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Mao M, Ahrens L, Luka J, Contreras F, Kurkina T, Bienstein M, Sárria Pereira de Passos M, Schirinzi G, Mehn D, Valsesia A, Desmet C, Serra MÁ, Gilliland D, Schwaneberg U. Material-specific binding peptides empower sustainable innovations in plant health, biocatalysis, medicine and microplastic quantification. Chem Soc Rev 2024; 53:6445-6510. [PMID: 38747901 DOI: 10.1039/d2cs00991a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
Material-binding peptides (MBPs) have emerged as a diverse and innovation-enabling class of peptides in applications such as plant-/human health, immobilization of catalysts, bioactive coatings, accelerated polymer degradation and analytics for micro-/nanoplastics quantification. Progress has been fuelled by recent advancements in protein engineering methodologies and advances in computational and analytical methodologies, which allow the design of, for instance, material-specific MBPs with fine-tuned binding strength for numerous demands in material science applications. A genetic or chemical conjugation of second (biological, chemical or physical property-changing) functionality to MBPs empowers the design of advanced (hybrid) materials, bioactive coatings and analytical tools. In this review, we provide a comprehensive overview comprising naturally occurring MBPs and their function in nature, binding properties of short man-made MBPs (<20 amino acids) mainly obtained from phage-display libraries, and medium-sized binding peptides (20-100 amino acids) that have been reported to bind to metals, polymers or other industrially produced materials. The goal of this review is to provide an in-depth understanding of molecular interactions between materials and material-specific binding peptides, and thereby empower the use of MBPs in material science applications. Protein engineering methodologies and selected examples to tailor MBPs toward applications in agriculture with a focus on plant health, biocatalysis, medicine and environmental monitoring serve as examples of the transformative power of MBPs for various industrial applications. An emphasis will be given to MBPs' role in detecting and quantifying microplastics in high throughput, distinguishing microplastics from other environmental particles, and thereby assisting to close an analytical gap in food safety and monitoring of environmental plastic pollution. In essence, this review aims to provide an overview among researchers from diverse disciplines in respect to material-(specific) binding of MBPs, protein engineering methodologies to tailor their properties to application demands, re-engineering for material science applications using MBPs, and thereby inspire researchers to employ MBPs in their research.
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Affiliation(s)
- Maochao Mao
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Leon Ahrens
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Julian Luka
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Francisca Contreras
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Tetiana Kurkina
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Marian Bienstein
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | | | | | - Dora Mehn
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Andrea Valsesia
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Cloé Desmet
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | | | | | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
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2
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Mukhopadhyay T, Ghosh A, Datta A. Screening 2D Materials for Their Nanotoxicity toward Nucleic Acids and Proteins: An In Silico Outlook. ACS PHYSICAL CHEMISTRY AU 2024; 4:97-121. [PMID: 38560753 PMCID: PMC10979489 DOI: 10.1021/acsphyschemau.3c00053] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/04/2023] [Accepted: 11/06/2023] [Indexed: 04/04/2024]
Abstract
Since the discovery of graphene, two-dimensional (2D) materials have been anticipated to demonstrate enormous potential in bionanomedicine. Unfortunately, the majority of 2D materials induce nanotoxicity via disruption of the structure of biomolecules. Consequently, there has been an urge to synthesize and identify biocompatible 2D materials. Before the cytotoxicity of 2D nanomaterials is experimentally tested, computational studies can rapidly screen them. Additionally, computational analyses can provide invaluable insights into molecular-level interactions. Recently, various "in silico" techniques have identified these interactions and helped to develop a comprehensive understanding of nanotoxicity of 2D materials. In this article, we discuss the key recent advances in the application of computational methods for the screening of 2D materials for their nanotoxicity toward two important categories of abundant biomolecules, namely, nucleic acids and proteins. We believe the present article would help to develop newer computational protocols for the identification of novel biocompatible materials, thereby paving the way for next-generation biomedical and therapeutic applications based on 2D materials.
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Affiliation(s)
- Titas
Kumar Mukhopadhyay
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A and 2B Raja S.C. Mullick Road,
Jadavpur, Kolkata 700032, West Bengal, India
| | - Anupam Ghosh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A and 2B Raja S.C. Mullick Road,
Jadavpur, Kolkata 700032, West Bengal, India
| | - Ayan Datta
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A and 2B Raja S.C. Mullick Road,
Jadavpur, Kolkata 700032, West Bengal, India
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3
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Lan J, Peng Y, Liang L, Duan X, Kong Z, Zhang L, Shen JW. Theoretical study of protein adsorption on graphene/h-BN heterostructures. Phys Chem Chem Phys 2023; 25:31206-31221. [PMID: 37955184 DOI: 10.1039/d3cp03303a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
The biological characteristics of planar heterojunction nanomaterials and their interactions with biomolecules are crucial for the potential application of these materials in the biomedical field. This study employed molecular dynamics (MD) simulations to investigate the interactions between proteins with distinct secondary structures (a single α-helix representing the minimal oligomeric domain protein, a single β-sheet representing the WW structural domain of the Yap65 protein, and a mixed α/β structure representing the BBA protein) and a planar two-dimensional heterojunction (a GRA/h-BN heterojunction consisting of a graphene nanoplate (GRA) and a hexagonal boron nitride nanoplate (h-BN)). The results indicate that all three kinds of protein can be quickly and stably adsorbed on the GRA/h-BN heterojunction due to the strong van der Waals interaction, regardless of their respective types, structures and initial orientations. Moreover, the proteins exhibit a pronounced binding preference for the hBN region of the GRA/h-BN heterojunction. Upon adsorption, the α-helix structure of the minimal oligomeric domain protein experiences partial or complete denaturation. Conversely, while the secondary structure of the single β-sheet and mixed α/β structure (BBA protein) undergoes slight changes (focus on the coil and turn regions), the main α-helix and β-sheet structures remain intact. The initial orientation significantly impacts the degree of protein adsorption and its position on the GRA/h-BN heterojunction. However, regardless of the initial orientation, proteins can ultimately be adsorbed onto the GRA/h-BN heterojunction. Furthermore, the initial orientation has a minor influence on the structural changes of proteins. Significantly, the combination of different secondary structures helps mitigate the denaturation of a single α-helix structure to some extent. Overall, the adsorption of proteins on GRA/h-BN is primarily driven by van der Waals and hydrophobic interactions. Proteins with β-sheet or mixed structures exhibit stronger biocompatibility on the GRA/h-BN heterojunction. Our research elucidated the biological characteristics of GRA/h-BN heterojunction nanomaterials and their interactions with proteins possessing diverse secondary structures. It offers a theoretical foundation for considering heterojunction nanomaterials as promising candidates for biomedical applications.
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Affiliation(s)
- Jun Lan
- College of Automation, Hangzhou Dianzi University, Hangzhou, 310018, China.
| | - Yiran Peng
- College of Automation, Hangzhou Dianzi University, Hangzhou, 310018, China.
| | - Lijun Liang
- College of Automation, Hangzhou Dianzi University, Hangzhou, 310018, China.
| | - Xing Duan
- Center of Advanced Optoelectronic Materials and Devices, Key Laboratory of Novel Materials for Sensor of Zhejiang Province, College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Zhe Kong
- Center of Advanced Optoelectronic Materials and Devices, Key Laboratory of Novel Materials for Sensor of Zhejiang Province, College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Li Zhang
- Department of Chemistry, Key Laboratory of Surface & Interface Science of Polymer Materials of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Jia-Wei Shen
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China.
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4
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Barria-Urenda M, Ruiz-Fernandez A, Gonzalez C, Oostenbrink C, Garate JA. Size Matters: Free-Energy Calculations of Amino Acid Adsorption over Pristine Graphene. J Chem Inf Model 2023; 63:6642-6654. [PMID: 37909535 DOI: 10.1021/acs.jcim.3c00418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
There is still growing interest in graphene interactions with proteins, both for its possible biological applications and due to concerns over detrimental effects at the cellular level. As with any process involving proteins, an understanding of amino acid composition is desirable. In this work, we systematically studied the adsorption process of amino acids onto pristine graphene via rigorous free-energy calculations. We characterized the free energy, potential energy, and entropy of the adsorption of all proteinogenic amino acids. The energetic components were further separated into pair interaction contributions. A linear correlation was found between the free energy and the solvent accessible surface area change during adsorption (ΔSASAads) over pristine graphene and uncharged amino acids. Free energies over pristine graphene were compared with adsorption onto graphene oxide, finding an almost complete loss of the favorability of amino acid adsorption onto graphene. Finally, the correlation with ΔSASAads was used to successfully predict the free energy of adsorption of several penta-l-peptides in different structural states and sequences. Due to the relative ease of calculating the ΔSASAads compared to free-energy calculations, it could prove to be a cost-effective predictor of the free energy of adsorption for proteins onto nonpolar surfaces.
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Affiliation(s)
- Mateo Barria-Urenda
- Centro Interdisciplinario de Neurociencia de Valparaíso, Pasaje Harrington 287, Playa Ancha, 2381850 Valparaíso, Chile
- Doctorado en Ciencias, Mención Biofísica y Biología Computacional, Facultad de Ciencias, Universidad de Valparaíso, 2360102 Valparaíso, Chile
- Millennium Nucleus in NanoBioPhysics (NNBP), Universidad San Sebastian, Bellavista, 7510602 Santiago, Chile
| | - Alvaro Ruiz-Fernandez
- Centro Científico y Tecnológico de Excelencia, Fundacion Ciencia & Vida, Santiago, Santiago 7780272, Chile
| | - Carlos Gonzalez
- Millennium Nucleus in NanoBioPhysics (NNBP), Universidad San Sebastian, Bellavista, 7510602 Santiago, Chile
| | - Chris Oostenbrink
- Institute for Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Jose Antonio Garate
- Centro Interdisciplinario de Neurociencia de Valparaíso, Pasaje Harrington 287, Playa Ancha, 2381850 Valparaíso, Chile
- Millennium Nucleus in NanoBioPhysics (NNBP), Universidad San Sebastian, Bellavista, 7510602 Santiago, Chile
- Centro Científico y Tecnológico de Excelencia, Fundacion Ciencia & Vida, Santiago, Santiago 7780272, Chile
- Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Bellavista, 7510602 Santiago, Chile
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5
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Vacek J, Zatloukalová M, Dorčák V, Cifra M, Futera Z, Ostatná V. Electrochemistry in sensing of molecular interactions of proteins and their behavior in an electric field. Mikrochim Acta 2023; 190:442. [PMID: 37847341 PMCID: PMC10582152 DOI: 10.1007/s00604-023-05999-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 09/12/2023] [Indexed: 10/18/2023]
Abstract
Electrochemical methods can be used not only for the sensitive analysis of proteins but also for deeper research into their structure, transport functions (transfer of electrons and protons), and sensing their interactions with soft and solid surfaces. Last but not least, electrochemical tools are useful for investigating the effect of an electric field on protein structure, the direct application of electrochemical methods for controlling protein function, or the micromanipulation of supramolecular protein structures. There are many experimental arrangements (modalities), from the classic configuration that works with an electrochemical cell to miniaturized electrochemical sensors and microchip platforms. The support of computational chemistry methods which appropriately complement the interpretation framework of experimental results is also important. This text describes recent directions in electrochemical methods for the determination of proteins and briefly summarizes available methodologies for the selective labeling of proteins using redox-active probes. Attention is also paid to the theoretical aspects of electron transport and the effect of an external electric field on the structure of selected proteins. Instead of providing a comprehensive overview, we aim to highlight areas of interest that have not been summarized recently, but, at the same time, represent current trends in the field.
