1
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Kamboukos A, Williams-Noonan BJ, Charchar P, Yarovsky I, Todorova N. Graphitic nanoflakes modulate the structure and binding of human amylin. NANOSCALE 2024; 16:16870-16886. [PMID: 39219407 DOI: 10.1039/d4nr01315h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Human amylin is an inherently disordered protein whose ability to form amyloid fibrils is linked to the onset of type II diabetes. Graphitic nanomaterials have potential in managing amyloid diseases as they can disrupt protein aggregation processes in biological settings, but optimising these materials to prevent fibrillation is challenging. Here, we employ bias-exchange molecular dynamics simulations to systematically study the structure and adsorption preferences of amylin on graphitic nanoflakes that vary in their physical dimensions and surface functionalisation. Our findings reveal that nanoflake size and surface oxidation both influence the structure and adsorption preferences of amylin. The purely hydrophobic substrate of pristine graphene (PG) nanoflakes encourages non-specific protein adsorption, leading to unrestricted lateral mobility once amylin adheres to the surface. Particularly on larger PG nanoflakes, this induces structural changes in amylin that may promote fibril formation, such as the loss of native helical content and an increase in β-sheet character. In contrast, oxidised graphene nanoflakes form hydrogen bonds between surface oxygen sites and amylin, and as such restricting protein mobility. Reduced graphene oxide (rGO) flakes, featuring lower amounts of surface oxidation, are amphiphilic and exhibit substantial regions of bare carbon which promote protein binding and reduced conformational flexibility, leading to conservation of the native structure of amylin. In comparison, graphene oxide (GO) nanoflakes, which are predominantly hydrophilic and have a high degree of surface oxidation, facilitate considerable protein structural variability, resulting in substantial contact area between the protein and GO, and subsequent protein unfolding. Our results indicate that tailoring the size, oxygen concentration and surface patterning of graphitic nanoflakes can lead to specific and robust protein binding, ultimately influencing the likelihood of fibril formation. These atomistic insights provide key design considerations for the development of graphitic nanoflakes that can modulate protein aggregation by sequestering protein monomers in the biological environment and inhibit conformational changes linked to amyloid fibril formation.
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Affiliation(s)
- Alexa Kamboukos
- School of Engineering, RMIT University, Melbourne, Victoria, 3001, Australia.
| | - Billy J Williams-Noonan
- School of Engineering, RMIT University, Melbourne, Victoria, 3001, Australia.
- School of Science, RMIT University, Melbourne, Victoria, 3001, Australia
| | - Patrick Charchar
- School of Engineering, RMIT University, Melbourne, Victoria, 3001, Australia.
| | - Irene Yarovsky
- School of Engineering, RMIT University, Melbourne, Victoria, 3001, Australia.
| | - Nevena Todorova
- School of Engineering, RMIT University, Melbourne, Victoria, 3001, Australia.
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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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Palierse E, Masse S, Laurent G, Le Griel P, Mosser G, Coradin T, Jolivalt C. Synthesis of Hybrid Polyphenol/Hydroxyapatite Nanomaterials with Anti-Radical Properties. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:3588. [PMID: 36296776 PMCID: PMC9612319 DOI: 10.3390/nano12203588] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Plant-derived natural bioactive molecules are of great therapeutic potential but, so far, their application in nanomedicine has scarcely been studied. This work aimed at comparing two methodologies, i.e., adsorption and in situ incorporation, to prepare hybrid polyphenol/hydroxyapatite nanoparticles. Two flavonoids, baicalin and its aglycone derivative baicalein, and two phenolic acids derived from caffeic acid, rosmarinic and chlorogenic acids, were studied. Adsorption of these polyphenols on pre-formed hydroxyapatite nanoparticles did not modify particle size or shape and loading was less than 10% (w/w). In contrast, presence of polyphenols during the synthesis of nanoparticles significantly impacted and sometimes fully inhibited hydroxyapatite formation but recovered particles could exhibit higher loadings. For most hybrid particles, release profiles consisted of a 24 h burst effect followed by a slow release over 2 weeks. Antioxidant properties of the polyphenols were preserved after adsorption but not when incorporated in situ. These results provide fruitful clues for the valorization of natural bioactive molecules in nanomedicine.
