic motion on the NMR time scale and the appearance of additional conformations at room temperature. While well-tempered metadynamics suggests only a modest difference in accessible conformational footprints of the protonated and deprotonated macrocycles, the shift in conformation(s) supports the stabilizing role that the protons adopt in the hydrogen-bonded network.
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Affiliation(s)
- Alexander J Menke
- Department of Chemistry & Biochemistry, Texas Christian University, Fort Worth, Texas 76129, United States
| | - Zachary P Jacobus
- Department of Chemistry & Biochemistry, Texas Christian University, Fort Worth, Texas 76129, United States
| | - Liam E Claton
- Department of Chemistry & Biochemistry, Texas Christian University, Fort Worth, Texas 76129, United States
| | - Onofrio Annunziata
- Department of Chemistry & Biochemistry, Texas Christian University, Fort Worth, Texas 76129, United States
| | - Riccardo Capelli
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, Milan 20133, Italy
| | - Giovanni M Pavan
- Department of Innovative Technologies, University of Applied Sciences and Arts of Southern Switzerland, Polo Universitario Lugano, Lugano-Viganello 6962, Switzerland
- Department of Applied Science and Technology, Politecnico di Torino, Torino 10129, Italy
| | - Eric E Simanek
- Department of Chemistry & Biochemistry, Texas Christian University, Fort Worth, Texas 76129, United States
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24
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Meuskens I, Kristiansen PE, Bardiaux B, Koynarev VR, Hatlem D, Prydz K, Lund R, Izadi-Pruneyre N, Linke D. A poly-proline II helix in YadA from Yersinia enterocolitica serotype O:9 facilitates heparin binding through electrostatic interactions. FEBS J 2024; 291:761-777. [PMID: 37953437 DOI: 10.1111/febs.17001] [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: 07/14/2023] [Revised: 10/25/2023] [Accepted: 11/09/2023] [Indexed: 11/14/2023]
Abstract
Poly-proline II helices are secondary structure motifs frequently found in ligand-binding sites. They exhibit increased flexibility and solvent exposure compared to the strongly hydrogen-bonded α-helices or β-strands and can therefore easily be misinterpreted as completely unstructured regions with an extremely high rotational freedom. Here, we show that the adhesin YadA of Yersinia enterocolitica serotype O:9 contains a poly-proline II helix interaction motif in the N-terminal region. The motif is involved in the interaction of YadAO:9 with heparin, a host glycosaminoglycan. We show that the basic residues within the N-terminal motif of YadA are required for electrostatic interactions with the sulfate groups of heparin. Biophysical methods including CD spectroscopy, solution-state NMR and SAXS all independently support the presence of a poly-proline helix allowing YadAO:9 binding to the rigid heparin. Lastly, we show that host cells deficient in sulfation of heparin and heparan sulfate are not targeted by YadAO:9 -mediated adhesion. We speculate that the YadAO:9 -heparin interaction plays an important and highly strain-specific role in the pathogenicity of Yersinia enterocolitica serotype O:9.
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Affiliation(s)
- Ina Meuskens
- Department of Biosciences, University of Oslo, Norway
| | | | - Benjamin Bardiaux
- Structural Bioinformatics Unit, CNRS UMR3528, Institut Pasteur, Université de Paris-Cité, France
| | | | - Daniel Hatlem
- Department of Biosciences, University of Oslo, Norway
| | | | - Reidar Lund
- Department of Chemistry, University of Oslo, Norway
| | - Nadia Izadi-Pruneyre
- Bacterial Transmembrane Systems Unit, CNRS UMR3528, Institut Pasteur, Université de Paris-Cité, France
| | - Dirk Linke
- Department of Biosciences, University of Oslo, Norway
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25
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Wilson CB, Yau WM, Tycko R. Experimental Evidence for Millisecond-Timescale Structural Evolution Following the Microsecond-Timescale Folding of a Small Protein. PHYSICAL REVIEW LETTERS 2024; 132:048402. [PMID: 38335342 PMCID: PMC11423860 DOI: 10.1103/physrevlett.132.048402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 10/27/2023] [Indexed: 02/12/2024]
Abstract
Prior work has shown that small proteins can fold (i.e., convert from unstructured to structured states) within 10 μs. Here we use time-resolved solid state nuclear magnetic resonance (ssNMR) methods to show that full folding of the 35-residue villin headpiece subdomain (HP35) requires a slow annealing process that has not been previously detected. ^{13}C ssNMR spectra of frozen HP35 solutions, acquired with a variable time τ_{e} at 30 °C after rapid cooling from 95 °C and before rapid freezing, show changes on the 3-10 ms timescale, attributable to slow rearrangements of protein sidechains during τ_{e}.
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Affiliation(s)
- C Blake Wilson
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
| | - Wai-Ming Yau
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
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26
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Schütz S, Bergsdorf C, Hänni-Holzinger S, Lingel A, Renatus M, Gossert AD, Jahnke W. Intrinsically Disordered Regions in the Transcription Factor MYC:MAX Modulate DNA Binding via Intramolecular Interactions. Biochemistry 2024. [PMID: 38264995 DOI: 10.1021/acs.biochem.3c00608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
The basic helix-loop-helix leucine zipper (bHLH-LZ) transcription factor (TF) MYC is in large part an intrinsically disordered oncoprotein. In complex with its obligate heterodimerization partner MAX, MYC preferentially binds E-Box DNA sequences (CANNTG). At promoters containing these sequence motifs, MYC controls fundamental cellular processes such as cell cycle progression, metabolism, and apoptosis. A vast network of proteins in turn regulates MYC function via intermolecular interactions. In this work, we establish another layer of MYC regulation by intramolecular interactions. We used nuclear magnetic resonance (NMR) spectroscopy to identify and map multiple binding sites for the C-terminal MYC:MAX DNA-binding domain (DBD) on the intrinsically disordered regions (IDRs) in the MYC N-terminus. We find that these binding events in trans are driven by electrostatic attraction, that they have distinct affinities, and that they are competitive with DNA binding. Thereby, we observe the strongest effects for the N-terminal MYC box 0 (Mb0), a conserved motif involved in MYC transactivation and target gene induction. We prepared recombinant full-length MYC:MAX complex and demonstrate that the interactions identified in this work are also relevant in cis, i.e., as intramolecular interactions. These findings are supported by surface plasmon resonance (SPR) experiments, which revealed that intramolecular IDR:DBD interactions in MYC decelerate the association of MYC:MAX complexes to DNA. Our work offers new insights into how bHLH-LZ TFs are regulated by intramolecular interactions, which open up new possibilities for drug discovery.
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Affiliation(s)
- Stefan Schütz
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Christian Bergsdorf
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Sandra Hänni-Holzinger
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Andreas Lingel
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Martin Renatus
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | | | - Wolfgang Jahnke
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
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27
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El Hajjar L, Bridot C, Nguyen M, Cantrelle FX, Landrieu I, Smet-Nocca C. Phosphorylation of Tau Protein by CDK2/cyclin A and GSK3β Recombinant Kinases: Analysis of Phosphorylation Patterns by Nuclear Magnetic Resonance Spectroscopy. Methods Mol Biol 2024; 2754:271-306. [PMID: 38512672 DOI: 10.1007/978-1-0716-3629-9_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
Posttranslational modifications (PTMs) of proteins can be investigated by Nuclear Magnetic Resonance (NMR) spectroscopy as a powerful analytical tool to define modification sites, their relative stoichiometry, and crosstalk between modifications. As a Structural Biology method, NMR provides important additional information on changes in protein conformation and dynamics upon modification as well as a mapping of binding sites upon biomolecular interactions. Indeed, PTMs not only mediate functional modulation in protein-protein interactions, but can also induce diverse structural responses with different biological outcomes. Here we present protocols that have been developed for the production and phosphorylation of the neuronal tau protein. Under its aggregated form, tau is a hallmark of Alzheimer's disease and other neurodegenerative diseases named tauopathies involving tau dysfunction and/or mutations. As a common feature shared by various tauopathies, tau aggregates are found into a form displaying an increased, abnormal phosphorylation, also referred to hyperphosphorylation. We have used NMR to investigate the phosphorylation patterns of tau induced by several kinases or cell extracts, how phosphorylation affects the local and overall conformation of tau, its interactions with partners (proteins, DNA, small-molecules, etc.) including tubulin and microtubules, and its capacity to form insoluble fibrillar aggregates. We present here detailed protocols for in vitro phosphorylation of tau by the recombinant kinases CDK2/cyclin A and GSK3β, the production of the recombinant kinases thereof, as well as the analytical characterization of phosphorylated tau by NMR spectroscopy.