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Affiliation(s)
- Jan Vacek
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska 3, 77515, Olomouc, Czech Republic.
| | - Martina Zatloukalová
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska 3, 77515, Olomouc, Czech Republic
| | - Vlastimil Dorčák
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska 3, 77515, Olomouc, Czech Republic
| | - Michal Cifra
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Chaberska 1014/57, 18200, Prague, Czech Republic
| | - Zdeněk Futera
- Faculty of Science, University of South Bohemia, Branisovska 1760, 37005, Ceske Budejovice, Czech Republic
| | - Veronika Ostatná
- Institute of Biophysics, The Czech Academy of Sciences, v.v.i., Kralovopolska 135, 61200, Brno, Czech Republic
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6
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Bergman M, Xiao X, Hall CK. In Silico Design and Analysis of Plastic-Binding Peptides. J Phys Chem B 2023; 127:8370-8381. [PMID: 37735840 PMCID: PMC10591858 DOI: 10.1021/acs.jpcb.3c04319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023]
Abstract
Peptides that bind to inorganic materials can be used to functionalize surfaces, control crystallization, or assist in interfacial self-assembly. In the past, inorganic-binding peptides have been found predominantly through peptide library screening. While this method has successfully identified peptides that bind to a variety of materials, an alternative design approach that can intelligently search for peptides and provide physical insight for peptide affinity would be desirable. In this work, we develop a computational, physics-based approach to design inorganic-binding peptides, focusing on peptides that bind to the common plastics polyethylene, polypropylene, polystyrene, and poly(ethylene terephthalate). The PepBD algorithm, a Monte Carlo method that samples peptide sequence and conformational space, was modified to include simulated annealing, relax hydration constraints, and an ensemble of conformations to initiate design. These modifications led to the discovery of peptides with significantly better scores compared to those obtained using the original PepBD. PepBD scores were found to improve with increasing van der Waals interactions, although strengthening the intermolecular van der Waals interactions comes at the cost of introducing unfavorable electrostatic interactions. The best designs are enriched in amino acids with bulky side chains and possess hydrophobic and hydrophilic patches whose location depends on the adsorbed conformation. Future work will evaluate the top peptide designs in molecular dynamics simulations and experiment, enabling their application in microplastic pollution remediation and plastic-based biosensors.
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Affiliation(s)
- Michael Bergman
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, 27606, USA
| | - Xingqing Xiao
- Department of Chemistry, School of Science, Hainan University, Longhua District, Haikou, Hainan, 571101, China
| | - Carol K. Hall
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, 27606, USA
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7
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Braz BA, Hospinal-Santiani M, Martins G, Beirão BCB, Bergamini MF, Marcolino-Junior LH, Soccol CR, Thomaz-Soccol V. Disposable electrochemical platform based on solid-binding peptides and carbon nanomaterials: an alternative device for leishmaniasis detection. Mikrochim Acta 2023; 190:321. [PMID: 37491620 DOI: 10.1007/s00604-023-05891-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 06/29/2023] [Indexed: 07/27/2023]
Abstract
Neglected tropical diseases are those caused by infectious agents or parasites and are considered endemic in low-income populations. These diseases also have unacceptable indicators and low investment in research, drug production, and control. Tropical diseases such as leishmaniasis are some of the main causes of morbidity and mortality around the globe. Electrochemical immunosensors are promising tools for diagnostics against these diseases. One such benefit is the possibility of assisting diagnosis in isolated regions, where laboratory infrastructure is lacking. In this work, different peptides were investigated to detect antibodies against Leishmania in human and canine serum samples. The peptides evaluated (395-KKG and 395-G) have the same recognition site but differ on their solid-binding domains, which ensure affinity to spontaneously bind to either graphene oxide (GO) or graphene quantum dots (GQD). Cyclic voltammetry and differential pulse voltammetry were employed to investigate the electrochemical behavior of each assembly step and the role of each solid-binding domain coupled to its anchoring material. The graphene affinity peptide (395-G) showed better reproducibility and selectivity when coupled to GQD. Under the optimized set of experimental conditions, negative and positive human serum samples responses were distinguished based on a cut-off value of 82.5% at a 95% confidence level. The immunosensor showed selective behavior to antibodies against Mycobacterium leprae and Mycobacterium tuberculosis, which are similar antibodies and potentially sources of false positive tests. Therefore, the use of the graphene affinity peptide as a recognition site achieved outstanding performance for the detection of Leishmania antibodies.
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Affiliation(s)
- Beatriz A Braz
- Laboratory of Electrochemical Sensors (LabSensE), Department of Chemistry, Federal University of Paraná (UFPR), CEP, CP 19032, Curitiba, PR, 81531-980, Brazil
- Molecular Biology Laboratory, Graduate Program in Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), CEP, Curitiba, PR, 81531-980, Brazil
| | - Manuel Hospinal-Santiani
- Molecular Biology Laboratory, Graduate Program in Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), CEP, Curitiba, PR, 81531-980, Brazil
| | - Gustavo Martins
- Laboratory of Electrochemical Sensors (LabSensE), Department of Chemistry, Federal University of Paraná (UFPR), CEP, CP 19032, Curitiba, PR, 81531-980, Brazil
| | - Breno C B Beirão
- Graduate Program in Microbiology, Parasitology, and Pathology, Federal University of Paraná (UFPR), CEP, Curitiba, PR, 81531-980, Brazil
| | - Márcio F Bergamini
- Laboratory of Electrochemical Sensors (LabSensE), Department of Chemistry, Federal University of Paraná (UFPR), CEP, CP 19032, Curitiba, PR, 81531-980, Brazil.
| | - Luiz H Marcolino-Junior
- Laboratory of Electrochemical Sensors (LabSensE), Department of Chemistry, Federal University of Paraná (UFPR), CEP, CP 19032, Curitiba, PR, 81531-980, Brazil.
| | - Carlos R Soccol
- Molecular Biology Laboratory, Graduate Program in Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), CEP, Curitiba, PR, 81531-980, Brazil
| | - Vanete Thomaz-Soccol
- Molecular Biology Laboratory, Graduate Program in Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), CEP, Curitiba, PR, 81531-980, Brazil
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8
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Ye T, Yang Y, Bai J, Wu FY, Zhang L, Meng LY, Lan Y. The mechanical, optical, and thermal properties of graphene influencing its pre-clinical use in treating neurological diseases. Front Neurosci 2023; 17:1162493. [PMID: 37360172 PMCID: PMC10288862 DOI: 10.3389/fnins.2023.1162493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 05/17/2023] [Indexed: 06/28/2023] Open
Abstract
Rapid progress in nanotechnology has advanced fundamental neuroscience and innovative treatment using combined diagnostic and therapeutic applications. The atomic scale tunability of nanomaterials, which can interact with biological systems, has attracted interest in emerging multidisciplinary fields. Graphene, a two-dimensional nanocarbon, has gained increasing attention in neuroscience due to its unique honeycomb structure and functional properties. Hydrophobic planar sheets of graphene can be effectively loaded with aromatic molecules to produce a defect-free and stable dispersion. The optical and thermal properties of graphene make it suitable for biosensing and bioimaging applications. In addition, graphene and its derivatives functionalized with tailored bioactive molecules can cross the blood-brain barrier for drug delivery, substantially improving their biological property. Therefore, graphene-based materials have promising potential for possible application in neuroscience. Herein, we aimed to summarize the important properties of graphene materials required for their application in neuroscience, the interaction between graphene-based materials and various cells in the central and peripheral nervous systems, and their potential clinical applications in recording electrodes, drug delivery, treatment, and as nerve scaffolds for neurological diseases. Finally, we offer insights into the prospects and limitations to aid graphene development in neuroscience research and nanotherapeutics that can be used clinically.
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Affiliation(s)
- Ting Ye
- Department of Physiology and Pathophysiology, College of Medicine, Yanbian University, Yanji, Jilin, China
- Interdisciplinary Program of Biological Functional Molecules, College of Intergration Science, Yanbian University, Yanji, Jilin, China
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Yi Yang
- Department of Physiology and Pathophysiology, College of Medicine, Yanbian University, Yanji, Jilin, China
| | - Jin Bai
- Department of Physiology and Pathophysiology, College of Medicine, Yanbian University, Yanji, Jilin, China
| | - Feng-Ying Wu
- Department of Physiology and Pathophysiology, College of Medicine, Yanbian University, Yanji, Jilin, China
- Interdisciplinary Program of Biological Functional Molecules, College of Intergration Science, Yanbian University, Yanji, Jilin, China
| | - Lu Zhang
- Department of Physiology and Pathophysiology, College of Medicine, Yanbian University, Yanji, Jilin, China
| | - Long-Yue Meng
- Department of Environmental Science, Department of Chemistry, Yanbian University, Yanji, Jilin, China
| | - Yan Lan
- Department of Physiology and Pathophysiology, College of Medicine, Yanbian University, Yanji, Jilin, China
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9
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Ghosh A, Mukhopadhyay TK, Datta A. Two dimensional materials are non-nanotoxic and biocompatible towards cyclotides: evidence from classical molecular dynamics simulations. NANOSCALE 2022; 15:321-336. [PMID: 36484694 DOI: 10.1039/d2nr05096j] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Cyclotides are backbone-cyclized peptides of plant origin enriched with disulfide bonds, having exceptional stability towards thermal denaturation and proteolytic degradation. They have a plethora of activities like antibacterial, antifungal, anti-tumor and anti-HIV properties predominantly owing to their selective interaction with certain phospholipids, thereby leading to the disruption of cellular membranes. On the other hand, low-dimensional materials like graphene and hexagonal boron nitride (h-BN) are also known to show membrane-proliferating activities through lipid extraction. A plausible and more effective antibacterial, anti-tumor and antifungal agent would be a composite of these 2D materials and cyclotides, provided the structures of the peptides remain unperturbed upon adsorption and interaction. In this study, classical molecular dynamics simulations are performed to understand the nature of adsorption of cyclotides belonging to different families on graphene and h-BN and analyze the resulting structural changes. It is revealed that, due to their exceptional structural stability, cyclotides maintain their structural integrity upon adsorption on the 2D materials. In addition, the aggregated states of the cyclotides, which are ubiquitous in plant organs, are also not disrupted upon adsorption. Extensive free energy calculations show that the adsorption strength of the cyclotides is moderate in comparison to those of other similar-sized biomolecules, and the larger the size of the aggregates, the weaker the binding of individual peptides with the 2D materials, thereby leading to their lower release times from the materials. It is predicted that graphene and h-BN may safely be used for the preparation of composites with cyclotides, which in turn may be envisaged to be probable candidates for manufacturing next-generation bionano agents for agricultural, antibacterial and therapeutic applications.