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Affiliation(s)
- Estelle Palierse
- Sorbonne Université, CNRS, Laboratoire de Chimie de la Matière Condensée de Paris, 75005 Paris, France
- Sorbonne Université, CNRS, Laboratoire de Réactivité de Surface, 75005 Paris, France
| | - Sylvie Masse
- Sorbonne Université, CNRS, Laboratoire de Chimie de la Matière Condensée de Paris, 75005 Paris, France
| | - Guillaume Laurent
- Sorbonne Université, CNRS, Laboratoire de Chimie de la Matière Condensée de Paris, 75005 Paris, France
| | - Patrick Le Griel
- Sorbonne Université, CNRS, Laboratoire de Chimie de la Matière Condensée de Paris, 75005 Paris, France
| | - Gervaise Mosser
- Sorbonne Université, CNRS, Laboratoire de Chimie de la Matière Condensée de Paris, 75005 Paris, France
| | - Thibaud Coradin
- Sorbonne Université, CNRS, Laboratoire de Chimie de la Matière Condensée de Paris, 75005 Paris, France
| | - Claude Jolivalt
- Sorbonne Université, CNRS, Laboratoire de Réactivité de Surface, 75005 Paris, France
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4
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Chen SH, Bell DR, Luan B. Understanding interactions between biomolecules and two-dimensional nanomaterials using in silico microscopes. Adv Drug Deliv Rev 2022; 186:114336. [PMID: 35597306 PMCID: PMC9212071 DOI: 10.1016/j.addr.2022.114336] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/08/2022] [Accepted: 05/06/2022] [Indexed: 12/28/2022]
Abstract
Two-dimensional (2D) nanomaterials such as graphene are increasingly used in research and industry for various biomedical applications. Extensive experimental and theoretical studies have revealed that 2D nanomaterials are promising drug delivery vehicles, yet certain materials exhibit toxicity under biological conditions. So far, it is known that 2D nanomaterials possess strong adsorption propensities for biomolecules. To mitigate potential toxicity and retain favorable physical and chemical properties of 2D nanomaterials, it is necessary to explore the underlying mechanisms of interactions between biomolecules and nanomaterials for the subsequent design of biocompatible 2D nanomaterials for nanomedicine. The purpose of this review is to integrate experimental findings with theoretical observations and facilitate the study of 2D nanomaterial interaction with biomolecules at the molecular level. We discuss the current understanding and progress of 2D nanomaterial interaction with proteins, lipid membranes, and DNA based on molecular dynamics (MD) simulation. In this review, we focus on the 2D graphene nanosheet and briefly discuss other 2D nanomaterials. With the ever-growing computing power, we can image nanoscale processes using MD simulation that are otherwise not observable in experiment. We expect that molecular characterization of the complex behavior between 2D nanomaterials and biomolecules will help fulfill the goal of designing effective 2D nanomaterials as drug delivery platforms.
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Affiliation(s)
- Serena H Chen
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - David R Bell
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Binquan Luan
- IBM Thomas J. Watson Research, Yorktown Heights, New York 10598, USA.
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5
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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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6
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Kamel M, Raissi H, Hashemzadeh H, Mohammadifard K. Theoretical elucidation of the amino acid interaction with graphene and functionalized graphene nanosheets: insights from DFT calculation and MD simulation. Amino Acids 2020; 52:1465-1478. [PMID: 33098474 DOI: 10.1007/s00726-020-02905-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 10/18/2020] [Indexed: 11/26/2022]
Affiliation(s)
- Maedeh Kamel
- Department of Chemistry, Payame Noor University, 19395-4697, Tehran, Iran
| | - Heidar Raissi
- Department of Chemistry, University of Birjand, Birjand, Iran.
| | | | - Kamal Mohammadifard
- Department of Chemical Engineering, Ferdowsi University of Mashhad, Mashhad, Iran
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7
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Wang X, Yang X, Chen H, Yang X, Xu Z. Entropy-Enthalpy Compensation in Peptide Adsorption on Solid Surfaces: Dependence on Surface Hydration. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:10822-10829. [PMID: 32813538 DOI: 10.1021/acs.langmuir.0c01845] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Although protein adsorption at the solid-water interface is of immense importance, understanding the crucial role of the water phase in mediating protein-surface interactions is lacking, particularly due to the lack of fundamental thermodynamic data. Herein, we have performed complicated free energy calculations and successfully extracted the entropy and enthalpy changes of molecular adsorption on solids. Using the gold and graphene as the surface models with distinct affinities to the water phase, we successfully unravel the sharply opposite manners of entropy-enthalpy compensation in driving water and tripeptide adsorptions on two surfaces. Though the thermodynamic features of water adsorption on surface are enthalpically dominated based on the positions of free energy barriers and minima, the favorable entropy term significantly decreases the free energy barrier and further stabilizes the adsorbate at the adsorption site on the graphene surface. For the peptide, the shape of the adsorption free energy profile is jointly determined by the enthalpy and entropy changes, which, however, alternatively act the driving force to promote the peptide adsorption on the Au surface and graphene surface. The distinct structural and dynamic properties of solid-liquid interfaces account for the special role of the interfacial water phase in regulating the competitive relationship between the entropy and enthalpy variations.
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Affiliation(s)
- Xiang Wang
- College of Chemical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Xinmofanmalu 30, Nanjing 210009, China
| | - Xiao Yang
- College of Chemical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Xinmofanmalu 30, Nanjing 210009, China
| | - Huijun Chen
- Obstetrics and Gynecology Department, Zhongnan Hospital of Wuhan University, #169 East Lake Road, Wuchang District, Wuhan 430017, China
| | - Xiaoning Yang
- College of Chemical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Xinmofanmalu 30, Nanjing 210009, China
| | - Zhijun Xu
- College of Chemical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Xinmofanmalu 30, Nanjing 210009, China
- Zhangjiagang Institute of Nanjing Tech University, Jiangfanlu 8, Zhangjiagang 215699, China
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8
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Penna M, Yarovsky I. Nanoscale in silico classification of ligand functionalised surfaces for protein adsorption resistance. NANOSCALE 2020; 12:7240-7255. [PMID: 32196038 DOI: 10.1039/c9nr10009a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Non-specific protein adsorption represents a significant challenge for the design of efficient and safe nanoparticles for biomedical applications since it may prevent functional ligands to target the desired specific receptors which can limit the efficacy of novel drug delivery systems and biosensors. The biofilm formation initiated by protein adsorption on surfaces limits the lifetime and safety of medical implants and tissue regenerative scaffolds. The development of biofouling resistant surfaces is therefore a major goal for the widespread uptake of nanomedicine. Here, we provide a relatively simple computational screening method based on the rational physically grounded criteria that may suffice in selection of surface grafted ligands for protein rejection, and test whether these criteria can be extrapolated from a specific protein to generic protein-resistant surfaces. Using all-atom molecular dynamics simulations we characterise four types of ligand functionalised surfaces at aqueous interfaces in terms of the surface hydrophobicity and ligand dynamics. We demonstrate how our hypothesised interfacial design based on the select physical characteristics of the ligated surfaces can enable the rejection of a protein from the surface. The ligand screening procedure and the detailed atomistic characterisation of the protein rejection process presented suggest that minimizing the adsorption of surface active proteins requires specific surface topographies and ligand chemistries that are able to maximise the entropic penalty associated with the restriction of the ligand dynamics and trapping interfacial water by adsorbed proteins.
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Affiliation(s)
- Matthew Penna
- School of Engineering, RMIT University, Melbourne, VIC 3000, Australia.
