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Makinde ZO, van der Heijden NJ, Domigan LJ, McGillivray DJ, Williams DE. Aligned Assembly in a 2-D Gel of a Water-Soluble Peptide. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:11292-11302. [PMID: 32882136 DOI: 10.1021/acs.langmuir.0c01944] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We demonstrate the assembly of a compact, gel-like Langmuir-Blodgett film of rods formed by self-assembly of a β-sheet-forming water-soluble peptide, Ac-IKHLSVN-NH2, at the surface of aqueous electrolytes. We characterize surface pressure hysteresis and demonstrate shear stiffening of the surface caused by area cycling, which we interpret as due to rearrangement and alignment of the rods. We show strong effects of the electrolyte on the assembly of the elementary rods, which can be related to the Hofmeister series and interpreted by effects on the interaction energies mediated by ions and water. Formation of β-sheet structures and assembly of these into surface-segregated semicrystalline gels was strongly promoted by ammonium sulfate electrolyte. With ammonium sulfate electrolyte as subphase for Langmuir-Blodgett film deposition, shear stiffening by surface area cycling resulted in very compact films on transfer to a substrate.
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Affiliation(s)
- Zainab O Makinde
- School of Chemical Sciences, The University of Auckland, Auckland 1010, New Zealand
- MacDiarmid Institute for Advanced Materials and Nanotechnology, Victoria University of Wellington, Wellington 6140, New Zealand
| | - Nadine J van der Heijden
- School of Chemical Sciences, The University of Auckland, Auckland 1010, New Zealand
- MacDiarmid Institute for Advanced Materials and Nanotechnology, Victoria University of Wellington, Wellington 6140, New Zealand
| | - Laura J Domigan
- MacDiarmid Institute for Advanced Materials and Nanotechnology, Victoria University of Wellington, Wellington 6140, New Zealand
- Department of Chemical and Materials Engineering, The University of Auckland, Auckland 1010, New Zealand
| | - Duncan J McGillivray
- School of Chemical Sciences, The University of Auckland, Auckland 1010, New Zealand
- MacDiarmid Institute for Advanced Materials and Nanotechnology, Victoria University of Wellington, Wellington 6140, New Zealand
| | - David E Williams
- School of Chemical Sciences, The University of Auckland, Auckland 1010, New Zealand
- MacDiarmid Institute for Advanced Materials and Nanotechnology, Victoria University of Wellington, Wellington 6140, New Zealand
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2
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Rinaldi S. The Diverse World of Foldamers: Endless Possibilities of Self-Assembly. Molecules 2020; 25:E3276. [PMID: 32708440 PMCID: PMC7397133 DOI: 10.3390/molecules25143276] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/13/2020] [Accepted: 07/16/2020] [Indexed: 02/07/2023] Open
Abstract
Different classes of foldamers, which are synthetic oligomers that adopt well-defined conformations in solution, have been the subject of extensive studies devoted to the elucidation of the forces driving their secondary structures and their potential as bioactive molecules. Regardless of the backbone type (peptidic or abiotic), the most important features of foldamers are the high stability, easy predictability and tunability of their folding, as well as the possibility to endow them with enhanced biological functions, with respect to their natural counterparts, by the correct choice of monomers. Foldamers have also recently started playing a starring role in the self-assembly of higher-order structures. In this review, selected articles will be analyzed to show the striking number of self-assemblies obtained for foldamers with different backbones, which will be analyzed in order of increasing complexity. Starting from the simplest self-associations in solution (e.g., dimers of β-strands or helices, bundles, interpenetrating double and multiple helices), the formation of monolayers, vesicles, fibers, and eventually nanostructured solid tridimensional morphologies will be subsequently described. The experimental techniques used in the structural investigation, and in the determination of the driving forces and mechanisms underlying the self-assemblies, will be systematically reported. Where applicable, examples of biomimetic self-assembled foldamers and their interactions with biological components will be described.
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Affiliation(s)
- Samuele Rinaldi
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
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3
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Baruch Leshem A, Isaacs S, Srivastava SK, Abdulhalim I, Kushmaro A, Rapaport H. Quantitative assessment of paraoxon adsorption to amphiphilic β-sheet peptides presenting the catalytic triad of esterases. J Colloid Interface Sci 2018; 530:328-337. [DOI: 10.1016/j.jcis.2018.06.065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/21/2018] [Accepted: 06/22/2018] [Indexed: 01/31/2023]
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4
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Chotera A, Sadihov H, Cohen-Luria R, Monnard PA, Ashkenasy G. Functional Assemblies Emerging in Complex Mixtures of Peptides and Nucleic Acid-Peptide Chimeras. Chemistry 2018; 24:10128-10135. [PMID: 29732630 DOI: 10.1002/chem.201800500] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 03/29/2018] [Indexed: 01/24/2023]
Abstract
Striking synergy between nucleic acids and proteins is exhibited in living cells. Whether such mutual activity can be performed using simple supramolecular nucleic acid-peptide (NA-pep) architectures remains a mystery. To shed light on this question, we studied the emergence of a primitive synergy in assemblies of short DNA-peptide chimeras. Specifically, we characterized multiple structures forming along gradual mixing trajectory, in which a peptide solution was seeded with increasing amounts of NA-pep chimeras. We report on the systematic change from β-sheet-peptide-based fibrillar architectures into the spherical structures formed by the conjugates. Remarkably, we find that through forming onion-like structures, the conjugates exhibit increased DNA hybridization stability and bind small molecules more efficiently than the peptides or DNA alone. A brief discussion highlights the implications of our findings for the production of new materials and for research on the origin of life.
