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Huang LB, Mamiya F, Baaden M, Yashima E, Barboiu M. Self-Assembling Peptide-Appended Metallomacrocycle Pores for Selective Water Translocation. ACS APPLIED MATERIALS & INTERFACES 2023; 15:40133-40139. [PMID: 37566758 DOI: 10.1021/acsami.3c09059] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/13/2023]
Abstract
Artificial water channels selectively transport water, excluding all ions. Unimolecular channels have been synthesized via complex synthetic steps. Ideally, simpler compounds requesting less synthetic steps should efficiently lead to selective channels by self-assembly. Herein, we report a self-assembled peptide-bound Ni2+ metallomacrocycle, 1, in which rim-peptide-bound units are connected to a central macrocycle obtained via condensation in the presence of Ni2+ ions. Compound 1 achieves a single-channel permeability up to 107-108 water/s/channel and insignificant ion transport, which is 1 order of magnitude lower than those for aquaporins. Molecular simulations probe that spongelike aggregates can form to generate transient cluster water pathways through the bilayer. Altogether, adaptive metallosupramolecular self-assembly is an efficient and simple way to construct selective channel superstructures.
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Affiliation(s)
- Li-Bo Huang
- Institut Europeen des Membranes, Adaptive Supramolecular Nanosystems Group, University of Montpellier, ENSCM-CNRS, UMR5635, Place E. Bataillon CC047, Montpellier 34095, France
- School of Chemical Engineering and Technology, Hainan University, Haikou 570228, China
| | - Fumihiko Mamiya
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University Chikusa-ku, Nagoya 464-8603, Japan
| | - Marc Baaden
- Laboratoire de Biochimie Théorique, CNRS, Université Paris Cité, 13 rue Pierre et Marie Curie, Paris F-75005, France
| | - Eiji Yashima
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University Chikusa-ku, Nagoya 464-8603, Japan
- Department of Molecular and Macromolecular Chemistry, Graduate School of Engineering, Nagoya University Chikusa-ku, Nagoya 464-8603, Japan
| | - Mihail Barboiu
- Institut Europeen des Membranes, Adaptive Supramolecular Nanosystems Group, University of Montpellier, ENSCM-CNRS, UMR5635, Place E. Bataillon CC047, Montpellier 34095, France
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2
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Fraser CS, Spetz JKE, Qin X, Presser A, Choiniere J, Li C, Yu S, Blevins F, Hata AN, Miller JW, Bradshaw GA, Kalocsay M, Sanchorawala V, Sarosiek S, Sarosiek KA. Exploiting endogenous and therapy-induced apoptotic vulnerabilities in immunoglobulin light chain amyloidosis with BH3 mimetics. Nat Commun 2022; 13:5789. [PMID: 36184661 PMCID: PMC9527241 DOI: 10.1038/s41467-022-33461-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 09/16/2022] [Indexed: 01/11/2023] Open
Abstract
Immunoglobulin light chain (AL) amyloidosis is an incurable hematologic disorder typically characterized by the production of amyloidogenic light chains by clonal plasma cells. These light chains misfold and aggregate in healthy tissues as amyloid fibrils, leading to life-threatening multi-organ dysfunction. Here we show that the clonal plasma cells in AL amyloidosis are highly primed to undergo apoptosis and dependent on pro-survival proteins MCL-1 and BCL-2. Notably, this MCL-1 dependency is indirectly targeted by the proteasome inhibitor bortezomib, currently the standard of care for this disease and the related plasma cell disorder multiple myeloma, due to upregulation of pro-apoptotic Noxa and its inhibitory binding to MCL-1. BCL-2 inhibitors sensitize clonal plasma cells to multiple front-line therapies including bortezomib, dexamethasone and lenalidomide. Strikingly, in mice bearing AL amyloidosis cell line xenografts, single agent treatment with the BCL-2 inhibitor ABT-199 (venetoclax) produces deeper remissions than bortezomib and triples median survival. Mass spectrometry-based proteomic analysis reveals rewiring of signaling pathways regulating apoptosis, proliferation and mitochondrial metabolism between isogenic AL amyloidosis and multiple myeloma cells that divergently alter their sensitivity to therapies. These findings provide a roadmap for the use of BH3 mimetics to exploit endogenous and induced apoptotic vulnerabilities in AL amyloidosis.