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Affiliation(s)
- Léa El Hajjar
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS EMR9002 Integrative Structural Biology, Lille, France
| | - Clarisse Bridot
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS EMR9002 Integrative Structural Biology, Lille, France
| | - Marine Nguyen
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS EMR9002 Integrative Structural Biology, Lille, France
| | - François-Xavier Cantrelle
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS EMR9002 Integrative Structural Biology, Lille, France
| | - Isabelle Landrieu
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS, EMR9002 BSI Integrative Structural Biology, Lille, France
- LabEx (Laboratory of Excellence) DISTALZ (Development of Innovative Strategies for a Transdisciplinary Approach to Alzheimer's Disease ANR-11-LABX-01), Lille, France
| | - Caroline Smet-Nocca
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France.
- CNRS EMR9002 Integrative Structural Biology, Lille, France.
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28
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El Hajjar L, Bridot C, Nguyen M, Cantrelle FX, Landrieu I, Smet-Nocca C. The O-GlcNAc Modification of Recombinant Tau Protein and Characterization of the O-GlcNAc Pattern for Functional Study. Methods Mol Biol 2024; 2754:237-269. [PMID: 38512671 DOI: 10.1007/978-1-0716-3629-9_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
The neuronal microtubule-associated tau protein is characterized in vivo by a large number of post-translational modifications along the entire primary sequence that modulates its function. The primary modification of tau is phosphorylation of serine/threonine or tyrosine residues that is involved in the regulation of microtubule binding and polymerization. In neurodegenerative disorders referred to as tauopathies including Alzheimer's disease, tau is abnormally hyperphosphorylated and forms fibrillar inclusions in neurons progressing throughout different brain area during the course of the disease. The O-β-linked N-acetylglucosamine (O-GlcNAc) is another reversible post-translational modification of serine/threonine residues that is installed and removed by the unique O-GlcNAc transferase (OGT) and O-GlcNAc hydrolase (OGA), respectively. This modification was described as a potential modulator of tau phosphorylation and functions in the physiopathology. Moreover, reducing protein O-GlcNAc levels in the brain upon treatment of tauopathy mouse models with an OGA inhibitor reveals a beneficial effect on tau pathology and neurodegeneration. However, whether the role of tau O-GlcNAcylation is responsible of the protective effect against tau toxicity remains to be determined. The production of O-GlcNAc modified recombinant tau protein is a valuable tool for the investigations of the impact of O-GlcNAcylation on tau functions, modulation of interactions with partners and crosstalk with other post-translational modifications, including but not restricted to phosphorylation. We describe here the in vitro O-GlcNAcylation of tau with recombinant OGT for which we provide an expression and purification protocol. The use of the O-GlcNAc tau protein in functional studies requires the analytical characterization of the O-GlcNAc pattern. Here, we describe a method for the O-GlcNAc modification of tau protein with recombinant OGT and the analytical characterization of the resulting O-GlcNAc pattern by a combination of methods for the overall characterization of tau O-GlcNAcylation by chemoenzymatic labeling and mass spectrometry, as well as the quantitative, site-specific pattern by NMR spectroscopy.
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Affiliation(s)
- Léa El Hajjar
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS EMR9002 Integrative Structural Biology, Lille, France
| | - Clarisse Bridot
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS EMR9002 Integrative Structural Biology, Lille, France
| | - Marine Nguyen
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS EMR9002 Integrative Structural Biology, Lille, France
| | - François-Xavier Cantrelle
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS EMR9002 Integrative Structural Biology, Lille, France
| | - Isabelle Landrieu
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS, EMR9002 BSI Integrative Structural Biology, Lille, France
- LabEx (Laboratory of Excellence) DISTALZ (Development of Innovative Strategies for a Transdisciplinary Approach to Alzheimer's Disease ANR-11-LABX-01), Lille, France
| | - Caroline Smet-Nocca
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France.
- CNRS EMR9002 Integrative Structural Biology, Lille, France.
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29
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Liang X, Liu M, Wei Y, Tong L, Guo S, Kang H, Zhang W, Yu Z, Zhang F, Duan JA. Structural characteristics and structure-activity relationship of four polysaccharides from Lycii fructus. Int J Biol Macromol 2023; 253:127256. [PMID: 37802446 DOI: 10.1016/j.ijbiomac.2023.127256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 09/22/2023] [Accepted: 10/03/2023] [Indexed: 10/09/2023]
Abstract
At present, the structure-activity relationship of polysaccharides is a common and important focus in the fields of glycobiology and carbohydrate chemistry. To better understand the effect of specific polysaccharide structures on bioactive orientation, four homogeneous polysaccharides from Lycii fructus, one neutral along with three acidic polysaccharides, were purified, structurally characterized and comparatively evaluated on the antioxidative and anti-aging activities. The GC-MS-based monosaccharide composition analysis and methylation results showed that the LFPs had similar glycosyl types but varied proportions. Nuclear magnetic resonance (NMR) spectroscopy showed that LFPs consisted of arabinogalactan, rhamnogalacturonan and homogalacturonan structural domains. The results of the structure-activity relationship indicated that the antioxidative activity was positively correlated with the galacturonic acid (GalA) content, while the neutral multi-branched chains might be responsible for the anti-aging activity. This study is the first time to compare the principal structures and multiple biological activities of LFPs, which provided a reference for the industrial development and deep excavation of the health value of LFPs.
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Affiliation(s)
- Xiaofei Liang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, PR China
| | - Mengqiu Liu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, PR China
| | - Yan Wei
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, PR China
| | - Limei Tong
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, PR China
| | - Sheng Guo
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, PR China
| | - Hongjie Kang
- Ningxia Innovation Center of Goji R & D, Yinchuan 750002, PR China
| | - Wenhua Zhang
- Bairuiyuan Gouqi Co., Ltd., Yinchuan 750200, PR China
| | - Zhexiong Yu
- Tianren Ningxia Wolfberry Biotechnology Co., Ltd., Zhongning 755100, PR China
| | - Fang Zhang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, PR China.
| | - Jin-Ao Duan
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, PR China.
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30
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Ferková S, Froehlich U, Nepveu-Traversy MÉ, Murza A, Azad T, Grandbois M, Sarret P, Lavigne P, Boudreault PL. Comparative Analysis of Cyclization Techniques in Stapled Peptides: Structural Insights into Protein-Protein Interactions in a SARS-CoV-2 Spike RBD/hACE2 Model System. Int J Mol Sci 2023; 25:166. [PMID: 38203338 PMCID: PMC10778704 DOI: 10.3390/ijms25010166] [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: 11/17/2023] [Revised: 12/15/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
Medicinal chemistry is constantly searching for new approaches to develop more effective and targeted therapeutic molecules. The design of peptidomimetics is a promising emerging strategy that is aimed at developing peptides that mimic or modulate the biological activity of proteins. Among these, stapled peptides stand out for their unique ability to stabilize highly frequent helical motifs, but they have failed to be systematically reported. Here, we exploit chemically diverse helix-inducing i, i + 4 constraints-lactam, hydrocarbon, triazole, double triazole and thioether-on two distinct short sequences derived from the N-terminal peptidase domain of hACE2 upon structural characterization and in silico alanine scan. Our overall objective was to provide a sequence-independent comparison of α-helix-inducing staples using circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy. We identified a 9-mer lactam stapled peptide derived from the hACE2 sequence (His34-Gln42) capable of reaching its maximal helicity of 55% with antiviral activity in bioreporter- and pseudovirus-based inhibition assays. To the best of our knowledge, this study is the first comprehensive investigation comparing several cyclization methods with the goal of generating stapled peptides and correlating their secondary structures with PPI inhibitions using a highly topical model system (i.e., the interaction of SARS-CoV-2 Spike RBD with hACE2).