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Affiliation(s)
- Anupam Ghosh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur - 700032, West Bengal, India.
| | - Titas Kumar Mukhopadhyay
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur - 700032, West Bengal, India.
| | - Ayan Datta
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur - 700032, West Bengal, India.
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10
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Jin R, Brljak N, Sangrigoli R, Walsh TR, Knecht MR. Achieving regioselective materials binding using multidomain peptides. NANOSCALE 2022; 14:14113-14121. [PMID: 36073151 DOI: 10.1039/d2nr03169h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The ability to integrate two disparate materials-binding domains into a single ligand to achieve regiospecific binding would be powerful to direct material assembly; however, this has proven challenging to achieve due to cross-materials binding. Accomplishing this goal might be achieved by harnessing the precision of biology to exploit the recognition between peptides and specific nanomaterials. Here, a designed bifunctional molecule termed Biomolecular Exfoliant and Assembly Motifs (BEAM) is introduced, featuring two different materials-binding peptide domains, one for graphene and one for hexagonal boron nitride (h-BN), at each end of the molecule, separated by a fatty acid spacer. The BEAM is demonstrated to bind strongly to both graphene and h-BN surfaces, and in each case the materials-binding peptide domain is shown to preferentially bind its target material. Critically, the two materials-binding domains exhibited limited cross-domain interaction. The BEAM design concept shows substantial potential to eventually guide self-organization of a range of materials in aqueous media.
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Affiliation(s)
- Ruitao Jin
- Institute for Frontier Materials, Deakin University, Geelong, 3216 VIC, Australia.
| | - Nermina Brljak
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146, USA.
| | - Robert Sangrigoli
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146, USA.
| | - Tiffany R Walsh
- Institute for Frontier Materials, Deakin University, Geelong, 3216 VIC, Australia.
| | - Marc R Knecht
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146, USA.
- Dr J.T. Macdonald Foundation Biomedical Nanotechnology Institute, University of Miami, UM Life Science Technology Building, 1951 NW 7th Ave, Suite 475, Miami, Florida, 33136, USA
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11
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Perdomo Y, Jin R, Parab AD, Knecht MR, Walsh TR. Manipulation of peptide-fatty acid bioconjugates on graphene: effects of fatty acid chain length and attachment point. J Mater Chem B 2022; 10:6018-6025. [PMID: 35894139 DOI: 10.1039/d2tb01104b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The non-destructive functionalisation of graphene in aqueous media is a critical process with the potential to enhance the versatility of the 2D nanosheet material as a technological enabler. This could also unlock strategies for a wider uptake of graphene in bio-related applications. Graphene functionalisation can be achieved using peptides that specifically recognise the carbon-based material, resulting in persistent non-covalent adsorption without damaging the nanosheet. Bio-conjugation of non-natural moieties with these peptides can incorporate multifunctionality, further extending the applicability of these interfaces. Here, bio-conjugates comprising a graphene-binding peptide with a fatty acid chain of varying length are investigated for their binding affinity and adsorbed structures at the aqueous graphene interface. Through an integration of quartz crystal microbalance and atomic force microscopy data with advanced sampling molecular simulations, variations in the binding of these bio-conjugates is determined. Conjugation at either terminus led to good interfacial contact, and for a given attachment point, the changes in the fatty acid length did not substantially disrupt the conformations of the adsorbed peptide domain. These findings provide a solid foundation for designing multi-functional bio-interfaces for sensing and healthcare.
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Affiliation(s)
- Yuliana Perdomo
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida, 33146, USA.
| | - Ruitao Jin
- Institute for Frontier Materials, Deakin University, Geelong, 3216 VIC, Australia.
| | - Atul D Parab
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida, 33146, USA.
| | - Marc R Knecht
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida, 33146, USA. .,Dr. J. T. Macdonald Foundation Biomedical Nanotechnology Institute, University of Miami, Miami, Florida, 33136, USA
| | - Tiffany R Walsh
- Institute for Frontier Materials, Deakin University, Geelong, 3216 VIC, Australia.
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Legleiter J, Thakkar R, Velásquez-Silva A, Miranda-Carvajal I, Whitaker S, Tomich J, Comer J. Design of Peptides that Fold and Self-Assemble on Graphite. J Chem Inf Model 2022; 62:4066-4082. [PMID: 35881533 PMCID: PMC9472279 DOI: 10.1021/acs.jcim.2c00419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The graphite-water interface provides a unique environment for polypeptides that generally favors ordered structures more than in solution. Therefore, systems consisting of designed peptides and graphitic carbon might serve as a convenient medium for controlled self-assembly of functional materials. Here, we computationally designed cyclic peptides that spontaneously fold into a β-sheet-like conformation at the graphite-water interface and self-assemble, and we subsequently observed evidence of such assembly by atomic force microscopy. Using a novel protocol, we screened nearly 2000 sequences, optimizing for formation of a unique folded conformation while discouraging unfolded or misfolded conformations. A head-to-tail cyclic peptide with the sequence GTGSGTGGPGGGCGTGTGSGPG showed the greatest apparent propensity to fold spontaneously, and this optimized sequence was selected for larger scale molecular dynamics simulations, rigorous free-energy calculations, and experimental validation. In simulations ranging from hundreds of nanoseconds to a few microseconds, we observed spontaneous folding of this peptide at the graphite-water interface under many different conditions, including multiple temperatures (295 and 370 K), with different initial orientations relative to the graphite surface, and using different molecular dynamics force fields (CHARMM and Amber). The thermodynamic stability of the folded conformation on graphite over a range of temperatures was verified by replica-exchange simulations and free-energy calculations. On the other hand, in free solution, the folded conformation was found to be unstable, unfolding in tens of picoseconds. Intermolecular hydrogen bonds promoted self-assembly of the folded peptides into linear arrangements where the peptide backbone exhibited a tendency to align along one of the six zigzag directions of the graphite basal plane. For the optimized peptide, atomic force microscopy revealed growth of single-molecule-thick linear patterns of 6-fold symmetry, consistent with the simulations, while no such patterns were observed for a control peptide with the same amino acid composition but a scrambled sequence.
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Affiliation(s)
- Justin Legleiter
- The C. Eugene Bennett Department of Chemistry, West Virginia University, 217 Clark Hall, Morgantown, West Virginia 26506, United States
| | - Ravindra Thakkar
- Nanotechnology Innovation Center of Kansas State, Institute of Computational Comparative Medicine, Department of Anatomy and Physiology, Kansas State University, Manhattan, Kansas 66506-5802, United States
| | - Astrid Velásquez-Silva
- Facultad de Ciencias de la Salud, Programa de Fisioterapia, Corporación Universitaria Iberoamericana, Calle 67 No. 5-27, 110231 Bogotá, Colombia
| | - Ingrid Miranda-Carvajal
- Centro de Innovación y Tecnología - Instituto Colombiano del Petróleo - Ecopetrol S.A., Km 7 vía Bucaramanga, 681011 Piedecuesta, Colombia
| | - Susan Whitaker
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506-5802, United States
| | - John Tomich
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506-5802, United States
| | - Jeffrey Comer
- Nanotechnology Innovation Center of Kansas State, Institute of Computational Comparative Medicine, Department of Anatomy and Physiology, Kansas State University, Manhattan, Kansas 66506-5802, United States
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13
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Thakkar R, Gajaweera S, Comer J. Organic contaminants and atmospheric nitrogen at the graphene-water interface: a simulation study. NANOSCALE ADVANCES 2022; 4:1741-1757. [PMID: 36132158 PMCID: PMC9417612 DOI: 10.1039/d1na00570g] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 03/07/2022] [Indexed: 06/15/2023]
Abstract
Ordered nanoscale patterns have been observed by atomic force microscopy at graphene-water and graphite-water interfaces. The two dominant explanations for these patterns are that (i) they consist of self-assembled organic contaminants or (ii) they are dense layers formed from atmospheric gases (especially nitrogen). Here we apply molecular dynamics simulations to study the behavior of dinitrogen and possible organic contaminants at the graphene-water interface. Despite the high concentration of N2 in ambient air, we find that its expected occupancy at the graphene-water interface is quite low. Although dense (disordered) aggregates of dinitrogen have been observed in previous simulations, our results suggest that they are stable only in the presence of supersaturated aqueous N2 solutions and dissipate rapidly when they coexist with nitrogen gas near atmospheric pressure. On the other hand, although heavy alkanes are present at only trace concentrations (micrograms per cubic meter) in typical indoor air, we predict that such concentrations can be sufficient to form ordered monolayers that cover the graphene-water interface. For octadecane, grand canonical Monte Carlo suggests nucleation and growth of monolayers above an ambient concentration near 6 μg m-3, which is less than some literature values for indoor air. The thermodynamics of the formation of these alkane monolayers includes contributions from the hydration free-energy (unfavorable), the free-energy of adsorption to the graphene-water interface (highly favorable), and integration into the alkane monolayer phase (highly favorable). Furthermore, the peak-to-peak distances in AFM force profiles perpendicular to the interface (0.43-0.53 nm), agree with the distances calculated in simulations for overlayers of alkane-like molecules, but not for molecules such as N2, water, or aromatics. Taken together, these results suggest that ordered domains observed on graphene, graphite, and other hydrophobic materials in water are consistent with alkane-like molecules occupying the interface.
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Affiliation(s)
- Ravindra Thakkar
- Nanotechnology Innovation Center of Kansas State, Department of Anatomy and Physiology 1620 Denison Avenue Mahattan Kansas USA
| | - Sandun Gajaweera
- Nanotechnology Innovation Center of Kansas State, Department of Anatomy and Physiology 1620 Denison Avenue Mahattan Kansas USA
| | - Jeffrey Comer
- Nanotechnology Innovation Center of Kansas State, Department of Anatomy and Physiology 1620 Denison Avenue Mahattan Kansas USA
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14
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Tewari M, Pareek P, Kumar S. Correlating Amino Acid Interaction with Graphene-Based Materials Regulating Cell Function. J Indian Inst Sci 2022. [DOI: 10.1007/s41745-021-00272-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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15
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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...
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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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16
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Benková Z, Cordeiro MNDS. Structural behavior of monomer of SARS-CoV-2 spike protein during initial stage of adsorption on graphene. MATERIALS TODAY. CHEMISTRY 2021; 22:100572. [PMID: 34485782 PMCID: PMC8405511 DOI: 10.1016/j.mtchem.2021.100572] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 08/22/2021] [Accepted: 08/26/2021] [Indexed: 05/14/2023]
Abstract
Spike glycoprotein of the SARS-CoV-2 virus and its structure play a crucial role in the infections of cells containing angiotensin-converting enzyme 2 (ACE2) as well as in the interactions of this virus with surfaces. Protection against viruses and often even their deactivation is one of the great varieties of graphene applications. The structural changes of the non-glycosylated monomer of the spike glycoprotein trimer (denoted as S-protein in this work) triggered by its adsorption onto graphene at the initial stage are investigated by means of atomistic molecular dynamics simulations. The adsorption of the S-protein happens readily during the first 10 ns. The shape of the S-protein becomes more prolate during the adsorption, but this trend, albeit less pronounced, is observed also for the freely relaxing S-protein in water. The receptor-binding domain (RBD) of the free and adsorbed S-protein manifests itself as the most rigid fragment of the whole S-protein. The adsorption even enhances the rigidity of the whole S-protein as well as its subunits. Only one residue of the RBD involved in the specific interactions with ACE2 during the cell infection is involved in the direct contact of the adsorbed S-protein with the graphene. The new intramolecular hydrogen bonds formed during the S-protein adsorption replace the S-protein-water hydrogen bonds; this trend, although less apparent, is observed also during the relaxation of the free S-protein in water. In the initial phase, the secondary structure of the RBD fragment specifically interacting with ACE2 receptor is not affected during the S-protein adsorption onto the graphene.