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Affiliation(s)
- Agata Chotera
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Hava Sadihov
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Rivka Cohen-Luria
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Pierre-Alain Monnard
- Institute for Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230, Odense M, Denmark
| | - Gonen Ashkenasy
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
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5
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Popescu MT, Liontos G, Avgeropoulos A, Tsitsilianis C. Stimuli responsive fibrous hydrogels from hierarchical self-assembly of a triblock copolypeptide. SOFT MATTER 2015; 11:331-342. [PMID: 25379651 DOI: 10.1039/c4sm02092h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In this work, the self-assembly behavior and pH responsiveness of a triblock copolypeptide in aqueous media are demonstrated. The copolypeptide was composed of a central pH responsive poly(l-glutamic acid) (PGA), flanked by two hydrophobic poly(l-alanine) blocks (PAla) (PAla5-PGA11-PAla5). This system showed a pH-responsive transition from short tapes to spherical aggregates by increasing the pH, as a result of deprotonation of the PGA block and a conformational change from α-helix to random coil. Increasing the ionic strength to physiological conditions (0.15 M) has triggered fibrillar self-assembly through intermolecular hydrogen bonding of PAla end-blocks that form β-sheet nanostructures, in conjunction with charge screening of the central random coil PGA segments. At elevated concentrations a thermo-responsive free supporting hydrogel was obtained, consisting of rigid β-sheet based twisted superfibers, resulting from hierarchical self-assembly of the copolypeptide. Yet, morphological transformation of this nanostructure was observed upon switching the pH from physiological conditions to pH 4. An unexpected morphology constituted of α-helix-based giant nanobelts was observed as a consequence of the secondary peptide transitions.
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Shlomo Z, Vinod TP, Jelinek R, Rapaport H. Stacking interactions by two Phe side chains stabilize and orient assemblies of even the minimal amphiphilic β-sheet motif. Chem Commun (Camb) 2015; 51:3154-7. [DOI: 10.1039/c4cc09673h] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here we demonstrate that the smallest possible motif of the amphiphilic and pleated β-strand structure can be generated using tri-peptides stabilized by π–π stacking interactions.
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Affiliation(s)
- Zarzhitsky Shlomo
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering
- Ben-Gurion University of the Negev
- Beer-Sheva 84105
- Israel
- Ilse Katz Institute for Nanoscale Science and Technology
| | - T. P. Vinod
- Ilse Katz Institute for Nanoscale Science and Technology
- Ben-Gurion University of the Negev
- Beer-Sheva 84105
- Israel
- Department of Chemistry
| | - Raz Jelinek
- Ilse Katz Institute for Nanoscale Science and Technology
- Ben-Gurion University of the Negev
- Beer-Sheva 84105
- Israel
- Department of Chemistry
| | - Hanna Rapaport
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering
- Ben-Gurion University of the Negev
- Beer-Sheva 84105
- Israel
- Ilse Katz Institute for Nanoscale Science and Technology
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7
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Liebes-Peer Y, Rapaport H, Ashkenasy N. Amplification of single molecule translocation signal using β-strand peptide functionalized nanopores. ACS NANO 2014; 8:6822-6832. [PMID: 24949890 DOI: 10.1021/nn501331u] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Changes in ionic current flowing through nanopores due to binding or translocation of single biopolymer molecules enable their detection and characterization. It is, however, much more challenging to detect small molecules due to their rapid and small signal signature. Here we demonstrate the use of de novo designed peptides for functionalization of nanopores that enable the detection of a small analytes at the single molecule level. The detection relies on cooperative peptide conformational change that is induced by the binding of the small molecule to a receptor domain on the peptide. This change results in alteration of the nanopore effective diameter and hence induces current perturbation signal. On the basis of this approach, we demonstrate here the detection of diethyl 4-nitrophenyl phosphate (paraoxon), a poisonous organophosphate molecule. Paraoxon binding is induced by the incorporation of the catalytic triad of acetylcholine esterase in the hydrophilic domain of a short amphiphilic peptide and promotes β-sheet assembly of the peptide both in solution and for peptide molecules immobilized on solid surfaces. Nanopores coated with this peptide allowed the detection of paraoxon at the single molecule level revealing two binding arrangements. This unique approach, hence, provides the ability to study interactions of small molecules with the corresponding engineered receptors at the single molecule level. Furthermore, the suggested versatile platform may be used for the development of highly sensitive small analytes sensors.