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Affiliation(s)
| | | | | | | | | | | | | | | | - Pierre-Luc Boudreault
- Department of Pharmacology and Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke, QC J1H 5N4, Canada; (S.F.); (M.-É.N.-T.); (A.M.); (T.A.)
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31
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Byeon CH, Wang PC, Byeon IJL, Akbey Ü. Solution-state NMR assignment and secondary structure propensity of the full length and minimalistic-truncated prefibrillar monomeric form of biofilm forming functional amyloid FapC from Pseudomonas aeruginosa. BIOMOLECULAR NMR ASSIGNMENTS 2023; 17:159-165. [PMID: 37162737 DOI: 10.1007/s12104-023-10135-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 04/28/2023] [Indexed: 05/11/2023]
Abstract
Functional bacterial amyloids provide structural scaffolding to bacterial biofilms. In contrast to the pathological amyloids, they have a role in vivo and are tightly regulated. Their presence is essential to the integrity of the bacterial communities surviving in biofilms and may cause serious health complications. Targeting amyloids in biofilms could be a novel approach to prevent chronic infections. However, structural information is very scarce on them in both soluble monomeric and insoluble fibrillar forms, hindering our molecular understanding and strategies to fight biofilm related diseases. Here, we present solution-state NMR assignment of 250 amino acid long biofilm-forming functional-amyloid FapC from Pseudomonas aeruginosa. We studied full-length (FL) and shorter minimalistic-truncated (L2R3C) FapC constructs without the signal-sequence that is required for secretion. 91% and 100% backbone NH resonance assignments for FL and L2R3C constructs, respectively, indicate that soluble monomeric FapC is predominantly disordered, with sizeable secondary structural propensities mostly as PP2 helices, but also as α-helices and β-sheets highlighting hotspots for fibrillation initiation interface. A shorter construct showing almost identical NMR chemical shifts highlights the promise of utilizing it for more demanding solid-state NMR studies that require methods to alleviate signal redundancy due to almost identical repeat units. This study provides key NMR resonance assignments for future structural studies of soluble, pre-fibrillar and fibrillar forms of FapC.
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Affiliation(s)
- Chang-Hyeock Byeon
- Department of Structural Biology, School of Medicine, Biomedical Science Tower 3, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, 15261, USA
| | - Pang C Wang
- Department of Structural Biology, School of Medicine, Biomedical Science Tower 3, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, 15261, USA
| | - In-Ja L Byeon
- Department of Structural Biology, School of Medicine, Biomedical Science Tower 3, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, 15261, USA
| | - Ümit Akbey
- Department of Structural Biology, School of Medicine, Biomedical Science Tower 3, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, 15261, USA.
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32
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Byeon CH, Kinney T, Saricayir H, Srinivasa S, Wells MK, Kim W, Akbey Ü. Tapping into the native Pseudomonas bacterial biofilm structure by high-resolution multidimensional solid-state NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 357:107587. [PMID: 37984030 PMCID: PMC10913148 DOI: 10.1016/j.jmr.2023.107587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/19/2023] [Accepted: 11/03/2023] [Indexed: 11/22/2023]
Abstract
We present a multidimensional magic-angle spinning (MAS) solid-state NMR (ssNMR) study to characterize native Pseudomonas fluorescens colony biofilms at natural abundance without isotope-labelling. By using a high-resolution INEPT-based 2D 1H-13C ssNMR spectrum and thorough peak deconvolution at the 1D ssNMR spectra, approximately 80/134 (in 1D/2D) distinct biofilm chemical sites were identified. We compared CP and INEPT 13C ssNMR spectra to differentiate signals originating from the mobile and rigid fractions of the biofilm, and qualitatively determined dynamical changes by comparing CP buildup behaviors. Protein and polysaccharide signals were differentiated and identified by utilizing FapC protein signals as a template, a biofilm forming functional amyloid from Pseudomonas. We identified several biofilm polysaccharide species such as glucose, mannan, galactose, heptose, rhamnan, fucose and N-acylated mannuronic acid by using 1H and 13C chemical shifts obtained from the 2D spectrum. To our knowledge, this study marks the first high-resolution multidimensional ssNMR characterization of a native bacterial biofilm. Our experimental pipeline can be readily applied to other in vitro biofilm model systems and natural biofilms and holds the promise of making a substantial impact on biofilm research, fostering new ideas and breakthroughs to aid in the development of strategic approaches to combat infections caused by biofilm-forming bacteria.
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Affiliation(s)
- Chang-Hyeock Byeon
- Department of Structural Biology, School of Medicine, University of Pittsburgh, Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15261, United States
| | - Ted Kinney
- Department of Structural Biology, School of Medicine, University of Pittsburgh, Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15261, United States
| | - Hakan Saricayir
- Department of Structural Biology, School of Medicine, University of Pittsburgh, Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15261, United States
| | - Sadhana Srinivasa
- Department of Biological Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA 15282, United States
| | - Meghan K Wells
- Department of Biological Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA 15282, United States
| | - Wook Kim
- Department of Biological Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA 15282, United States
| | - Ümit Akbey
- Department of Structural Biology, School of Medicine, University of Pittsburgh, Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15261, United States.
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33
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Byeon CH, Akbey Ü. Solution-state NMR assignment and secondary structure analysis of the monomeric Pseudomonas biofilm-forming functional amyloid accessory protein FapA. BIOMOLECULAR NMR ASSIGNMENTS 2023; 17:275-280. [PMID: 37798606 DOI: 10.1007/s12104-023-10155-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 09/20/2023] [Indexed: 10/07/2023]
Abstract
FapA is an accessory protein within the biofilm forming functional bacterial amyloid related fap-operon in Pseudomonas, and maybe a chaperone for FapC controlling its fibrillization. To allow further structural analysis, here we present a complete sequential assignment of 1Hamide, 13Cα, 13Cβ, and 15N NMR resonances for the functional form of the monomeric soluble FapA protein, comprising amino acids between 29 and 152. From these observed chemical shifts, the secondary structure propensities (SSPs) were determined. FapA predominantly adopts a random coil conformation, however, we also identified small propensities for α-helical and β-strand conformations. Notably, these observed SSPs are smaller compared to the ones we recently observed for the monomeric soluble FapC protein. These NMR results provide valuable insights into the activity of FapA in functional amyloid formation and regulation, that will also aid developing strategies targeting amyloid formation within biofilms and addressing chronic infections.
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Affiliation(s)
- Chang-Hyeock Byeon
- Department of Structural Biology, School of Medicine, University of Pittsburgh, Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, 15261, USA
| | - Ümit Akbey
- Department of Structural Biology, School of Medicine, University of Pittsburgh, Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, 15261, USA.
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34
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Nuti F, Larregola M, Staśkiewicz A, Retzl B, Tomašević N, Macchia L, Street ME, Jewgiński M, Lequin O, Latajka R, Rovero P, Gruber CW, Chorev M, Papini AM. Design, synthesis, conformational analysis, and biological activity of Cα 1-to-Cα 6 1,4- and 4,1-disubstituted 1 H-[1,2,3]triazol-1-yl-bridged oxytocin analogues. J Enzyme Inhib Med Chem 2023; 38:2254019. [PMID: 37735942 PMCID: PMC10519257 DOI: 10.1080/14756366.2023.2254019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 08/26/2023] [Indexed: 09/23/2023] Open
Abstract
Oxytocin (OT) is a neurohypophyseal peptide hormone containing a disulphide-bridged pseudocyclic conformation. The biomedical use of OT peptides is limited amongst others by disadvantageous pharmacokinetic parameters. To increase the stability of OT by replacing the disulphide bridge with the stable and more rigid [1,2,3]triazol-1-yl moiety, we employed the Cu2+-catalysed side chain-to-side chain azide-alkyne 1,3-cycloaddition. Here we report the design, synthesis, conformational analysis, and in vitro pharmacological activity of a homologous series of Cα1-to-Cα6 side chain-to-side chain [1,2,3]triazol-1-yl-containing OT analogues differing in the length of the bridge, location, and orientation of the linking moiety. Exploiting this macrocyclisation approach, it was possible to generate a systematic series of compounds providing interesting insight into the structure-conformation-function relationship of OT. Most analogues were able to adopt similar conformation to endogenous OT in water, namely, a type I β-turn. This approach may in the future generate stabilised pharmacological peptide tools to advance understanding of OT physiology.