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Affiliation(s)
- Z Benková
- Polymer Institute, Slovak Academy of Sciences, Dúbravská Cesta 9, 845 41 Bratislava, Slovakia
| | - M N D S Cordeiro
- LAQV@REQUIMTE, Department of Chemistry and Biochemistry, University of Porto, Rua Do Campo Alegre 687, 4168-007 Porto, Portugal
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17
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Gallegos A, Wu J. Molecular thermodynamics for amino‐acid adsorption at inorganic surfaces. AIChE J 2021. [DOI: 10.1002/aic.17432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Alejandro Gallegos
- Department of Chemical and Environmental Engineering University of California Riverside California USA
| | - Jianzhong Wu
- Department of Chemical and Environmental Engineering University of California Riverside California USA
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18
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19
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Pushpavanam K, Ma J, Cai Y, Naser NY, Baneyx F. Solid-Binding Proteins: Bridging Synthesis, Assembly, and Function in Hybrid and Hierarchical Materials Fabrication. Annu Rev Chem Biomol Eng 2021; 12:333-357. [PMID: 33852353 DOI: 10.1146/annurev-chembioeng-102020-015923] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
There is considerable interest in the development of hybrid organic-inorganic materials because of the potential for harvesting the unique capabilities that each system has to offer. Proteins are an especially attractive organic component owing to the high amount of chemical information encoded in their amino acid sequence, their amenability to molecular and computational (re)design, and the many structures and functions they specify. Genetic installation of solid-binding peptides (SBPs) within protein frameworks affords control over the position and orientation of adhesive and morphogenetic segments, and a path toward predictive synthesis and assembly of functional materials and devices, all while harnessing the built-in properties of the host scaffold. Here, we review the current understanding of the mechanisms through which SBPs bind to technologically relevant interfaces, with an emphasis on the variables that influence the process, and highlight the last decade of progress in the use of solid-binding proteins for hybrid and hierarchical materials synthesis.
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Affiliation(s)
- Karthik Pushpavanam
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98115, USA;
| | - Jinrong Ma
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington 98115, USA
| | - Yifeng Cai
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98115, USA;
| | - Nada Y Naser
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98115, USA;
| | - François Baneyx
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98115, USA; .,Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington 98115, USA
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20
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Brljak N, Jin R, Walsh TR, Knecht MR. Selective manipulation of peptide orientation on hexagonal boron nitride nanosheets. NANOSCALE 2021; 13:5670-5678. [PMID: 33725079 DOI: 10.1039/d1nr00609f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The bio-recognition capabilities of materials-specific peptides offer a promising route to obtaining and organizing 2D nanosheet materials in aqueous media. Although significant advances have been made for graphene, little is currently understood regarding how to apply this strategy to hexagonal boron nitride (h-BN) due to a lack of knowledge regarding peptide/h-BN interactions. Here, one of the few peptide sequences known with affinity for h-BN, BP7, is the focus of mutation studies and bio-conjugation. A combination of experimental methods and modeling reveals the importance of Tyrosine in peptide/h-BN interactions. This residue is identified as the key anchoring species, which is then leveraged via bio-conjugation of BP7 to a fatty acid to create new interfacial properties. Specific placement of the fatty acid in the bio-conjugate results in dramatic manipulation of the surface-bound biotic overlayer to generate a highly viscoelastic interface. This viscoelasticity is a consequence of the fatty acid binding, which also down-modulates Tyrosine contact to h-BN, resulting in presentation of the extended peptide to solution. In this orientation, the biomolecule is available for subsequent bioconjugation, providing new pathways to programmable organization and conjugation of h-BN nanosheets in liquid water.
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Affiliation(s)
- Nermina Brljak
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146, USA.
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21
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Abstract
Understanding peptide-surface interactions is crucial for programming self-assembly of peptides at surfaces and in realizing their applications, such as biosensors and biomimetic materials. In this study, we developed insights into the dependence of a residue's interaction with a surface on its neighboring residue in a tripeptide using molecular dynamics simulations. This knowledge is integral for designing rational mutations to control peptide-surface complexes. Using graphene as our model surface, we estimated the free energy of adsorption (ΔAads) and extracted predominant conformations of 26 tripeptides with the motif LNR-CR-Gly, where LNR and CR are variable left-neighboring and central residues, respectively. We considered a combination of strongly adsorbing (Phe, Trp, and Arg) and weakly adsorbing (Ala, Val, Leu, Ser, and Thr) amino acids on graphene identified in a prior study to form the tripeptides. Our results indicate that ΔAads of a tripeptide cannot be estimated as the sum of ΔAads of each residue indicating that the residues in a tripeptide do not behave as independent entities. We observed that the contributions from the strongly adsorbing amino acids were dominant, which suggests that such residues could be used for strengthening peptide-graphene interactions irrespective of their neighboring residues. In contrast, the adsorption of weakly adsorbing central residues is dependent on their neighboring residues. Our structural analysis revealed that the dihedral angles of LNR are more correlated with that of CR in the adsorbed state than in bulk state. Together with ΔAads trends, this implies that different backbone structures of a given CR can be accessed for a similar ΔAads by varying the LNR. Therefore, incorporation of context effects in designing mutations can lead to desired peptide structure at surfaces. Our results also emphasize that these cooperative effects in ΔAads and structure are not easily predicted a priori. The collective results have applications in guiding rational mutagenesis techniques to control orientation of peptides at surfaces and in developing peptide structure prediction algorithms in adsorbed state from its sequence.
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Affiliation(s)
- Siva Dasetty
- Department of Chemical & Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Sapna Sarupria
- Department of Chemical & Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634, United States
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22
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Thodkar K, Cazade PA, Bergmann F, Lopez-Calle E, Thompson D, Heindl D. Self-Assembled Pyrene Stacks and Peptide Monolayers Tune the Electronic Properties of Functionalized Electrolyte-Gated Graphene Field-Effect Transistors. ACS APPLIED MATERIALS & INTERFACES 2021; 13:9134-9142. [PMID: 33573369 DOI: 10.1021/acsami.0c18485] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Aromatic molecules such as pyrenes are a unique class of building units for graphene functionalization, forming highly ordered π-π stacks while peptides provide more complex, biocompatible linkers. Understanding the adsorption and stacking behavior of these molecules and their influence on material properties is an essential step in enabling highly repeatable 2D material-based applications, such as biosensors, gas sensors, and solar cells. In this work, we characterize pyrene and peptide self-assembly on graphene substrates using fluorescence microscopy, atomic force microscopy and electrolyte-gated field-effect measurements supported by quantum mechanical calculations. We find distinct binding and assembly modes for pyrenes versus peptides with corresponding distinct electronic signatures in their characteristic charge neutrality point and field-effect slope responses. Our data demonstrates that pyrene- and peptide-based self-assembly platforms can be highly beneficial for precisely customizing graphene electronic properties for desired device technologies such as transport-based biosensing graphene field-effect transistors.
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Affiliation(s)
- Kishan Thodkar
- BioMed X Institute, Im Neuenheimer Feld 515, 69120 Heidelberg, Germany
| | - Pierre-Andre Cazade
- Department of Physics, Bernal Institute, University of Limerick, V94 T9PX Limerick, Ireland
| | - Frank Bergmann
- Roche Diagnostics GmbH, Nonnenwald 2, 82377 Penzberg, Germany
| | | | - Damien Thompson
- Department of Physics, Bernal Institute, University of Limerick, V94 T9PX Limerick, Ireland
| | - Dieter Heindl
- Roche Diagnostics GmbH, Nonnenwald 2, 82377 Penzberg, Germany
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23
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Osella S. Artificial Photosynthesis: Is Computation Ready for the Challenge Ahead? NANOMATERIALS 2021; 11:nano11020299. [PMID: 33498961 PMCID: PMC7911014 DOI: 10.3390/nano11020299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 12/13/2022]
Abstract
A tremendous effort is currently devoted to the generation of novel hybrid materials with enhanced electronic properties for the creation of artificial photosynthetic systems. This compelling and challenging problem is well-defined from an experimental point of view, as the design of such materials relies on combining organic materials or metals with biological systems like light harvesting and redox-active proteins. Such hybrid systems can be used, e.g., as bio-sensors, bio-fuel cells, biohybrid photoelectrochemical cells, and nanostructured photoelectronic devices. Despite these efforts, the main bottleneck is the formation of efficient interfaces between the biological and the organic/metal counterparts for efficient electron transfer (ET). It is within this aspect that computation can make the difference and improve the current understanding of the mechanisms underneath the interface formation and the charge transfer efficiency. Yet, the systems considered (i.e., light harvesting protein, self-assembly monolayer and surface assembly) are more and more complex, reaching (and often passing) the limit of current computation power. In this review, recent developments in computational methods for studying complex interfaces for artificial photosynthesis will be provided and selected cases discussed, to assess the inherent ability of computation to leave a mark in this field of research.
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Affiliation(s)
- Silvio Osella
- Chemical and Biological Systems Simulation Lab, Center of New Technologies, University of Warsaw, Banacha 2C, 02-097 Warsaw, Poland
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24
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Vaidyanathan A, Mathew M, Radhakrishnan S, Rout CS, Chakraborty B. Theoretical Insight on the Biosensing Applications of 2D Materials. J Phys Chem B 2020; 124:11098-11122. [PMID: 33232607 DOI: 10.1021/acs.jpcb.0c08539] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The research on the design of efficient, reliable, and cost-effective biosensors is expanding given its high demand in various fields such as health care, environmental surveillance, agriculture, diagnostics, industries, and so forth. In the last decade, various fascinating and interesting 2D materials with extraordinary properties have been experimentally synthesized and theoretically predicted. 2D materials have been explored for the sensing of different biomolecules because of their large surface area and strong interaction with different biomolecules. Theoretical simulations can bring important insight on the interaction of biomolecules on 2D materials, charge transfer, orbital interactions, and so forth and may play an important role in the development of efficient biosensors. Quantum simulation techniques, such as density functional theory (DFT), are very powerful and are gaining popularity especially with the advent of high-speed computing facilities. This review article provides theoretical insight regarding the interaction of various biomolecules on different 2D materials and the charge transfer between the biomolecules and 2D materials leading to electrochemical signals, which can then provide experimentalists the useful design parameters for fabrication of biosensors. It also includes an overview of quantum simulations, use of the DFT method for simulating biomolecules on 2D materials, parameters obtained from theoretical simulations and sensitivity, and limitations of computational techniques for sensing biomolecules on 2D materials. Furthermore, this review summarizes the recent work in first-principles investigation of 2D materials for the purpose of biomolecule sensing. Beyond the traditional graphene or 2D transition-metal dichalcogenides, some novel and recently proposed 2D materials such as pentagraphene, haeckelite, MXenes, and so forth which have exhibited good sensing applications have also been highlighted.