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Affiliation(s)
- Yael Liebes-Peer
- Department of Biotechnology Engineering, ‡Department of Materials Engineering, and §The Ilze Katz Institute for Nanoscale Technology, Ben-Gurion University of the Negev , P.O. Box 653, Beer-Sheva 84105, Israel
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8
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Hwang W, Eryilmaz E. Kinetic signature of fractal-like filament networks formed by orientational linear epitaxy. PHYSICAL REVIEW LETTERS 2014; 113:025502. [PMID: 25062204 DOI: 10.1103/physrevlett.113.025502] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Indexed: 06/03/2023]
Abstract
We study a broad class of epitaxial assembly of filament networks on lattice surfaces. Over time, a scale-free behavior emerges with a 2.5-3 power-law exponent in filament length distribution. Partitioning between the power-law and exponential behaviors in a network can be used to find the stage and kinetic parameters of the assembly process. To analyze real-world networks, we develop a computer program that measures the network architecture in experimental images. Application to triaxial networks of collagen fibrils shows quantitative agreement with our model. Our unifying approach can be used for characterizing and controlling the network formation that is observed across biological and nonbiological systems.
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Affiliation(s)
- Wonmuk Hwang
- Departments of Biomedical Engineering and Materials Science & Engineering, Texas A&M University, College Station, Texas 77845, USA and School of Computational Sciences, Korea Institute for Advanced Study, Seoul 130-722, Korea
| | - Esma Eryilmaz
- Department of Physics, Texas A&M University, College Station, Texas 77845, USA
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9
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Joshi KB, Singh P. l-Proline induced self-assembly of indolicidin derived palindromic tripeptide. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.04.090] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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10
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Cavalli S, Overhand M, Kros A. Assembly into β-Sheet Structures upon Peptide-Liposome Conjugation through Copper(I)-Catalyzed [3+2] Azide-Alkyne Cycloaddition. Chempluschem 2014; 79:564-568. [DOI: 10.1002/cplu.201300354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 01/03/2014] [Indexed: 11/12/2022]
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11
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Chen J, Zhao J, Ning J, Liu Y, Xu J, Tian S, Zhang L, Sun MX. NtProRP1, a novel proline-rich protein, is an osmotic stress-responsive factor and specifically functions in pollen tube growth and early embryogenesis in Nicotiana tabacum. PLANT, CELL & ENVIRONMENT 2014; 37:499-511. [PMID: 23937639 DOI: 10.1111/pce.12174] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 07/19/2013] [Accepted: 07/24/2013] [Indexed: 06/02/2023]
Abstract
Proline-rich proteins (PRPs) are known to play important roles in sexual plant reproduction. Most of the known proteins in the family were found in styles or pollen and modulate pollen tube growth. Here, we identified a novel member of the gene family, NtProRP1, which is preferentially expressed in tobacco pollen grains, pollen tubes and zygotes. NtProRP1 could be secreted into the extracellular space including the cell wall, and the predicted N-terminal signal peptide is crucial for its secretion. In NtProRP1-RNAi plants, pollen germination and pollen tube growth were significantly slower and showed zigzag or swell morphology in vitro. Early embryogenesis also exhibited aberrant development, indicative of its critical role in both pollen tube growth and early embryogenesis. Further investigation revealed that NtProRP1 plays a crucial role in osmotic stress response during pollen tube growth and is likely regulated by Tsi, a stress-responsive gene, suggesting that the regulatory mechanism is also involved in the stress response during sexual plant reproduction. These data provide evidence that NtProRP1 functions as a downstream factor of Tsi1 in the stress response and converges the stress signal into the modulation of pollen tube growth and early embryogenesis.
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Affiliation(s)
- Junyi Chen
- Department of Cell and Development Biology, College of Life Science, State Key Laboratory of Plant Hybrid Rice, Wuhan University, Wuhan, 430072, China
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12
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Dalgicdir C, Sensoy O, Peter C, Sayar M. A transferable coarse-grained model for diphenylalanine: How to represent an environment driven conformational transition. J Chem Phys 2013; 139:234115. [DOI: 10.1063/1.4848675] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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13
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Yaakobi K, Liebes-Peer Y, Kushmaro A, Rapaport H. Designed amphiphilic β-sheet peptides as templates for paraoxon adsorption and detection. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:6840-6848. [PMID: 23631528 DOI: 10.1021/la401280e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Amphiphilic peptides were designed to fold into a β-sheet monolayer structure while presenting the catalytic triad residues of the enzyme, acetylcholinesterase (Glu, His, and Ser), to a solution containing the organophosphate, paraoxon. Three peptides, in which the catalytic triad residues were arranged in different orders along the strand, were generated to reveal potential differences in interactions with paraoxon as a function of the order of these amino acids. One additional peptide with amino acids introduced in random order was studied to highlight the contribution of the β-sheet secondary structure to any interactions with paraoxon. Langmuir isotherms, Brewster angle microscope at interfaces, and circular dichroism measurements in bulk showed that both the β-sheet conformation and the order of the amino acids along the strand influenced the interactions of paraoxon with the peptides. Compression isotherm curves as well as Brewster angle microscopy images provided evidence for enhanced adsorption of the paraoxon to the monolayers of peptides, which present neighboring Glu and Ser residues along the hydrophilic face of the β-strand. Circular dichroism revealed that the peptide most sensitive to interactions with paraoxon was that with the triad residues in the order Glu, Ser, and His, which appears to be appropriate for supporting a catalytic mechanism similar to that in the acetylcholinesterase enzyme. These rationally designed peptides may be further used for the development of technologies for organophosphate adsorption and detection.
