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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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Khavani M, Mehranfar A, Mofrad MRK. On the interactions of peptides with gold nanoparticles: effects of sequence and size. J Biomol Struct Dyn 2024; 42:4429-4441. [PMID: 37306472 DOI: 10.1080/07391102.2023.2220816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 05/28/2023] [Indexed: 06/13/2023]
Abstract
Peptide-based self-assembly and synthesis techniques have emerged as a viable approach to designing active and stable inorganic nanostructures in aqueous media. In the present study, we use all-atom molecular dynamic (MD) simulations to study the interactions of ten short peptides (namely A3, AgBP1, AgBP2, AuBP1, AuBP2, GBP1, Midas2, Pd4, Z1, and Z2) with different gold nanoparticles (of different diameters ranging from 2 to 8 nm). Our MD simulation results imply that the gold nanoparticles have a remarkable effect on the stability and conformational properties of peptides. Moreover, the size of the gold nanoparticles and the type of peptide amino acid sequences play important roles in the stability of the peptide-AuNP complexes. Our results reveal that some amino acids such as Tyr, Phe, Met, Lys, Arg, and Gln have direct contact with the metal surface in comparison with Gly, Ala, Pro, Thr, and Val residues. The peptide adsorption on the surface of the gold nanoparticles is favorable from the energetic viewpoint, in which the van der Waals (vdW) interactions between the peptides and metal surface can be considered as one of the driving forces for the complexation process. The calculated Gibbs binding energies indicate that AuNPs have more sensitivity against the GBP1 peptide in the presence of different peptides. Overall, the results of this study can provide new insight into the peptide interaction with the gold nanoparticles from the molecular viewpoint, which can be important for designing new biomaterials based on the peptides and gold nanoparticles.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohammad Khavani
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California Berkeley, Berkeley, California, USA
| | - Aliyeh Mehranfar
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California Berkeley, Berkeley, California, USA
| | - Mohammad R K Mofrad
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California Berkeley, Berkeley, California, USA
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3
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Redondo-Gómez C, Parreira P, Martins MCL, Azevedo HS. Peptide-based self-assembled monolayers (SAMs): what peptides can do for SAMs and vice versa. Chem Soc Rev 2024; 53:3714-3773. [PMID: 38456490 DOI: 10.1039/d3cs00921a] [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: 03/09/2024]
Abstract
Self-assembled monolayers (SAMs) represent highly ordered molecular materials with versatile biochemical features and multidisciplinary applications. Research on SAMs has made much progress since the early begginings of Au substrates and alkanethiols, and numerous examples of peptide-displaying SAMs can be found in the literature. Peptides, presenting increasing structural complexity, stimuli-responsiveness, and biological relevance, represent versatile functional components in SAMs-based platforms. This review examines the major findings and progress made on the use of peptide building blocks displayed as part of SAMs with specific functions, such as selective cell adhesion, migration and differentiation, biomolecular binding, advanced biosensing, molecular electronics, antimicrobial, osteointegrative and antifouling surfaces, among others. Peptide selection and design, functionalisation strategies, as well as structural and functional characteristics from selected examples are discussed. Additionally, advanced fabrication methods for dynamic peptide spatiotemporal presentation are presented, as well as a number of characterisation techniques. All together, these features and approaches enable the preparation and use of increasingly complex peptide-based SAMs to mimic and study biological processes, and provide convergent platforms for high throughput screening discovery and validation of promising therapeutics and technologies.
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Affiliation(s)
- Carlos Redondo-Gómez
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, Porto, 4200-135, Portugal.
- INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen, 208, Porto, 4200-135, Portugal
| | - Paula Parreira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, Porto, 4200-135, Portugal.
- INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen, 208, Porto, 4200-135, Portugal
| | - M Cristina L Martins
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, Porto, 4200-135, Portugal.
- INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen, 208, Porto, 4200-135, Portugal
- ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 4050-313 Porto, Portugal
| | - Helena S Azevedo
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, Porto, 4200-135, Portugal.
- INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen, 208, Porto, 4200-135, Portugal
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4
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Xie M, Shimogawa R, Liu Y, Zhang L, Foucher AC, Routh PK, Stach EA, Frenkel AI, Knecht MR. Biomimetic Control over Bimetallic Nanoparticle Structure and Activity via Peptide Capping Ligand Sequence. ACS NANO 2024; 18:3286-3294. [PMID: 38227802 DOI: 10.1021/acsnano.3c10016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
The controlled design of bimetallic nanoparticles (BNPs) is a key goal in tailoring their catalytic properties. Recently, biomimetic pathways demonstrated potent control over the distribution of different metals within BNPs, but a direct understanding of the peptide effect on the compositional distribution at the interparticle and intraparticle levels remains lacking. We synthesized two sets of PtAu systems with two peptides and correlated their structure, composition, and distributions with the catalytic activity. Structural and compositional analyses were performed by a combined machine learning-assisted refinement of X-ray absorption spectra and Z-contrast measurements by scanning transmission electron microscopy. The difference in the catalytic activities between nanoparticles synthesized with different peptides was attributed to the details of interparticle distribution of Pt and Au across these markedly heterogeneous systems, comprising Pt-rich, Au-rich, and Au core/Pt shell nanoparticles. The total amount of Pt in the shells of the BNPs was proposed to be the key catalytic activity descriptor. This approach can be extended to other systems of metals and peptides to facilitate the targeted design of catalysts with the desired activity.
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Affiliation(s)
- Maichong Xie
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Ryuichi Shimogawa
- Department of Materials Science and Chemical Engineering, Stony Brook University, Stony Brook, New York 11794, United States
- Mitsubishi Chemical Corporation, Science & Innovation Center, 1000, Kamoshida-cho, Aoba-ku, Yokohama 227-8502, Japan
| | - Yang Liu
- Department of Materials Science and Chemical Engineering, Stony Brook University, Stony Brook, New York 11794, United States
| | - Lihua Zhang
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Alexandre C Foucher
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Prahlad K Routh
- Department of Materials Science and Chemical Engineering, Stony Brook University, Stony Brook, New York 11794, United States
| | - Eric A Stach
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Anatoly I Frenkel
- Department of Materials Science and Chemical Engineering, Stony Brook University, Stony Brook, New York 11794, United States
- Chemistry Division, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Marc R Knecht
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
- Dr. J.T. Macdonald Foundation Biomedical Nanotechnology Institute, University of Miami, Miami, Florida 33136, United States
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5
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Völkle Nee Evgrafov E, Schulz F, Kanold JM, Michaelis M, Wissel K, Brümmer F, Schenk AS, Ludwigs S, Bill J, Rothenstein D. Functional mimicry of sea urchin biomineralization proteins with CaCO 3-binding peptides selected by phage display. J Mater Chem B 2023; 11:10174-10188. [PMID: 37850271 DOI: 10.1039/d3tb01584j] [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: 10/19/2023]
Abstract
The intricate process of biomineralization, e.g. in sea urchins, involves the precise interplay of highly regulated mineralization proteins and the spatiotemporal coordination achieved through compartmentalization. However, the investigation of biomineralization effector molecules, e.g. proteins, is challenging, due to their very low abundance. Therefore, we investigate the functional mimicry in the bioinspired precipitation of calcium carbonate (CaCO3) with artificial peptides selected from a peptide library by phage display based on peptide-binding to calcite and aragonite, respectively. The structure-directing effects of the identified peptides were compared to those of natural protein mixes isolated from skeletal (test) structures of two sea urchin species (Arbacia lixula and Paracentrotus lividus). The calcium carbonate samples deposited in the absence or presence of peptides were analyzed with a set of complementary techniques with regard to morphology, polymorph, and nanostructural motifs. Remarkably, some of the CaCO3-binding peptides induced morphological features in calcite that appeared similar to those obtained in the presence of the natural protein mixes. Many of the peptides identified as most effective in exerting a structure-directing effect on calcium carbonate crystallization were rich in basic amino acid residues. Hence, our in vitro mineralization study further highlights the important, but often neglected, role of positively charged soluble organic matrices associated with biological and bioinspired CaCO3 deposition.
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Affiliation(s)
- Elke Völkle Nee Evgrafov
- Dept. Bioinspired Materials, Institute for Materials Science, University of Stuttgart, Heisenbergstraße 3, 70569 Stuttgart, Germany.
| | - Fabian Schulz
- Dept. Bioinspired Materials, Institute for Materials Science, University of Stuttgart, Heisenbergstraße 3, 70569 Stuttgart, Germany.
| | - Julia Maxi Kanold
- Institute for Biomaterials and Biomolecular Systems & Scientific Diving Group (WiTUS), University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Monika Michaelis
- Biomolecular and Materials Interface Research Group, Interdisciplinary Biomedical Research Centre, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK
| | - Kerstin Wissel
- Dept. Chemical Materials Synthesis, Institute for Materials Science, University of Stuttgart, Heisenbergstraβe 3, 70569 Stuttgart, Germany
| | - Franz Brümmer
- Institute for Biomaterials and Biomolecular Systems & Scientific Diving Group (WiTUS), University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Anna S Schenk
- Physical Chemistry IV, Department of Chemistry, University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Sabine Ludwigs
- IPOC - Functional Polymers, Institute of Polymer Chemistry (IPOC), University of Stuttgart, Stuttgart 70569, Germany
| | - Joachim Bill
- Dept. Bioinspired Materials, Institute for Materials Science, University of Stuttgart, Heisenbergstraße 3, 70569 Stuttgart, Germany.
| | - Dirk Rothenstein
- Dept. Bioinspired Materials, Institute for Materials Science, University of Stuttgart, Heisenbergstraße 3, 70569 Stuttgart, Germany.
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6
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Lee H, Bang Y, Chang IS. Orientation-Controllable Enzyme Cascade on Electrode for Bioelectrocatalytic Chain Reaction. ACS APPLIED MATERIALS & INTERFACES 2023; 15:40355-40368. [PMID: 37552888 DOI: 10.1021/acsami.3c03077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
The accomplishment of concurrent interenzyme chain reaction and direct electric communication in a multienzyme-electrode is challenging since the required condition of multienzymatic binding conformation is quite complex. In this study, an enzyme cascade-induced bioelectrocatalytic system has been constructed using solid binding peptide (SBP) as a molecular binder that coimmobilizes the invertase (INV) and flavin adenine dinucleotide (FAD)-dependent glucose dehydrogenase gamma-alpha complex (GDHγα) cascade system on a single electrode surface. The SBP-fused enzyme cascade was strategically designed to induce diverse relative orientations of coupling enzymes while enabling efficient direct electron transfer (DET) at the FAD cofactor of GDHγα and the electrode interface. The interenzyme relative orientation was found to determine the intermediate delivery route and affect overall chain reaction efficiency. Moreover, interfacial DET between the fusion GDHγα and the electrode was altered by the binding conformation of the coimmobilized enzyme and fusion INVs. Collectively, this work emphasizes the importance of interenzyme orientation when incorporating enzymatic cascade in an electrocatalytic system and demonstrates the efficacy of SBP fusion technology as a generic tool for developing cascade-induced direct bioelectrocatalytic systems. The proposed approach is applicable to enzyme cascade-based bioelectronics such as biofuel cells, biosensors, and bioeletrosynthetic systems utilizing or producing complex biomolecules.
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Affiliation(s)
- Hyeryeong Lee
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, 123 Cheomdan-gwagiro, Buk-gu, Gwangju 61005, Republic of Korea
- Research Center for Innovative Energy and Carbon Optimized Synthesis for Chemicals (inn-ECOSysChem), Gwangju Institute of Science and Technology, 123 Cheomdan-gwagiro, Buk-gu, Gwangju 61005, Republic of Korea
| | - Yuna Bang
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, 123 Cheomdan-gwagiro, Buk-gu, Gwangju 61005, Republic of Korea
| | - In Seop Chang
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, 123 Cheomdan-gwagiro, Buk-gu, Gwangju 61005, Republic of Korea
- Research Center for Innovative Energy and Carbon Optimized Synthesis for Chemicals (inn-ECOSysChem), Gwangju Institute of Science and Technology, 123 Cheomdan-gwagiro, Buk-gu, Gwangju 61005, Republic of Korea
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7
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Wang L, Li H, Wang X, Yang X, Tian C, Sun D, Liu L, Li J. Modification of Low-Energy Surfaces Using Bicyclic Peptides Discovered by Phage Display. J Am Chem Soc 2023; 145:17613-17620. [PMID: 37531461 DOI: 10.1021/jacs.3c02943] [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: 08/04/2023]
Abstract
Solid-binding peptides are a simple and versatile tool for the non-covalent modification of solid material surfaces, and a variety of peptides have been developed by reference to natural proteins or de novo design. Here, for the first time, we report the discovery of a bicyclic peptide targeting the heterogeneous material polypropylene by combining phage display technology and next-generation sequencing. We find that the enrichment properties of bicyclic peptides capable of binding to polypropylene are distinct from linear peptides, as reflected in amino acid abundance and a trend toward negative net charges and high hydrophobicity. The selected bicyclic peptide has a higher binding affinity for polypropylene compared with a previously reported linear peptide, enabling the hydrophilic and adhesive properties of the polypropylene to be more effectively enhanced. Our work paves the way for the exploration and utilization of conformational-restricted cyclic peptides as a new family of functionally evolvable agents for material surface modification.
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Affiliation(s)
- Lingxiao Wang
- Department of Chemistry, Center for BioAnalytical Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Haodong Li
- Department of Chemistry, Center for BioAnalytical Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Xinyan Wang
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Xichu Yang
- Center for BioAnalytical Chemistry, Hefei National Laboratory of Physical Science at Microscale, University of Science and Technology of China, Hefei 230026, China
| | - Changlin Tian
- Center for BioAnalytical Chemistry, Hefei National Laboratory of Physical Science at Microscale, University of Science and Technology of China, Hefei 230026, China
| | - Demeng Sun
- Center for BioAnalytical Chemistry, Hefei National Laboratory of Physical Science at Microscale, University of Science and Technology of China, Hefei 230026, China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Jinghong Li
- Department of Chemistry, Center for BioAnalytical Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
- New Cornerstone Science Laboratory, Shenzhen 518054, China
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8
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Michaelis M, Cupellini L, Mensch C, Perry CC, Delle Piane M, Colombi Ciacchi L. Tidying up the conformational ensemble of a disordered peptide by computational prediction of spectroscopic fingerprints. Chem Sci 2023; 14:8483-8496. [PMID: 37592980 PMCID: PMC10430726 DOI: 10.1039/d3sc02202a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 07/15/2023] [Indexed: 08/19/2023] Open
Abstract
The most advanced structure prediction methods are powerless in exploring the conformational ensemble of disordered peptides and proteins and for this reason the "protein folding problem" remains unsolved. We present a novel methodology that enables the accurate prediction of spectroscopic fingerprints (circular dichroism, infrared, Raman, and Raman optical activity), and by this allows for "tidying up" the conformational ensembles of disordered peptides and disordered regions in proteins. This concept is elaborated for and applied to a dodecapeptide, whose spectroscopic fingerprint is measured and theoretically predicted by means of enhanced-sampling molecular dynamics coupled with quantum mechanical calculations. Following this approach, we demonstrate that peptides lacking a clear propensity for ordered secondary-structure motifs are not randomly, but only conditionally disordered. This means that their conformational landscape, or phase-space, can be well represented by a basis-set of conformers including about 10 to 100 structures. The implications of this finding have profound consequences both for the interpretation of experimental electronic and vibrational spectral features of peptides in solution and for the theoretical prediction of these features using accurate and computationally expensive techniques. The here-derived methods and conclusions are expected to fundamentally impact the rationalization of so-far elusive structure-spectra relationships for disordered peptides and proteins, towards improved and versatile structure prediction methods.
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Affiliation(s)
- Monika Michaelis
- Hybrid Materials Interfaces Group, Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), and MAPEX Center for Materials and Processes, University of Bremen Am Fallturm 1 Bremen 28359 Germany
- Biomolecular and Materials Interface Research Group, Interdisciplinary Biomedical Research Centre, School of Science and Technology, Nottingham Trent University Clifton Lane Nottingham NG11 8NS UK
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, University of Pisa Via G. Moruzzi 13 Pisa I-56124 Italy
| | - Carl Mensch
- Molecular Spectroscopy Research Group, Department of Chemistry, University of Antwerp Groenenborgerlaan 171 Antwerp 2020 Belgium
| | - Carole C Perry
- Biomolecular and Materials Interface Research Group, Interdisciplinary Biomedical Research Centre, School of Science and Technology, Nottingham Trent University Clifton Lane Nottingham NG11 8NS UK
| | - Massimo Delle Piane
- Hybrid Materials Interfaces Group, Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), and MAPEX Center for Materials and Processes, University of Bremen Am Fallturm 1 Bremen 28359 Germany
- Department of Applied Science and Technology, Politecnico di Torino Corso Duca degli Abruzzi 24 Torino 10129 Italy
| | - Lucio Colombi Ciacchi
- Hybrid Materials Interfaces Group, Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), and MAPEX Center for Materials and Processes, University of Bremen Am Fallturm 1 Bremen 28359 Germany
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9
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Perdomo Y, Slocik JM, Phillips DM, Knecht MR. Peptide/Nanoparticle Biointerfaces for Multistep Tandem Catalysis. J Am Chem Soc 2023. [PMID: 37478168 DOI: 10.1021/jacs.3c04097] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2023]
Abstract
The realization of multifunctional nanoparticle systems is essential to achieve highly efficient catalytic materials for specific applications; however, their production remains quite challenging. They are typically achieved through the incorporation of multiple inorganic components; however, incorporation of functionality could also be achieved at the organic ligand layer. In this work, we demonstrate the generation of multifunctional nanoparticle catalysts using peptide-based ligands for tandem catalytic functionality. To this end, chimeric peptides were designed that incorporated a Au binding sequence and a catalytic sequence that can drive ester hydrolysis. Using this chimera, Au nanoparticles were prepared, which sufficiently presented the catalytic domain of the peptide to drive tandem catalytic processes occurring at the peptide ligand layer and the Au nanoparticle surface. This work represents unique pathways to achieve multifunctionality from nanoparticle systems tuned by both the inorganic and bio/organic components, which could be highly important for applications beyond catalysis, including theranostics, sensing, and energy technologies.
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Affiliation(s)
- Yuliana Perdomo
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
- Dr. J.T. Macdonald Foundation Biomedical Nanotechnology Institute, University of Miami, Miami, Florida 33136, United States
| | - Joseph M Slocik
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Dayton, Ohio 45433, United States
| | - David M Phillips
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Dayton, Ohio 45433, United States
| | - Marc R Knecht
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
- Dr. J.T. Macdonald Foundation Biomedical Nanotechnology Institute, University of Miami, Miami, Florida 33136, United States
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10
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Zheng C, Alvisi N, de Haas RJ, Zhang Z, Zuilhof H, de Vries R. Modular Design for Proteins Assembling into Antifouling Coatings: Case of Gold Surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023. [PMID: 37366321 DOI: 10.1021/acs.langmuir.3c00389] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
We analyze modularity for a B-M-E triblock protein designed to self-assemble into antifouling coatings. Previously, we have shown that the design performs well on silica surfaces when B is taken to be a silica-binding peptide, M is a thermostable trimer domain, and E is the uncharged elastin-like polypeptide (ELP), E = (GSGVP)40. Here, we demonstrate that we can modulate the nature of the substrate on which the coatings form by choosing different solid-binding peptides as binding domain B and that we can modulate antifouling properties by choosing a different hydrophilic block E. Specifically, to arrive at antifouling coatings for gold surfaces, as binding block B we use the gold-binding peptide GBP1 (with the sequence MHGKTQATSGTIQS), while we replace the antifouling blocks E by zwitterionic ELPs of different lengths, EZn = (GDGVP-GKGVP)n/2, with n = 20, 40, or 80. We find that even the B-M-E proteins with the shortest E blocks make coatings on gold surfaces with excellent antifouling against 1% human serum (HS) and reasonable antifouling against 10% HS. This suggests that the B-M-E triblock protein can be easily adapted to form antifouling coatings on any substrate for which solid-binding peptide sequences are available.
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Affiliation(s)
- Chuanbao Zheng
- Physical Chemistry and Soft Matter, Wageningen University & Research, Stippeneng 4, Wageningen 6708 WE, The Netherlands
- Laboratory of Organic Chemistry, Wageningen University & Research, Stippeneng 4, Wageningen 6708 WE, The Netherlands
| | - Nicolò Alvisi
- Physical Chemistry and Soft Matter, Wageningen University & Research, Stippeneng 4, Wageningen 6708 WE, The Netherlands
| | - Robbert Jan de Haas
- Physical Chemistry and Soft Matter, Wageningen University & Research, Stippeneng 4, Wageningen 6708 WE, The Netherlands
| | - Zhisen Zhang
- Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Laboratory for Soft Functional Materials Research, Department of Physics, Xiamen University, Xiamen 361005, China
| | - Han Zuilhof
- Laboratory of Organic Chemistry, Wageningen University & Research, Stippeneng 4, Wageningen 6708 WE, The Netherlands
- School of Pharmaceutical Sciences and Technology, Tianjin University, 92 Weijin Road, Tianjin 300072, China
| | - Renko de Vries
- Physical Chemistry and Soft Matter, Wageningen University & Research, Stippeneng 4, Wageningen 6708 WE, The Netherlands
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11
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Han SI, Sarkes DA, Hurley MM, Renberg R, Huang C, Li Y, Jahnke JP, Sumner JJ, Stratis-Cullum DN, Han A. Identification of Microorganisms that Bind Specifically to Target Materials of Interest Using a Magnetophoretic Microfluidic Platform. ACS APPLIED MATERIALS & INTERFACES 2023; 15:11391-11402. [PMID: 36847552 PMCID: PMC10848205 DOI: 10.1021/acsami.2c15192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
Discovery of microorganisms and their relevant surface peptides that specifically bind to target materials of interest can be achieved through iterative biopanning-based screening of cellular libraries having high diversity. Recently, microfluidics-based biopanning methods have been developed and exploited to overcome the limitations of conventional methods where controlling the shear stress applied to remove cells that do not bind or only weakly bind to target surfaces is difficult and the overall experimental procedure is labor-intensive. Despite the advantages of such microfluidic methods and successful demonstration of their utility, these methods still require several rounds of iterative biopanning. In this work, a magnetophoretic microfluidic biopanning platform was developed to isolate microorganisms that bind to target materials of interest, which is gold in this case. To achieve this, gold-coated magnetic nanobeads, which only attached to microorganisms that exhibit high affinity to gold, were used. The platform was first utilized to screen a bacterial peptide display library, where only the cells with surface peptides that specifically bind to gold could be isolated by the high-gradient magnetic field generated within the microchannel, resulting in enrichment and isolation of many isolates with high affinity and high specificity toward gold even after only a single round of separation. The amino acid profile of the resulting isolates was analyzed to provide a better understanding of the distinctive attributes of peptides that contribute to their specific material-binding capabilities. Next, the microfluidic system was utilized to screen soil microbes, a rich source of extremely diverse microorganisms, successfully isolating many naturally occurring microorganisms that show strong and specific binding to gold. The results show that the developed microfluidic platform is a powerful screening tool for identifying microorganisms that specifically bind to a target material surface of interest, which can greatly accelerate the development of new peptide-driven biological materials and hybrid organic-inorganic materials.
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Affiliation(s)
- Song-I Han
- Department
of Electrical and Computer Engineering, Texas A&M University, College
Station, Texas 77843, USA
| | - Deborah A. Sarkes
- Biotechnology
Branch, U.S. Army Combat Capabilities Development Command (DEVCOM), Army Research Laboratory (ARL), Adelphi, Maryland 20783, USA
| | - Margaret M. Hurley
- Biotechnology
Branch, U.S. Army Combat Capabilities Development Command (DEVCOM), Army Research Laboratory (ARL), Adelphi, Maryland 20783, USA
| | - Rebecca Renberg
- Biotechnology
Branch, U.S. Army Combat Capabilities Development Command (DEVCOM), Army Research Laboratory (ARL), Adelphi, Maryland 20783, USA
| | - Can Huang
- Department
of Electrical and Computer Engineering, Texas A&M University, College
Station, Texas 77843, USA
| | - Yuwen Li
- Department
of Electrical and Computer Engineering, Texas A&M University, College
Station, Texas 77843, USA
| | - Justin P. Jahnke
- Biotechnology
Branch, U.S. Army Combat Capabilities Development Command (DEVCOM), Army Research Laboratory (ARL), Adelphi, Maryland 20783, USA
| | - James J. Sumner
- Biotechnology
Branch, U.S. Army Combat Capabilities Development Command (DEVCOM), Army Research Laboratory (ARL), Adelphi, Maryland 20783, USA
| | - Dimitra N. Stratis-Cullum
- Biotechnology
Branch, U.S. Army Combat Capabilities Development Command (DEVCOM), Army Research Laboratory (ARL), Adelphi, Maryland 20783, USA
| | - Arum Han
- Department
of Electrical and Computer Engineering, Texas A&M University, College
Station, Texas 77843, USA
- Department
of Biomedical Engineering, Texas A&M
University, College Station, Texas 77843, USA
- Department
of Chemical Engineering, Texas A&M University, College Station, Texas 77843, USA
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12
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Jarosova R, Woolfolk SK, Martinez-Rivera N, Jaeschke MW, Rosa-Molinar E, Tamerler C, Johnson MA. Spatiotemporal Imaging of Zinc Ions in Zebrafish Live Brain Tissue Enabled by Fluorescent Bionanoprobes. Molecules 2023; 28:molecules28052260. [PMID: 36903504 PMCID: PMC10005619 DOI: 10.3390/molecules28052260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/11/2023] [Accepted: 02/19/2023] [Indexed: 03/05/2023] Open
Abstract
The zebrafish is a powerful model organism to study the mechanisms governing transition metal ions within whole brain tissue. Zinc is one of the most abundant metal ions in the brain, playing a critical pathophysiological role in neurodegenerative diseases. The homeostasis of free, ionic zinc (Zn2+) is a key intersection point in many of these diseases, including Alzheimer's disease and Parkinson's disease. A Zn2+ imbalance can eventuate several disturbances that may lead to the development of neurodegenerative changes. Therefore, compact, reliable approaches that allow the optical detection of Zn2+ across the whole brain would contribute to our current understanding of the mechanisms that underlie neurological disease pathology. We developed an engineered fluorescence protein-based nanoprobe that can spatially and temporally resolve Zn2+ in living zebrafish brain tissue. The self-assembled engineered fluorescence protein on gold nanoparticles was shown to be confined to defined locations within the brain tissue, enabling site specific studies, compared to fluorescent protein-based molecular tools, which diffuse throughout the brain tissue. Two-photon excitation microscopy confirmed the physical and photometrical stability of these nanoprobes in living zebrafish (Danio rerio) brain tissue, while the addition of Zn2+ quenched the nanoprobe fluorescence. Combining orthogonal sensing methods with our engineered nanoprobes will enable the study of imbalances in homeostatic Zn2+ regulation. The proposed bionanoprobe system offers a versatile platform to couple metal ion specific linkers and contribute to the understanding of neurological diseases.
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Affiliation(s)
- Romana Jarosova
- Department of Chemistry and R.N. Adams Institute for Bioanalytical Chemistry, University of Kansas, Lawrence, KS 66045, USA
- UNESCO Laboratory of Environmental Electrochemistry, Department of Analytical Chemistry, Charles University, 12843 Prague 2, Czech Republic
| | - Sarah K. Woolfolk
- Institute for Bioengineering Research, University of Kansas, Lawrence, KS 66045, USA
- Bioengineering Program, University of Kansas, Lawrence, KS 66045, USA
| | - Noraida Martinez-Rivera
- Microscopy and Analytical Imaging Research Resource Core Laboratory, University of Kansas, Lawrence, KS 66045, USA
| | - Mathew W. Jaeschke
- Institute for Bioengineering Research, University of Kansas, Lawrence, KS 66045, USA
- Department of Mechanical Engineering, University of Kansas, Lawrence, KS 66045, USA
| | - Eduardo Rosa-Molinar
- Microscopy and Analytical Imaging Research Resource Core Laboratory, University of Kansas, Lawrence, KS 66045, USA
- Department of Pharmacology & Toxicology, University of Kansas, Lawrence, KS 66045, USA
| | - Candan Tamerler
- Institute for Bioengineering Research, University of Kansas, Lawrence, KS 66045, USA
- Bioengineering Program, University of Kansas, Lawrence, KS 66045, USA
- Department of Mechanical Engineering, University of Kansas, Lawrence, KS 66045, USA
- Correspondence: (M.A.J.); (C.T.)
| | - Michael A. Johnson
- Department of Chemistry and R.N. Adams Institute for Bioanalytical Chemistry, University of Kansas, Lawrence, KS 66045, USA
- Correspondence: (M.A.J.); (C.T.)
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13
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Biomedical applications of solid-binding peptides and proteins. Mater Today Bio 2023; 19:100580. [PMID: 36846310 PMCID: PMC9950531 DOI: 10.1016/j.mtbio.2023.100580] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/06/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
Over the past decades, solid-binding peptides (SBPs) have found multiple applications in materials science. In non-covalent surface modification strategies, solid-binding peptides are a simple and versatile tool for the immobilization of biomolecules on a vast variety of solid surfaces. Especially in physiological environments, SBPs can increase the biocompatibility of hybrid materials and offer tunable properties for the display of biomolecules with minimal impact on their functionality. All these features make SBPs attractive for the manufacturing of bioinspired materials in diagnostic and therapeutic applications. In particular, biomedical applications such as drug delivery, biosensing, and regenerative therapies have benefited from the introduction of SBPs. Here, we review recent literature on the use of solid-binding peptides and solid-binding proteins in biomedical applications. We focus on applications where modulating the interactions between solid materials and biomolecules is crucial. In this review, we describe solid-binding peptides and proteins, providing background on sequence design and binding mechanism. We then discuss their application on materials relevant for biomedicine (calcium phosphates, silicates, ice crystals, metals, plastics, and graphene). Although the limited characterization of SBPs still represents a challenge for their design and widespread application, our review shows that SBP-mediated bioconjugation can be easily introduced into complex designs and on nanomaterials with very different surface chemistries.
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14
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Lu Q, Zhang B, Sun M, Lu L, Chen B, Wong HH, Chan CH, Wu T, Huang B. Probing the affinity of noble metal nanoparticles to the segments of the SARS-CoV-2 spike protein. iScience 2023; 26:106110. [PMID: 36776935 PMCID: PMC9898944 DOI: 10.1016/j.isci.2023.106110] [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: 11/28/2022] [Revised: 12/16/2022] [Accepted: 01/28/2023] [Indexed: 02/05/2023] Open
Abstract
Currently, scientists have devoted great efforts to finding effective treatments to combat COVID-19 infections. Although noble metal nanoparticles are able to realize protein modifications, their interactions with the protein are still unclear from the atomic perspective. To supply a general understanding, in this work, we have carried out theoretical calculations to investigate the interaction between protein segments (RBD1, RBD2, RBD3) of SARS-Cov-2 spike protein and a series of noble metal (Au, Ag, Cu, Pd, Pt) surfaces regarding the binding strength, protein orientations, and electronic modulations. In particular, the Au surface has shown the strongest binding preferences for the protein segments, which induces electron transfer between the Au and receptor-binding domain (RBD) segments. This further leads to the polarization of segments for virus denaturation. This work has offered a direct visualization of protein interactions with noble metal surfaces from the atomic level, which will benefit anti-virus material developments in the future.
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Affiliation(s)
- Qiuyang Lu
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Baiyang Zhang
- Chinese International School, Hong Kong, Hong Kong, China
| | - Mingzi Sun
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Lu Lu
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Baian Chen
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Hon Ho Wong
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Cheuk Hei Chan
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Tong Wu
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Bolong Huang
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China,Research Centre for Carbon-Strategic Catalysis, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China,Corresponding author
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15
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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: 10] [Impact Index Per Article: 5.0] [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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16
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Hintzen KW, Simons C, Schaffrath K, Roessler G, Johnen S, Jakob F, Walter P, Schwaneberg U, Lohmann T. BioAdhere: tailor-made bioadhesives for epiretinal visual prostheses. Biomater Sci 2022; 10:3282-3295. [PMID: 35583519 DOI: 10.1039/d1bm01946e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Introduction: Visual prostheses, i.e. epiretinal stimulating arrays, are a promising therapy in treating retinal dystrophies and degenerations. In the wake of a new generation of devices, an innovative method for epiretinal fixation of stimulator arrays is required. We present the development of tailor-made bioadhesive peptides (peptesives) for fixating epiretinal stimulating arrays omitting the use of traumatic retinal tacks. Materials and methods: Binding motifs on the stimulating array (poly[chloro-p-xylylene] (Parylene C)) and in the extracellular matrix of the retinal surface (collagens I and IV, laminin, fibronectin) were identified. The anchor peptides cecropin A (CecA), KH1, KH2 (author's initials) and osteopontin (OPN) were genetically fused to reporter proteins to assess their binding behavior to coated microtiter plates via fluorescence-based assays. Domain Z (DZ) of staphylococcal protein A was used as a separator to generate a bioadhesive peptide. Following ISO 10993 "biological evaluation of medical materials", direct and non-direct cytotoxicity testing (L-929 and R28 retinal progenitor cells) was performed. Lastly, the fixating capabilities of the peptesives were tested in proof-of-principle experiments. Results: The generation of the bioadhesive peptide required evaluation of the N- and C-anchoring of investigated APs. The YmPh-CecA construct showed the highest activity on Parylene C in comparison with the wildtype phytase without the anchor peptide. eGFP-OPN was binding to all four investigated ECM proteins (collagen I, laminin > collagen IV, fibronectin). The strongest binding to collagen I was observed for eGFP-KH1, while the strongest binding to fibronectin was observed for eGFP-KH2. The selectivity of binding was checked by incubating eGFP-CecA and eGFP-OPN on ECM proteins and on Parylene C, respectively. Direct and non-direct cytotoxicity testing of the peptide cecropin-A-DZ-OPN using L-929 and R28 cells showed good biocompatibility properties. Proof-of-concept experiments in post-mortem rabbit eyes suggested an increased adhesion of CecA-DZ-OPN-coated stimulating arrays. Conclusion: This is the first study to prove the applicability and biocompatibility of peptesives for the fixation of macroscopic objects.
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Affiliation(s)
- Kai-Wolfgang Hintzen
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany.,DWI - Leibniz-Institute for Interactive Materials, Aachen, Germany
| | - Christian Simons
- DWI - Leibniz-Institute for Interactive Materials, Aachen, Germany
| | - Kim Schaffrath
- