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Russell MJ. A self-sustaining serpentinization mega-engine feeds the fougerite nanoengines implicated in the emergence of guided metabolism. Front Microbiol 2023; 14:1145915. [PMID: 37275164 PMCID: PMC10236563 DOI: 10.3389/fmicb.2023.1145915] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 03/22/2023] [Indexed: 06/07/2023] Open
Abstract
The demonstration by Ivan Barnes et al. that the serpentinization of fresh Alpine-type ultramafic rocks results in the exhalation of hot alkaline fluids is foundational to the submarine alkaline vent theory (AVT) for life's emergence to its 'improbable' thermodynamic state. In AVT, such alkaline fluids ≤ 150°C, bearing H2 > CH4 > HS--generated and driven convectively by a serpentinizing exothermic mega-engine operating in the ultramafic crust-exhale into the iron-rich, CO2> > > NO3--bearing Hadean ocean to result in hydrothermal precipitate mounds comprising macromolecular ferroferric-carbonate oxyhydroxide and minor sulfide. As the nanocrystalline minerals fougerite/green rust and mackinawite (FeS), they compose the spontaneously precipitated inorganic membranes that keep the highly contrasting solutions apart, thereby maintaining redox and pH disequilibria. They do so in the form of fine chimneys and chemical gardens. The same disequilibria drive the reduction of CO2 to HCOO- or CO, and the oxidation of CH4 to a methyl group-the two products reacting to form acetate in a sequence antedating the 'energy-producing' acetyl coenzyme-A pathway. Fougerite is a 2D-layered mineral in which the hydrous interlayers themselves harbor 2D solutions, in effect constricted to ~ 1D by preferentially directed electron hopping/tunneling, and proton Gröthuss 'bucket-brigading' when subject to charge. As a redox-driven nanoengine or peristaltic pump, fougerite forces the ordered reduction of nitrate to ammonium, the amination of pyruvate and oxalate to alanine and glycine, and their condensation to short peptides. In turn, these peptides have the flexibility to sequester the founding inorganic iron oxyhydroxide, sulfide, and pyrophosphate clusters, to produce metal- and phosphate-dosed organic films and cells. As the feed to the hydrothermal mound fails, the only equivalent sustenance on offer to the first autotrophs is the still mildly serpentinizing upper crust beneath. While the conditions here are very much less bountiful, they do offer the similar feed and disequilibria the survivors are accustomed to. Sometime during this transition, a replicating non-ribosomal guidance system is discovered to provide the rules to take on the incrementally changing surroundings. The details of how these replicating apparatuses emerged are the hard problem, but by doing so the progenote archaea and bacteria could begin to colonize what would become the deep biosphere. Indeed, that the anaerobic nitrate-respiring methanotrophic archaea and the deep-branching Acetothermia presently comprise a portion of that microbiome occupying serpentinizing rocks offers circumstantial support for this notion. However, the inescapable, if jarring conclusion is drawn that, absent fougerite/green rust, there would be no structured channelway to life.
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Affiliation(s)
- Michael J. Russell
- Dipartimento di Chimica, Università degli Studi di Torino, Torino, Italy
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Zhang L, Li M, Wang M, Li L, Guo M, Ke Y, Zhou P, Wang W. Tailored Cross-β Assemblies Establish Peptide "Dominos" Structures for Anchoring Undruggable Pharmacophores. Angew Chem Int Ed Engl 2022; 61:e202212527. [PMID: 36102014 DOI: 10.1002/anie.202212527] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Indexed: 12/15/2022]
Abstract
β-sheets have the ability to hierarchically stack into assemblies, and much effort has been spent on designing different peptides to regulate their assembly behaviors. Although the progress is remarkable, it remains challenging to manipulate them in a controllable way for achieving both tailored structures and specific functions. In this study, we obtained bola-like peptides using de novo design and combinatorial chemical screening. By regulating the solvent-accessible surface area of the peptide chain, a series of assemblies with different tilt angles and active sites of the β-sheet were obtained, resembling collapsed dominos. The structure-activity relationship of the optimized peptide NQ40 system was established and its ability to target the PD-L1 was demonstrated. This study successfully established the structure-function relationship of β-sheets assemblies and has positive implications on the rational design of peptide assemblies that possess recognition abilities.