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Affiliation(s)
- Keren Yaakobi
- Unit of Environmental Engineering, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
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14
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Hall H, Ellis B. Transcriptional programming during cell wall maturation in the expanding Arabidopsis stem. BMC PLANT BIOLOGY 2013; 13:14. [PMID: 23350960 PMCID: PMC3635874 DOI: 10.1186/1471-2229-13-14] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 01/21/2013] [Indexed: 05/18/2023]
Abstract
BACKGROUND Plant cell walls are complex dynamic structures that play a vital role in coordinating the directional growth of plant tissues. The rapid elongation of the inflorescence stem in the model plant Arabidopsis thaliana is accompanied by radical changes in cell wall structure and chemistry, but analysis of the underlying mechanisms and identification of the genes that are involved has been hampered by difficulties in accurately sampling discrete developmental states along the developing stem. RESULTS By creating stem growth kinematic profiles for individual expanding Arabidopsis stems we have been able to harvest and pool developmentally-matched tissue samples, and to use these for comparative analysis of global transcript profiles at four distinct phases of stem growth: the period of elongation rate increase, the point of maximum growth rate, the point of stem growth cessation and the fully matured stem. The resulting profiles identify numerous genes whose expression is affected as the stem tissues pass through these defined growth transitions, including both novel loci and genes identified in earlier studies. Of particular note is the preponderance of highly active genes associated with secondary cell wall deposition in the region of stem growth cessation, and of genes associated with defence and stress responses in the fully mature stem. CONCLUSIONS The use of growth kinematic profiling to create tissue samples that are accurately positioned along the expansion growth continuum of Arabidopsis inflorescence stems establishes a new standard for transcript profiling analyses of such tissues. The resulting expression profiles identify a substantial number of genes whose expression is correlated for the first time with rapid cell wall extension and subsequent fortification, and thus provide an important new resource for plant biologists interested in gene discovery related to plant biomass accumulation.
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Affiliation(s)
- Hardy Hall
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Currently: Swedish University of Agricultural Sciences (SLU), Umeå, 901 83, Sweden
| | - Brian Ellis
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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15
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Raz Y, Rubinov B, Matmor M, Rapaport H, Ashkenasy G, Miller Y. Effects of mutations in de novo designed synthetic amphiphilic β-sheet peptides on self-assembly of fibrils. Chem Commun (Camb) 2013; 49:6561-3. [DOI: 10.1039/c3cc42879f] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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16
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Rubinov B, Wagner N, Matmor M, Regev O, Ashkenasy N, Ashkenasy G. Transient fibril structures facilitating nonenzymatic self-replication. ACS NANO 2012; 6:7893-901. [PMID: 22856322 DOI: 10.1021/nn302223v] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
An emerging new direction of research focuses on developing "self-synthesizing materials", those supramolecular structures that can promote their own formation by accelerating the synthesis of building blocks and/or an entire assembly. It was postulated recently that practical design of such systems can benefit from the ability to control the assembly of amphiphilic molecules into nanostructures. We describe here the self-assembly pathway of short amphiphilic peptides into various forms of soluble β-sheet structures--β-plates, fibrils, and hollow nanotubes--and their consequent activity as autocatalysts for the synthesis of monomeric peptides from simpler building blocks. A detailed kinetic analysis of both the self-assembly and self-replication processes allows us to suggest a full model and simulate the replication process, revealing that only specific structures, primarily fibrils that are stable within the solution for a time shorter than a few hours, can be active as catalysts. Interestingly, we have found that such a process also induces fibril reproduction, in a mechanism very similar to the propagation of prion proteins by transmission of misfolded states.
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Affiliation(s)
- Boris Rubinov
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel
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17
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Cavalli S, Robson Marsden H, Albericio F, Kros A. Peptide Self-Assembly. Supramol Chem 2012. [DOI: 10.1002/9780470661345.smc088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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19
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Bourbo V, Matmor M, Shtelman E, Rubinov B, Ashkenasy N, Ashkenasy G. Self-assembly and self-replication of short amphiphilic β-sheet peptides. ORIGINS LIFE EVOL B 2011; 41:563-7. [PMID: 22139518 DOI: 10.1007/s11084-011-9257-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 08/28/2011] [Indexed: 12/01/2022]
Abstract
Most self-replicating peptide systems are made of α-helix forming sequences. However, it has been postulated that shorter and simpler peptides may also serve as templates for replication when arranged into well-defined structures. We describe here the design and characterization of new peptides that form soluble β-sheet aggregates that serve to significantly accelerate their ligation and self-replication. We then discuss the relevance of these phenomena to early molecular evolution, in light of additional functionality associated with β-sheet assemblies.
