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Noguchi H, Nakamura Y, Tezuka S, Seki T, Yatsu K, Narimatsu T, Nakata Y, Hayamizu Y. Self-assembled GA-Repeated Peptides as a Biomolecular Scaffold for Biosensing with MoS 2 Electrochemical Transistors. ACS APPLIED MATERIALS & INTERFACES 2023; 15. [PMID: 36892269 PMCID: PMC10037235 DOI: 10.1021/acsami.2c23227] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 02/17/2023] [Indexed: 06/16/2023]
Abstract
Biosensors with two-dimensional materials have gained wide interest due to their high sensitivity. Among them, single-layer MoS2 has become a new class of biosensing platform owing to its semiconducting property. Immobilization of bioprobes directly onto the MoS2 surface with chemical bonding or random physisorption has been widely studied. However, these approaches potentially cause a reduction of conductivity and sensitivity of the biosensor. In this work, we designed peptides that spontaneously align into monomolecular-thick nanostructures on electrochemical MoS2 transistors in a non-covalent fashion and act as a biomolecular scaffold for efficient biosensing. These peptides consist of repeated domains of glycine and alanine in the sequence and form self-assembled structures with sixfold symmetry templated by the lattice of MoS2. We investigated electronic interactions of self-assembled peptides with MoS2 by designing their amino acid sequence with charged amino acids at both ends. Charged amino acids in the sequence showed a correlation with the electrical properties of single-layer MoS2, where negatively charged peptides caused a shift of threshold voltage in MoS2 transistors and neutral and positively charged peptides had no significant effect on the threshold voltage. The transconductance of transistors had no decrease due to the self-assembled peptides, indicating that aligned peptides can act as a biomolecular scaffold without degrading the intrinsic electronic properties for biosensing. We also investigated the impact of peptides on the photoluminescence (PL) of single-layer MoS2 and found that the PL intensity changed sensitively depending on the amino acid sequence of peptides. Finally, we demonstrated a femtomolar-level sensitivity of biosensing using biotinylated peptides to detect streptavidin.
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Affiliation(s)
- Hironaga Noguchi
- Department
of Materials Science and Engineering, School of Materials and Chemical
Technology, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Yoshiki Nakamura
- Department
of Materials Science and Engineering, School of Materials and Chemical
Technology, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Sayaka Tezuka
- Department
of Materials Science and Engineering, School of Materials and Chemical
Technology, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Takakazu Seki
- Department
of Frontier Materials Chemistry, Faculty of Science and Technology, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori 036-8561, Japan
| | - Kazuki Yatsu
- Department
of Materials Science and Engineering, School of Materials and Chemical
Technology, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Takuma Narimatsu
- Department
of Materials Science and Engineering, School of Materials and Chemical
Technology, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Yasuaki Nakata
- Department
of Materials Science and Engineering, School of Materials and Chemical
Technology, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Yuhei Hayamizu
- Department
of Materials Science and Engineering, School of Materials and Chemical
Technology, Tokyo Institute of Technology, Tokyo 152-8550, Japan
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2
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Ruan Y, Sohail M, Zhao J, Hu F, Li Y, Wang P, Zhang L. Applications of Material-Binding Peptides: A Review. ACS Biomater Sci Eng 2022; 8:4738-4750. [PMID: 36229413 DOI: 10.1021/acsbiomaterials.2c00651] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Material-binding peptides (MBPs) are functionalized adhesive materials consisting of a few to several dozen amino acids. This affinity between MBPs and materials is regulated by multiple interactions, including hydrogen bonding, electrostatic, hydrophobic interactions, and π-π stacking. They show selective binding and high affinity to a diverse range of inorganic and organic materials, such as silicon-based materials, metals, metal compounds, carbon materials, and polymers. They are used to improve the biocompatibility of materials, increase the efficiency of material synthesis, and guide the controlled synthesis of nanomaterials. In addition, these can be used for precise targeting of proteins by conjugating to target biomolecules. In this review, we summarize the main designs and applications of MBPs in recent years. The discussions focus on more efficient and functional peptides, including evolution and overall design of MBPs. We have also highlighted the recent applications of MBPs, such as functionalization of material surfaces, synthesis of nanomaterials, drug delivery, cancer therapy, and plastic degradation. Besides, we also discussed the development trend of MBPs. This interpretation will accelerate future investigations to bottleneck the drawbacks of available MBPs, promoting their commercial applications.