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Affiliation(s)
- Antara Vaidyanathan
- Department of Chemistry, Ramnarain Ruia Autonomous College, Matunga, Mumbai 400019, India
| | - Minu Mathew
- Centre for Nano and Material Science, Jain University, Jain Global Campus, Jakkasandra, Ramanagara, Bangalore 562112, India
| | - Sithara Radhakrishnan
- Centre for Nano and Material Science, Jain University, Jain Global Campus, Jakkasandra, Ramanagara, Bangalore 562112, India
| | - Chandra Sekhar Rout
- Centre for Nano and Material Science, Jain University, Jain Global Campus, Jakkasandra, Ramanagara, Bangalore 562112, India
| | - Brahmananda Chakraborty
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India.,Homi Bhabha National Institute, Mumbai 400094, India
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25
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Awuah JB, Walsh TR. Side-chain effects on the co-existence of emergent nanopatterns in amino acid adlayers on graphene. NANOSCALE 2020; 12:13662-13673. [PMID: 32568329 DOI: 10.1039/d0nr01333a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The spontaneous tendency of amino acid adlayers to self-assemble into ordered patterns on non-reactive surfaces is thought to be chiefly influenced by amino acid termination state. Experiments have shown that different side chains can produce different patterns, with a distinction drawn between side chains that can support hydrogen bonds or electrostatic interactions, and those that are hydrophobic. However, as is demonstrated in this work, this distinction is not clear cut, implying that there is currently no way to predict in advance what type of pattern will be formed. Here, we use molecular dynamics simulations of amino acid adlayers in neutral, zwitterion, and neutral-zwitterion states for two types of amino acids, either histidine or alanine, adsorbed at the in-vacuo graphene interface. In contrast to earlier studies on adlayers of tryptophan and methionine on graphene that reveal the presence of only a single type of pattern motif, the canonical dimer row, here we find that emergent patterns of histidine and alanine adlayers supported the co-existence of several different types of motifs, influenced by the different side-chain characteristics. For alanine, the compact side-chain does not support hydrogen bonding and engages weakly with the surface, leading to the emergence of a new dimer row configuration in addition to the canonical dimer row motif. On the contrary, for histidine, the side-chain supports hydrogen bonding, leading to the emergence of a dimer row motif different from the canonical dimer row, co-existing with several different monomer row motifs. On this basis, we propose that emergent canonical dimer row patterns are more likely for amino acids with side-chains that are non-compact and that also lack extensive hydrogen bonding capacity, and that engage strongly with the underlying substrate. These findings provide a fundamental basis to rationally guide the design of desired self-assembled nanostructures on planar surfaces.
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Affiliation(s)
- Joel B Awuah
- Institute for Frontier Materials, Deakin University, Geelong, VIC 3216, Australia.
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26
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Awuah JB, Walsh TR. Predictions of Pattern Formation in Amino Acid Adlayers at the In Vacuo Graphene Interface: Influence of Termination State. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1903403. [PMID: 31663292 DOI: 10.1002/smll.201903403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 09/17/2019] [Indexed: 06/10/2023]
Abstract
Controlled self-assembly of biomolecules on graphene offers a pathway for realizing its full potential in biological applications. Microscopy has revealed the self-assembly of amino acid adlayers into dimer rows on nonreactive substrates. However, neither the spontaneous formation of these patterns, nor the influence of amino acid termination state on the formation of patterns has been directly resolved to date. Molecular dynamics simulations, with the ability to reveal atomic level details and exert full control over the termination state, are used here to model initially disordered adlayers of neutral, zwitterionic, and neutral-zwitterionic mixtures for two types of amino acids, tryptophan and methionine, adsorbed on graphene in vacuo. The simulations of the zwitterion-containing adlayers exhibit the spontaneous emergence of dimer row ordering, mediated by charge-driven intermolecular interactions. In contrast, adlayers containing only neutral species do not assemble into ordered patterns. It is also found that the presence of trace amounts of water reduces the interamino acid interactions in the adlayers, but does not induce or disrupt pattern formation. Overall, the findings reveal the balance between the lateral interamino acid interactions and amino acid-graphene interactions, providing foundational insights for ultimately realizing the predictable pattern formation of biomolecules adsorbed on unreactive surfaces.
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Affiliation(s)
- Joel B Awuah
- Institute for Frontier Materials, Deakin University, Geelong, VIC, 3216, Australia
| | - Tiffany R Walsh
- Institute for Frontier Materials, Deakin University, Geelong, VIC, 3216, Australia
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27
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Zhang C, Li X, Wang Z, Huang X, Ge Z, Hu B. Influence of Structured Water Layers on Protein Adsorption Process: A Case Study of Cytochrome c and Carbon Nanotube Interactions and Its Implications. J Phys Chem B 2020; 124:684-694. [PMID: 31880460 DOI: 10.1021/acs.jpcb.9b10192] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cytochrome c, an essential protein of the electron transport chain, is known to be capable of amplifying the toxicity of carbon nanomaterials via free-radical generation. To understand their interaction, as well as the more general protein-nanoparticle interaction at molecular levels, we investigate the adsorptions between cytochrome c and carbon nanotubes (CNTs) in dynamic and thermodynamic ways using molecular dynamics simulations. The results reveal a well-defined three-phase process separated by two transition points: the diffusion phase where the protein diffuses in the water box, the lockdown phase I where the protein inserts into the surface-bound water layers and rearranges its conformation to fit to the surface of the CNT, and the lockdown phase II where cytochrome c repels the water molecules standing in its way to the surface of CNT and reaches stable adsorption states. The structured water layers affect the movement of atoms by electrostatic forces. In lockdown phase I, the conformation adjustment of the protein dominates the adsorption process. The most thermally favorable adsorption conformation is determined. It shows that except for the deformation of short β sheets and some portions of α helixes, most of the secondary structures of cytochrome c remain unchanged, implying that most of the functions of cytochrome c are preserved. During these processes, the energy contributions of the hydrophilic residues of cytochrome c are much larger than those of hydrophobic residues. Interestingly, the structured water layers at the CNT surface allow more hydrophilic residues such as Lys to get into close contact with the CNT, which plays a significant role during the anchoring process of adsorption. Our results demonstrate that the heme group is in close contact with the CNT in some of the adsorbed states, which hence provides a way for electron transfer from cytochrome c to the CNT surface.
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Affiliation(s)
- Chi Zhang
- Center of Materials Science and Optoelectronics Engineering, College of Materials Science and Opto-Electronic Technology , University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Xiaoyi Li
- Center of Materials Science and Optoelectronics Engineering, College of Materials Science and Opto-Electronic Technology , University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Zichen Wang
- Center of Materials Science and Optoelectronics Engineering, College of Materials Science and Opto-Electronic Technology , University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Xuqi Huang
- Center of Materials Science and Optoelectronics Engineering, College of Materials Science and Opto-Electronic Technology , University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Zhenpeng Ge
- Center of Materials Science and Optoelectronics Engineering, College of Materials Science and Opto-Electronic Technology , University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Benfeng Hu
- Center of Materials Science and Optoelectronics Engineering, College of Materials Science and Opto-Electronic Technology , University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
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28
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Jorgenson TD, Yucesoy DT, Sarikaya M, Overney RM. Thermal Selection of Aqueous Molecular Conformations for Tailored Energetics of Peptide Assemblies at Solid Interfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:318-327. [PMID: 31829632 DOI: 10.1021/acs.langmuir.9b02425] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Key to the development of functional bioinorganic soft interfaces is the predictive control over the micron-scale assembly structure and energetics of biomolecules at solid interfaces. While assembly of labile biomolecules, such as short peptides, at interfaces is a great deal affected by the shape of the molecule, biomolecular conformations are prompted by external solution conditions, involving temperature, pH, and salt concentration. In this light, one can expect that the environmental conformational selection of aqueous biomolecules could potentially allow for fine-tuning of the equilibrium assembly structure at interfaces, as well as, the binding strength and molecular mobility within these assemblies. Here, we demonstrate the energetic and structural tailoring of two-dimensional surface assemblies of graphite-binding dodecapeptides, through the thermal selection of aqueous peptide conformations. Our findings based on a scanning probe energetic analysis, supplemented by molecular dynamics modeling, show that peptide-graphite and peptide-peptide intermolecular interactions strongly depend on the thermally selected molecular conformation and that the extent of the conformational change is directly related to the observed assembled structure. Enabled by these results was the design of a peptide with predictable binding and assembled structure, thus, suggesting environmental preconditioning of peptides as a means for controlling self-assembling active bioinorganic interfaces for bioelectronic implementations such as biomolecular fuel cells and biosensors.