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Affiliation(s)
- Valery Bourbo
- Department of Chemistry, Ben Gurion University of Negev, Beer Sheva, Israel
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20
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Zarzhitsky S, Rapaport H. The interactions between doxorubicin and amphiphilic and acidic β-sheet peptides towards drug delivery hydrogels. J Colloid Interface Sci 2011; 360:525-31. [DOI: 10.1016/j.jcis.2011.04.091] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2011] [Revised: 04/20/2011] [Accepted: 04/21/2011] [Indexed: 10/18/2022]
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21
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Grigoryan G, Kim YH, Acharya R, Axelrod K, Jain RM, Willis L, Drndic M, Kikkawa JM, DeGrado WF. Computational design of virus-like protein assemblies on carbon nanotube surfaces. Science 2011; 332:1071-6. [PMID: 21617073 PMCID: PMC3264056 DOI: 10.1126/science.1198841] [Citation(s) in RCA: 164] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
There is a general need for the engineering of protein-like molecules that organize into geometrically specific superstructures on molecular surfaces, directing further functionalization to create richly textured, multilayered assemblies. Here we describe a computational approach whereby the surface properties and symmetry of a targeted surface define the sequence and superstructure of surface-organizing peptides. Computational design proceeds in a series of steps that encode both surface recognition and favorable intersubunit packing interactions. This procedure is exemplified in the design of peptides that assemble into a tubular structure surrounding single-walled carbon nanotubes (SWNTs). The geometrically defined, virus-like coating created by these peptides converts the smooth surfaces of SWNTs into highly textured assemblies with long-scale order, capable of directing the assembly of gold nanoparticles into helical arrays along the SWNT axis.
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Affiliation(s)
- Gevorg Grigoryan
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
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22
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Lamport DT, Kieliszewski MJ, Chen Y, Cannon MC. Role of the extensin superfamily in primary cell wall architecture. PLANT PHYSIOLOGY 2011; 156:11-9. [PMID: 21415277 PMCID: PMC3091064 DOI: 10.1104/pp.110.169011] [Citation(s) in RCA: 174] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Accepted: 03/13/2011] [Indexed: 05/17/2023]
Affiliation(s)
| | | | | | - Maura C. Cannon
- School of Life Sciences, University of Sussex, Brighton BN1 9QG, United Kingdom (D.T.A.L.); Department of Chemistry and Biochemistry, Ohio University, Athens, Ohio 45701 (M.J.K., Y.C.); and Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003 (M.C.C.)
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23
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Ligrone R, Vaughn KC, Rascio N. A cytochemical and immunocytochemical analysis of the wall labyrinth apparatus in leaf transfer cells in Elodea canadensis. ANNALS OF BOTANY 2011; 107:717-22. [PMID: 21289025 PMCID: PMC3064542 DOI: 10.1093/aob/mcr010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
BACKGROUND AND AIMS Transfer cells are plant cells specialized in apoplast/symplast transport and characterized by a distinctive wall labyrinth apparatus. The molecular architecture and biochemistry of the labyrinth apparatus are poorly known. The leaf lamina in the aquatic angiosperm Elodea canadensis consists of only two cell layers, with the abaxial cells developing as transfer cells. The present study investigated biochemical properties of wall ingrowths and associated plasmalemma in these cells. METHODS Leaves of Elodea were examined by light and electron microscopy and ATPase activity was localized cytochemically. Immunogold electron microscopy was employed to localize carbohydrate epitopes associated with major cell wall polysaccharides and glycoproteins. KEY RESULTS The plasmalemma associated with the wall labyrinth is strongly enriched in light-dependent ATPase activity. The wall ingrowths and an underlying wall layer share an LM11 epitope probably associated with glucuronoarabinoxylan and a CCRC-M7 epitope typically associated with rhamnogalacturonan I. No labelling was observed with LM10, an antibody that recognizes low-substituted and unsubstituted xylan, a polysaccharide consistently associated with secondary cell walls. The JIM5 and JIM7 epitopes, associated with homogalacturonan with different degrees of methylation, appear to be absent in the wall labyrinth but present in the rest of cell walls. CONCLUSIONS The wall labyrinth apparatus of leaf transfer cells in Elodea is a specialized structure with distinctive biochemical properties. The high level of light-dependent ATPase activity in the plasmalemma lining the wall labyrinth is consistent with a formerly suggested role of leaf transfer cells in enhancing inorganic carbon inflow. The wall labyrinth is a part of the primary cell wall. The discovery that the wall ingrowths in Elodea have an antibody-binding pattern divergent, in part, from that of the rest of cell wall suggests that their carbohydrate composition is modulated in relation to transfer cell functioning.