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Affiliation(s)
- Yongqiang Ruan
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Muhammad Sohail
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Jindi Zhao
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Fanghui Hu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Yunhan Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Panlin Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Lihui Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, China
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3
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Simultaneous Visualization of MiRNA-221 and Caspase-3 in Cancer Cells for Investigating the Feasibility of MiRNA-Targeted Therapy with a Dual-Color Fluorescent Nanosensor. BIOSENSORS 2022; 12:bios12070444. [PMID: 35884247 PMCID: PMC9312853 DOI: 10.3390/bios12070444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/16/2022] [Accepted: 06/20/2022] [Indexed: 11/22/2022]
Abstract
MiRNA-targeted therapy holds great promise for precision cancer therapy. It is important to investigate the effect of changes in miRNA expression on apoptosis in order to evaluate miRNA-targeted therapy and achieve personalized therapy. In this study, we designed a dual-color fluorescent nanosensor consisting of grapheme oxide modified with a molecular beacon and peptide. The nanosensor can simultaneously detect and image miRNA-221 and apoptotic protein caspase-3 in living cells. Intracellular experiments showed that the nanosensor could be successfully applied for in situ monitoring of the effect of miRNA-221 expression changes on apoptosis by dual-color imaging. The current strategy could provide new avenues for investigating the feasibility of miRNA-targeted therapy, screening new anti-cancer drugs targeting miRNA and developing personalized treatment plans.
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4
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Pham LN, Walsh TR. Predicting biomolecule adsorption on MoS 2 nanosheets with high structural fidelity. Chem Sci 2022; 13:5186-5195. [PMID: 35655578 PMCID: PMC9093178 DOI: 10.1039/d1sc06814h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 03/15/2022] [Indexed: 11/21/2022] Open
Abstract
A new force field, MoSu-CHARMM, for the description of bio-interfacial structures at the aqueous MoS2 interface is developed, based on quantum chemical data. The force field describes non-covalent interactions between the MoS2 surface and a wide range of chemistries including hydrocarbon, alcohol, aldehyde, ketone, carboxylic acid, amine, thiol, and amino acid groups. Density functional theory (DFT), using the vdW-DF2 functional, is employed to create training and validation datasets, comprising 330 DFT binding energies for 21 organic compounds. Development of MoSu-CHARMM is guided by two criteria: (i) minimisation of energetic differences compared to target DFT data and (ii) preservation of the DFT energetic rankings of the different binding configurations. Force-field performance is validated against existing high-quality structural experimental data regarding adsorption of four 26-residue peptides at the aqueous MoS2 interface. Adsorption free energies for all twenty amino acids in liquid water are calculated to provide guidance for future peptide design, and interpret the properties of existing experimentally-identified MoS2-binding peptides. This force field will enable large-scale simulations of biological interactions with MoS2 surfaces in aqueous media where an emphasis on structural fidelity is prioritised.
