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Amit M, Yuran S, Gazit E, Reches M, Ashkenasy N. Tailor-Made Functional Peptide Self-Assembling Nanostructures. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1707083. [PMID: 29989255 DOI: 10.1002/adma.201707083] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 04/05/2018] [Indexed: 05/08/2023]
Abstract
Noncovalent interactions are the main driving force in the folding of proteins into a 3D functional structure. Motivated by the wish to reveal the mechanisms of the associated self-assembly processes, scientists are focusing on studying self-assembly processes of short protein segments (peptides). While this research has led to major advances in the understanding of biological and pathological process, only in recent years has the applicative potential of the resulting self-assembled peptide assemblies started to be explored. Here, major advances in the development of biomimetic supramolecular peptide assemblies as coatings, gels, and as electroactive materials, are highlighted. The guiding lines for the design of helical peptides, β strand peptides, as well as surface binding monolayer-forming peptides that can be utilized for a specific function are highlighted. Examples of their applications in diverse immerging applications in, e.g., ecology, biomedicine, and electronics, are described. Taking into account that, in addition to extraordinary design flexibility, these materials are naturally biocompatible and ecologically friendly, and their production is cost effective, the emergence of devices incorporating these biomimetic materials in the market is envisioned in the near future.
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Affiliation(s)
- Moran Amit
- Department of Materials Engineering, Ben Gurion University of the Negev, Beer-Sheva, 84105, Israel
- Department of Electrical and Computer Engineering, UC San Diego, La Jolla, CA, 92093-0407, USA
| | - Sivan Yuran
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, Department of Materials Science and Engineering, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Meital Reches
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Nurit Ashkenasy
- Department of Materials Engineering, Ben Gurion University of the Negev, Beer-Sheva, 84105, Israel
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Han P, Guo R, Wang Y, Yao L, Liu C. Bidirectional Electron-Transfer in Polypeptides with Various Secondary Structures. Sci Rep 2017; 7:16445. [PMID: 29180651 PMCID: PMC5703997 DOI: 10.1038/s41598-017-16678-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 11/16/2017] [Indexed: 12/25/2022] Open
Abstract
The protein-mediated bidirectional electron transfer (ET) is the foundation of protein molecular wire, and plays an important role in the rapid detection of oxo-guanine-adenine DNA mismatches by MutY glycosylase. However, the influences of structural transitions on bidirectional ET are still not clear. In this work, the modified through-bond coupling (MTBC) model was further refined to correlate the structural transition and ET rate more quantitatively. With this model, various polyglycine structures (310-helix, α-helix, β-sheets, linear, polyproline helical I and II) were studied to explore the influences of structural transitions on bidirectional ET. It was found that the HOMO-LUMO gaps (ΔE) in CN (from the carboxyl to amino terminus) direction are much lower than that in opposite direction, except for polypro I. However, with the equal tunneling energy, the differences between bidirectional ET rates are slight for all structures. In structural transitions, we found that the ET rates are not only affected by the Ramachandran angles, but also correlated to the alignment of C = O vectors, the alignment of peptide planes and the rearrangement of other structure factors. The detailed information can be used to rationalize the inhomogeneous ET across different protein structures and design more efficient protein molecular wires.
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Affiliation(s)
- Ping Han
- Department of Neurology, Haici Hospital Affiliated to Medical College of Qingdao University, Qingdao, 266033, Shandong, P.R. China
| | - Ruiyou Guo
- Department of Neurology, Haici Hospital Affiliated to Medical College of Qingdao University, Qingdao, 266033, Shandong, P.R. China
| | - Yefei Wang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, P.R. China.
| | - Lishan Yao
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, P.R. China
| | - Chengbu Liu
- Institute of Theoretical Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, Shandong, China
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Joy S, Sureshbabu VV, Periyasamy G. Computational Studies on Structural, Excitation, and Charge-Transfer Properties of Ureidopeptidomimetics. J Phys Chem B 2016; 120:6469-78. [PMID: 27314639 DOI: 10.1021/acs.jpcb.6b02210] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Peptides with ureido group enclosing backbones are considered peptidomimetics and are known for their higher stabilities, biocompatibilities, antibiotic, inhibitor, and charge-transduction activities. These peptidomimetics have some unique applications, which are quite different from those of natural peptides. Hence, it is imperative to appreciate their properties at a microscopic level. In this regard, this work outlines, in detail, the charge transfer (CT) properties, hole-migration dynamics, and electronic structures of various experimentally comprehended ureidopeptidomimetic models using density functional theory (DFT). Time-dependent DFT and complete active space self-consistent field computations on basic models provide the necessary evidence for the viability of CT from the end enfolding the ureido group to the other end with a carboxylate entity. This donor-to-acceptor CT has been reflected in excitation studies, in which the higher intensity band corresponds to CT from the π orbital of the ureido group to the π* orbital of the carboxylate entity. Further, hole-migration studies have shown that charge can evolve from the ureido end, whereas the hole generated at the carboxylate end does not migrate. However, hole migration has been reported to occur from both ends (amino and carboxylate ends) in glycine oligopeptides, and our studies show that the ability to transfer and migrate charge can be tuned by modifying the donor and acceptor functional groups in both the neutral and cationic charge states. We have analyzed the possibility of hole migration following ionization using DFT-based wave-packet propagation and found its occurrence on a ∼2-5 fs time scale, which reflects the charge-transduction ability of peptidomimetics.