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Affiliation(s)
- Cameron S. Fraser
- grid.38142.3c000000041936754XJohn B. Little Center for Radiation Sciences, Harvard TH Chan School of Public Health, Boston, MA 02115 USA ,grid.38142.3c000000041936754XProgram in Molecular and Integrative Physiological Sciences, Harvard TH Chan School of Public Health, Boston, MA 02115 USA ,grid.38142.3c000000041936754XLaboratory of Systems Pharmacology, Harvard Medical School, Boston, 02115 USA
| | - Johan K. E. Spetz
- grid.38142.3c000000041936754XJohn B. Little Center for Radiation Sciences, Harvard TH Chan School of Public Health, Boston, MA 02115 USA ,grid.38142.3c000000041936754XProgram in Molecular and Integrative Physiological Sciences, Harvard TH Chan School of Public Health, Boston, MA 02115 USA ,grid.38142.3c000000041936754XLaboratory of Systems Pharmacology, Harvard Medical School, Boston, 02115 USA
| | - Xingping Qin
- grid.38142.3c000000041936754XJohn B. Little Center for Radiation Sciences, Harvard TH Chan School of Public Health, Boston, MA 02115 USA ,grid.38142.3c000000041936754XProgram in Molecular and Integrative Physiological Sciences, Harvard TH Chan School of Public Health, Boston, MA 02115 USA ,grid.38142.3c000000041936754XLaboratory of Systems Pharmacology, Harvard Medical School, Boston, 02115 USA
| | - Adam Presser
- grid.38142.3c000000041936754XJohn B. Little Center for Radiation Sciences, Harvard TH Chan School of Public Health, Boston, MA 02115 USA ,grid.38142.3c000000041936754XProgram in Molecular and Integrative Physiological Sciences, Harvard TH Chan School of Public Health, Boston, MA 02115 USA ,grid.38142.3c000000041936754XLaboratory of Systems Pharmacology, Harvard Medical School, Boston, 02115 USA
| | - Jonathan Choiniere
- grid.38142.3c000000041936754XJohn B. Little Center for Radiation Sciences, Harvard TH Chan School of Public Health, Boston, MA 02115 USA ,grid.38142.3c000000041936754XProgram in Molecular and Integrative Physiological Sciences, Harvard TH Chan School of Public Health, Boston, MA 02115 USA ,grid.38142.3c000000041936754XLaboratory of Systems Pharmacology, Harvard Medical School, Boston, 02115 USA
| | - Chendi Li
- grid.32224.350000 0004 0386 9924Massachusetts General Hospital Cancer Center, Charlestown, MA 02129 USA ,grid.38142.3c000000041936754XDepartment of Medicine, Harvard Medical School, Boston, MA 02115 USA
| | - Stacey Yu
- grid.38142.3c000000041936754XJohn B. Little Center for Radiation Sciences, Harvard TH Chan School of Public Health, Boston, MA 02115 USA ,grid.38142.3c000000041936754XProgram in Molecular and Integrative Physiological Sciences, Harvard TH Chan School of Public Health, Boston, MA 02115 USA ,grid.38142.3c000000041936754XLaboratory of Systems Pharmacology, Harvard Medical School, Boston, 02115 USA
| | - Frances Blevins
- grid.239424.a0000 0001 2183 6745Section of Hematology & Medical Oncology, Boston Medical Center, Boston, MA 02118 USA ,grid.189504.10000 0004 1936 7558Amyloidosis Center, Boston University School of Medicine, Boston, MA 02118 USA
| | - Aaron N. Hata
- grid.32224.350000 0004 0386 9924Massachusetts General Hospital Cancer Center, Charlestown, MA 02129 USA ,grid.38142.3c000000041936754XDepartment of Medicine, Harvard Medical School, Boston, MA 02115 USA
| | - Jeffrey W. Miller
- grid.38142.3c000000041936754XDepartment of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA 02115 USA
| | - Gary A. Bradshaw
- grid.38142.3c000000041936754XLaboratory of Systems Pharmacology, Harvard Medical School, Boston, 02115 USA
| | - Marian Kalocsay
- grid.38142.3c000000041936754XLaboratory of Systems Pharmacology, Harvard Medical School, Boston, 02115 USA ,grid.240145.60000 0001 2291 4776Present Address: Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Vaishali Sanchorawala
- grid.239424.a0000 0001 2183 6745Section of Hematology & Medical Oncology, Boston Medical Center, Boston, MA 02118 USA ,grid.189504.10000 0004 1936 7558Amyloidosis Center, Boston University School of Medicine, Boston, MA 02118 USA
| | - Shayna Sarosiek
- grid.239424.a0000 0001 2183 6745Section of Hematology & Medical Oncology, Boston Medical Center, Boston, MA 02118 USA ,grid.189504.10000 0004 1936 7558Amyloidosis Center, Boston University School of Medicine, Boston, MA 02118 USA ,grid.65499.370000 0001 2106 9910Present Address: Dana-Farber Cancer Institute, Harvard Cancer Center, Boston, 02215 USA
| | - Kristopher A. Sarosiek
- grid.38142.3c000000041936754XJohn B. Little Center for Radiation Sciences, Harvard TH Chan School of Public Health, Boston, MA 02115 USA ,grid.38142.3c000000041936754XProgram in Molecular and Integrative Physiological Sciences, Harvard TH Chan School of Public Health, Boston, MA 02115 USA ,grid.38142.3c000000041936754XLaboratory of Systems Pharmacology, Harvard Medical School, Boston, 02115 USA
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3
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Yudina ON, Gening ML, Talukdar P, Gerbst AG, Tsvetkov YE, Nifantiev NE. Synthesis of a cyclic tetramer of 3-amino-3-deoxyallose with axially oriented amino groups. Carbohydr Res 2021; 511:108476. [PMID: 34800752 DOI: 10.1016/j.carres.2021.108476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/02/2021] [Accepted: 11/03/2021] [Indexed: 12/01/2022]
Abstract
A linear tetramer of β-(1 → 6)-linked 3-azido-3-deoxy-d-allose containing glycosyl donor and glycosyl acceptor functions in the terminal monosaccharide units was prepared starting from 3-azido-3-deoxy-1,2:5,6-di-O-isopropylidene-α-d-allofuranose. Cyclization of the linear tetramer under glycosylation conditions afforded the corresponding cyclic tetrasaccharide in 77% yield; its deprotection and reduction of the azido groups resulted in the formation of the cyclic tetramer of 3-amino-3-deoxy-d-allose with axial amino groups, a potential scaffold for the synthesis of tetravalent functional clusters.