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Affiliation(s)
- Le Nhan Pham
- Institute for Frontier Materials, Deakin University Geelong Victoria 3216 Australia
| | - Tiffany R Walsh
- Institute for Frontier Materials, Deakin University Geelong Victoria 3216 Australia
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5
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High-Gradient Magnetic Separation of Compact Fluorescent Lamp Phosphors: Elucidation of the Removal Dynamics in a Rotary Permanent Magnet Separator. MINERALS 2021. [DOI: 10.3390/min11101116] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In an ongoing effort towards a more sustainable rare-earth element market, there is a high potential for an efficient recycling of rare-earth elements from end-of-life compact fluorescent lamps by physical separation of the individual phosphors. In this study, we investigate the separation of five fluorescent lamp particles by high-gradient magnetic separation in a rotary permanent magnet separator. We thoroughly characterize the phosphors by ICP-MS, laser diffraction analysis, gas displacement pycnometry, surface area analysis, SQUID-VSM, and Time-Resolved Laser-Induced Fluorescence Spectroscopy. We present a fast and reliable quantification method for mixtures of the investigated phosphors, based on a combination of Time-Resolved Laser-Induced Fluorescence Spectroscopy and parallel factor analysis. With this method, we were able to monitor each phosphors’ removal dynamics in the high-gradient magnetic separator and we estimate that the particles’ removal efficiencies are proportional to (d2·χ)1/3. Finally, we have found that the removed phosphors can readily be recovered easily from the separation cell by backwashing with an intermittent air–water flow. This work should contribute to a better understanding of the phosphors’ separability by high-gradient magnetic separation and can simultaneously be considered to be an important preparation for an upscalable separation process with (bio)functionalized superparamagnetic carriers.
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6
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Ccorahua R, Noguchi H, Hayamizu Y. Cosolvents Restrain Self-Assembly of a Fibroin-Like Peptide on Graphite. J Phys Chem B 2021; 125:10893-10899. [PMID: 34559528 DOI: 10.1021/acs.jpcb.1c02594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Controllable self-assembly of peptides on solid surfaces has been investigated for establishing functional bio/solid interfaces. In this work, we study the influence of organic solvents on the self-assembly of a fibroin-like peptide on a graphite surface. The peptide has been designed by mimicking fibroin proteins to have strong hydrogen bonds among peptides enabling their self-assembly. We have employed cosolvents of water and organic solvents with a wide range of dielectric constants to control peptide self-assembly on the surface. Atomic force microscopy has revealed that the peptides self-assemble into highly ordered monolayer-thick linear structures on graphite after incubation in pure water, where the coverage of peptides on the surface is more than 85%. When methanol is mixed, the peptide coverage becomes zero at a threshold concentration of 30% methanol on graphite and 25% methanol on MoS2. The threshold concentration in ethanol, isopropanol, dimethyl sulfoxide, and acetone varies depending on the dielectric constant with restraining self-assembly of the peptides, and particularly low dielectric-constant protic solvents prevent the peptide self-assembly significantly. The observed phenomena are explained by competitive surface adsorption of the organic solvents and peptides and the solvation effect of the peptide assembly.
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Affiliation(s)
- Robert Ccorahua
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Hironaga Noguchi
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Yuhei Hayamizu
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Tokyo 152-8550, Japan
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7
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Sun L, Li P, Seki T, Tsuchiya S, Yatsu K, Narimatsu T, Sarikaya M, Hayamizu Y. Chiral Recognition of Self-Assembled Peptides on MoS 2 via Lattice Matching. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:8696-8704. [PMID: 34278791 DOI: 10.1021/acs.langmuir.1c00792] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Chiral recognition of peptides on solid surfaces has been studied for a better understanding of their assembly mechanism toward its applications in stereochemistry and enantioselective catalysis. However, moving from small peptides such as dipeptides, understanding the chiral recognition of larger biomolecules such as oligopeptides or peptides with a larger sequence is challenging. Furthermore, their intrinsic mechanism for chiral recognition in liquid conditions was poorly investigated experimentally. Here, we used in/ex situ atomic force microscopy (AFM) to investigate the chiral recognition of self-assembled structures of l/d-type peptides on molybdenum disulfide (MoS2). We chose single-layer MoS2 with a triangular shape as a substrate for the self-assembly of peptides. The facet edges of MoS2 were utilized as a landmark to identify the crystallographic orientation of their ordered structures. We found both peptide enantiomers formed nanowires on MoS2 with a mirror symmetry according to the facet edges of MoS2. From in situ AFM measurements, we found a dimension of a unit cell in the self-assembled structure and proposed a model of lattice matching between peptides and MoS2 lattice. The lattice matching for chiral recognition was further investigated by changing peptide sequences and surface lattice from MoS2 to graphite. This work further deepened the understanding of biomolecular chiral recognition and will lead us to rationally design specific morphologies and conformations of chiral self-assembled structures of peptides with expected functions in the future.
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Affiliation(s)
- Linhao Sun
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
- Department of Materials Science and Engineering, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Peiying Li
- Department of Materials Science and Engineering, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Takakazu Seki
- Department of Materials Science and Engineering, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Shohei Tsuchiya
- Department of Materials Science and Engineering, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Kazuki Yatsu
- Department of Materials Science and Engineering, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Takuma Narimatsu
- Department of Materials Science and Engineering, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Mehmet Sarikaya
- GEMSEC, Genetically Engineered Materials Science and Engineering Center, Materials Science and Engineering, University of Washington, Seattle WA98195, United States
| | - Yuhei Hayamizu
- Department of Materials Science and Engineering, Tokyo Institute of Technology, Tokyo 152-8550, Japan
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8
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Schönberger N, Taylor C, Schrader M, Drobot B, Matys S, Lederer FL, Pollmann K. Gallium-binding peptides as a tool for the sustainable treatment of industrial waste streams. JOURNAL OF HAZARDOUS MATERIALS 2021; 414:125366. [PMID: 33636447 DOI: 10.1016/j.jhazmat.2021.125366] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 01/31/2021] [Accepted: 02/05/2021] [Indexed: 06/12/2023]
Abstract
Here we provide a proof of principle for an application-oriented concept for the peptide-based recovery of gallium in industrial wastewater, which was supported by biosorption studies with a real wastewater sample. We investigated the interaction of the gallium-binding peptides TMHHAAIAHPPH, NYLPHQSSSPSR, SQALSTSRQDLR, HTQHIQSDDHLA, and NDLQRHRLTAGP with gallium and arsenic through different experimental and computational approaches. Data obtained from isothermal titration microcalorimetry indicated a competitive influence by the presence of acetate ions with an exothermic contribution to the otherwise endothermic peptide gallium interactions. For peptide HTQHIQSDDHLA, a stabilizing influence of acetate ions on the metal peptide interaction was found. Peptide NYLPHQSSSPSR showed the highest affinity for gallium in ITC studies. Computational modeling of peptide NYLPHQSSSPSR was used to determine interaction parameters and to explain a possible binding mechanism. Furthermore, the peptides were immobilized on polystyrene beads. Thus, we created a novel and exceptionally robust peptide-based material for the biosorption of gallium from an aqueous solution. Data obtained from isothermal titration microcalorimetry indicated a competitive influence by the presence of acetate ions with an exothermic contribution to the otherwise endothermic peptide gallium interactions. For peptide HTQHIQSDDHLA, a stabilizing influence of acetate ions on the metal peptide interaction was found. Peptide NYLPHQSSSPSR showed the highest affinity for gallium in ITC studies. Computational modeling of peptide NYLPHQSSSPSR was used to determine interaction parameters and to explain a possible binding mechanism. Furthermore, the peptides were immobilized on polystyrene beads. Thus, we created a novel and exceptionally robust peptide-based material for the biosorption of gallium from an aqueous solution.
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Affiliation(s)
- Nora Schönberger
- Institute of Nonferrous Metallurgy and Purest Materials, TU Bergakademie Freiberg, Leipziger Str. 32, 09599 Freiberg, Germany; Helmholtz Institute Freiberg for Resource Technology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328 Dresden, Germany.