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Affiliation(s)
- Francesca Nuti
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Florence, Italy
| | - Maud Larregola
- CNRS, BioCIS, CY Cergy Paris Université, Cergy Pontoise and Paris Saclay Université, Orsay, France
| | - Agnieszka Staśkiewicz
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Florence, Italy
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Bernhard Retzl
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Nataša Tomašević
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Lorenzo Macchia
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Florence, Italy
| | - Maria E. Street
- Dipartimento di Medicina e Chirurgia, Università di Parma e Clinica Pediatrica, AOU di Parma, Parma, Italy
| | - Michał Jewgiński
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Olivier Lequin
- Laboratoire des Biomolécules, Sorbonne Université, Ecole Normale Supérieure, PSL University, CNRS, Paris, France
| | - Rafal Latajka
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Paolo Rovero
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of NeuroFarBa, University of Florence, Sesto Fiorentino, Florence, Italy
| | - Christian W. Gruber
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Michael Chorev
- Laboratory for Translational Research, Department of Medicine, Division of Hematology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Anna Maria Papini
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Florence, Italy
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35
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Fan X, Qin R, Yuan W, Fan JS, Lin Z. Chemical shift assignments of wildtype human leptin. BIOMOLECULAR NMR ASSIGNMENTS 2023; 17:265-268. [PMID: 37796383 DOI: 10.1007/s12104-023-10153-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 09/12/2023] [Indexed: 10/06/2023]
Abstract
Leptin is an adipose tissue-expressed 16-kDa hormone encoded by the ob/ob gene. It serves a crucial role in regulating diverse physiological processes, including body weight control, energy homeostasis regulation, promotion of cell proliferation, and more. Emerging research has also revealed potential implications of leptin in various aging-related diseases, suggesting multifaceted physiological roles of leptin. Structural investigation of wild-type leptin in apo form is of particular importance to understand its conformational plasticity for receptor interaction and recognition. Here, we report backbone and side-chain resonance assignments of wild-type human leptin as a basis for structural and functional studies on leptin-mediated signaling.
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Affiliation(s)
- Xiao Fan
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
| | - Ruiqi Qin
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
| | - Wensu Yuan
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
| | - Jing-Song Fan
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN, 38105, USA.
| | - Zhi Lin
- School of Life Sciences, Tianjin University, Tianjin, 300072, China.
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36
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Al-Danoon O, Mohanty S. Backbone and side chain NMR assignments and secondary structure calculation of the pheromone binding protein3 of Ostrinia nubilalis, an agricultural pest. BIOMOLECULAR NMR ASSIGNMENTS 2023; 17:223-227. [PMID: 37498448 DOI: 10.1007/s12104-023-10145-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/12/2023] [Indexed: 07/28/2023]
Abstract
Ostrinia nubilalis, also known as European Corn Borer (ECB), is a serious pest in Europe and North America, as well as in Central Asia and Northern Africa. It damages a variety of agricultural crops such as corn, oats, buckwheat, millet, and soybeans. causing annually at least one billion dollars in loss. The Ostrinia nubilalis pheromone-binding protein3 (OnubPBP3), preferentially expressed in the male moth antenna, has been implicated in the detection of the female-secreted pheromone blend during the mating process. Understanding the structure of and function of OnubPBP3, including the mechanism of pheromone binding and its release at the dendritic olfactory neuron (ORN), is essential if integrated pest management through sensory inhibition is to be achieved. We report here the backbone and side-chain resonance assignments of OnubPBP3 at pH 6.5 using various triple resonance NMR experiments on a 13C, 15N-labeled protein sample. The secondary structure of OnubPBP3 consists of six α-helices and an unstructured C-terminus based on backbone chemical shifts.
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Affiliation(s)
- Omar Al-Danoon
- Department of Chemistry, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Smita Mohanty
- Department of Chemistry, Oklahoma State University, Stillwater, OK, 74078, USA.
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37
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Dongol Y, Wilson DT, Daly NL, Cardoso FC, Lewis RJ. Structure-function and rational design of a spider toxin Ssp1a at human voltage-gated sodium channel subtypes. Front Pharmacol 2023; 14:1277143. [PMID: 38034993 PMCID: PMC10682951 DOI: 10.3389/fphar.2023.1277143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 10/23/2023] [Indexed: 12/02/2023] Open
Abstract
The structure-function and optimization studies of NaV-inhibiting spider toxins have focused on developing selective inhibitors for peripheral pain-sensing NaV1.7. With several NaV subtypes emerging as potential therapeutic targets, structure-function analysis of NaV-inhibiting spider toxins at such subtypes is warranted. Using the recently discovered spider toxin Ssp1a, this study extends the structure-function relationships of NaV-inhibiting spider toxins beyond NaV1.7 to include the epilepsy target NaV1.2 and the pain target NaV1.3. Based on these results and docking studies, we designed analogues for improved potency and/or subtype-selectivity, with S7R-E18K-rSsp1a and N14D-P27R-rSsp1a identified as promising leads. S7R-E18K-rSsp1a increased the rSsp1a potency at these three NaV subtypes, especially at NaV1.3 (∼10-fold), while N14D-P27R-rSsp1a enhanced NaV1.2/1.7 selectivity over NaV1.3. This study highlights the challenge of developing subtype-selective spider toxin inhibitors across multiple NaV subtypes that might offer a more effective therapeutic approach. The findings of this study provide a basis for further rational design of Ssp1a and related NaSpTx1 homologs targeting NaV1.2, NaV1.3 and/or NaV1.7 as research tools and therapeutic leads.
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Affiliation(s)
- Yashad Dongol
- Centre for Chemistry and Drug Discovery, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - David T. Wilson
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Norelle L. Daly
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Fernanda C. Cardoso
- Centre for Chemistry and Drug Discovery, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Richard J. Lewis
- Centre for Chemistry and Drug Discovery, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
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38
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Yang C, Kim Y, Kim SO, Lee SJ, Choi J, Ihee H. Length and Charge of the N-terminus Regulate the Lifetime of the Signaling State of Photoactive Yellow Protein. J Phys Chem B 2023; 127:9001-9013. [PMID: 37819381 DOI: 10.1021/acs.jpcb.3c03841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Photoactive yellow protein (PYP) is one of the most extensively studied photoreceptors. Nevertheless, the role of the N-terminus in the photocycle and structural transitions is still elusive. Here, we attached additional amino acids to the N-terminus of PYP and investigated the effect of the length and charge of additional N-terminal residues using circular dichroism, two-dimensional nuclear magnetic resonance (2D-NMR), transient absorption (TA), and transient grating (TG) spectroscopic techniques. TA experiments showed that, except for negatively charged residues (5D-PYP), additional N-terminal residues of PYP generally enable faster dark recovery from the putative signaling state (pB2) to the ground state (pG). TG data showed that although the degree of structural changes can be controlled by adjusting specific amino acid residues in the extended N-terminus of N-terminal extended PYPs (NE-PYPs), the dark recovery times of wt-PYP and NE-PYPs, except for 5D-PYP, are independent of the structural differences between pG and pB2 states. These results demonstrate that the recovery time and the degree of structural change can be regulated by controlling the length and sequence of N-terminal residues of PYP. The findings in this study emphasize the need for careful attention to the remaining amino acid residues when designing recombinant proteins for genetic engineering purposes.