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Affiliation(s)
- Limin Zhang
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electro-photonic Conversion Materials, School of Chemistry and Chemical Engineering, Institute of Engineering Medicine, Beijing Institute of Technology, Beijing, 100081, P. R. China
| | - Mengzhen Li
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electro-photonic Conversion Materials, School of Chemistry and Chemical Engineering, Institute of Engineering Medicine, Beijing Institute of Technology, Beijing, 100081, P. R. China
| | - Minxuan Wang
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electro-photonic Conversion Materials, School of Chemistry and Chemical Engineering, Institute of Engineering Medicine, Beijing Institute of Technology, Beijing, 100081, P. R. China
| | - Lingyun Li
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electro-photonic Conversion Materials, School of Chemistry and Chemical Engineering, Institute of Engineering Medicine, Beijing Institute of Technology, Beijing, 100081, P. R. China
| | - Mingmei Guo
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electro-photonic Conversion Materials, School of Chemistry and Chemical Engineering, Institute of Engineering Medicine, Beijing Institute of Technology, Beijing, 100081, P. R. China
| | - Yubin Ke
- Spallation Neutron Source Science Center, Dongguan, 523803, P. R. China
| | - Peng Zhou
- College of Chemical Engineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao, 266580, P. R. China
| | - Weizhi Wang
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electro-photonic Conversion Materials, School of Chemistry and Chemical Engineering, Institute of Engineering Medicine, Beijing Institute of Technology, Beijing, 100081, P. R. China
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Alves ED, de Andrade DX, de Almeida AR, Colherinhas G. Atomistic molecular dynamics study on the influence of high temperatures on the structure of peptide nanomembranes candidates for organic supercapacitor electrode. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116126] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Wang H, Feng Z, Lu A, Jiang Y, Wu H, Xu B. Instant Hydrogelation Inspired by Inflammasomes. Angew Chem Int Ed Engl 2017; 56:7579-7583. [PMID: 28481474 PMCID: PMC5551645 DOI: 10.1002/anie.201702783] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Indexed: 11/10/2022]
Abstract
Based on the recent near-atomic structures of the PYRIN domain of ASC in the protein filament of inflammasomes and the observation that the active form of vitamin B6 (pyridoxal phosphate, P5P) modulates the self-assembly of ASC, we rationally designed an N-terminal capped nonapeptide (Nap-FFKKFKLKL, 1) to form supramolecular nanofibers consisting of α-helix. The addition of P5P to the solution of 1 results in a hydrogel almost instantly (about 4 seconds). Several other endogenous small molecules (for example, pyridoxal, folinic acid, ATP, and AMP) also convert the solution of 1 into a hydrogel. As the demonstration of correlating assemblies of peptides and the relevant protein epitopes, this work illustrates a bioinspired approach to develop supramolecular structures modulated by endogenous small molecules.
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Affiliation(s)
- Huaimin Wang
- Department of chemistry, Brandeis University, 415 South St, Waltham, MA, 02454, USA
| | - Zhaoqianqi Feng
- Department of chemistry, Brandeis University, 415 South St, Waltham, MA, 02454, USA
| | - Alvin Lu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Yujie Jiang
- Department of chemistry, Brandeis University, 415 South St, Waltham, MA, 02454, USA
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Bing Xu
- Department of chemistry, Brandeis University, 415 South St, Waltham, MA, 02454, USA
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5
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Wang H, Feng Z, Lu A, Jiang Y, Wu H, Xu B. Instant Hydrogelation Inspired by Inflammasomes. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702783] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Huaimin Wang
- Department of chemistry Brandeis University 415 South St Waltham MA 02454 USA
| | - Zhaoqianqi Feng
- Department of chemistry Brandeis University 415 South St Waltham MA 02454 USA
| | - Alvin Lu
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School, and Program in Cellular and Molecular Medicine, Boston Children's Hospital Boston MA USA
| | - Yujie Jiang
- Department of chemistry Brandeis University 415 South St Waltham MA 02454 USA
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School, and Program in Cellular and Molecular Medicine, Boston Children's Hospital Boston MA USA
| | - Bing Xu
- Department of chemistry Brandeis University 415 South St Waltham MA 02454 USA
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Pellach M, Mondal S, Harlos K, Mance D, Baldus M, Gazit E, Shimon LJW. A Two-Tailed Phosphopeptide Crystallizes to Form a Lamellar Structure. Angew Chem Int Ed Engl 2017; 56:3252-3255. [PMID: 28191715 PMCID: PMC5412914 DOI: 10.1002/anie.201609877] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Indexed: 11/29/2022]
Abstract
The crystal structure of a designed phospholipid-inspired amphiphilic phosphopeptide at 0.8 Å resolution is presented. The phosphorylated β-hairpin peptide crystallizes to form a lamellar structure that is stabilized by intra- and intermolecular hydrogen bonding, including an extended β-sheet structure, as well as aromatic interactions. This first reported crystal structure of a two-tailed peptidic bilayer reveals similarities in thickness to a typical phospholipid bilayer. However, water molecules interact with the phosphopeptide in the hydrophilic region of the lattice. Additionally, solid-state NMR was used to demonstrate correlation between the crystal structure and supramolecular nanostructures. The phosphopeptide was shown to self-assemble into semi-elliptical nanosheets, and solid-state NMR provides insight into the self-assembly mechanisms. This work brings a new dimension to the structural study of biomimetic amphiphilic peptides with determination of molecular organization at the atomic level.