| | - Corey Taylor
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328 Dresden, Germany
| | - Martin Schrader
- Helmholtz Institute Freiberg for Resource Technology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328 Dresden, Germany
| | - Björn Drobot
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328 Dresden, Germany
| | - Sabine Matys
- Helmholtz Institute Freiberg for Resource Technology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328 Dresden, Germany
| | - Franziska L Lederer
- Helmholtz Institute Freiberg for Resource Technology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328 Dresden, Germany
| | - Katrin Pollmann
- Helmholtz Institute Freiberg for Resource Technology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328 Dresden, Germany
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9
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Dhas N, Kudarha R, Garkal A, Ghate V, Sharma S, Panzade P, Khot S, Chaudhari P, Singh A, Paryani M, Lewis S, Garg N, Singh N, Bangar P, Mehta T. Molybdenum-based hetero-nanocomposites for cancer therapy, diagnosis and biosensing application: Current advancement and future breakthroughs. J Control Release 2020; 330:257-283. [PMID: 33345832 DOI: 10.1016/j.jconrel.2020.12.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/11/2020] [Indexed: 02/08/2023]
Abstract
In recent years, there have been significant advancements in the nanotechnology for cancer therapy. Even though molybdenum disulphide (MoS2)-based nanocomposites demonstrated extensive applications in biosensing, bioimaging, phototherapy, the review article focusing on MoS2 nanocomposite platform has not been accounted for yet. The review summarizes recent strategies on design and fabrication of MoS2-based nanocomposites and their modulated properties in cancer treatment. The review also discussed several therapeutic strategies (photothermal, photodynamic, immunotherapy, gene therapy and chemotherapy) and their combinations for efficient cancer therapy along with certain case studies. The review also inculcates various diagnostic techniques viz. magnetic resonance imaging, computed tomography, photoacoustic imaging and fluorescence imaging for diagnosis of cancer.
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Affiliation(s)
- Namdev Dhas
- Department of Pharmaceutics, Institute of Pharmacy, Nirma University, Ahmedabad, Gujarat 382481, India
| | - Ritu Kudarha
- Faculty of Pharmacy, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat 390002, India
| | - Atul Garkal
- Department of Pharmaceutics, Institute of Pharmacy, Nirma University, Ahmedabad, Gujarat 382481, India
| | - Vivek Ghate
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka 576104, India
| | - Shilpa Sharma
- Department of Chemistry, Indian Institute of Technology, Ropar, Rupnagar, Punjab 140001, India
| | - Prabhakar Panzade
- Department of Pharmaceutics, Srinath College of Pharmacy, Dr. Babasaheb Ambedkar Technological University, Aurangabad, Maharashtra 431133, India
| | - Shubham Khot
- Sinhgad Institute of Pharmacy, Narhe, Pune, Maharashtra 411041, India
| | - Pinal Chaudhari
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka 576104, India
| | - Ashutosh Singh
- School of Basic Sciences, Indian Institute of Technology, Mandi, Kamand, Himachal Pradesh 175005, India
| | - Mitali Paryani
- Department of Pharmaceutics, Institute of Pharmacy, Nirma University, Ahmedabad, Gujarat 382481, India
| | - Shaila Lewis
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka 576104, India
| | - Neha Garg
- Department of Medicinal Chemistry, Faculty of Ayurveda, Institute of Medical Sciences, BHU, Varanasi, Uttar Pradesh 221005, India
| | - Narinder Singh
- Department of Chemistry, Indian Institute of Technology, Ropar, Rupnagar, Punjab 140001, India
| | - Priyanka Bangar
- Intas Pharmaceuticals Ltd., Ahmedabad, Gujarat 382213, India
| | - Tejal Mehta
- Department of Pharmaceutics, Institute of Pharmacy, Nirma University, Ahmedabad, Gujarat 382481, India.