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Affiliation(s)
- Roberto Ligrone
- Dipartimento di Scienze Ambientali, Seconda Università di Napoli, via Vivaldi 43, Caserta, Italy.
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Dexter AF. Interfacial and emulsifying properties of designed β-strand peptides. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:17997-18007. [PMID: 21058648 DOI: 10.1021/la103471j] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The structural and surfactant properties of a series of amphipathic β-strand peptides have been studied as a function of pH. Each nine-residue peptide has a framework of hydrophobic proline and phenylalanine amino acid residues, alternating with acidic or basic amino acids to give a sequence closely related to known β-sheet formers. Surface activity, interfacial mechanical properties, electronic circular dichroism (ECD), droplet sizing and zeta potential measurements were used to gain an overview of the peptide behavior as the molecular charge varied from ±4 to 0 with pH. ECD data suggest that the peptides form polyproline-type helices in bulk aqueous solution when highly charged, but may fold to β-hairpins rather than β-sheets when uncharged. In the uncharged state, the peptides adsorb readily at a macroscopic fluid interface to form mechanically strong interfacial films, but tend to give large droplet sizes on emulsification, apparently due to flocculation at a low droplet zeta potential. In contrast, highly charged peptide states gave a low interfacial coverage, but retained good emulsifying activity as judged by droplet size. Best emulsification was generally seen for intermediate charged states of the peptides, possibly representing a compromise between droplet zeta potential and interfacial binding affinity. The emulsifying properties of β-strand peptides have not been previously reported. Understanding the interfacial properties of such peptides is important to their potential development as biosurfactants.
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Affiliation(s)
- Annette F Dexter
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia QLD 4072, Australia.
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Engin O, Villa A, Sayar M, Hess B. Driving Forces for Adsorption of Amphiphilic Peptides to the Air−Water Interface. J Phys Chem B 2010; 114:11093-101. [DOI: 10.1021/jp1024922] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Ozge Engin
- College of Engineering, Koc University, Istanbul, Turkey, Max-Planck Institute for Polymer Research, D-55128, Mainz, Germany, Karolinska Institutet, SE-14157, Huddinge, Sweden, Stockholm Center for Biomembrane Research, Stockholm University, SE-10691 Stockholm, Sweden, and Center of Smart Interfaces, Technical University of Darmstadt, D-64287 Darmstadt, Germany
| | - Alessandra Villa
- College of Engineering, Koc University, Istanbul, Turkey, Max-Planck Institute for Polymer Research, D-55128, Mainz, Germany, Karolinska Institutet, SE-14157, Huddinge, Sweden, Stockholm Center for Biomembrane Research, Stockholm University, SE-10691 Stockholm, Sweden, and Center of Smart Interfaces, Technical University of Darmstadt, D-64287 Darmstadt, Germany
| | - Mehmet Sayar
- College of Engineering, Koc University, Istanbul, Turkey, Max-Planck Institute for Polymer Research, D-55128, Mainz, Germany, Karolinska Institutet, SE-14157, Huddinge, Sweden, Stockholm Center for Biomembrane Research, Stockholm University, SE-10691 Stockholm, Sweden, and Center of Smart Interfaces, Technical University of Darmstadt, D-64287 Darmstadt, Germany
| | - Berk Hess
- College of Engineering, Koc University, Istanbul, Turkey, Max-Planck Institute for Polymer Research, D-55128, Mainz, Germany, Karolinska Institutet, SE-14157, Huddinge, Sweden, Stockholm Center for Biomembrane Research, Stockholm University, SE-10691 Stockholm, Sweden, and Center of Smart Interfaces, Technical University of Darmstadt, D-64287 Darmstadt, Germany
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Montanha E, Pavinatto F, Caseli L, Kaczmarek O, Liebscher J, Huster D, Oliveira O. Properties of lipophilic nucleoside monolayers at the air–water interface. Colloids Surf B Biointerfaces 2010; 77:161-5. [DOI: 10.1016/j.colsurfb.2010.01.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2010] [Revised: 01/22/2010] [Accepted: 01/25/2010] [Indexed: 11/25/2022]
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Barman AK, Verma S. Sunlight mediated disruption of peptide-based soft structures decorated with gold nanoparticles. Chem Commun (Camb) 2010; 46:6992-4. [DOI: 10.1039/c0cc02604b] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Lee BC, Zuckermann RN. Templated display of biomolecules and inorganic nanoparticles by metal ion-induced peptide nanofibers. Chem Commun (Camb) 2010; 46:1634-6. [DOI: 10.1039/b925395e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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Segman S, Lee MR, Vaiser V, Gellman S, Rapaport H. Highly Stable Pleated-Sheet Secondary Structure in Assemblies of Amphiphilic α/β-Peptides at the Air-Water Interface. Angew Chem Int Ed Engl 2009; 49:716-9. [DOI: 10.1002/anie.200904566] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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30
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Segman S, Lee MR, Vaiser V, Gellman S, Rapaport H. Highly Stable Pleated-Sheet Secondary Structure in Assemblies of Amphiphilic α/β-Peptides at the Air-Water Interface. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200904566] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Rubinov B, Wagner N, Rapaport H, Ashkenasy G. Self-replicating amphiphilic beta-sheet peptides. Angew Chem Int Ed Engl 2009; 48:6683-6. [PMID: 19644990 DOI: 10.1002/anie.200902790] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Boris Rubinov
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, 84105, Israel