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Affiliation(s)
- Cheolhee Yang
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Youngmin Kim
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Seong Ok Kim
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
- Department of Chemistry and KI for the BioCentury, KAIST, Daejeon 34141, Republic of Korea
| | - Sang Jin Lee
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
- Department of Chemistry and KI for the BioCentury, KAIST, Daejeon 34141, Republic of Korea
| | - Jungkweon Choi
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
- Department of Chemistry and KI for the BioCentury, KAIST, Daejeon 34141, Republic of Korea
| | - Hyotcherl Ihee
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
- Department of Chemistry and KI for the BioCentury, KAIST, Daejeon 34141, Republic of Korea
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39
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Nazzaro A, Lu B, Sawyer N, Watkins AM, Arora PS. Macrocyclic β-Sheets Stabilized by Hydrogen Bond Surrogates. Angew Chem Int Ed Engl 2023; 62:e202303943. [PMID: 37170337 PMCID: PMC10592574 DOI: 10.1002/anie.202303943] [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: 03/18/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 05/13/2023]
Abstract
Mimics of protein secondary and tertiary structure offer rationally-designed inhibitors of biomolecular interactions. β-Sheet mimics have a storied history in bioorganic chemistry and are typically designed with synthetic or natural turn segments. We hypothesized that replacement of terminal inter-β-strand hydrogen bonds with hydrogen bond surrogates (HBS) may lead to conformationally-defined macrocyclic β-sheets without the requirement for natural or synthetic β-turns, thereby providing a minimal mimic of a protein β-sheet. To access turn-less antiparallel β-sheet mimics, we developed a facile solid phase synthesis protocol. We surveyed a dataset of protein β-sheets for naturally observed interstrand side chain interactions. This bioinformatics survey highlighted an over-abundance of aromatic-aromatic, cation-π and ionic interactions in β-sheets. In correspondence with natural β-sheets, we find that minimal HBS mimics show robust β-sheet formation when specific amino acid residue pairings are incorporated. In isolated β-sheets, aromatic interactions endow superior conformational stability over ionic or cation-π interactions. Circular dichroism and NMR spectroscopies, along with high-resolution X-ray crystallography, support our design principles.
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Affiliation(s)
- Alex Nazzaro
- Department of Chemistry, New York University, 100 Washington Square East, NY 10013, New York, USA
| | - Brandon Lu
- Department of Chemistry, New York University, 100 Washington Square East, NY 10013, New York, USA
| | - Nicholas Sawyer
- Department of Chemistry, New York University, 100 Washington Square East, NY 10013, New York, USA
| | | | - Paramjit S Arora
- Department of Chemistry, New York University, 100 Washington Square East, NY 10013, New York, USA
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40
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Byeon CH, Kinney T, Saricayir H, Srinivasa S, Wells MK, Kim W, Akbey Ü. Tapping into the native Pseudomonas Bacterial Biofilm Structure by High-Resolution 1D and 2D MAS solid-state NMR. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.02.560490. [PMID: 37873242 PMCID: PMC10592892 DOI: 10.1101/2023.10.02.560490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
We present a high-resolution 1D and 2D magic-angle spinning (MAS) solid-state NMR (ssNMR) study to characterize native Pseudomonas fluorescens colony biofilms at natural abundance without isotope-labelling. By using a high-resolution INEPT-based 2D 1 H- 13 C ssNMR spectrum and thorough peak deconvolution approach at the 1D ssNMR spectra, approximately 80/134 (in 1D/2D) distinct biofilm chemical sites were identified. We compared CP and INEPT 13 C ssNMR spectra to different signals originating from the mobile and rigid fractions of the biofilm, and qualitative determined dynamical changes by comparing CP buildup behaviors. Protein and polysaccharide signals were differentiated and identified by utilizing FapC signals as a template, a biofilm forming functional amyloid from Pseudomonas . We also attempted to identify biofilm polysaccharide species by using 1 H/ 13 C chemical shifts obtained from the 2D spectrum. This study marks the first demonstration of high-resolution 2D ssNMR spectroscopy for characterizing native bacterial biofilms and expands the scope of ssNMR in studying biofilms. Our experimental pipeline can be readily applied to other in vitro biofilm model systems and natural biofilms and holds the promise of making a substantial impact on biofilm research, fostering new ideas and breakthroughs to aid in the development of strategic approaches to combat infections caused by biofilm-forming bacteria.
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41
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Marques Dos Santos M, Pivniouk V, Rankl B, Walker A, Pagani G, Hertkorn N, Schmitt-Kopplin P, Müller C, Bracher F, Merl-Pham J, Hauck SM, Schloter M, Michael AN, Anderson D, Honeker L, Gozdz J, Pivniouk O, Ober C, Holbreich M, Martinez FD, Snyder SA, von Mutius E, Vercelli D. Asthma-protective agents in dust from traditional farm environments. J Allergy Clin Immunol 2023; 152:610-621. [PMID: 37271318 PMCID: PMC10680491 DOI: 10.1016/j.jaci.2023.05.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 04/05/2023] [Accepted: 05/05/2023] [Indexed: 06/06/2023]
Abstract
BACKGROUND Growing up on traditional European or US Amish dairy farms in close contact with cows and hay protects children against asthma, and airway administration of extracts from dust collected from cowsheds of those farms prevents allergic asthma in mice. OBJECTIVES This study sought to begin identifying farm-derived asthma-protective agents. METHODS Our work unfolded along 2 unbiased and independent but complementary discovery paths. Dust extracts (DEs) from protective and nonprotective farms (European and Amish cowsheds vs European sheep sheds) were analyzed by comparative nuclear magnetic resonance profiling and differential proteomics. Bioactivity-guided size fractionation focused on protective Amish cowshed DEs. Multiple in vitro and in vivo functional assays were used in both paths. Some of the proteins thus identified were characterized by in-solution and in-gel sodium dodecyl sulfate-polyacrylamide gel electrophoresis enzymatic digestion/peptide mapping followed by liquid chromatography/mass spectrometry. The cargo carried by these proteins was analyzed by untargeted liquid chromatography-high-resolution mass spectrometry. RESULTS Twelve carrier proteins of animal and plant origin, including the bovine lipocalins Bos d 2 and odorant binding protein, were enriched in DEs from protective European cowsheds. A potent asthma-protective fraction of Amish cowshed DEs (≈0.5% of the total carbon content of unfractionated extracts) contained 7 animal and plant proteins, including Bos d 2 and odorant binding protein loaded with fatty acid metabolites from plants, bacteria, and fungi. CONCLUSIONS Animals and plants from traditional farms produce proteins that transport hydrophobic microbial and plant metabolites. When delivered to mucosal surfaces, these agents might regulate airway responses.
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Affiliation(s)
| | - Vadim Pivniouk
- Department of Cellular and Molecular Medicine, The University of Arizona, Tucson, Ariz; Asthma and Airway Disease Research Center, The University of Arizona, Tucson, Ariz
| | - Bettina Rankl
- Institute for Asthma and Allergy Prevention, IAP, Helmholtz Center Munich, Munich, Germany
| | - Alesia Walker
- Research Unit Analytical Biogeochemistry, BGC, Helmholtz Center Munich, Munich, Germany
| | - Giulia Pagani
- Institute for Asthma and Allergy Prevention, IAP, Helmholtz Center Munich, Munich, Germany
| | - Norbert Hertkorn
- Research Unit Analytical Biogeochemistry, BGC, Helmholtz Center Munich, Munich, Germany
| | | | - Christoph Müller
- Department of Pharmacy, Center for Drug Research, Ludwig-Maximilians University Munich, Munich, Germany
| | - Franz Bracher
- Department of Pharmacy, Center for Drug Research, Ludwig-Maximilians University Munich, Munich, Germany
| | - Juliane Merl-Pham
- Research Unit Protein Science and Metabolomics and Proteomics Core, Helmholtz Center Munich, Munich, Germany
| | - Stefanie M Hauck
- Research Unit Protein Science and Metabolomics and Proteomics Core, Helmholtz Center Munich, Munich, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Center Munich, Munich, Germany; ZIEL-Institute for Food & Health, Technical University of Munich, Freising, Germany
| | - Ashley N Michael
- Asthma and Airway Disease Research Center, The University of Arizona, Tucson, Ariz
| | - Dayna Anderson
- Asthma and Airway Disease Research Center, The University of Arizona, Tucson, Ariz
| | - Linnea Honeker
- Asthma and Airway Disease Research Center, The University of Arizona, Tucson, Ariz; Biosphere2, The University of Arizona, Tucson, Ariz
| | - Justyna Gozdz
- Asthma and Airway Disease Research Center, The University of Arizona, Tucson, Ariz
| | - Oksana Pivniouk
- Asthma and Airway Disease Research Center, The University of Arizona, Tucson, Ariz
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, Ill
| | | | - Fernando D Martinez
- Asthma and Airway Disease Research Center, The University of Arizona, Tucson, Ariz
| | - Shane A Snyder
- Department of Chemical & Environmental Engineering, The University of Arizona, Tucson, Ariz; The BIO5 Institute, The University of Arizona, Tucson, Ariz.
