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Pitz ME, Nukovic AM, Elpers MA, Alexander-Bryant AA. Factors Affecting Secondary and Supramolecular Structures of Self-Assembling Peptide Nanocarriers. Macromol Biosci 2021; 22:e2100347. [PMID: 34800001 DOI: 10.1002/mabi.202100347] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/19/2021] [Indexed: 01/12/2023]
Abstract
Self-assembling peptides are a popular vector for therapeutic cargo delivery due to their versatility, tunability, and biocompatibility. Accurately predicting secondary and supramolecular structures of self-assembling peptides is essential for de novo peptide design. However, computational modeling of such assemblies is not yet able to accurately predict structure formation for many peptide sequences. This review identifies patterns in literature between secondary and supramolecular structures, primary sequences, and applications to provide a guide for informed peptide design. An overview of peptide structures, their applications as nanocarriers, and analytical methods for characterizing secondary and supramolecular structure is examined. A top-down approach is then used to identify trends between peptide sequence and assembly structure from the current literature, including an analysis of the drivers at work, such as local and nonlocal sequence effects and solution conditions.
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Affiliation(s)
- Megan E Pitz
- Department of Bioengineering, 301 Rhodes Research Center, Clemson University, Clemson, SC, 29634-0905, USA
| | - Alexandra M Nukovic
- Department of Bioengineering, 301 Rhodes Research Center, Clemson University, Clemson, SC, 29634-0905, USA
| | - Margaret A Elpers
- Department of Bioengineering, 301 Rhodes Research Center, Clemson University, Clemson, SC, 29634-0905, USA
| | - Angela A Alexander-Bryant
- Department of Bioengineering, 301 Rhodes Research Center, Clemson University, Clemson, SC, 29634-0905, USA
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2
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New self-assembled archetypes in crown ether substituted $$\Delta ^\mathrm{{Z}}\hbox {Phe}$$ containing tripeptides. J CHEM SCI 2019. [DOI: 10.1007/s12039-019-1623-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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3
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Nikoofard N, Maghsoodi F. Dynamic stability of nano-fibers self-assembled from short amphiphilic A 6D peptides. J Chem Phys 2018; 148:134903. [PMID: 29626855 DOI: 10.1063/1.5019766] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Self-assembly of A6D amphiphilic peptides in explicit water is studied by using coarse-grained molecular dynamics simulations. It is observed that the self-assembly of randomly distributed A6D peptides leads to the formation of a network of nano-fibers. Two other simulations with cylindrical nano-fibers as the initial configuration show the dynamic stability of the self-assembled nano-fibers. As a striking feature, notable fluctuations occur along the axes of the nano-fibers. Depending on the number of peptides per unit length of the nano-fiber, flat-shaped bulges or spiral shapes along the nano-fiber axis are observed at the fluctuations. Analysis of the particle distribution around the nano-fiber indicates that the hydrophobic core and the hydrophilic shell of the nano-structure are preserved in both simulations. The size of the deformations and their correlation times are different in the two simulations. This study gives new insights into the dynamics of the self-assembled nano-structures of short amphiphilic peptides.
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Affiliation(s)
- Narges Nikoofard
- Institute of Nanoscience and Nanotechnology, University of Kashan, Kashan 51167-87317, Iran
| | - Fahimeh Maghsoodi
- Institute of Nanoscience and Nanotechnology, University of Kashan, Kashan 51167-87317, Iran
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4
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Sun Y, Qian Z, Guo C, Wei G. Amphiphilic Peptides A6K and V6K Display Distinct Oligomeric Structures and Self-Assembly Dynamics: A Combined All-Atom and Coarse-Grained Simulation Study. Biomacromolecules 2015; 16:2940-9. [PMID: 26301845 DOI: 10.1021/acs.biomac.5b00850] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Amphiphilic peptides can self-assemble into ordered nanostructures with different morphologies. However, the assembly mechanism and the structures of the early assemblies prior to nanostructure formation remain elusive. In this study, we investigated the oligomeric structures of two amphiphilic heptapeptides A6K and V6K by all-atom explicit-solvent replica-exchange molecular dynamics (REMD) simulations, and then examined the assembly dynamics of large aggregates by coarse-grained (CG) MD simulations. Our 200 ns REMD simulations show that A6K peptides predominantly adopt loosely packed disordered coil aggregates, whereas V6K peptides mostly assemble into compact β-sheet-rich conformations, consistent with the signal measured experimentally in aqueous solution. Well-organized β-sheet-rich conformations, albeit with low population, are also populated for V6K octamers, including bilayer β-sheets and β-barrels. These ordered β-sheet-rich conformations are observed for the first time for amphiphilic peptides. Our 10-μs CG-MD simulations on 200 peptide chains demonstrate that A6K and V6K peptides follow two different self-assembly processes, and the former form monolayer lamellas while the latter assemble into plate-like assemblies. CG-MD simulations also show that V6K peptides display higher assembly capability than A6K, in support of our all-atom REMD simulation results. Interpeptide interaction analyses reveal that the marked differences in oligomeric structures and assembly dynamics between A6K and V6K result from the subtle interplay of competition among hydrophobic, hydrogen-bonding, and electrostatic interactions of the two peptides. Our study provides structural and mechanistic insights into the initial self-assembly process of A6K and V6K at the molecular level.