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Rubinov B, Wagner N, Rapaport H, Ashkenasy G. Self-Replicating Amphiphilic β-Sheet Peptides. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200902790] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Miller CA, Abbott NL, de Pablo JJ. Surface activity of amphiphilic helical beta-peptides from molecular dynamics simulation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:2811-2823. [PMID: 19437698 DOI: 10.1021/la802973e] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The surface activity of beta-peptides is investigated using molecular simulations. The type and display of hydrophobic and hydrophilic groups on helical beta-peptides is varied systematically. Peptides with 2/3 hydrophobic groups are found to be surface active, and to adopt an orientation parallel to the air-water interface. For select beta-peptides, we also determine the potential of mean force required to bring a peptide to the air-water interface. Facially amphiphilic helices with 2/3 hydrophobic groups are found to exhibit the lowest free energy of adsorption. The adsorption process is driven by a favorable energetic term and opposed by negative entropic changes. The temperature dependence of adsorption is also investigated; facially amphiphilic helices are found to adopt orientations that are largely independent of temperature, while nonfacially amphiphilic helices sample a broader range of interfacial orientations at elevated temperatures. The thermodynamics of adsorption of beta-peptides is compared to that of 1-octanol, a well-known surfactant, and ovispirin, a naturally occurring antimicrobial peptide. It is found that the essential difference lies in the sign of the entropy of adsorption, which is negative for beta- and alpha-peptides and positive for traditional surfactants such as octanol.
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Affiliation(s)
- Clark A Miller
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706-1691, USA
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Gras SL. Surface- and Solution-Based Assembly of Amyloid Fibrils for Biomedical and Nanotechnology Applications. ENGINEERING ASPECTS OF SELF-ORGANIZING MATERIALS 2009. [DOI: 10.1016/s0065-2377(08)00206-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Muenter AH, Hentschel J, Börner HG, Brezesinski G. Characterization of peptide-guided polymer assembly at the air/water interface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2008; 24:3306-3316. [PMID: 18290677 DOI: 10.1021/la701909m] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
An organo-soluble, peptide-polymer conjugate that combines poly(n-butyl acrylate) with a beta-sheet-forming peptide is spread at the water surface to investigate peptide-guided self-assembly in a two-dimensional environment. Single layers of the conjugate are studied to gain information on the packing, orientation, and structure of the conjugate molecules using standard monolayer techniques: isotherms, grazing incidence X-ray diffraction (GIXD), and infrared reflection absorption spectroscopy (IRRAS). At all conditions studied, the stabilizing beta-sheet network consists of antiparallel beta-sheets oriented parallel to the air/water interface. The incorporation of temporary switch defects in the peptide segment enables beta-sheet assembly to be triggered at different packing densities. Stable monolayers, with low compressibilities similar to peptide monolayers, form when beta-sheet assembly occurs in monolayers that contain closely packed conjugate molecules. Langmuir-Schaefer transfer of the switched monolayer seeded with 1/1000 part stearic acid results in a transferred monolayer containing ordered domains with 7 nm wide stripes, a width in agreement with the end-to-end distance of the conjugate molecule. In this interfacial system, high packing densities and a hydrophobic seed molecule play an important role in beta-sheet network and structure formation. Both effects likely direct the highly ordered beta-sheet structure because of beta-strand prealignment. Insights gained from self-assembly in this system can be applied to peptide aggregation mechanisms in more complex interfacial environments.
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Affiliation(s)
- Annabel H Muenter
- Max Planck Institute of Colloids and Interfaces, MPI KG Golm, D-14424 Potsdam, Germany.
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Middelberg APJ, He L, Dexter AF, Shen HH, Holt SA, Thomas RK. The interfacial structure and Young's modulus of peptide films having switchable mechanical properties. J R Soc Interface 2008; 5:47-54. [PMID: 17550885 PMCID: PMC2605502 DOI: 10.1098/rsif.2007.1063] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We report the structure and Young's modulus of switchable films formed by peptide self-assembly at the air-water interface. Peptide surfactant AM1 forms an interfacial film that can be switched, reversibly, from a high- to low-elasticity state, with rapid loss of emulsion and foam stability. Using neutron reflectometry, we find that the AM1 film comprises a thin (approx. 15A) layer of ordered peptide in both states, confirming that it is possible to drastically alter the mechanical properties of an interfacial ensemble without significantly altering its concentration or macromolecular organization. We also report the first experimentally determined Young's modulus of a peptide film self-assembled at the air-water interface (E=80MPa for AM1, switching to E<20MPa). These findings suggest a fundamental link between E and the macroscopic stability of peptide-containing foam. Finally, we report studies of a designed peptide surfactant, Lac21E, which we find forms a stronger switchable film than AM1 (E=335MPa switching to E<4MPa). In contrast to AM1, Lac21E switching is caused by peptide dissociation from the interface (i.e. by self-disassembly). This research confirms that small changes in molecular design can lead to similar macroscopic behaviour via surprisingly different mechanisms.