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Affiliation(s)
- Olga N Yudina
- Laboratory of Glycoconjugate Chemistry, N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky Prosp, 119991, Moscow, Russian Federation
| | - Marina L Gening
- Laboratory of Glycoconjugate Chemistry, N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky Prosp, 119991, Moscow, Russian Federation
| | - Pinaki Talukdar
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune, 411008, Maharashtra, India
| | - Alexey G Gerbst
- Laboratory of Glycoconjugate Chemistry, N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky Prosp, 119991, Moscow, Russian Federation
| | - Yury E Tsvetkov
- Laboratory of Glycoconjugate Chemistry, N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky Prosp, 119991, Moscow, Russian Federation
| | - Nikolay E Nifantiev
- Laboratory of Glycoconjugate Chemistry, N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky Prosp, 119991, Moscow, Russian Federation.
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4
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Esmaeilpour D, Hussein A, Almalki F, Shityakov S, Bordbar A. Probing inclusion complexes of 2-hydroxypropyl-β-cyclodextrin with mono-amino mono-carboxylic acids: physicochemical specification, characterization and molecular modeling. Heliyon 2020; 6:e03360. [PMID: 32322699 PMCID: PMC7160434 DOI: 10.1016/j.heliyon.2020.e03360] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 11/20/2019] [Accepted: 01/31/2020] [Indexed: 01/28/2023] Open
Abstract
Density (ρ), viscosity (η) and surface tension (γ) of three amino acids (valine, alanine, and glycine) have been measured at a different mass fraction (0.002 - 0.009) of aqueous hydroxypropyl-β-cyclodextrin (HPβCD) mixtures and different temperatures (278.15 - 295.15 K). The formation of inclusion complexes has been analyzed via evaluating the amounts of apparent and limiting apparent molar volumes, limiting apparent molar expansibilities, activation energy, kinematic, relative, intrinsic, spatial, and dynamic viscosities. The surface tension studies indicated that the inclusion complexes have been formed with 1:1 stoichiometry and mediated by hydrophobic effects and electrostatic forces. Additionally, the ρ and η parameters were evaluated by molecular modeling experiments to provide more details on the mechanisms of the complexation.
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Affiliation(s)
| | - A.A. Hussein
- College of Dentistry, University of Al-Ameed, Karbala, Iraq
- Department of Chemistry, University of Southampton, Southampton, Hampshire, UK
| | - F.A. Almalki
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - S. Shityakov
- Department of Bioinformatics, University of Würzburg, Germany
- Corresponding author.
| | - A.K. Bordbar
- Department of Chemistry, University of Isfahan, Iran
- California Institute of Quantitative Biosciences, University of California, Berkeley, California, USA
- Corresponding author.