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10
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Liu J, Zeng J, Zhu C, Miao J, Huang Y, Heinz H. Interpretable molecular models for molybdenum disulfide and insight into selective peptide recognition. Chem Sci 2020; 11:8708-8722. [PMID: 34094188 PMCID: PMC8162032 DOI: 10.1039/d0sc01443e] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 07/16/2020] [Indexed: 12/14/2022] Open
Abstract
Molybdenum disulfide (MoS2) is a layered material with outstanding electrical and optical properties. Numerous studies evaluate the performance in sensors, catalysts, batteries, and composites that can benefit from guidance by simulations in all-atom resolution. However, molecular simulations remain difficult due to lack of reliable models. We introduce an interpretable force field for MoS2 with record performance that reproduces structural, interfacial, and mechanical properties in 0.1% to 5% agreement with experiments. The model overcomes structural instability, deviations in interfacial and mechanical properties by several 100%, and empirical fitting protocols in earlier models. It is compatible with several force fields for molecular dynamics simulation, including the interface force field (IFF), CVFF, DREIDING, PCFF, COMPASS, CHARMM, AMBER, and OPLS-AA. The parameters capture polar covalent bonding, X-ray structure, cleavage energy, infrared spectra, bending stability, bulk modulus, Young's modulus, and contact angles with polar and nonpolar solvents. We utilized the models to uncover the binding mechanism of peptides to the MoS2 basal plane. The binding strength of several 7mer and 8mer peptides scales linearly with surface contact and replacement of surface-bound water molecules, and is tunable in a wide range from -86 to -6 kcal mol-1. The binding selectivity is multifactorial, including major contributions by van-der-Waals coordination and charge matching of certain side groups, orientation of hydrophilic side chains towards water, and conformation flexibility. We explain the relative attraction and role of the 20 amino acids using computational and experimental data. The force field can be used to screen and interpret the assembly of MoS2-based nanomaterials and electrolyte interfaces up to a billion atoms with high accuracy, including multiscale simulations from the quantum scale to the microscale.
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Affiliation(s)
- Juan Liu
- Department of Chemical and Biological Engineering, University of Colorado- Boulder Boulder CO 80309 USA
| | - Jin Zeng
- Department of Chemical and Biological Engineering, University of Colorado- Boulder Boulder CO 80309 USA
| | - Cheng Zhu
- Department of Chemical and Biological Engineering, University of Colorado- Boulder Boulder CO 80309 USA
| | - Jianwei Miao
- Department of Physics and Astronomy, University of California Los Angeles California 90095 USA
- California NanoSystems Institute, University of California, Los Angeles CA 90095 USA
| | - Yu Huang
- California NanoSystems Institute, University of California, Los Angeles CA 90095 USA
- Department of Materials Science and Engineering, University of California, Los Angeles 90095 USA
| | - Hendrik Heinz
- Department of Chemical and Biological Engineering, University of Colorado- Boulder Boulder CO 80309 USA
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11
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Datta LP, Manchineella S, Govindaraju T. Biomolecules-derived biomaterials. Biomaterials 2020; 230:119633. [DOI: 10.1016/j.biomaterials.2019.119633] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 11/12/2019] [Accepted: 11/14/2019] [Indexed: 12/22/2022]
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12
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Walsh TR, Knecht MR. Biomolecular Material Recognition in Two Dimensions: Peptide Binding to Graphene, h-BN, and MoS 2 Nanosheets as Unique Bioconjugates. Bioconjug Chem 2019; 30:2727-2750. [PMID: 31593454 DOI: 10.1021/acs.bioconjchem.9b00593] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Two-dimensional nanosheet-based materials such as graphene, hexagonal boron nitride, and MoS2 represent intriguing structures for a variety of biological applications ranging from biosensing to nanomedicine. Recent advances have demonstrated that peptides can be identified with affinity for these three materials, thus generating a highly unique bioconjugate interfacial system. This Review focuses on recent advances in the formation of bioconjugates of these types, paying particular attention to the structure/function relationship of the peptide overlayer. This is achieved through the amino acid composition of the nanosheet binding peptides, thus allowing for precise control over the properties of the final materials. Such bioconjugate systems offer rapid advances via direct property control that remain difficult to achieve for biological applications using nonbiological approaches.