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Affiliation(s)
- A P J Middelberg
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia.
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Abstract
Cytokinesis partitions the cell by a cleavage furrow in animals but by a new cross wall in plants. How this new wall assembles at the molecular level and connects with the mother cell wall remains unclear. A lethal Arabidopsis embryogenesis mutant designated root-, shoot-, hypocotyl-defective (rsh) provides some clues: RSH encodes extensin AtEXT3, a structural glycoprotein located in the nascent cross wall or "cell plate" and also in mature cell walls. Here we report that electron micrographs of rsh mutant cells lacking RSH extensin correspond to a wall phenotype typified by incomplete cross wall assembly. Biochemical characterization of the purified RSH glycoprotein isolated from wild-type Arabidopsis cell cultures confirmed its identity as AtEXT3: a (hydroxy)proline-rich glyco protein comprising 11 identical amphiphilic peptide repeats with a 28-residue periodicity: SOOOOKKHYVYKSOOOOVKHYSOOOVYH (O = Hyp), each repeat containing a hydrophobic isodityrosine cross-link motif (YVY, underlined). Atomic force microscopy of RSH glycoprotein imaged its propensity for self-assembly into a dendritic scaffold. Extensin peroxidase catalyzed in vitro formation of insoluble RSH gels with concomitant tyrosine cross-linking, hence this likelihood in muro. We conclude that self-assembling amphiphiles of lysine-rich RSH extensin form positively charged scaffolds in the cell plate. These react with negatively charged pectin to create an extensin pectate coacervate that may template further orderly deposition of the new cross wall at cytokinesis.
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Lepère M, Chevallard C, Hernandez JF, Mitraki A, Guenoun P. Multiscale surface self-assembly of an amyloid-like peptide. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2007; 23:8150-5. [PMID: 17579468 DOI: 10.1021/la701042t] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
We present the 2D self-assembly properties of an amyloid-like peptide (LSFDNSGAITIG-NH2) (i.e., LSFD) over a whole range of spatial scales. This peptide is known to adopt an amyloid-like behavior in water where it aggregates into fibrils. Monolayers of this 12 amino acid peptide were built by direct spreading and compression of an organic unstructured LSFD solution at the air/water interface. Investigation by infrared spectroscopy of the peptide secondary structure reveals beta-sheet formation at the water surface. As evidenced by Brewster angle microscopy, compression of the peptidic film results in the formation of large condensed domains. We used atomic force microscopy to show that these domains are made of rather monodisperse, elongated domains of monomolecular thickness, which are about 1 microm long and hundred of nanometers wide. These nanodomains can be compacted up to the formation of a homogeneous monolayer on the micrometer scale. These bidimensional structures appear as a surface-induced counterpart of the bulk amyloid fibrils that do not form at the air/water interface. These self-assembled peptide nanostructures are also very promising for building organized nanomaterials.
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Affiliation(s)
- Mathilde Lepère
- CEA Saclay, Service de Chimie Moléculaire, LIONS, Bâtiment 125, 91191 Gif-sur-Yvette Cedex, France.
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Abstract
Designed amphiphilic beta-sheet peptides with the sequence Pro-Glu-(Phe-Glu)(n)-Pro (n = 2-7) were previously shown by grazing incidence X-ray diffraction (GIXD), to form ordered two-dimensional (2-D) monolayer structures at interfaces induced by the proline residues at peptide termini. The GIXD diffraction pattern was modeled with two coexisting lattice arrangements, suggesting structural flexibility exhibited in the multiple ways by which beta-strands and their amino acid side chains pack into ordered 2-D structures. Here, we find by in-situ GIXD measurements that the ordered beta-sheet assemblies may undergo a quasi-reversible compression and expansion cycle at the air-water interface. The diffraction measurements indicate that on compression the repeat distance that corresponds to the long axes of the peptide strands may decrease by up to 37% in length. Upon expansion the compressed beta-sheet assemblies revert elastically to their original conformation. The interstrand repeat distance along the peptide hydrogen bonds apparently does not change along the film compression and expansion. Based on the GIXD data, at surface pressures higher than approximately 3 mN/m, beyond the peptide limiting area per molecule, the compressibility is 7.4 +/- 0.6 m/N. The out-of-plane Bragg rod diffraction patterns imply that in the compressed state the beta-strands buckle up in reaction to the increase in surface pressure. At low surface pressure, the 2-D compressibility of the crystalline beta-sheet was estimated at approximately 32 m/N attributed to interdomain rearrangements.
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Affiliation(s)
- Hila Isenberg
- Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
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