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Affiliation(s)
- Tyler D Jorgenson
- Molecular Engineering and Sciences Institute , University of Washington , Box 351653, Seattle , Washington 98195-1653 , United States
- GEMSEC, Genetically Engineered Materials Science and Engineering Center , University of Washington , Seattle , Washington 98195 , United States
| | - Deniz T Yucesoy
- GEMSEC, Genetically Engineered Materials Science and Engineering Center , University of Washington , Seattle , Washington 98195 , United States
- Department of Material Science and Engineering , University of Washington , Roberts Hall , Box 352120, Seattle , Washington 98195-2120 , United States
| | - Mehmet Sarikaya
- Molecular Engineering and Sciences Institute , University of Washington , Box 351653, Seattle , Washington 98195-1653 , United States
- GEMSEC, Genetically Engineered Materials Science and Engineering Center , University of Washington , Seattle , Washington 98195 , United States
- Department of Material Science and Engineering , University of Washington , Roberts Hall , Box 352120, Seattle , Washington 98195-2120 , United States
- Department of Chemical Engineering , University of Washington , Benson Hall , Box 351750, Seattle , Washington 98195-1750 , United States
| | - René M Overney
- Molecular Engineering and Sciences Institute , University of Washington , Box 351653, Seattle , Washington 98195-1653 , United States
- Department of Chemical Engineering , University of Washington , Benson Hall , Box 351750, Seattle , Washington 98195-1750 , United States
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29
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Srivastava R. Interactions, electronic and optical properties of nanographene–peptide complexes: a theoretical study. RSC Adv 2020; 10:38654-38662. [PMID: 35517564 PMCID: PMC9057264 DOI: 10.1039/d0ra07961h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 10/09/2020] [Indexed: 12/22/2022] Open
Abstract
We studied the interaction of planar phenylalanine (phe), tryptophan (try), tyrosine (tyr); amide asparagine (asn) and glutamine (gln); arginine (arg) side-chains, charged histidine (his-c) and charged lysine (lys-c) side-chains on a nanographene (g) surface by Density Functional theory (DFT) and Time Dependent Density Functional Theory (TDDFT). The occupied number of states by the system at each energy level and relative contribution of a particular atom/orbital has been studied by Density of States (DOS) and Partial Density of States (PDOS) respectively. Atom-in Molecules (AIM) analysis and non-covalent interaction (NCI) PLOT are used to study the interactions in these complexes. The absorption spectra and HOMO–LUMO (HL) gaps are quantitatively analysed to study the correlation between the optical properties of the studied complexes. The HL gap of peptides is larger than the HL gap of graphene–peptide complexes, indicating strong interactions. All the peptides interact from the above the nanographene surfaces. garg, glys-c, gtry and gtyr complexes have smaller bond distance as compared to gasn, ggln, ghis-c and gphe complexes. AIM analysis and (NCI) PLOT showed noncovalent interactions for these complexes. TDDFT calculations indicated the applicability of these complexes as biosensors. We studied interactions of planar phenylalanine, tryptophan, tyrosine; amide asparagine and glutamine; arginine side-chains, charged histidine and charged lysine side-chains on a nanographene surface by density functional theory and time dependent density functional theory.![]()
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Affiliation(s)
- Ruby Srivastava
- CSIR-Centre for Cellular and Molecular Biology
- Hyderabad
- India
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30
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Budi A, Walsh TR. A Bespoke Force Field To Describe Biomolecule Adsorption at the Aqueous Boron Nitride Interface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:16234-16243. [PMID: 31714785 DOI: 10.1021/acs.langmuir.9b03121] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Reliable manipulation of the interface between 2D nanomaterials and biomolecules represents a current frontier in nanoscience. The ability to resolve the molecular-level structures of these biointerfaces would provide a fundamental data set that is needed to enable systematic and knowledge-based progress in this area. These structures are challenging to obtain via experiment alone, and molecular simulations offer a complementary approach to address this problem. Compared with graphene, the interface between hexagonal boron nitride (h-BN) and biomolecules is relatively understudied at present. While several force fields are currently available for modeling the h-BN/water interface, there is a lack of a suitable force field that can describe the interactions between h-BN, liquid water, and biomolecules. Here, we use density functional theory calculations to create a force field, BoNi-CHARMM, to describe biomolecular interactions at the aqueous h-BN interface. Verifying our force field presents an additional challenge, given the scarcity of available experimental data for these interfaces. We test our force field against experimental evidence regarding the water/surface contact angle and confirm that the force field provides experimentally consistent values. We also present preliminary data regarding predictions of the free energy of adsorption of a selection of amino acids at the aqueous h-BN interface, revealing arginine and tryptophan to be among the strongest binders. This force field provides an opportunity to initiate a systematic progression in our current understanding of how to capture the intermolecular interactions at the h-BN biointerface.
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Affiliation(s)
- Akin Budi
- Institute for Frontier Materials , Deakin University , 75 Pigdon's Rd. , Geelong , Victoria 3216 , Australia
| | - Tiffany R Walsh
- Institute for Frontier Materials , Deakin University , 75 Pigdon's Rd. , Geelong , Victoria 3216 , Australia
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31
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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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32
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Jorgenson TD, Milligan M, Sarikaya M, Overney RM. Conformationally directed assembly of peptides on 2D surfaces mediated by thermal stimuli. SOFT MATTER 2019; 15:7360-7368. [PMID: 31355403 DOI: 10.1039/c9sm00426b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Dynamic and environmentally directed assembly of molecules in biological systems is essential for the fabrication of micronscale, hierarchical, functional structures. Here, we demonstrate the directed assembly of genetically selected graphite binding peptides on 2D solid surfaces upon thermal stimuli. Structural and kinetic analyses as well as molecular dynamics simulations yield the self-assembly process as thermally controllable upon tuning the solvated peptide conformational states. The ability to tailor the structure of two-dimensional soft bio/nano interfaces via external stimuli shows the potential for the bottom-up fabrication of complex materials with nanotechnological importance, such as biosensors, bioelectronics, and biomolecular fuel cells.
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Affiliation(s)
- Tyler D Jorgenson
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA.
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33
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Goel K, Zuñiga-Bustos M, Lazurko C, Jacques E, Galaz-Araya C, Valenzuela-Henriquez F, Pacioni NL, Couture JF, Poblete H, Alarcon EI. Nanoparticle Concentration vs Surface Area in the Interaction of Thiol-Containing Molecules: Toward a Rational Nanoarchitectural Design of Hybrid Materials. ACS APPLIED MATERIALS & INTERFACES 2019; 11:17697-17705. [PMID: 31013043 DOI: 10.1021/acsami.9b03942] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The effect of accounting for the total surface in the association of thiol-containing molecules to nanosilver was assessed using isothermal titration calorimetry, along with a new open access algorithm that calculates the total surface area for samples of different polydispersity. Further, we used advanced molecular dynamic calculations to explore the underlying mechanisms for the interaction of the studied molecules in the presence of a nanosilver surface in the form of flat surfaces or as three-dimensional pseudospherical nanostructures. Our data indicate that not only is the total surface area available for binding but also the supramolecular arrangements of the molecules in the near proximity of the nanosilver surface strongly affects the affinity of thiol-containing molecules to nanosilver surfaces.
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Affiliation(s)
- Keshav Goel
- Division of Cardiac Surgery , University of Ottawa Heart Institute , 40 Ruskin Street , Ottawa , Ontario , Canada K1Y 4W7
- Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine , University of Ottawa , 451 Smyth Road , Ottawa , Ontario , Canada K1H 8M5
| | - Matias Zuñiga-Bustos
- Center for Bioinformatics and Molecular Simulations, Facultad de Ingeniería , Universidad de Talca , Campus Lircay s/n , Talca 3460000 , Chile
| | - Caitlin Lazurko
- Division of Cardiac Surgery , University of Ottawa Heart Institute , 40 Ruskin Street , Ottawa , Ontario , Canada K1Y 4W7
- Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine , University of Ottawa , 451 Smyth Road , Ottawa , Ontario , Canada K1H 8M5
| | - Erik Jacques
- Division of Cardiac Surgery , University of Ottawa Heart Institute , 40 Ruskin Street , Ottawa , Ontario , Canada K1Y 4W7
| | - Constanza Galaz-Araya
- Center for Bioinformatics and Molecular Simulations, Facultad de Ingeniería , Universidad de Talca , Campus Lircay s/n , Talca 3460000 , Chile
| | - Francisco Valenzuela-Henriquez
- Instituto de Matemática , Pontificia Universidad Católica de Valparaíso , Blanco Viel 596, Cerro Barón , Valparaíso 2350026 , Chile
| | - Natalia L Pacioni
- Facultad de Ciencias Químicas, Departamento de Química Orgánica , Universidad Nacional de Córdoba , Haya de la Torre y Medina Allende s/n, Ciudad Universitaria , Córdoba X5000HUA , Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), INFIQC , Buenos Aires 1418 , Córdoba X5000IND , Argentina
| | - Jean-François Couture
- Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine , University of Ottawa , 451 Smyth Road , Ottawa , Ontario , Canada K1H 8M5
| | - Horacio Poblete
- Center for Bioinformatics and Molecular Simulations, Facultad de Ingeniería , Universidad de Talca , Campus Lircay s/n , Talca 3460000 , Chile
- Núcleo Científico Multidisciplinario, Dirección de Investigación , Universidad de Talca , Talca 3460000 , Chile
- Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD) , Talca 3460000 , Chile
| | - Emilio I Alarcon
- Division of Cardiac Surgery , University of Ottawa Heart Institute , 40 Ruskin Street , Ottawa , Ontario , Canada K1Y 4W7
- Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine , University of Ottawa , 451 Smyth Road , Ottawa , Ontario , Canada K1H 8M5
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34
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Dasetty S, Barrows JK, Sarupria S. Adsorption of amino acids on graphene: assessment of current force fields. SOFT MATTER 2019; 15:2359-2372. [PMID: 30789189 DOI: 10.1039/c8sm02621a] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We compare the free energies of adsorption (ΔAads) and the structural preferences of amino acids on graphene obtained using the non-polarizable force fields-Amberff99SB-ILDN/TIP3P, CHARMM36/modified-TIP3P, OPLS-AA/M/TIP3P, and Amber03w/TIP4P/2005. The amino acid-graphene interactions are favorable irrespective of the force field. While the magnitudes of ΔAads differ between the force fields, the relative free energy of adsorption across amino acids is similar for the studied force fields. ΔAads positively correlates with amino acid-graphene and negatively correlates with graphene-water interaction energies. Using a combination of principal component analysis and density-based clustering technique, we grouped the structures observed in the graphene adsorbed state. The resulting population of clusters, and the conformation in each cluster indicate that the structures of the amino acid in the graphene adsorbed state vary across force fields. The differences in the conformations of amino acids are more severe in the graphene adsorbed state compared to the bulk state for all the force fields. Our findings suggest that the force fields studied will give qualitatively consistent relative strength of adsorption across proteins but different structural preferences in the graphene adsorbed state.
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Affiliation(s)
- Siva Dasetty
- Department of Chemical & Biomolecular Engineering, Clemson University, Clemson, SC 29634, USA.
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35
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Sumaryada T, Sandy Gunawan M, Perdana S, Arjo S, Maddu A. A Molecular Interaction Analysis Reveals the Possible Roles of Graphene Oxide in a Glucose Biosensor. BIOSENSORS 2019; 9:E18. [PMID: 30696069 PMCID: PMC6468508 DOI: 10.3390/bios9010018] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 01/22/2019] [Accepted: 01/24/2019] [Indexed: 11/16/2022]
Abstract
In this paper, we report the molecular docking study of graphene oxide and glucose oxidase (GOx) enzyme for a potential glucose biosensing application. The large surface area and good electrical properties have made graphene oxide as one of the best candidates for an enzyme immobilizer and transducer in the biosensing system. Our molecular docking results revealed that graphene oxide plays a role as a GOx enzyme immobilizer in the glucose biosensor system since it can spontaneously bind with GOx at specific regions separated from the active sites of glucose and not interfering or blocking the glucose sensing by GOx in an enzyme-assisted biosensor system. The strongest binding affinity of GOx-graphene oxide interaction is -11.6 kCal/mol and dominated by hydrophobic interaction. Other modes of interactions with a lower binding affinity have shown the existence of some hydrogen bonds (H-bonds). A possibility of direct sensing (interaction) model of glucose by graphene oxide (non-enzymatic sensing mechanism) was also studied in this paper, and showed a possible direct glucose sensing by graphene oxide through the H-bond interaction, even though with a much lower binding affinity of -4.2 kCal/mol. It was also found that in a direct glucose sensing mechanism, the sensing interaction can take place anywhere on the graphene oxide surface with almost similar binding affinity.
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Affiliation(s)
- Tony Sumaryada
- Department of Physics, Bogor Agricultural University, Bogor 16680, Indonesia.
| | | | - Salahuddin Perdana
- Department of Physics, Bogor Agricultural University, Bogor 16680, Indonesia.
| | - Sugianto Arjo
- Program Studi Pendidikan Fisika, FKIP, Universitas HAMKA, Jakarta 13830, Indonesia.
| | - Akhiruddin Maddu
- Department of Physics, Bogor Agricultural University, Bogor 16680, Indonesia.