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5
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Mayer SF, Ducrey J, Dupasquier J, Haeni L, Rothen-Rutishauser B, Yang J, Fennouri A, Mayer M. Targeting specific membranes with an azide derivative of the pore-forming peptide ceratotoxin A. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:183023. [DOI: 10.1016/j.bbamem.2019.07.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 07/01/2019] [Accepted: 07/09/2019] [Indexed: 10/26/2022]
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6
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Understanding the antimicrobial activity of water soluble γ-cyclodextrin/alamethicin complex. Colloids Surf B Biointerfaces 2018; 172:451-458. [DOI: 10.1016/j.colsurfb.2018.08.065] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 08/06/2018] [Accepted: 08/29/2018] [Indexed: 02/03/2023]
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7
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Das S, Ben Haj Salah K, Djibo M, Inguimbert N. Peptaibols as a model for the insertions of chemical modifications. Arch Biochem Biophys 2018; 658:16-30. [DOI: 10.1016/j.abb.2018.09.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 09/05/2018] [Accepted: 09/18/2018] [Indexed: 12/13/2022]
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8
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Vurgun N, Nitz M. Highly Functionalized β-Cyclodextrins by Solid-Supported Synthesis. Chemistry 2018; 24:4459-4467. [PMID: 29389050 DOI: 10.1002/chem.201800028] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Indexed: 12/26/2022]
Abstract
Using covalent capture, a high yielding selective mono-functionalization of heptakis-[6-deoxy-6-(2-aminoethylsulfanyl)]-β-CD with a 5-mercaptopentyl functional group has been achieved. Here, we demonstrate the immobilization of the mono-thiol functionalized β-CD on PEGA resin via a disulfide bond, enabling solid-phase elaboration of the remaining six primary amines. To showcase the potential of this method, the amines were elaborated to tripeptides through standard Fmoc-peptide chemistry. A small library of CD-tripeptide conjugates was generated which, when reduced from the solid support, could be tagged at the released thiol with an environmentally sensitive fluorophore. The resulting library of sensors showed potential for the differential sensing of various bile salts. The described methodology provides a rapid and versatile route to synthesize highly functionalized libraries of CD derivatives that may be tailored towards applications in sensing, catalysis, and multivalent displays.
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Affiliation(s)
- Nesrin Vurgun
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada
| | - Mark Nitz
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada
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9
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Adam C, Peters AD, Lizio MG, Whitehead GFS, Diemer V, Cooper JA, Cockroft SL, Clayden J, Webb SJ. The Role of Terminal Functionality in the Membrane and Antibacterial Activity of Peptaibol-Mimetic Aib Foldamers. Chemistry 2018; 24:2249-2256. [PMID: 29210477 DOI: 10.1002/chem.201705299] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Indexed: 01/04/2023]
Abstract
Peptaibols are peptide antibiotics that typically feature an N-terminal acetyl cap, a C-terminal aminoalcohol, and a high proportion of α-aminoisobutyric acid (Aib) residues. To establish how each feature might affect the membrane-activity of peptaibols, biomimetic Aib foldamers with different lengths and terminal groups were synthesised. Vesicle assays showed that long foldamers (eleven Aib residues) with hydrophobic termini had the highest ionophoric activity. C-terminal acids or primary amides inhibited activity, while replacement of an N-terminal acetyl with an azide group made little difference. Crystallography showed that N3 Aib11 CH2 OTIPS folded into a 310 helix 2.91 nm long, which is close to the bilayer hydrophobic width. Planar bilayer conductance assays showed discrete ion channels only for N-acetylated foldamers. However long foldamers with hydrophobic termini had the highest antibacterial activity, indicating that ionophoric activity in vesicles was a better indicator of antibacterial activity than the observation of discrete ion channels.
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Affiliation(s)
- Catherine Adam
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Anna D Peters
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, UK.,Manchester Institute of Biotechnology, University of Manchester, 131 Princess St, Manchester, M1 7DN, UK
| | - M Giovanna Lizio
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, UK.,Manchester Institute of Biotechnology, University of Manchester, 131 Princess St, Manchester, M1 7DN, UK
| | - George F S Whitehead
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Vincent Diemer
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, UK.,Manchester Institute of Biotechnology, University of Manchester, 131 Princess St, Manchester, M1 7DN, UK
| | - James A Cooper
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, UK
| | - Scott L Cockroft
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, UK
| | - Jonathan Clayden
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Simon J Webb
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, UK.,Manchester Institute of Biotechnology, University of Manchester, 131 Princess St, Manchester, M1 7DN, UK
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10
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Du L, Risinger AL, Mitchell CA, You J, Stamps BW, Pan N, King JB, Bopassa JC, Judge SIV, Yang Z, Stevenson BS, Cichewicz RH. Unique amalgamation of primary and secondary structural elements transform peptaibols into potent bioactive cell-penetrating peptides. Proc Natl Acad Sci U S A 2017; 114:E8957-E8966. [PMID: 29073092 PMCID: PMC5664515 DOI: 10.1073/pnas.1707565114] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Mass-spectrometry-based metabolomics and molecular phylogeny data were used to identify a metabolically prolific strain of Tolypocladium that was obtained from a deep-water Great Lakes sediment sample. An investigation of the isolate's secondary metabolome resulted in the purification of a 22-mer peptaibol, gichigamin A (1). This peptidic natural product exhibited an amino acid sequence including several β-alanines that occurred in a repeating ααβ motif, causing the compound to adopt a unique right-handed 311 helical structure. The unusual secondary structure of 1 was confirmed by spectroscopic approaches including solution NMR, electronic circular dichroism (ECD), and single-crystal X-ray diffraction analyses. Artificial and cell-based membrane permeability assays provided evidence that the unusual combination of structural features in gichigamins conferred on them an ability to penetrate the outer membranes of mammalian cells. Compound 1 exhibited potent in vitro cytotoxicity (GI50 0.55 ± 0.04 µM) and in vivo antitumor effects in a MIA PaCa-2 xenograft mouse model. While the primary mechanism of cytotoxicity for 1 was consistent with ion leakage, we found that it was also able to directly depolarize mitochondria. Semisynthetic modification of 1 provided several analogs, including a C-terminus-linked coumarin derivative (22) that exhibited appreciably increased potency (GI50 5.4 ± 0.1 nM), but lacked ion leakage capabilities associated with a majority of naturally occurring peptaibols such as alamethicin. Compound 22 was found to enter intact cells and induced cell death in a process that was preceded by mitochondrial depolarization.