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Affiliation(s)
- Tiffany R Walsh
- Institute for Frontier Materials , Deakin University , Waurn Ponds , Victoria 3216 VIC , Australia
| | - Marc R Knecht
- Department of Chemistry , University of Miami , 1301 Memorial Drive , Coral Gables , Florida 33146 , United States.,Dr. J.T. Macdonald Foundation Biomedical Nanotechnology Institute , University of Miami , UM Life Science Technology Building, 1951 NW Seventh Ave, Suite 475 , Miami , Florida 33136 , United States
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13
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Zhang L, Luan B, Zhou R. Parameterization of Molybdenum Disulfide Interacting with Water Using the Free Energy Perturbation Method. J Phys Chem B 2019; 123:7243-7252. [PMID: 31369702 DOI: 10.1021/acs.jpcb.9b02797] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Water contact angles (WCA) are often used to parametrize force field parameters of novel 2D nanomaterials, such as molybdenum disulfide (MoS2), which has emerged as a promising nanomaterial in many biomedical applications due to its unique and impressive properties. However, there is a wide range of water-MoS2 contact angles in the literature depending on the aging process on the surface of a MoS2 nanosheet and/or substrate material. In this study, we revisit and optimize existing parameters for the basal plane of MoS2 with two popular water models, TIP3P and SPC/E, using the wide range of WCAs from various experiments. We develop and deploy the free energy perturbation method for parametrizing MoS2 with experimentally determined WCAs for both fresh and aged surfaces. Energy decomposition analysis on the simulation trajectories reveals that MoS2-water interaction is dominated by van der Waals interaction, which mainly comes from the top layer of MoS2. We conclude that to describe both fresh and aged MoS2 surfaces it is convenient to only adjust the Lennard-Jones parameter εS (the depth of the potential well of a sulfur atom), which displays a surprisingly linear correlation with WCAs.
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Affiliation(s)
- Leili Zhang
- Computational Biology Center , IBM Thomas J. Watson Research Center , Yorktown Heights , New York 10598 , United States
| | - Binquan Luan
- Computational Biology Center , IBM Thomas J. Watson Research Center , Yorktown Heights , New York 10598 , United States
| | - Ruhong Zhou
- Computational Biology Center , IBM Thomas J. Watson Research Center , Yorktown Heights , New York 10598 , United States
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Apitius L, Rübsam K, Jakesch C, Jakob F, Schwaneberg U. Ultrahigh‐throughput screening system for directed polymer binding peptide evolution. Biotechnol Bioeng 2019; 116:1856-1867. [DOI: 10.1002/bit.26990] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 03/28/2019] [Accepted: 04/11/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Lina Apitius
- DWI – Leibniz‐Institute for Interactive MaterialsAachen Germany
- RWTH Aachen UniversityAachen Germany
| | - Kristin Rübsam
- DWI – Leibniz‐Institute for Interactive MaterialsAachen Germany
| | | | - Felix Jakob
- DWI – Leibniz‐Institute for Interactive MaterialsAachen Germany
- RWTH Aachen UniversityAachen Germany
| | - Ulrich Schwaneberg
- DWI – Leibniz‐Institute for Interactive MaterialsAachen Germany
- RWTH Aachen UniversityAachen Germany
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15
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Aminpour M, Montemagno C, Tuszynski JA. An Overview of Molecular Modeling for Drug Discovery with Specific Illustrative Examples of Applications. Molecules 2019; 24:E1693. [PMID: 31052253 PMCID: PMC6539951 DOI: 10.3390/molecules24091693] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 04/17/2019] [Accepted: 04/23/2019] [Indexed: 01/29/2023] Open
Abstract
In this paper we review the current status of high-performance computing applications in the general area of drug discovery. We provide an introduction to the methodologies applied at atomic and molecular scales, followed by three specific examples of implementation of these tools. The first example describes in silico modeling of the adsorption of small molecules to organic and inorganic surfaces, which may be applied to drug delivery issues. The second example involves DNA translocation through nanopores with major significance to DNA sequencing efforts. The final example offers an overview of computer-aided drug design, with some illustrative examples of its usefulness.
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Affiliation(s)
- Maral Aminpour
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB T6G 2R3, Canada.
- Ingenuity Lab, Edmonton, AB T6G 2R3, Canada.
- Department of Oncology, University of Alberta, Edmonton, AB T6G 1Z2, Canada.
| | - Carlo Montemagno
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB T6G 2R3, Canada.
- Ingenuity Lab, Edmonton, AB T6G 2R3, Canada.
- Southern Illinois University, Carbondale, IL 62901, USA.
| | - Jack A Tuszynski
- Department of Oncology, University of Alberta, Edmonton, AB T6G 1Z2, Canada.
- Department of Physics, University of Alberta, Edmonton, AB T6G 2E1, Canada.