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Affiliation(s)
- Yunxiang Sun
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), and Department of Physics, Fudan University , 220 Handan Road, Shanghai, 200433, China
| | - Zhenyu Qian
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), and Department of Physics, Fudan University , 220 Handan Road, Shanghai, 200433, China
| | - Cong Guo
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), and Department of Physics, Fudan University , 220 Handan Road, Shanghai, 200433, China
| | - Guanghong Wei
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), and Department of Physics, Fudan University , 220 Handan Road, Shanghai, 200433, China
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Lechner CC, Becker CFW. Silaffins in Silica Biomineralization and Biomimetic Silica Precipitation. Mar Drugs 2015; 13:5297-333. [PMID: 26295401 PMCID: PMC4557024 DOI: 10.3390/md13085297] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 07/17/2015] [Accepted: 07/20/2015] [Indexed: 12/05/2022] Open
Abstract
Biomineralization processes leading to complex solid structures of inorganic material in biological systems are constantly gaining attention in biotechnology and biomedical research. An outstanding example for biomineral morphogenesis is the formation of highly elaborate, nano-patterned silica shells by diatoms. Among the organic macromolecules that have been closely linked to the tightly controlled precipitation of silica in diatoms, silaffins play an extraordinary role. These peptides typically occur as complex posttranslationally modified variants and are directly involved in the silica deposition process in diatoms. However, even in vitro silaffin-based peptides alone, with and without posttranslational modifications, can efficiently mediate biomimetic silica precipitation leading to silica material with different properties as well as with encapsulated cargo molecules of a large size range. In this review, the biomineralization process of silica in diatoms is summarized with a specific focus on silaffins and their in vitro silica precipitation properties. Applications in the area of bio- and nanotechnology as well as in diagnostics and therapy are discussed.
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Affiliation(s)
- Carolin C Lechner
- Swiss Federal Institute of Technology in Lausanne (EPFL), Fondation Sandoz Chair in Biophysical Chemistry of Macromolecules, 1015 Lausanne, Switzerland.
| | - Christian F W Becker
- Institute of Biological Chemistry, Department of Chemistry, University of Vienna, Währinger Straße 38, 1090 Vienna, Austria.
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6
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Dehsorkhi A, Castelletto V, Hamley IW. Self-assembling amphiphilic peptides. J Pept Sci 2014; 20:453-67. [PMID: 24729276 PMCID: PMC4237179 DOI: 10.1002/psc.2633] [Citation(s) in RCA: 271] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 02/27/2014] [Accepted: 03/04/2014] [Indexed: 01/08/2023]
Abstract
The self-assembly of several classes of amphiphilic peptides is reviewed, and selected applications are discussed. We discuss recent work on the self-assembly of lipopeptides, surfactant-like peptides and amyloid peptides derived from the amyloid-β peptide. The influence of environmental variables such as pH and temperature on aggregate nanostructure is discussed. Enzyme-induced remodelling due to peptide cleavage and nanostructure control through photocleavage or photo-cross-linking are also considered. Lastly, selected applications of amphiphilic peptides in biomedicine and materials science are outlined.