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Affiliation(s)
- Lin Du
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, OK 73019-5251
- Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, University of Oklahoma, Norman, OK 73019-5251
| | - April L Risinger
- Department of Pharmacology, University of Texas Health Science Center, San Antonio, TX 78229
- Cancer Therapy & Research Center, University of Texas Health Science Center, San Antonio, TX 78229
| | - Carter A Mitchell
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, OK 73019-5251
- Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, University of Oklahoma, Norman, OK 73019-5251
| | - Jianlan You
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, OK 73019-5251
- Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, University of Oklahoma, Norman, OK 73019-5251
| | - Blake W Stamps
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019-5251
| | - Ning Pan
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, OK 73019-5251
| | - Jarrod B King
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, OK 73019-5251
- Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, University of Oklahoma, Norman, OK 73019-5251
| | - Jean C Bopassa
- Department of Physiology, School of Medicine, University of Texas Health Science Center, San Antonio, TX 78229
| | - Susan I V Judge
- Department of Biochemistry, High Throughput Screening Facility, Center for Innovative Drug Discovery, University of Texas Health Science Center, San Antonio, TX 78229
- CytoBioscience Incorporated, San Antonio, TX 78229
| | - Zhibo Yang
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, OK 73019-5251
| | - Bradley S Stevenson
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, OK 73019-5251
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019-5251
| | - Robert H Cichewicz
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, OK 73019-5251;
- Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, University of Oklahoma, Norman, OK 73019-5251
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11
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Pohorille A, Wilson MA, Shannon G. Flexible Proteins at the Origin of Life. Life (Basel) 2017; 7:E23. [PMID: 28587235 PMCID: PMC5492145 DOI: 10.3390/life7020023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 05/10/2017] [Accepted: 05/24/2017] [Indexed: 11/17/2022] Open
Abstract
Almost all modern proteins possess well-defined, relatively rigid scaffolds that provide structural preorganization for desired functions. Such scaffolds require the sufficient length of a polypeptide chain and extensive evolutionary optimization. How ancestral proteins attained functionality, even though they were most likely markedly smaller than their contemporary descendants, remains a major, unresolved question in the origin of life. On the basis of evidence from experiments and computer simulations, we argue that at least some of the earliest water-soluble and membrane proteins were markedly more flexible than their modern counterparts. As an example, we consider a small, evolved in vitro ligase, based on a novel architecture that may be the archetype of primordial enzymes. The protein does not contain a hydrophobic core or conventional elements of the secondary structure characteristic of modern water-soluble proteins, but instead is built of a flexible, catalytic loop supported by a small hydrophilic core containing zinc atoms. It appears that disorder in the polypeptide chain imparts robustness to mutations in the protein core. Simple ion channels, likely the earliest membrane protein assemblies, could also be quite flexible, but still retain their functionality, again in contrast to their modern descendants. This is demonstrated in the example of antiamoebin, which can serve as a useful model of small peptides forming ancestral ion channels. Common features of the earliest, functional protein architectures discussed here include not only their flexibility, but also a low level of evolutionary optimization and heterogeneity in amino acid composition and, possibly, the type of peptide bonds in the protein backbone.
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Affiliation(s)
- Andrew Pohorille
- Exobiology Branch, MS 239-4, NASA Ames Research Center, Moffett Field, CA 94035, USA.
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94132, USA.
| | - Michael A Wilson
- Exobiology Branch, MS 239-4, NASA Ames Research Center, Moffett Field, CA 94035, USA.
- SETI Institute, 189 N Bernardo Ave #200, Mountain View, CA 94043, USA.
| | - Gareth Shannon
- Exobiology Branch, MS 239-4, NASA Ames Research Center, Moffett Field, CA 94035, USA.
- NASA Postdoctoral Program Fellow, NASA Ames Research Center, Moffett Field, CA 94035, USA.
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12
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2011-2012. MASS SPECTROMETRY REVIEWS 2017; 36:255-422. [PMID: 26270629 DOI: 10.1002/mas.21471] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 01/15/2015] [Indexed: 06/04/2023]
Abstract
This review is the seventh update of the original article published in 1999 on the application of MALDI mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2012. General aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, and fragmentation are covered in the first part of the review and applications to various structural types constitute the remainder. The main groups of compound are oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Much of this material is presented in tabular form. Also discussed are medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 36:255-422, 2017.