| | - Erika von Mutius
- Institute for Asthma and Allergy Prevention, IAP, Helmholtz Center Munich, Munich, Germany; Department of Pediatrics, Dr. von Hauner Children's Hospital, LMU University Hospital, Ludwig-Maximilians University Munich, Munich, Germany; Comprehensive Pneumology Center-Munich (CPC-M), German Center for Lung Research (DZL), Munich, Germany.
| | - Donata Vercelli
- Department of Cellular and Molecular Medicine, The University of Arizona, Tucson, Ariz; Asthma and Airway Disease Research Center, The University of Arizona, Tucson, Ariz; The BIO5 Institute, The University of Arizona, Tucson, Ariz; Arizona Center for the Biology of Complex Diseases, The University of Arizona, Tucson, Ariz.
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Miyamoto Y, Nakatsuji M, Yoshida T, Ohkubo T, Inui T. Structural and interaction analysis of human lipocalin-type prostaglandin D synthase with the poorly water-soluble drug NBQX. FEBS J 2023; 290:3983-3996. [PMID: 37021622 DOI: 10.1111/febs.16791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/24/2023] [Accepted: 04/03/2023] [Indexed: 04/07/2023]
Abstract
Lipocalin-type prostaglandin D synthase (L-PGDS) is a secretory lipid-transporter protein that was shown to bind a wide variety of hydrophobic ligands in vitro. Exploiting this function, we previously examined the feasibility of using L-PGDS as a novel delivery vehicle for poorly water-soluble drugs. However, the mechanism by which human L-PGDS binds to poorly water-soluble drugs is unclear. In this study, we determined the solution structure of human L-PGDS and investigated the mechanism of L-PGDS binding to 6-nitro-7-sulfamoyl-benzo[f]quinoxalin-2,3-dione (NBQX), an α-amino-3-hydroxy-5-methyl-4-isoxazole-propionic acid receptor antagonist. NMR experiments showed that human L-PGDS has an eight-stranded antiparallel β-barrel structure that forms a central cavity, a short 310 -helix and two α-helices. Titration with NBQX was monitored using 1 H-15 N HSQC spectroscopy. At higher NBQX concentrations, some cross-peaks of the protein exhibited fast-exchanging shifts with a curvature, indicating at least two binding sites. These residues were located in the upper portion of the cavity. Singular value decomposition analysis revealed that human L-PGDS has two NBQX binding sites. Large chemical shift changes were observed in the H2-helix and A-, B-, C-, D-, H- and I-strands and H2-helix upon NBQX binding. Calorimetric experiments revealed that human L-PGDS binds two NBQX molecules with dissociation constants of 46.7 μm for primary binding and 185.0 μm for secondary binding. Molecular docking simulations indicated that these NBQX binding sites are located within the β-barrel. These results provide new insights into the interaction between poorly water-soluble drugs and human L-PGDS as a drug carrier.
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Affiliation(s)
- Yuya Miyamoto
- Laboratory of Biological Macromolecules, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Japan
- Japan Society for the Promotion of Science, Chiyoda-ku, Japan
| | - Masatoshi Nakatsuji
- Laboratory of Biological Macromolecules, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Japan
- Japan Society for the Promotion of Science, Chiyoda-ku, Japan
| | - Takuya Yoshida
- Laboratory of Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Japan
| | - Tadayasu Ohkubo
- Laboratory of Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Japan
| | - Takashi Inui
- Laboratory of Biological Macromolecules, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Japan
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43
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Zhou Y, Harvey PJ, Koehbach J, Chan LY, Jones A, Andersson Å, Vetter I, Durek T, Craik DJ. A Chemoenzymatic Approach To Produce a Cyclic Analogue of the Analgesic Drug MVIIA (Ziconotide). Angew Chem Int Ed Engl 2023; 62:e202302812. [PMID: 37148162 PMCID: PMC10952433 DOI: 10.1002/anie.202302812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/05/2023] [Accepted: 05/05/2023] [Indexed: 05/07/2023]
Abstract
Ziconotide (ω-conotoxin MVIIA) is an approved analgesic for the treatment of chronic pain. However, the need for intrathecal administration and adverse effects have limited its widespread application. Backbone cyclization is one way to improve the pharmaceutical properties of conopeptides, but so far chemical synthesis alone has been unable to produce correctly folded and backbone cyclic analogues of MVIIA. In this study, an asparaginyl endopeptidase (AEP)-mediated cyclization was used to generate backbone cyclic analogues of MVIIA for the first time. Cyclization using six- to nine-residue linkers did not perturb the overall structure of MVIIA, and the cyclic analogues of MVIIA showed inhibition of voltage-gated calcium channels (CaV 2.2) and substantially improved stability in human serum and stimulated intestinal fluid. Our study reveals that AEP transpeptidases are capable of cyclizing structurally complex peptides that chemical synthesis cannot achieve and paves the way for further improving the therapeutic value of conotoxins.
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Affiliation(s)
- Yan Zhou
- ARC Centre of Excellence for Innovations in Peptide and Protein ScienceInstitute for Molecular BioscienceThe University of QueenslandBrisbaneQLD4072Australia
| | - Peta J. Harvey
- ARC Centre of Excellence for Innovations in Peptide and Protein ScienceInstitute for Molecular BioscienceThe University of QueenslandBrisbaneQLD4072Australia
| | - Johannes Koehbach
- ARC Centre of Excellence for Innovations in Peptide and Protein ScienceInstitute for Molecular BioscienceThe University of QueenslandBrisbaneQLD4072Australia
| | - Lai Yue Chan
- ARC Centre of Excellence for Innovations in Peptide and Protein ScienceInstitute for Molecular BioscienceThe University of QueenslandBrisbaneQLD4072Australia
| | - Alun Jones
- Institute for Molecular BioscienceThe University of QueenslandBrisbaneQLD4072Australia
| | - Åsa Andersson
- Institute for Molecular BioscienceThe University of QueenslandBrisbaneQLD4072Australia
| | - Irina Vetter
- School of PharmacyInstitute for Molecular BioscienceThe University of QueenslandBrisbaneQLD4072Australia
| | - Thomas Durek
- ARC Centre of Excellence for Innovations in Peptide and Protein ScienceInstitute for Molecular BioscienceThe University of QueenslandBrisbaneQLD4072Australia
| | - David J. Craik
- ARC Centre of Excellence for Innovations in Peptide and Protein ScienceInstitute for Molecular BioscienceThe University of QueenslandBrisbaneQLD4072Australia
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44
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Plut E, Calderón JC, Stanojlović V, Gattor AO, Höring C, Humphrys LJ, Konieczny A, Kerres S, Schubert M, Keller M, Cabrele C, Clark T, Reiser O. Stereochemistry-Driven Interactions of α,γ-Peptide Ligands with the Neuropeptide Y Y 4-Receptor. J Med Chem 2023. [PMID: 37440703 DOI: 10.1021/acs.jmedchem.3c00363] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/15/2023]
Abstract
The G-protein-coupled Y4-receptor (Y4R) and its endogenous ligand, pancreatic polypeptide (PP), suppress appetite in response to food intake and, thus, are attractive drug targets for body-weight control. The C-terminus of human PP (hPP), T32-R33-P34-R35-Y36-NH2, penetrates deep into the binding pocket with its tyrosine-amide and di-arginine motif. Here, we present two C-terminally amidated α,γ-hexapeptides (1a/b) with sequence Ac-R31-γ-CBAA32-R33-L34-R35-Y36-NH2, where γ-CBAA is the (1R,2S,3R)-configured 2-(aminomethyl)-3-phenylcyclobutanecarboxyl moiety (1a) or its mirror image (1b). Both peptides bind the Y4R (Ki of 1a/b: 0.66/12 nM) and act as partial agonists (intrinsic activity of 1a/b: 50/39%). Their induced-fit binding poses in the Y4R pocket are unique and build ligand-receptor contacts distinct from those of the C-terminus of the endogenous ligand hPP. We conclude that energetically favorable interactions, although they do not match those of the native ligand hPP, still guarantee high binding affinity (with 1a rivaling hPP) but not the maximum receptor activation.