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9
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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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10
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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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11
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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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12
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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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13
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Bansal R, Care A, Lord MS, Walsh TR, Sunna A. Experimental and theoretical tools to elucidate the binding mechanisms of solid-binding peptides. N Biotechnol 2019; 52:9-18. [PMID: 30954671 DOI: 10.1016/j.nbt.2019.04.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 03/31/2019] [Accepted: 04/01/2019] [Indexed: 12/19/2022]
Abstract
The interactions between biomolecules and solid surfaces play an important role in designing new materials and applications which mimic nature. Recently, solid-binding peptides (SBPs) have emerged as potential molecular building blocks in nanobiotechnology. SBPs exhibit high selectivity and binding affinity towards a wide range of inorganic and organic materials. Although these peptides have been widely used in various applications, there is a need to understand the interaction mechanism between the peptide and its material substrate, which is challenging both experimentally and theoretically. This review describes the main characterisation techniques currently available to study SBP-surface interactions and their contribution to gain a better insight for designing new peptides for tailored binding.
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Affiliation(s)
- Rachit Bansal
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia; ARC Centre of Excellence for Nanoscale Biophotonics, Macquarie University, Sydney, NSW 2109, Australia
| | - Andrew Care
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia; ARC Centre of Excellence for Nanoscale Biophotonics, Macquarie University, Sydney, NSW 2109, Australia
| | - Megan S Lord
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, NSW 2052, Australia
| | - Tiffany R Walsh
- Institute for Frontier Materials, Deakin University, Geelong, Victoria 3216, Australia
| | - Anwar Sunna
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia; ARC Centre of Excellence for Nanoscale Biophotonics, Macquarie University, Sydney, NSW 2109, Australia; Biomolecular Discovery and Design Research Centre, Macquarie University, Sydney, NSW 2109, Australia.
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14
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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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15
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16
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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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17
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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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18
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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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19
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Cetinel S, Shen WZ, Aminpour M, Bhomkar P, Wang F, Borujeny ER, Sharma K, Nayebi N, Montemagno C. Biomining of MoS 2 with Peptide-based Smart Biomaterials. Sci Rep 2018; 8:3374. [PMID: 29463859 PMCID: PMC5820330 DOI: 10.1038/s41598-018-21692-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 02/06/2018] [Indexed: 11/09/2022] Open
Abstract
Biomining of valuable metals using a target specific approach promises increased purification yields and decreased cost. Target specificity can be implemented with proteins/peptides, the biological molecules, responsible from various structural and functional pathways in living organisms by virtue of their specific recognition abilities towards both organic and inorganic materials. Phage display libraries are used to identify peptide biomolecules capable of specifically recognizing and binding organic/inorganic materials of interest with high affinities. Using combinatorial approaches, these molecular recognition elements can be converted into smart hybrid biomaterials and harnessed for biotechnological applications. Herein, we used a commercially available phage-display library to identify peptides with specific binding affinity to molybdenite (MoS2) and used them to decorate magnetic NPs. These peptide-coupled NPs could capture MoS2 under a variety of environmental conditions. The same batch of NPs could be re-used multiple times to harvest MoS2, clearly suggesting that this hybrid material was robust and recyclable. The advantages of this smart hybrid biomaterial with respect to its MoS2-binding specificity, robust performance under environmentally challenging conditions and its recyclability suggests its potential application in harvesting MoS2 from tailing ponds and downstream mining processes.