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Affiliation(s)
- David J Harvey
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, Oxford, OX1 3QU, UK
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13
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Andersen TL, Nordeman P, Christoffersen HF, Audrain H, Antoni G, Skrydstrup T. Application of Methyl Bisphosphine-Ligated Palladium Complexes for Low Pressure N
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C-Acetylation of Peptides. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201700446] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Thomas L. Andersen
- Carbon Dioxide Activation Center (CADIAC); Department of Chemistry and the Interdisciplinary Nanoscience Center (iNANO); Aarhus University; Gustav Wieds Vej 14 8000 Aarhus C Denmark
| | - Patrik Nordeman
- Department of Medicinal Chemistry; Uppsala University; 75123 Uppsala Sweden
| | - Heidi F. Christoffersen
- Carbon Dioxide Activation Center (CADIAC); Department of Chemistry and the Interdisciplinary Nanoscience Center (iNANO); Aarhus University; Gustav Wieds Vej 14 8000 Aarhus C Denmark
| | - Hélène Audrain
- Department of Nuclear Medicine and PET Center; Aarhus University Hospital; 8000 Aarhus Denmark
| | - Gunnar Antoni
- Department of Medicinal Chemistry; Uppsala University; 75123 Uppsala Sweden
| | - Troels Skrydstrup
- Carbon Dioxide Activation Center (CADIAC); Department of Chemistry and the Interdisciplinary Nanoscience Center (iNANO); Aarhus University; Gustav Wieds Vej 14 8000 Aarhus C Denmark
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14
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Andersen TL, Nordeman P, Christoffersen HF, Audrain H, Antoni G, Skrydstrup T. Application of Methyl Bisphosphine-Ligated Palladium Complexes for Low Pressure N
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C-Acetylation of Peptides. Angew Chem Int Ed Engl 2017; 56:4549-4553. [DOI: 10.1002/anie.201700446] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Revised: 02/12/2017] [Indexed: 12/26/2022]
Affiliation(s)
- Thomas L. Andersen
- Carbon Dioxide Activation Center (CADIAC); Department of Chemistry and the Interdisciplinary Nanoscience Center (iNANO); Aarhus University; Gustav Wieds Vej 14 8000 Aarhus C Denmark
| | - Patrik Nordeman
- Department of Medicinal Chemistry; Uppsala University; 75123 Uppsala Sweden
| | - Heidi F. Christoffersen
- Carbon Dioxide Activation Center (CADIAC); Department of Chemistry and the Interdisciplinary Nanoscience Center (iNANO); Aarhus University; Gustav Wieds Vej 14 8000 Aarhus C Denmark
| | - Hélène Audrain
- Department of Nuclear Medicine and PET Center; Aarhus University Hospital; 8000 Aarhus Denmark
| | - Gunnar Antoni
- Department of Medicinal Chemistry; Uppsala University; 75123 Uppsala Sweden
| | - Troels Skrydstrup
- Carbon Dioxide Activation Center (CADIAC); Department of Chemistry and the Interdisciplinary Nanoscience Center (iNANO); Aarhus University; Gustav Wieds Vej 14 8000 Aarhus C Denmark
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15
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Pohorille A, Wilson MA, Wei C. Validity of the Electrodiffusion Model for Calculating Conductance of Simple Ion Channels. J Phys Chem B 2016; 121:3607-3619. [PMID: 27936743 DOI: 10.1021/acs.jpcb.6b09598] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We examine the validity and utility of the electrodiffusion (ED) equation, i.e., the generalized Nernst-Planck equation, to characterize, in combination with molecular dynamics, the electrophysiological behavior of simple ion channels. As models, we consider three systems-two naturally occurring channels formed by α-helical bundles of peptaibols, trichotoxin, and alamethicin, and a synthetic, hexameric channel, formed by a peptide that contains only leucine and serine. All these channels mediate transport of potassium and chloride ions. Starting with equilibrium properties, such as the potential of mean force experienced by an ion traversing the channel and diffusivity, obtained from molecular dynamics simulations, the ED equation can be used to determine the full current-voltage dependence with modest or no additional effort. The potential of mean force can be obtained not only from equilibrium simulations, but also, with comparable accuracy, from nonequilibrium simulations at a single voltage. The main assumptions underlying the ED equation appear to hold well for the channels and voltages studied here. To expand the utility of the ED equation, we examine what are the necessary and sufficient conditions for Ohmic and nonrectifying behavior and relate deviations from this behavior to the shape of the ionic potential of mean force.