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Affiliation(s)
- Eva Plut
- Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Regensburg, 93053 Regensburg, Germany
| | - Jacqueline C Calderón
- Department of Chemistry and Pharmacy, Computer-Chemistry-Center, Friedrich-Alexander-University Erlangen-Nürnberg, 91052 Erlangen, Germany
| | - Vesna Stanojlović
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
| | - Albert O Gattor
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, 93053 Regensburg, Germany
| | - Carina Höring
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, 93053 Regensburg, Germany
| | - Laura J Humphrys
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, 93053 Regensburg, Germany
| | - Adam Konieczny
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, 93053 Regensburg, Germany
| | - Sabine Kerres
- Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Regensburg, 93053 Regensburg, Germany
| | - Mario Schubert
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
| | - Max Keller
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, 93053 Regensburg, Germany
| | - Chiara Cabrele
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
| | - Timothy Clark
- Department of Chemistry and Pharmacy, Computer-Chemistry-Center, Friedrich-Alexander-University Erlangen-Nürnberg, 91052 Erlangen, Germany
| | - Oliver Reiser
- Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Regensburg, 93053 Regensburg, Germany
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45
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Coleman OD, Macdonald J, Thomson B, Ward JA, Stubbs CJ, McAllister TE, Clark S, Amin S, Cao Y, Abboud MI, Zhang Y, Sanganee H, Huber KVM, Claridge TDW, Kawamura A. Cyclic peptides target the aromatic cage of a PHD-finger reader domain to modulate epigenetic protein function. Chem Sci 2023; 14:7136-7146. [PMID: 37416723 PMCID: PMC10321576 DOI: 10.1039/d2sc05944d] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 04/15/2023] [Indexed: 07/08/2023] Open
Abstract
Plant homeodomain fingers (PHD-fingers) are a family of reader domains that can recruit epigenetic proteins to specific histone modification sites. Many PHD-fingers recognise methylated lysines on histone tails and play crucial roles in transcriptional regulation, with their dysregulation linked to various human diseases. Despite their biological importance, chemical inhibitors for targeting PHD-fingers are very limited. Here we report a potent and selective de novo cyclic peptide inhibitor (OC9) targeting the Nε-trimethyllysine-binding PHD-fingers of the KDM7 histone demethylases, developed using mRNA display. OC9 disrupts PHD-finger interaction with histone H3K4me3 by engaging the Nε-methyllysine-binding aromatic cage through a valine, revealing a new non-lysine recognition motif for the PHD-fingers that does not require cation-π interaction. PHD-finger inhibition by OC9 impacted JmjC-domain mediated demethylase activity at H3K9me2, leading to inhibition of KDM7B (PHF8) but stimulation of KDM7A (KIAA1718), representing a new approach for selective allosteric modulation of demethylase activity. Chemoproteomic analysis showed selective engagement of OC9 with KDM7s in T cell lymphoblastic lymphoma SUP T1 cells. Our results highlight the utility of mRNA-display derived cyclic peptides for targeting challenging epigenetic reader proteins to probe their biology, and the broader potential of this approach for targeting protein-protein interactions.
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Affiliation(s)
- Oliver D Coleman
- School of Natural and Environmental Sciences - Chemistry, Newcastle University Newcastle NE1 7RU UK
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
- Radcliffe Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford Roosevelt Drive Old Road Campus Oxford OX3 7BN UK
| | - Jessica Macdonald
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
| | - Ben Thomson
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
| | - Jennifer A Ward
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford Old Road Campus Oxford OX3 7FZ UK
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford Oxford OX3 7FZ UK
| | - Christopher J Stubbs
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca Cambridge CB4 0WG UK
| | - Tom E McAllister
- School of Natural and Environmental Sciences - Chemistry, Newcastle University Newcastle NE1 7RU UK
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
- Radcliffe Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford Roosevelt Drive Old Road Campus Oxford OX3 7BN UK
| | - Shane Clark
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
| | - Siddique Amin
- School of Natural and Environmental Sciences - Chemistry, Newcastle University Newcastle NE1 7RU UK
| | - Yimang Cao
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
| | - Martine I Abboud
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
| | - Yijia Zhang
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
| | - Hitesh Sanganee
- Emerging Innovations Unit, Discovery Sciences, R&D, AstraZeneca Cambridge UK
| | - Kilian V M Huber
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford Old Road Campus Oxford OX3 7FZ UK
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford Oxford OX3 7FZ UK
| | - Tim D W Claridge
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
| | - Akane Kawamura
- School of Natural and Environmental Sciences - Chemistry, Newcastle University Newcastle NE1 7RU UK
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
- Radcliffe Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford Roosevelt Drive Old Road Campus Oxford OX3 7BN UK
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46
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Wang CK, Huang YH, Shabbir F, Pham HT, Lawrence N, Benfield AH, van der Donk W, Henriques ST, Turner MS, Craik DJ. The Circular Bacteriocin enterocin NKR-5-3B has an Improved Stability Profile over Nisin. Peptides 2023:171049. [PMID: 37390898 DOI: 10.1016/j.peptides.2023.171049] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/22/2023] [Accepted: 06/23/2023] [Indexed: 07/02/2023]
Abstract
Bacteriocins are a large family of bacterial peptides that have antimicrobial activity and potential applications as clinical antibiotics or food preservatives. Circular bacteriocins are a unique class of these biomolecules distinguished by a seamless circular topology, and are widely assumed to be ultra-stable based on this constraining structural feature. However, without quantitative studies of their susceptibility to defined thermal, chemical, and enzymatic conditions, their stability characteristics remain poorly understood, limiting their translational development. Here, we produced the circular bacteriocin enterocin NKR-5-3B (Ent53B) in mg/L quantities using a heterologous Lactococcus expression system, and characterized its thermal stability by NMR, chemical stability by circular dichroism and analytical HPLC, and enzymatic stability by analytical HPLC. We demonstrate that Ent53B is ultra-stable, resistant to temperatures approaching boiling, acidic (pH 2.6) and alkaline (pH 9.0) conditions, the chaotropic agent 6M urea, and following incubation with a range of proteases (i.e., trypsin, chymotrypsin, pepsin, and papain), conditions under which most peptides and proteins degrade. Ent53B is stable across a broader range of pH conditions and proteases than nisin, the most widely used bacteriocin in food manufacturing. Antimicrobial assays showed that differences in stability correlated with differences in bactericidal activity. Overall, this study provides quantitative support for circular bacteriocins being an ultra-stable class of peptide molecules, suggesting easier handling and distribution options available to them in practical applications as antimicrobial agents.