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Affiliation(s)
- Michal Pellach
- Department of Molecular Microbiology and BiotechnologyGeorge S. Wise Faculty of Life SciencesTel Aviv UniversityRamat Aviv69978Israel
| | - Sudipta Mondal
- Department of Molecular Microbiology and BiotechnologyGeorge S. Wise Faculty of Life SciencesTel Aviv UniversityRamat Aviv69978Israel
| | - Karl Harlos
- Division of Structural BiologyWellcome Trust Centre for Human GeneticsUniversity of OxfordRoosevelt DriveOxfordOX3 7BNUK
| | - Deni Mance
- NMR SpectroscopyBijvoet Center for Biomolecular ResearchUtrecht UniversityPadualaan 83584 CHUtrechtThe Netherlands
| | - Marc Baldus
- NMR SpectroscopyBijvoet Center for Biomolecular ResearchUtrecht UniversityPadualaan 83584 CHUtrechtThe Netherlands
| | - Ehud Gazit
- Department of Molecular Microbiology and BiotechnologyGeorge S. Wise Faculty of Life SciencesTel Aviv UniversityRamat Aviv69978Israel
- Department of Materials Science and EngineeringIby and Aladar Fleischman Faculty of EngineeringTel Aviv UniversityRamat Aviv69978Israel
| | - Linda J. W. Shimon
- Department of Chemical Research SupportWeizmann Institute of ScienceRehovot76100Israel
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7
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Pellach M, Mondal S, Harlos K, Mance D, Baldus M, Gazit E, Shimon LJW. A Two-Tailed Phosphopeptide Crystallizes to Form a Lamellar Structure. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201609877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Michal Pellach
- Department of Molecular Microbiology and Biotechnology; George S. Wise Faculty of Life Sciences; Tel Aviv University; Ramat Aviv 69978 Israel
| | - Sudipta Mondal
- Department of Molecular Microbiology and Biotechnology; George S. Wise Faculty of Life Sciences; Tel Aviv University; Ramat Aviv 69978 Israel
| | - Karl Harlos
- Division of Structural Biology; Wellcome Trust Centre for Human Genetics; University of Oxford; Roosevelt Drive Oxford OX3 7BN UK
| | - Deni Mance
- NMR Spectroscopy; Bijvoet Center for Biomolecular Research; Utrecht University; Padualaan 8 3584 CH Utrecht The Netherlands
| | - Marc Baldus
- NMR Spectroscopy; Bijvoet Center for Biomolecular Research; Utrecht University; Padualaan 8 3584 CH Utrecht The Netherlands
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology; George S. Wise Faculty of Life Sciences; Tel Aviv University; Ramat Aviv 69978 Israel
- Department of Materials Science and Engineering; Iby and Aladar Fleischman Faculty of Engineering; Tel Aviv University; Ramat Aviv 69978 Israel
| | - Linda J. W. Shimon
- Department of Chemical Research Support; Weizmann Institute of Science; Rehovot 76100 Israel
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8
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Kapil N, Singh A, Das D. Cross-β Amyloid Nanohybrids Loaded With Cytochrome C Exhibit Superactivity in Organic Solvents. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201500981] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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9
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Kapil N, Singh A, Das D. Cross-β Amyloid Nanohybrids Loaded With Cytochrome C Exhibit Superactivity in Organic Solvents. Angew Chem Int Ed Engl 2015; 54:6492-5. [DOI: 10.1002/anie.201500981] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 03/03/2015] [Indexed: 01/15/2023]
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10
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Huang Z, Yao Y, Han L, Che S. Control of Chiral Nanostructures by Self-Assembly of Designed Amphiphilic Peptides and Silica Biomineralization. Chemistry 2014; 20:17068-76. [DOI: 10.1002/chem.201403498] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Indexed: 11/08/2022]
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11
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pH-controlled aggregation polymorphism of amyloidogenic Aβ(16-22): insights for obtaining peptide tapes and peptide nanotubes, as function of the N-terminal capping moiety. Eur J Med Chem 2014; 88:55-65. [PMID: 25087966 DOI: 10.1016/j.ejmech.2014.07.089] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 07/24/2014] [Accepted: 07/24/2014] [Indexed: 11/23/2022]
Abstract
Peptide and protein self-assembly resulting in the formation of amyloidogenic aggregates is generally thought of as a pathological event associated with severe diseases. However, amyloid formation may also provide a basis for advanced bionanomaterials, since amyloid fibrils combine unique material-like properties that make them very useful for design of new types of conducting nanowires, bioactive ligands, and biodegradable coatings as drug-encapsulating materials. The morphology of the supramolecular aggregates determines the properties and application range of these bionanomaterials. An important parameter to control the supramolecular morphology, is the overall charge of the peptide, which is related to the pH of the environment. Herein, we describe the design, synthesis and morphological analysis of a series of N-terminally functionalized Aβ(16-22) peptides (∼Lys-Leu-Val-Phe-Phe-Ala-Glu-OH), that underwent a pH-induced polymorphism, ranging from lamellar sheets, helical tapes, peptide nanotubes, and amyloid fibrils as was observed by transmission electron microscopy. Infrared spectroscopy and wide angle X-ray scattering studies showed that peptide self-assembly was driven by β-sheet formation, and that the supramolecular morphology was directed by subtle variations in electrostatic interactions. Finally, a structural model and hierarchy of self-assembly of a peptide nanotube, assembled at pH 1, is proposed.