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Affiliation(s)
- Andrew Pohorille
- Exobiology Branch, MS 239-4, NASA Ames Research Center , Moffett Field, California 94035, United States.,Department of Pharmaceutical Chemistry University of California , San Francisco, California 94132, United States
| | - Michael A Wilson
- Exobiology Branch, MS 239-4, NASA Ames Research Center , Moffett Field, California 94035, United States.,SETI Institute , 189 N Bernardo Ave #200, Mountain View, California 94043, United States
| | - Chenyu Wei
- Exobiology Branch, MS 239-4, NASA Ames Research Center , Moffett Field, California 94035, United States.,Department of Pharmaceutical Chemistry University of California , San Francisco, California 94132, United States
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16
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Liu Y, Williams MG, Miller TJ, Teplyakov AV. Nanoparticle layer deposition for highly controlled multilayer formation based on high- coverage monolayers of nanoparticles. THIN SOLID FILMS 2016; 598:16-24. [PMID: 26726273 PMCID: PMC4696505 DOI: 10.1016/j.tsf.2015.11.082] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
This paper establishes a strategy for chemical deposition of functionalized nanoparticles onto solid substrates in a layer-by-layer process based on self-limiting surface chemical reactions leading to complete monolayer formation within the multilayer system without any additional intermediate layers - nanoparticle layer deposition (NPLD). This approach is fundamentally different from previously established traditional layer-by-layer deposition techniques and is conceptually more similar to well-known atomic and molecular - layer deposition processes. The NPLD approach uses efficient chemical functionalization of the solid substrate material and complementary functionalization of nanoparticles to produce a nearly 100% coverage of these nanoparticles with the use of "click chemistry". Following this initial deposition, a second complete monolayer of nanoparticles is deposited using a copper-catalyzed "click reaction" with the azide-terminated silica nanoparticles of a different size. This layer-by-layer growth is demonstrated to produce stable covalently-bound multilayers of nearly perfect structure over macroscopic solid substrates. The formation of stable covalent bonds is confirmed spectroscopically and the stability of the multilayers produced is tested by sonication in a variety of common solvents. The 1-, 2- and 3-layer structures are interrogated by electron microscopy and atomic force microscopy and the thickness of the multilayers formed is fully consistent with that expected for highly efficient monolayer formation with each cycle of growth. This approach can be extended to include a variety of materials deposited in a predesigned sequence on different substrates with a highly conformal filling.
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Affiliation(s)
- Yue Liu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Mackenzie G. Williams
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Timothy J. Miller
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Andrew V. Teplyakov
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
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17
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Hansen SK, Bertelsen K, Paaske B, Nielsen NC, Vosegaard T. Solid-state NMR methods for oriented membrane proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2015; 88-89:48-85. [PMID: 26282196 DOI: 10.1016/j.pnmrs.2015.05.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 04/27/2015] [Indexed: 06/04/2023]
Abstract
Oriented-sample solid-state NMR represents one of few experimental methods capable of characterising the membrane-bound conformation of proteins in the cell membrane. Since the technique was developed 25 years ago, the technique has been applied to study the structure of helix bundle membrane proteins and antimicrobial peptides, characterise protein-lipid interactions, and derive information on dynamics of the membrane anchoring of membrane proteins. We will review the major developments in various aspects of oriented-sample solid-state NMR, including sample-preparation methods, pulse sequences, theory required to interpret the experiments, perspectives for and guidelines to new experiments, and a number of representative applications.
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Affiliation(s)
- Sara K Hansen
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Kresten Bertelsen
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Berit Paaske
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Niels Chr Nielsen
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Thomas Vosegaard
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark.
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18
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Sahariah P, Sørensen KK, Hjálmarsdóttir MÁ, Sigurjónsson ÓE, Jensen KJ, Másson M, Thygesen MB. Antimicrobial peptide shows enhanced activity and reduced toxicity upon grafting to chitosan polymers. Chem Commun (Camb) 2015; 51:11611-4. [PMID: 26096124 DOI: 10.1039/c5cc04010h] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Here we report that grafting of a short antimicrobial peptide, anoplin, to chitosan polymers is a strategy for abolishing the hemolytic propensity, and at the same time increasing the activity of the parent peptide. Anoplin-chitosan conjugates were synthesized by CuAAC reaction of multiple peptides through 2-azidoacetyl groups on chitosan.