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Affiliation(s)
- Conan K Wang
- Institute for Molecular Bioscience and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science,.
| | - Yen-Hua Huang
- Institute for Molecular Bioscience and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science
| | - Fatima Shabbir
- Institute for Molecular Bioscience and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science
| | - Huong T Pham
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Nicole Lawrence
- Institute for Molecular Bioscience and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science
| | - Aurélie H Benfield
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Translational Research Institute, Brisbane, QLD 4102, Australia
| | - Wilfred van der Donk
- Department of Chemistry and the Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Sónia T Henriques
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Translational Research Institute, Brisbane, QLD 4102, Australia
| | - Mark S Turner
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - David J Craik
- Institute for Molecular Bioscience and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science
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47
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Nicolini F, Todorovski T, Puig E, Díaz-Lobo M, Vilaseca M, García J, Andreu D, Giralt E. How Do Cancer-Related Mutations Affect the Oligomerisation State of the p53 Tetramerisation Domain? Curr Issues Mol Biol 2023; 45:4985-5004. [PMID: 37367066 DOI: 10.3390/cimb45060317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 05/29/2023] [Accepted: 06/02/2023] [Indexed: 06/28/2023] Open
Abstract
Tumour suppressor p53 plays a key role in the development of cancer and has therefore been widely studied in recent decades. While it is well known that p53 is biologically active as a tetramer, the tetramerisation mechanism is still not completely understood. p53 is mutated in nearly 50% of cancers, and mutations can alter the oligomeric state of the protein, having an impact on the biological function of the protein and on cell fate decisions. Here, we describe the effects of a number of representative cancer-related mutations on tetramerisation domain (TD) oligomerisation defining a peptide length that permits having a folded and structured domain, thus avoiding the effect of the flanking regions and the net charges at the N- and C-terminus. These peptides have been studied under different experimental conditions. We have applied a variety of techniques, including circular dichroism (CD), native mass spectrometry (MS) and high-field solution NMR. Native MS allows us to detect the native state of complexes maintaining the peptide complexes intact in the gas phase; the secondary and quaternary structures were analysed in solution by NMR, and the oligomeric forms were assigned by diffusion NMR experiments. A significant destabilising effect and a variable monomer population were observed for all the mutants studied.
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Affiliation(s)
- Federica Nicolini
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Toni Todorovski
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, 08028 Barcelona, Spain
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Eduard Puig
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Mireia Díaz-Lobo
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Marta Vilaseca
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Jesús García
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, 08028 Barcelona, Spain
| | - David Andreu
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Ernest Giralt
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, 08028 Barcelona, Spain
- Department of Inorganic and Organic Chemistry, University of Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
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48
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Politi MD, Gallo A, Bouras G, Birkou M, Canard B, Coutard B, Spyroulias GA. 1H, 13C, 15N backbone resonance assignment of apo and ADP-ribose bound forms of the macro domain of Hepatitis E virus through solution NMR spectroscopy. BIOMOLECULAR NMR ASSIGNMENTS 2023; 17:1-8. [PMID: 36272047 PMCID: PMC9589693 DOI: 10.1007/s12104-022-10111-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 09/28/2022] [Indexed: 06/02/2023]
Abstract
The genome of Hepatitis E virus (HEV) is 7.2 kilobases long and has three open reading frames. The largest one is ORF1, encoding a non-structural protein involved in the replication process, and whose processing is ill-defined. The ORF1 protein is a multi-modular protein which includes a macro domain (MD). MDs are evolutionarily conserved structures throughout all kingdoms of life. MDs participate in the recognition and removal of ADP-ribosylation, and specifically viral MDs have been identified as erasers of ADP-ribose moieties interpreting them as important players at escaping the early stages of host-immune response. A detailed structural analysis of the apo and bound to ADP-ribose state of the native HEV MD would provide the structural information to understand how HEV MD is implicated in virus-host interplay and how it interacts with its intracellular partner during viral replication. In the present study we present the high yield expression of the native macro domain of HEV and its analysis by solution NMR spectroscopy. The HEV MD is folded in solution and we present a nearly complete backbone and sidechains assignment for apo and bound states. In addition, a secondary structure prediction by TALOS + analysis was performed. The results indicated that HEV MD has a α/β/α topology very similar to that of most viral macro domains.
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Affiliation(s)
- Maria D Politi
- Department of Pharmacy, University of Patras, 26504, Patras, Greece
| | - Angelo Gallo
- Department of Chemistry, University of Torino, 10126, Torino, Italy
| | - Georgios Bouras
- Department of Pharmacy, University of Patras, 26504, Patras, Greece
| | - Maria Birkou
- Department of Pharmacy, University of Patras, 26504, Patras, Greece
| | - Bruno Canard
- Université Aix-Marseille, Architecture et Fonction des Macromolécules Biologiques (AFMB) - UMR7257 CNRS - Case 932, 163 avenue de Luminy, 13288, Marseille CEDEX 09, France
| | - Bruno Coutard
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France.
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49
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Moises JE, Regl C, Hinterholzer A, Huber CG, Schubert M. Unambiguous Identification of Glucose-Induced Glycation in mAbs and other Proteins by NMR Spectroscopy. Pharm Res 2023; 40:1341-1353. [PMID: 36510116 PMCID: PMC10338404 DOI: 10.1007/s11095-022-03454-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Glycation is a non-enzymatic and spontaneous post-translational modification (PTM) generated by the reaction between reducing sugars and primary amine groups within proteins. Because glycation can alter the properties of proteins, it is a critical quality attribute of therapeutic monoclonal antibodies (mAbs) and should therefore be carefully monitored. The most abundant product of glycation is formed by glucose and lysine side chains resulting in fructoselysine after Amadori rearrangement. In proteomics, which routinely uses a combination of chromatography and mass spectrometry to analyze PTMs, there is no straight-forward way to distinguish between glycation products of a reducing monosaccharide and an additional hexose within a glycan, since both lead to a mass difference of 162 Da. METHODS To verify that the observed mass change is indeed a glycation product, we developed an approach based on 2D NMR spectroscopy spectroscopy and full-length protein samples denatured using high concentrations of deuterated urea. RESULTS The dominating β-pyranose form of the Amadori product shows a characteristic chemical shift correlation pattern in 1H-13C HSQC spectra suited to identify glucose-induced glycation. The same pattern was observed in spectra of a variety of artificially glycated proteins, including two mAbs, as well as natural proteins. CONCLUSION Based on this unique correlation pattern, 2D NMR spectroscopy can be used to unambiguously identify glucose-induced glycation in any protein of interest. We provide a robust method that is orthogonal to MS-based methods and can also be used for cross-validation.
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Affiliation(s)
- Jennifer E Moises
- Department of Biosciences and Medical Biology, University of Salzburg, Hellbrunner Strasse 34, 5020, Salzburg, Austria
| | - Christof Regl
- Department of Biosciences and Medical Biology, University of Salzburg, Hellbrunner Strasse 34, 5020, Salzburg, Austria
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Strasse 34, 5020, Salzburg, Austria
| | - Arthur Hinterholzer
- Department of Biosciences and Medical Biology, University of Salzburg, Hellbrunner Strasse 34, 5020, Salzburg, Austria
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Strasse 34, 5020, Salzburg, Austria
| | - Christian G Huber
- Department of Biosciences and Medical Biology, University of Salzburg, Hellbrunner Strasse 34, 5020, Salzburg, Austria
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Strasse 34, 5020, Salzburg, Austria
| | - Mario Schubert
- Department of Biosciences and Medical Biology, University of Salzburg, Hellbrunner Strasse 34, 5020, Salzburg, Austria.
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Strasse 34, 5020, Salzburg, Austria.
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Jeon J, Yau WM, Tycko R. Early events in amyloid-β self-assembly probed by time-resolved solid state NMR and light scattering. Nat Commun 2023; 14:2964. [PMID: 37221174 DOI: 10.1038/s41467-023-38494-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/04/2023] [Indexed: 05/25/2023] Open
Abstract
Self-assembly of amyloid-β peptides leads to oligomers, protofibrils, and fibrils that are likely instigators of neurodegeneration in Alzheimer's disease. We report results of time-resolved solid state nuclear magnetic resonance (ssNMR) and light scattering experiments on 40-residue amyloid-β (Aβ40) that provide structural information for oligomers that form on time scales from 0.7 ms to 1.0 h after initiation of self-assembly by a rapid pH drop. Low-temperature ssNMR spectra of freeze-trapped intermediates indicate that β-strand conformations within and contacts between the two main hydrophobic segments of Aβ40 develop within 1 ms, while light scattering data imply a primarily monomeric state up to 5 ms. Intermolecular contacts involving residues 18 and 33 develop within 0.5 s, at which time Aβ40 is approximately octameric. These contacts argue against β-sheet organizations resembling those found previously in protofibrils and fibrils. Only minor changes in the Aβ40 conformational distribution are detected as larger assemblies develop.
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Affiliation(s)
- Jaekyun Jeon
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA
- Institute for Bioscience and Biotechnology Research, University of Maryland/National Institute of Standards and Technology, Rockville, MD, 20850, USA
| | - Wai-Ming Yau
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA.
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