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Affiliation(s)
- Sherin Joy
- Department of Chemistry, Central College Campus, Bangalore University , Bangalore 560 001, Karnataka, India
| | - Vommina V Sureshbabu
- Department of Chemistry, Central College Campus, Bangalore University , Bangalore 560 001, Karnataka, India
| | - Ganga Periyasamy
- Department of Chemistry, Central College Campus, Bangalore University , Bangalore 560 001, Karnataka, India
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Lee C, Mertz B. Theoretical Evidence for Multiple Charge Transfer Pathways in Bacteriorhodopsin. J Chem Theory Comput 2016; 12:1639-46. [PMID: 26950405 DOI: 10.1021/acs.jctc.6b00033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Choongkeun Lee
- C. Eugene Bennett Department
of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Blake Mertz
- C. Eugene Bennett Department
of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
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Kuś T, Mignolet B, Levine RD, Remacle F. Pump and Probe of Ultrafast Charge Reorganization in Small Peptides: A Computational Study through Sudden Ionizations. J Phys Chem A 2013; 117:10513-25. [DOI: 10.1021/jp407295t] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- T. Kuś
- Department
of Chemistry, B6c, University of Liege, B4000 Liege, Belgium
| | - B. Mignolet
- Department
of Chemistry, B6c, University of Liege, B4000 Liege, Belgium
| | - R. D. Levine
- Fritz Haber Research
Centre for Molecular Dynamics, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - F. Remacle
- Department
of Chemistry, B6c, University of Liege, B4000 Liege, Belgium
- Fritz Haber Research
Centre for Molecular Dynamics, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
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Moritoh R, Morita T, Kimura S. Photocurrent generation by helical peptide monolayers integrating light harvesting and charge-transport functions. Biopolymers 2013; 100:1-13. [DOI: 10.1002/bip.22174] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Revised: 10/01/2012] [Accepted: 10/08/2012] [Indexed: 11/08/2022]
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Yew SY, Shekhawat G, Wangoo N, Mhaisalkar S, Suri CR, Dravid VP, Lam YM. Design of single peptides for self-assembled conduction channels. NANOTECHNOLOGY 2011; 22:215606. [PMID: 21451229 DOI: 10.1088/0957-4484/22/21/215606] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Self-assembly of peptides provides the possibility of achieving relatively long range order on surfaces. These ordered peptides can also form channels that can be used as conduction channels. In the past, studies were focused on electron conduction through the secondary structure and amine bond of peptides and these restrict conduction of electrons over a short range (a few nanometers). In this work, we demonstrate the realization of electron conduction over a longer range of a few hundred nanometers via π-π stacking of the phenyl groups in the tyrosine residue of a single peptide. The peptide used in this work was designed with a phenyl ring for π-π stacking at one end and a carboxylic group at the other end for binding to aminopropyltriethoxysilane (APTES) treated silicon wafer. The distance between the peptides is controlled by a disulfide bond formed between neighboring cysteine residue and also by the amine groups of aminopropyltriethoxysilane. We demonstrate that the self-assembled peptide is conducting in the dry state over hundreds of nanometers, realizing the possibility of using peptide as a molecular wire.
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Affiliation(s)
- Sok Yee Yew
- School of Materials Science and Engineering, Nanyang Technological University, Block N4.1, 50 Nanyang Avenue, 639798, Singapore
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Arikuma Y, Nakayama H, Morita T, Kimura S. Ultra-long-range electron transfer through a self-assembled monolayer on gold composed of 120-Å-long α-helices. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:1530-1535. [PMID: 21090665 DOI: 10.1021/la103882r] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Electron transfer through α-helices has attracted much attention from the viewpoints of their contributions to efficient long-range electron transfer occurring in biological systems and their utility as molecular-electronics elements. In this study, we synthesized a long 80mer helical peptide carrying a redox-active ferrocene unit at the terminal and immobilized the helical peptide on a gold surface. The molecular length is calculated to be 134 Å, in which the helix accounts for 120 Å. The preparation conditions of the self-assembled monolayers were intentionally changed to obtain monolayers with different physical states to study the correlation between molecular motions and electron transfer. Ellipsometry and infrared spectroscopy showed that the helical peptide forms a self-assembled monolayer with vertical orientation. Electrochemical measurements revealed that an electron is transferred from the ferrocene unit to gold through the monolayer composed of this long helical peptide, and the experimental data are well explained by theoretical results calculated under the assumption that electron transfer occurs by a unique hopping mechanism with the amide groups as hopping sites. Furthermore, we have observed a unique dependence of electron transfer on the monolayer packing, suggesting the importance of structural fluctuations of peptides on the electron transfer controlled by the hopping mechanism.
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Affiliation(s)
- Yoko Arikuma
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto, Japan
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Arikuma Y, Takeda K, Morita T, Ohmae M, Kimura S. Linker Effects on Monolayer Formation and Long-Range Electron Transfer in Helical Peptide Monolayers. J Phys Chem B 2009; 113:6256-66. [DOI: 10.1021/jp810200x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yoko Arikuma
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku-Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Kazuki Takeda
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku-Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Tomoyuki Morita
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku-Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Masashi Ohmae
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku-Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Shunsaku Kimura
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku-Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
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Zbiri M, Johnson MR, Kearley GJ, Mulder FM. Density functional calculations of potential energy surface and charge transfer integrals in molecular triphenylene derivative HAT6. Theor Chem Acc 2009. [DOI: 10.1007/s00214-009-0559-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Santhanamoorthi N, Kolandaivel P, Senthilkumar K. Effect of conformational degrees of freedom on the charge transfer in model tripeptide. J Mol Graph Model 2009; 27:784-91. [DOI: 10.1016/j.jmgm.2008.11.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2008] [Revised: 11/18/2008] [Accepted: 11/21/2008] [Indexed: 10/21/2022]
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Santhanamoorthi N, Kolandaivel P, Senthilkumar K. Theoretical investigation on intramolecular electron transfer in polypeptides. Chem Phys Lett 2007. [DOI: 10.1016/j.cplett.2007.04.050] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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