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Affiliation(s)
- Priyanka Sahariah
- Faculty of Pharmaceutical Sciences, School of Health Sciences, University of Iceland, Hofsvallagata 53, IS-107 Reykjavík, Iceland
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The natural, peptaibolic peptide SPF-5506-A4 adopts a β-bend spiral structure, shows low hemolytic activity and targets membranes through formation of large pores. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:882-9. [PMID: 25796141 DOI: 10.1016/j.bbapap.2015.03.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 03/04/2015] [Accepted: 03/06/2015] [Indexed: 12/23/2022]
Abstract
The medium-length fungal peptaibol SPF-5506-A(4) has been shown to inhibit formation of the Aβ peptide involved in Alzheimer''s disease. As Aβ is a cleavage-product from the membrane-bound APP protein, we hypothesized that SPF-5506-A(4)'s activity might be linked to membrane interactions in general. Here we describe the synthesis, structure and membrane interactions of SPF-5506-A4. The challenging synthesis was carried out on solid phase and a detailed conformational analysis in solution revealed a β-bend ribbon spiral core structure with flexible termini. Investigations of its membrane activity revealed low hemolytic activity, limited inhibition of both Gram-positive and Gram-negative cell growth and a preference for an overall negatively charged membrane surface mimicking the bacterial cell surface. SPF-5506-A(4) is the first peptaibol to be shown to facilitate leakage of large (4.6 nm diameter) fluorescence-labeled dextran from vesicles while leaving the vesicles intact. We conclude that SPF-5506-A(4) follows the toroidal pore model in its mode of action.
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Skals M, Bjaelde RG, Reinholdt J, Poulsen K, Vad BS, Otzen DE, Leipziger J, Praetorius HA. Bacterial RTX toxins allow acute ATP release from human erythrocytes directly through the toxin pore. J Biol Chem 2014; 289:19098-109. [PMID: 24860098 DOI: 10.1074/jbc.m114.571414] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
ATP is as an extracellular signaling molecule able to amplify the cell lysis inflicted by certain bacterial toxins including the two RTX toxins α-hemolysin (HlyA) from Escherichia coli and leukotoxin A (LtxA) from Aggregatibacter actinomycetemcomitans. Inhibition of P2X receptors completely blocks the RTX toxin-induced hemolysis over a larger concentration range. It is, however, at present not known how the ATP that provides the amplification is released from the attacked cells. Here we show that both HlyA and LtxA trigger acute release of ATP from human erythrocytes that preceded and were not caused by cell lysis. This early ATP release did not occur via previously described ATP-release pathways in the erythrocyte. Both HlyA and LtxA were capable of triggering ATP release in the presence of the pannexin 1 blockers carbenoxolone and probenecid, and the HlyA-induced ATP release was found to be similar in erythrocytes from pannexin 1 wild type and knock-out mice. Moreover, the voltage-dependent anion channel antagonist TRO19622 had no effect on ATP release by either of the toxins. Finally, we showed that both HlyA and LtxA were able to release ATP from ATP-loaded lipid (1-palmitoyl-2-oleoyl-phosphatidylcholine) vesicles devoid of any erythrocyte channels or transporters. Again we were able to show that this happened in a non-lytic fashion, using calcein-containing vesicles as controls. These data show that both toxins incorporate into lipid vesicles and allow ATP to be released. We suggest that both toxins cause acute ATP release by letting ATP pass the toxin pores in both human erythrocytes and artificial membranes.
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Affiliation(s)
| | | | | | | | - Brian S Vad
- the Department of Molecular Biology and Genetics, Interdisciplinary Nanoscience Center (iNANO), Center for Insoluble Proteins (inSPIN), Aarhus University, Aarhus C 8000, Denmark
| | - Daniel E Otzen
- the Department of Molecular Biology and Genetics, Interdisciplinary Nanoscience Center (iNANO), Center for Insoluble Proteins (inSPIN), Aarhus University, Aarhus C 8000, Denmark
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Abstract
Seventeen derivatives of α- and β-cyclodextrins were prepared from the cyclodextrin per-6-azide by "click" cyclization with terminal alkynes. Sixteen of these "half-channel" compounds showed significant activity as ion channels in planar bilayer members as assessed by the voltage-clamp technique. Activity ranged from persistent square-top openings to highly erratic conductance; mixed behaviours were evident in virtually all data recorded. Some of the erratic behaviours were shown to follow an apparent power-law distribution of open duration times. The activities observed for the suite were summarized using a model-free activity grid method which displays conductance, duration, and opening behaviour. The overall activity shows the clustering of conductance-duration indicating that activity arises from system properties rather that solely as a property of the compound. The activity grids also support an analysis of structure-activity relationships as they apply to the global behaviour of the compounds and reveal the complexity of a single structure change in controlling the distribution of concurrent conductance behaviours. Transient blockage of channel activity by the hydrophobic guest of the cyclodextrin (1-adamantyl carboxylate) is consistent with the formation of an end-to-end dimer channel among several other competing and interconverting structures.
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Affiliation(s)
- Jonathan K W Chui
- Department of Chemistry, University of Victoria, PO Box 3065, Victoria, BC, Canada V8W 3P6.
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Kredics L, Szekeres A, Czifra D, Vágvölgyi C, Leitgeb B. Recent results in alamethicin research. Chem Biodivers 2013; 10:744-71. [PMID: 23681724 DOI: 10.1002/cbdv.201200390] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Indexed: 12/20/2022]
Affiliation(s)
- László Kredics
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged.
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