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Affiliation(s)
- Sibel Cetinel
- Ingenuity Lab, 11421 Saskatchewan Drive, T6G 2M9, Edmonton, AB, Canada.,Department of Chemical and Materials Engineering, University of Alberta, T6G 2V4, Edmonton, AB, Canada
| | - Wei-Zheng Shen
- Ingenuity Lab, 11421 Saskatchewan Drive, T6G 2M9, Edmonton, AB, Canada.,Department of Chemical and Materials Engineering, University of Alberta, T6G 2V4, Edmonton, AB, Canada
| | - Maral Aminpour
- Ingenuity Lab, 11421 Saskatchewan Drive, T6G 2M9, Edmonton, AB, Canada.,Department of Chemical and Materials Engineering, University of Alberta, T6G 2V4, Edmonton, AB, Canada
| | - Prasanna Bhomkar
- Ingenuity Lab, 11421 Saskatchewan Drive, T6G 2M9, Edmonton, AB, Canada.,National Institute of Nanotechnology (NINT), University of Alberta, T6G 2M9, Edmonton, AB, Canada
| | - Feng Wang
- Ingenuity Lab, 11421 Saskatchewan Drive, T6G 2M9, Edmonton, AB, Canada.,National Institute of Nanotechnology (NINT), University of Alberta, T6G 2M9, Edmonton, AB, Canada
| | - Elham Rafie Borujeny
- Ingenuity Lab, 11421 Saskatchewan Drive, T6G 2M9, Edmonton, AB, Canada.,Department of Chemical and Materials Engineering, University of Alberta, T6G 2V4, Edmonton, AB, Canada
| | - Kumakshi Sharma
- Ingenuity Lab, 11421 Saskatchewan Drive, T6G 2M9, Edmonton, AB, Canada.,Department of Chemical and Materials Engineering, University of Alberta, T6G 2V4, Edmonton, AB, Canada
| | - Niloofar Nayebi
- Ingenuity Lab, 11421 Saskatchewan Drive, T6G 2M9, Edmonton, AB, Canada.,Department of Chemical and Materials Engineering, University of Alberta, T6G 2V4, Edmonton, AB, Canada
| | - Carlo Montemagno
- Ingenuity Lab, 11421 Saskatchewan Drive, T6G 2M9, Edmonton, AB, Canada. .,Department of Chemical and Materials Engineering, University of Alberta, T6G 2V4, Edmonton, AB, Canada. .,Southern Illinois University, 62901, Carbondale, IL, USA.
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20
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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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21
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Ross-Naylor JA, Mijajlovic M, Zhang H, Biggs MJ. Characterizing the Switching Transitions of an Adsorbed Peptide by Mapping the Potential Energy Surface. J Phys Chem B 2017; 121:11455-11464. [DOI: 10.1021/acs.jpcb.7b10319] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- James A. Ross-Naylor
- School of Chemical Engineering, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Milan Mijajlovic
- School of Chemical Engineering, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Hu Zhang
- School of Chemical Engineering, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Mark J. Biggs
- School of Chemical Engineering, The University of Adelaide, Adelaide, South Australia 5005, Australia
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22
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Walsh TR, Knecht MR. Biointerface Structural Effects on the Properties and Applications of Bioinspired Peptide-Based Nanomaterials. Chem Rev 2017; 117:12641-12704. [DOI: 10.1021/acs.chemrev.7b00139] [Citation(s) in RCA: 132] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Tiffany R. Walsh
- Institute
for Frontier Materials, Deakin University, Geelong, Victoria 3216, Australia
| | - Marc R. Knecht
- Department
of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146, United States
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23
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Guo J, Tardy BL, Christofferson AJ, Dai Y, Richardson JJ, Zhu W, Hu M, Ju Y, Cui J, Dagastine RR, Yarovsky I, Caruso F. Modular assembly of superstructures from polyphenol-functionalized building blocks. NATURE NANOTECHNOLOGY 2016; 11:1105-1111. [PMID: 27723730 DOI: 10.1038/nnano.2016.172] [Citation(s) in RCA: 243] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 08/15/2016] [Indexed: 05/21/2023]
Abstract
The organized assembly of particles into superstructures is typically governed by specific molecular interactions or external directing factors associated with the particle building blocks, both of which are particle-dependent. These superstructures are of interest to a variety of fields because of their distinct mechanical, electronic, magnetic and optical properties. Here, we establish a facile route to a diverse range of superstructures based on the polyphenol surface-functionalization of micro- and nanoparticles, nanowires, nanosheets, nanocubes and even cells. This strategy can be used to access a large number of modularly assembled superstructures, including core-satellite, hollow and hierarchically organized supraparticles. Colloidal-probe atomic force microscopy and molecular dynamics simulations provide detailed insights into the role of surface functionalization and how this facilitates superstructure construction. Our work provides a platform for the rapid generation of superstructured assemblies across a wide range of length scales, from nanometres to centimetres.