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36
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Brown AH, Walsh TR. Elucidating Polymorph-Selective Bioadsorption on Chitin Surfaces. ACS Biomater Sci Eng 2019; 5:594-602. [DOI: 10.1021/acsbiomaterials.8b01260] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Aaron H. Brown
- 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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37
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Li K, Li P, Fan Y. The assembly of silk fibroin and graphene-based nanomaterials with enhanced mechanical/conductive properties and their biomedical applications. J Mater Chem B 2019; 7:6890-6913. [DOI: 10.1039/c9tb01733j] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The assembly of silk fibroin and graphene-based nanomaterials would present fantastic properties and functions via optimizing the interaction between each other, and can be processed into various formats to tailor specific biomedical applications.
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Affiliation(s)
- Kun Li
- School of Biological Science and Medical Engineering
- Beihang University
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education
- Beijing 100083
- China
| | - Ping Li
- School of Biological Science and Medical Engineering
- Beihang University
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education
- Beijing 100083
- China
| | - Yubo Fan
- School of Biological Science and Medical Engineering
- Beihang University
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education
- Beijing 100083
- China
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38
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Azhagiya Singam ER, Zhang Y, Magnin G, Miranda-Carvajal I, Coates L, Thakkar R, Poblete H, Comer J. Thermodynamics of Adsorption on Graphenic Surfaces from Aqueous Solution. J Chem Theory Comput 2018; 15:1302-1316. [DOI: 10.1021/acs.jctc.8b00830] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- E. R. Azhagiya Singam
- Institute of Computational Comparative Medicine, Nanotechnology Innovation Center of Kansas State, Department of Anatomy and Physiology, Kansas State University, Manhattan, Kansas 66506-5802, United States
| | - Yuntao Zhang
- Institute of Computational Comparative Medicine, Nanotechnology Innovation Center of Kansas State, Department of Anatomy and Physiology, Kansas State University, Manhattan, Kansas 66506-5802, United States
| | - Geraldine Magnin
- Institute of Computational Comparative Medicine, Nanotechnology Innovation Center of Kansas State, Department of Anatomy and Physiology, Kansas State University, Manhattan, Kansas 66506-5802, United States
| | - Ingrid Miranda-Carvajal
- Universidad Nacional de Colombia, sede Bogotá, Facultad de Ciencias, Departamento de Química, Carrera 30 No. 45-03, Bogotá 111321, Colombia
| | - Logan Coates
- Institute of Computational Comparative Medicine, Nanotechnology Innovation Center of Kansas State, Department of Anatomy and Physiology, Kansas State University, Manhattan, Kansas 66506-5802, United States
| | - Ravindra Thakkar
- Institute of Computational Comparative Medicine, Nanotechnology Innovation Center of Kansas State, Department of Anatomy and Physiology, Kansas State University, Manhattan, Kansas 66506-5802, United States
| | - Horacio Poblete
- Center for Bioinformatics and Molecular Simulation, Facultad de Ingeniería, Nucleo Científico Multidiciplinario-DI, Millennium Nucleus of Ion Channel-Associated Diseases (MiNICAD), Universidad de Talca, 3460000 Talca, Chile
| | - Jeffrey Comer
- Institute of Computational Comparative Medicine, Nanotechnology Innovation Center of Kansas State, Department of Anatomy and Physiology, Kansas State University, Manhattan, Kansas 66506-5802, United States
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39
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Peng E, Todorova N, Yarovsky I. Effects of Size and Functionalization on the Structure and Properties of Graphene Oxide Nanoflakes: An in Silico Investigation. ACS OMEGA 2018; 3:11497-11503. [PMID: 31459251 PMCID: PMC6645247 DOI: 10.1021/acsomega.8b00866] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 09/07/2018] [Indexed: 05/29/2023]
Abstract
Graphitic nanoparticles, specifically, graphene oxide (GO) nanoflakes, are of major interest in the field of nanotechnology, with potential applications ranging from drug delivery systems to energy storage devices. These applications are possible largely because of the properties imparted by various functional groups attached to the GO surface by relatively simple production methods compared to pristine graphene. We investigated how varying the size and oxidation of GO flakes can affect their structural and dynamic properties in an aqueous solution. The all-atom modeling of the GO nanoflakes of different sizes suggested that the curvature and roughness of relatively small (3 × 3 nm) GO flakes are not affected by their degree of oxidation. However, the larger (7 × 7 nm) flakes exhibited an increase in surface roughness as their oxidation increased. The analysis of water structure around the graphitic nanoparticles revealed that the degree of oxidation does not affect the water dipole orientations past the first hydration layer. Nevertheless, oxygen functionalization induced a well-structured first hydration layer, which manifested in identifiable hydrophobic and hydrophilic patches on GO. The detailed all-atom models of GO nanoflakes will guide a rational design of functional graphitic nanoparticles for biomedical and industrial applications.
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Affiliation(s)
- Enxi Peng
- School of Engineering, RMIT
University, GPO Box 2476V, 3001 Melbourne, Victoria, Australia
| | - Nevena Todorova
- School of Engineering, RMIT
University, GPO Box 2476V, 3001 Melbourne, Victoria, Australia
| | - Irene Yarovsky
- School of Engineering, RMIT
University, GPO Box 2476V, 3001 Melbourne, Victoria, Australia
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40
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Effect of calcium ions on peptide adsorption at the aqueous rutile titania (110) interface. Biointerphases 2018; 13:06D403. [PMID: 30180596 DOI: 10.1116/1.5046531] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
How the presence of Ca2+ ions at the aqueous TiO2 interface influences the binding modes of two experimentally identified titania-binding peptides, Ti-1 and Ti-2, is investigated using replica exchange with solute tempering molecular dynamics simulations. The findings are compared with available experimental data, and the results are contrasted with those obtained under NaCl solution conditions. For Ti-1, Ca2+ ions enhance the adsorption of the negatively charged Asp8 residue in this sequence to the negatively charged surface, via Asp–Ca2+–TiO2 bridging. This appears to generate a nonlocal impact on the adsorption of Lys12 in Ti-1, which then pins the peptide to the surface via direct surface contact. For Ti-2, fewer residues were predicted to adsorb directly to the surface in CaCl2, compared with predictions made for NaCl solution, possibly due to competition between the other peptide residues and Ca2+ ions to adsorb to the surface. This reduction in direct surface contact gives rise to a more extensive solvent-mediated contact for Ti-2. In general, the presence of Ca2+ ions resulted in a loss of conformational diversity of the surface-adsorbed conformational ensembles of these peptides, compared to counterpart data predicted for NaCl solution. The findings provide initial insights into how peptide–TiO2 interactions might be tuned at the molecular level via modification of the salt composition of the liquid medium.
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41
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Tran DP, Lam VT, Tran TL, Nguyen TNS, Thi Tran HT. In silico study of Bombyx mori fibroin enhancement by graphene in acidic environment. Phys Chem Chem Phys 2018; 20:19240-19249. [PMID: 29989136 DOI: 10.1039/c8cp01886c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Bombyx mori fibroin has been widely used since a long time ago and has become a popular material. Here, we carry out a molecular dynamics simulation-based docking simulation of a small fragment of graphene in order to seek the best binding position on the N-termini domain of Bombyx mori fibroin. We report the best binding position, of which binding free energy falls at -54.8 kJ mol-1, indicating the strong binding. The further analysis of the binding pathway shows that this position is selective for single layered graphene rather than multi-layered graphene within our limited simulation times. Via comparing the RAMAN spectra of the corresponding binding pose of atomic clusters, we report the change in the bands compared with free standing graphene fragments, implying the change in molecular orbitals.
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Affiliation(s)
- Duy Phuoc Tran
- Department for Management of Science and Technology Development, Ton Duc Thang University, Ho Chi Minh City, Vietnam.
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42
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Xu Z, Yang X, Wei Q, Zhao W, Cui B, Yang X, Sahai N. Quantitatively Identifying the Roles of Interfacial Water and Solid Surface in Governing Peptide Adsorption. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:7932-7941. [PMID: 29888924 DOI: 10.1021/acs.langmuir.8b01189] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Understanding the molecular mechanism of protein adsorption on solids is critical to their applications in materials synthesis and tissue engineering. Although the water phase at the surface/water interface has been recognized as three types: bulk water, intermediate water phase and surface-bound water layers, the roles of the water and surface in determining the protein adsorption are not clearly identified, particularly at the quantitative level. Herein, we provide a methodology involving the combination of microsecond strengthen sampling simulation and force integration to quantitatively characterize the water-induced contribution and the peptide-surface interactions into the adsorption free energy. Using hydroxyapatite and graphene surfaces as examples, we demonstrate how the distinct interfacial features dominate the delicate force balance between these two thermodynamics parameters, leading to surface preference/resistance to peptide adsorption. Specifically, the water layer provides sustained repelling force against peptide adsorption, as indicated by a monotonic increase in the water-induced free energy profile, whereas the contribution from the surface-peptide interactions is thermodynamically favorable to peptide adsorptions. More importantly, the revealed adsorption mechanism is critically dictated by the distribution of water phase, which plays a crucial role in establishing the force balance between the interactions of the peptide with the water layer and the surface. For the HAP surface, the charged peptide exhibits strong binding affinity to the surface, due to the controlling contribution of peptide-surface interaction in the intermediate water phase. The surface-bound water layers are observed as the origin of bioresistance of solid surfaces toward the adsorption of charge-neutral peptides. The preferred peptide adsorption on the graphene, however, is dominated by the surface-induced component at the water layers adjacent to the surface. Our results further elucidate that the intermediate water phase significantly shortens the effective range of the surface dispersion force, in contrast to the observation on the hydrophilic surface.
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Affiliation(s)
| | | | | | - Weilong Zhao
- Department of Polymer Science , University of Akron , Akron , Ohio 44325-3909 , United States
| | | | | | - Nita Sahai
- Department of Polymer Science , University of Akron , Akron , Ohio 44325-3909 , United States
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Bramini M, Alberini G, Colombo E, Chiacchiaretta M, DiFrancesco ML, Maya-Vetencourt JF, Maragliano L, Benfenati F, Cesca F. Interfacing Graphene-Based Materials With Neural Cells. Front Syst Neurosci 2018; 12:12. [PMID: 29695956 PMCID: PMC5904258 DOI: 10.3389/fnsys.2018.00012] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 03/26/2018] [Indexed: 12/12/2022] Open
Abstract
The scientific community has witnessed an exponential increase in the applications of graphene and graphene-based materials in a wide range of fields, from engineering to electronics to biotechnologies and biomedical applications. For what concerns neuroscience, the interest raised by these materials is two-fold. On one side, nanosheets made of graphene or graphene derivatives (graphene oxide, or its reduced form) can be used as carriers for drug delivery. Here, an important aspect is to evaluate their toxicity, which strongly depends on flake composition, chemical functionalization and dimensions. On the other side, graphene can be exploited as a substrate for tissue engineering. In this case, conductivity is probably the most relevant amongst the various properties of the different graphene materials, as it may allow to instruct and interrogate neural networks, as well as to drive neural growth and differentiation, which holds a great potential in regenerative medicine. In this review, we try to give a comprehensive view of the accomplishments and new challenges of the field, as well as which in our view are the most exciting directions to take in the immediate future. These include the need to engineer multifunctional nanoparticles (NPs) able to cross the blood-brain-barrier to reach neural cells, and to achieve on-demand delivery of specific drugs. We describe the state-of-the-art in the use of graphene materials to engineer three-dimensional scaffolds to drive neuronal growth and regeneration in vivo, and the possibility of using graphene as a component of hybrid composites/multi-layer organic electronics devices. Last but not least, we address the need of an accurate theoretical modeling of the interface between graphene and biological material, by modeling the interaction of graphene with proteins and cell membranes at the nanoscale, and describing the physical mechanism(s) of charge transfer by which the various graphene materials can influence the excitability and physiology of neural cells.