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Affiliation(s)
- Ashkan Dehsorkhi
- Department of Chemistry, University of ReadingWhiteknights, Reading, RG6 6AD, UK
| | - Valeria Castelletto
- Department of Chemistry, University of ReadingWhiteknights, Reading, RG6 6AD, UK
| | - Ian W Hamley
- Department of Chemistry, University of ReadingWhiteknights, Reading, RG6 6AD, UK
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7
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Fatouros D, Lamprou DA, Urquhart AJ, Yannopoulos SN, Vizirianakis IS, Zhang S, Koutsopoulos S. Lipid-like self-assembling peptide nanovesicles for drug delivery. ACS APPLIED MATERIALS & INTERFACES 2014; 6:8184-9. [PMID: 24821330 PMCID: PMC4059226 DOI: 10.1021/am501673x] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 05/12/2014] [Indexed: 05/19/2023]
Abstract
Amphiphilic self-assembling peptides are functional materials, which, depending on the amino acid sequence, the peptide length, and the physicochemical conditions, form a variety of nanostructures including nanovesicles, nanotubes, and nanovalves. We designed lipid-like peptides with an aspartic acid or lysine hydrophilic head and a hydrophobic tail composed of six alanines (i.e., ac-A6K-CONH2, KA6-CONH2, ac-A6D-COOH, and DA6-COOH). The resulting novel peptides have a length similar to biological lipids and form nanovesicles at physiological conditions. AFM microscopy and light scattering analyses of the positively charged lipid-like ac-A6K-CONH2, KA6-CONH2 peptide formulations showed individual nanovesicles. The negatively charged ac-A6D-COOH and DA6-COOH peptides self-assembled into nanovesicles that formed clusters that upon drying were organized into necklace-like formations of nanovesicles. Encapsulation of probe molecules and release studies through the peptide bilayer suggest that peptide nanovesicles may be good candidates for sustained release of pharmaceutically active hydrophilic and hydrophobic compounds. Lipid-like peptide nanovesicles represent a paradigm shifting system that may complement liposomes for the delivery of diagnostic and therapeutic agents.
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Affiliation(s)
- Dimitrios
G. Fatouros
- School
of Pharmacy, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece
| | - Dimitrios A. Lamprou
- Strathclyde
Institute of Pharmacy and Biomedical Sciences (SIPBS), University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, United Kingdom
| | - Andrew J. Urquhart
- Strathclyde
Institute of Pharmacy and Biomedical Sciences (SIPBS), University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, United Kingdom
| | - Spyros N. Yannopoulos
- Foundation
for Research and Technology, Hellas −
Institute of Chemical Engineering Sciences (FORTH/ICE-HT), P.O. Box 1414, GR-26504 Patra, Greece
| | | | - Shuguang Zhang
- Center
for Bits & Atoms, Massachusetts Institute
of Technology, 77 Massachusetts
Avenue, Cambridge, Massachusetts 02139, United States
| | - Sotirios Koutsopoulos
- Center
for Biomedical Engineering, Massachusetts
Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Tel.: +1-617-752-2042. Fax: +1-617-258-5239.
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8
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Dehsorkhi A, Hamley IW. Silica templating of a self-assembling peptide amphiphile that forms nanotapes. SOFT MATTER 2014; 10:1660-4. [PMID: 24651874 DOI: 10.1039/c3sm52324a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The peptide amphiphile C16-KTTKS templates silica polymerization, enabling the production of silica nanotape structures, imaged via electron microscopy (TEM and SEM). X-ray scattering shows that the nanotapes comprise stacked layers, as for the parent peptide amphiphile, but with a substantially increased layer spacing resulting from silica polymerization.
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Affiliation(s)
- Ashkan Dehsorkhi
- School of Chemistry, Pharmacy and Food Biosciences, University of Reading, Whiteknights, Reading, RG6 6AD, UK
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9
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Lechner CC, Becker CFW. A sequence-function analysis of the silica precipitating silaffin R5 peptide. J Pept Sci 2014; 20:152-8. [DOI: 10.1002/psc.2577] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Accepted: 09/30/2013] [Indexed: 11/05/2022]
Affiliation(s)
- Carolin C. Lechner
- University of Vienna; Department of Chemistry, Institute of Biological Chemistry; Währinger Straße 38 1090 Vienna Austria
| | - Christian F. W. Becker
- University of Vienna; Department of Chemistry, Institute of Biological Chemistry; Währinger Straße 38 1090 Vienna Austria
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Liu C, Jiang Z, Tong Z, Li Y, Yang D. Biomimetic synthesis of inorganic nanocomposites by a de novo designed peptide. RSC Adv 2014. [DOI: 10.1039/c3ra44630a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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11
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Wang Q, Zhang X, Zheng J, Liu D. Self-assembled peptide nanotubes as potential nanocarriers for drug delivery. RSC Adv 2014. [DOI: 10.1039/c4ra03304c] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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12
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Wang Q, Yu J, Zheng J, Liu D, Jiang F, Zhang X, Li W. Morphology-controlled synthesis of silica materials templated by self-assembled short amphiphilic peptides. RSC Adv 2013. [DOI: 10.1039/c3ra42183j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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