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Affiliation(s)
- Junling Guo
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of Melbourne, Parkville, Victoria 3010, Australia
- Department of Chemical and Biomolecular Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Blaise L Tardy
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of Melbourne, Parkville, Victoria 3010, Australia
- Department of Chemical and Biomolecular Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | | | - Yunlu Dai
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of Melbourne, Parkville, Victoria 3010, Australia
- Department of Chemical and Biomolecular Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Joseph J Richardson
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Wei Zhu
- Department of Chemical and Biomolecular Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Ming Hu
- Department of Chemical and Biomolecular Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Yi Ju
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of Melbourne, Parkville, Victoria 3010, Australia
- Department of Chemical and Biomolecular Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Jiwei Cui
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of Melbourne, Parkville, Victoria 3010, Australia
- Department of Chemical and Biomolecular Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Raymond R Dagastine
- Department of Chemical and Biomolecular Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Irene Yarovsky
- School of Engineering, RMIT University, GPO Box 2476, Melbourne, Victoria 3001, Australia
| | - Frank Caruso
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of Melbourne, Parkville, Victoria 3010, Australia
- Department of Chemical and Biomolecular Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
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24
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Penna M, Ley K, Maclaughlin S, Yarovsky I. Surface heterogeneity: a friend or foe of protein adsorption – insights from theoretical simulations. Faraday Discuss 2016; 191:435-464. [DOI: 10.1039/c6fd00050a] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A lack in the detailed understanding of mechanisms through which proteins adsorb or are repelled at various solid/liquid interfaces limits the capacity to rationally design and produce more sophisticated surfaces with controlled protein adsorption in both biomedical and industrial settings. To date there are three main approaches to achieve anti biofouling efficacy, namely chemically adjusting the surface hydrophobicity and introducing various degrees of surface roughness, or a combination of both. More recently, surface nanostructuring has been shown to have an effect on protein adsorption. However, the current resolution of experimental techniques makes it difficult to investigate these three phase systems at the molecular level. In this molecular dynamics study we explore in all-atom detail the adsorption process of one of the most surface active proteins, EAS hydrophobin, known for its versatile ability to self-assemble on both hydrophobic and hydrophilic surfaces forming stable monolayers that facilitate further biofilm growth. We model the adsorption of this protein on organic ligand protected silica surfaces with varying degrees of chemical heterogeneity and roughness, including fully homogenous hydrophobic and hydrophilic surfaces for comparison. We present a detailed characterisation of the functionalised surface structure and dynamics for each of these systems, and the effect the ligands have on interfacial water, the adsorption process and conformational rearrangements of the protein. Results suggest that the ligand arrangement that produces the highest hydrophilic chain mobility and the lack of significant hydrophobic patches shows the most promising anti-fouling efficacy toward hydrophobin. However, the presence on the protein surface of a flexible loop with amphipathic character (the Cys3–Cys4 loop) is seen to facilitate EAS adsorption on all surfaces by enabling the protein to match the surface pattern.
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Affiliation(s)
- Matthew Penna
- School of Engineering
- RMIT University
- Melbourne
- Australia
- ARC Research Hub for Australian Steel Manufacturing
| | - Kamron Ley
- School of Engineering
- RMIT University
- Melbourne
- Australia
| | - Shane Maclaughlin
- BlueScope Steel Research Laboratories
- Port Kembla
- Australia
- ARC Research Hub for Australian Steel Manufacturing
- Australia
| | - Irene Yarovsky
- School of Engineering
- RMIT University
- Melbourne
- Australia
- ARC Research Hub for Australian Steel Manufacturing
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