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Affiliation(s)
- Mattia Bramini
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy.,Graphene Labs, Istituto Italiano di Tecnologia, Genova, Italy
| | - Giulio Alberini
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy.,Department of Experimental Medicine, Università degli Studi di Genova, Genova, Italy
| | - Elisabetta Colombo
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy.,Graphene Labs, Istituto Italiano di Tecnologia, Genova, Italy
| | - Martina Chiacchiaretta
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy.,Department of Experimental Medicine, Università degli Studi di Genova, Genova, Italy
| | - Mattia L DiFrancesco
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy.,Graphene Labs, Istituto Italiano di Tecnologia, Genova, Italy
| | - José F Maya-Vetencourt
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy
| | - Luca Maragliano
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy
| | - Fabio Benfenati
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy.,Graphene Labs, Istituto Italiano di Tecnologia, Genova, Italy.,Department of Experimental Medicine, Università degli Studi di Genova, Genova, Italy
| | - Fabrizia Cesca
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy.,Graphene Labs, Istituto Italiano di Tecnologia, Genova, Italy
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Prakash A, Sprenger K, Pfaendtner J. Essential slow degrees of freedom in protein-surface simulations: A metadynamics investigation. Biochem Biophys Res Commun 2018; 498:274-281. [DOI: 10.1016/j.bbrc.2017.07.066] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 07/09/2017] [Accepted: 07/11/2017] [Indexed: 12/20/2022]
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45
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Wei Q, Zhao W, Yang Y, Cui B, Xu Z, Yang X. Method Evaluations for Adsorption Free Energy Calculations at the Solid/Water Interface through Metadynamics, Umbrella Sampling, and Jarzynski's Equality. Chemphyschem 2018; 19:690-702. [DOI: 10.1002/cphc.201701241] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 12/18/2017] [Indexed: 12/18/2022]
Affiliation(s)
- Qichao Wei
- College of Chemical Engineering; State Key Laboratory of Materials-Oriented Chemical Engineering; Nanjing Tech University; Nanjing 210009 P.R. China
| | - Weilong Zhao
- Department of Polymer Science; University of Akron; Akron OH 44325-3909 USA
| | - Yang Yang
- Department of Chemistry; Haverford College; Haverford PA 19041 USA
| | - Beiliang Cui
- Network Information Center; Nanjing Tech University; Nanjing 210009 P.R. China
| | - Zhijun Xu
- College of Chemical Engineering; State Key Laboratory of Materials-Oriented Chemical Engineering; Nanjing Tech University; Nanjing 210009 P.R. China
| | - Xiaoning Yang
- College of Chemical Engineering; State Key Laboratory of Materials-Oriented Chemical Engineering; Nanjing Tech University; Nanjing 210009 P.R. China
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Hughes ZE, Walsh TR. Probing nano-patterned peptide self-organisation at the aqueous graphene interface. NANOSCALE 2017; 10:302-311. [PMID: 29210426 DOI: 10.1039/c7nr06441a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The peptide sequence GrBP5, IMVTESSDYSSY, is found experimentally to bind to graphene, and ex situ atomic force microscopy indicates the formation of an ordered over-layer on graphite. However, under aqueous conditions neither the molecular conformations of the adsorbed peptide chains, nor the molecular-level spatial ordering of the over-layer, has been directly resolved. Here, we use advanced molecular dynamics simulations of GrBP5, and related mutant sequences, to elucidate the adsorbed structures of both the peptide and the adsorbed peptide over-layer at the aqueous graphene interface. In agreement with a previous hypothesis, we find GrBP5 binds at the aqueous graphene interface chiefly via the tyrosine-rich C-terminal region. Our simulations of the adsorbed peptide over-layers reveal that the peptide chains form an aggregate that does not evolve further into ordered patterns. Instead, we find that the inter-chain interactions are driven by hydrogen bonding and charge-charge interactions that are not sufficiently specific to support pattern formation. Overall, we suggest that the experimentally-observed over-layer pattern may be due to the drying of the sample, and may not be prevalent at the solvated interface. However, our simulations indicate sequence modifications of GrBP5 to promote over-layer ordering under aqueous conditions.
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Affiliation(s)
- Zak E Hughes
- Institute for Frontier Materials, Deakin University, Geelong, VIC 3216, Australia.
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Thyparambil AA, Bazin I, Guiseppi-Elie A. Molecular Modeling and Simulation Tools in the Development of Peptide-Based Biosensors for Mycotoxin Detection: Example of Ochratoxin. Toxins (Basel) 2017. [PMCID: PMC5744115 DOI: 10.3390/toxins9120395] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Mycotoxin contamination of food and feed is now ubiquitous. Exposures to mycotoxin via contact or ingestion can potentially induce adverse health outcomes. Affordable mycotoxin-monitoring systems are highly desired but are limited by (a) the reliance on technically challenging and costly molecular recognition by immuno-capture technologies; and (b) the lack of predictive tools for directing the optimization of alternative molecular recognition modalities. Our group has been exploring the development of ochratoxin detection and monitoring systems using the peptide NFO4 as the molecular recognition receptor in fluorescence, electrochemical and multimodal biosensors. Using ochratoxin as the model mycotoxin, we share our perspective on addressing the technical challenges involved in biosensor fabrication, namely: (a) peptide receptor design; and (b) performance evaluation. Subsequently, the scope and utility of molecular modeling and simulation (MMS) approaches to address the above challenges are described. Informed and enabled by phage display, the subsequent application of MMS approaches can rationally guide subsequent biomolecular engineering of peptide receptors, including bioconjugation and bioimmobilization approaches to be used in the fabrication of peptide biosensors. MMS approaches thus have the potential to reduce biosensor development cost, extend product life cycle, and facilitate multi-analyte detection of mycotoxins, each of which positively contributes to the overall affordability of mycotoxin biosensor monitoring systems.
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Affiliation(s)
- Aby A. Thyparambil
- Center for Bioelectronics, Biosensors and Biochips (C3B), Texas A&M University, College Station, TX 77843, USA;
- Department of Biomedical Engineering, College of Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Ingrid Bazin
- Laboratoire de Génie de l’Environnement Industriel( LGEI), Institut Mines Telecom (IMT) Mines Ales, University of Montpellier, 30100 Ales, France;
| | - Anthony Guiseppi-Elie
- Center for Bioelectronics, Biosensors and Biochips (C3B), Texas A&M University, College Station, TX 77843, USA;
- Department of Biomedical Engineering, College of Engineering, Texas A&M University, College Station, TX 77843, USA
- ABTECH Scientific, Inc., Biotechnology Research Park, 800 East Leigh Street, Richmond, VA 23219, USA
- Correspondence: ; Tel.: +1-979-458-1239; Fax: +1-979-458-8219
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48
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Hughes ZE, Walsh TR. Structural Disruption of an Adenosine-Binding DNA Aptamer on Graphene: Implications for Aptasensor Design. ACS Sens 2017; 2:1602-1611. [PMID: 29063764 DOI: 10.1021/acssensors.7b00435] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We report on the predicted structural disruption of an adenosine-binding DNA aptamer adsorbed via noncovalent interactions on aqueous graphene. The use of surface-adsorbed biorecognition elements on device substrates is needed for integration in nanofluidic sensing platforms. Upon analyte binding, the conformational change in the adsorbed aptamer may perturb the surface properties, which is essential for the signal generation mechanism in the sensor. However, at present, these graphene-adsorbed aptamer structure(s) are unknown, and are challenging to experimentally elucidate. Here we use molecular dynamics simulations to investigate the structure and analyte-binding properties of this aptamer, in the presence and absence of adenosine, both free in solution and adsorbed at the aqueous graphene interface. We predict this aptamer to support a variety of stable binding modes, with direct base-graphene contact arising from regions located in the terminal bases, the centrally located binding pockets, and the distal loop region. Considerable retention of the in-solution aptamer structure in the adsorbed state indicates that strong intra-aptamer interactions compete with the graphene-aptamer interactions. However, in some adsorbed configurations the analyte adenosines detach from the binding pockets, facilitated by strong adenosine-graphene interactions.
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Affiliation(s)
- Zak E. Hughes
- 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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Hughes ZE, Wei G, Drew KLM, Colombi Ciacchi L, Walsh TR. Adsorption of DNA Fragments at Aqueous Graphite and Au(111) via Integration of Experiment and Simulation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:10193-10204. [PMID: 28885033 DOI: 10.1021/acs.langmuir.7b02480] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We combine single molecule force spectroscopy measurements with all-atom metadynamics simulations to investigate the cross-materials binding strength trends of DNA fragments adsorbed at the aqueous graphite C(0001) and Au(111) interfaces. Our simulations predict this adsorption at the level of the nucleobase, nucleoside, and nucleotide. We find that despite challenges in making clear, careful connections between the experimental and simulation data, reasonable consistency between the binding trends between the two approaches and two substrates was evident. On C(0001), our simulations predict a binding trend of dG > dA ≈ dT > dC, which broadly aligns with the experimental trend. On Au(111), the simulation-based binding strength trends reveal stronger adsorption for the purines relative to the pyrimadines, with dG ≈ dA > dT ≈ dC. Moreover, our simulations provide structural insights into the origins of the similarities and differences in adsorption of the nucleic acid fragments at the two interfaces. In particular, our simulation data offer an explanation for the differences observed in the relative binding trend between adenosine and guanine on the two substrates.
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Affiliation(s)
- Zak E Hughes
- Institute for Frontier Materials, Deakin University , Geelong, VIC 3216, Australia
| | - Gang Wei
- Hybrid Materials Interface Group, Faculty of Production Engineering, University of Bremen , D-28359 Bremen, Germany
| | - Kurt L M Drew
- Institute for Frontier Materials, Deakin University , Geelong, VIC 3216, Australia
| | - Lucio Colombi Ciacchi
- Hybrid Materials Interface Group, Faculty of Production Engineering, University of Bremen , D-28359 Bremen, Germany
| | - Tiffany R Walsh
- Institute for Frontier Materials, Deakin University , Geelong, VIC 3216, Australia
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50
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Adsorption patterns of aromatic amino acids on monolayer MoS 2 and Au-modified MoS 2 surfaces: A first-principles study. COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2017.09.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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