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13
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Abstract
The self-assembly of different classes of peptide, including cyclic peptides, amyloid peptides and surfactant-like peptides into nanotube structures is reviewed. The modes of self-assembly are discussed. Additionally, applications in bionanotechnology and synthetic materials science are summarized.
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Affiliation(s)
- Ian W Hamley
- Department of Chemistry, University of Reading, Whiteknights, Reading, RG6 6AD (UK).
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14
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Huang Z, Yao Y, Che S. Design of Amphiphilic Peptide Geometry towards Biomimetic Self-Assembly of Chiral Mesoporous Silica. Chemistry 2014; 20:3273-6. [DOI: 10.1002/chem.201304400] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Revised: 01/09/2014] [Indexed: 12/18/2022]
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15
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Middleton DA, Madine J, Castelletto V, Hamley IW. Insights into the molecular architecture of a peptide nanotube using FTIR and solid-state NMR spectroscopic measurements on an aligned sample. Angew Chem Int Ed Engl 2013; 52:10537-40. [PMID: 23955926 PMCID: PMC4672711 DOI: 10.1002/anie.201301960] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Indexed: 11/05/2022]
Abstract
Queuing up: Molecular orientation within macroscopically aligned nanotubes of the peptide AAAAAAK can be studied by solid-state NMR and IR spectroscopy. Line shape analysis of the NMR spectra indicates that the peptide N-H bonds are tilted 65-70° relative to the nanotube long axis. Re-evaluation of earlier X-ray fiber diffraction data suggests that the peptide molecules are hydrogen-bonded in a helical arrangement along the nanotube axis.
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Affiliation(s)
- David A Middleton
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB (UK).
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16
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Middleton DA, Madine J, Castelletto V, Hamley IW. Insights into the Molecular Architecture of a Peptide Nanotube Using FTIR and Solid-State NMR Spectroscopic Measurements on an Aligned Sample. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201301960] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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17
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Ni R, Childers WS, Hardcastle KI, Mehta AK, Lynn DG. Remodeling cross-β nanotube surfaces with peptide/lipid chimeras. Angew Chem Int Ed Engl 2013; 51:6635-8. [PMID: 22736642 DOI: 10.1002/anie.201201173] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Rong Ni
- Center for Fundamental and Applied Molecular Evolution, NSF/NASA Center for Chemical Evolution, and Department of Chemistry, Emory University, Atlanta, GA 30322, USA
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Morris KL, Zibaee S, Chen L, Goedert M, Sikorski P, Serpell LC. The Structure of Cross-β Tapes and Tubes Formed by an Octapeptide, αSβ1. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201207699] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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19
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Morris KL, Zibaee S, Chen L, Goedert M, Sikorski P, Serpell LC. The structure of cross-β tapes and tubes formed by an octapeptide, αSβ1. Angew Chem Int Ed Engl 2013; 52:2279-83. [PMID: 23307646 PMCID: PMC4279883 DOI: 10.1002/anie.201207699] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Revised: 11/22/2012] [Indexed: 01/27/2023]
Affiliation(s)
- Kyle L Morris
- School of Life Sciences, University of Sussex, Falmer, Brighton, East Sussex, BN1 9QG, UK
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Ni R, Childers WS, Hardcastle KI, Mehta AK, Lynn DG. Remodeling Cross-β Nanotube Surfaces with Peptide/Lipid Chimeras. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201201173] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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