- Department of Mechanical Engineering and Aerospace Engineering (DIMEAS), Politecnico di Torino, 10129 Turin, Italy.
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Bansal R, Care A, Lord MS, Walsh TR, Sunna A. Experimental and theoretical tools to elucidate the binding mechanisms of solid-binding peptides. N Biotechnol 2019; 52:9-18. [PMID: 30954671 DOI: 10.1016/j.nbt.2019.04.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 03/31/2019] [Accepted: 04/01/2019] [Indexed: 12/19/2022]
Abstract
The interactions between biomolecules and solid surfaces play an important role in designing new materials and applications which mimic nature. Recently, solid-binding peptides (SBPs) have emerged as potential molecular building blocks in nanobiotechnology. SBPs exhibit high selectivity and binding affinity towards a wide range of inorganic and organic materials. Although these peptides have been widely used in various applications, there is a need to understand the interaction mechanism between the peptide and its material substrate, which is challenging both experimentally and theoretically. This review describes the main characterisation techniques currently available to study SBP-surface interactions and their contribution to gain a better insight for designing new peptides for tailored binding.
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Affiliation(s)
- Rachit Bansal
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia; ARC Centre of Excellence for Nanoscale Biophotonics, Macquarie University, Sydney, NSW 2109, Australia
| | - Andrew Care
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia; ARC Centre of Excellence for Nanoscale Biophotonics, Macquarie University, Sydney, NSW 2109, Australia
| | - Megan S Lord
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, NSW 2052, Australia
| | - Tiffany R Walsh
- Institute for Frontier Materials, Deakin University, Geelong, Victoria 3216, Australia
| | - Anwar Sunna
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia; ARC Centre of Excellence for Nanoscale Biophotonics, Macquarie University, Sydney, NSW 2109, Australia; Biomolecular Discovery and Design Research Centre, Macquarie University, Sydney, NSW 2109, Australia.
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Islam S, Apitius L, Jakob F, Schwaneberg U. Targeting microplastic particles in the void of diluted suspensions. ENVIRONMENT INTERNATIONAL 2019; 123:428-435. [PMID: 30622067 DOI: 10.1016/j.envint.2018.12.029] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 12/10/2018] [Accepted: 12/13/2018] [Indexed: 05/22/2023]
Abstract
Accumulation of microplastic in the environment and food chain will be a grand challenge for our society. Polyurethanes are widely used synthetic polymers in medical (e.g. catheters) and industrial products (especially as foams). Polyurethane is not abundant in nature and only a few microbial strains (fungi and bacteria) and enzymes (polyurethaneases and cutinases) have been reported to efficiently degrade polyurethane. Notably, in nature a long period of time (from 50 to >100 years depending on the literature) is required for degradation of plastics. Material binding peptides (e.g. anchor peptides) bind strongly to polymers such as polypropylene, polyethylene terephthalate, and polyurethane and can target specifically polymers. In this study we report the fusion of the anchor peptide Tachystatin A2 to the bacterial cutinase Tcur1278 which accelerated the degradation of polyester-polyurethane nanoparticles by a factor of 6.6 in comparison to wild-type Tcur1278. Additionally, degradation half-lives of polyester-polyurethane nanoparticles were reduced from 41.8 h to 6.2 h (6.7-fold) in a diluted polyester-polyurethane suspension (0.04% w/v).
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Affiliation(s)
- Shohana Islam
- DWI - Leibniz-Institut für Interaktive Materialien e.V., Forckenbeckstraße 50, 52056 Aachen, Germany; Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Lina Apitius
- DWI - Leibniz-Institut für Interaktive Materialien e.V., Forckenbeckstraße 50, 52056 Aachen, Germany; Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Felix Jakob
- DWI - Leibniz-Institut für Interaktive Materialien e.V., Forckenbeckstraße 50, 52056 Aachen, Germany; Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Ulrich Schwaneberg
- DWI - Leibniz-Institut für Interaktive Materialien e.V., Forckenbeckstraße 50, 52056 Aachen, Germany; Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
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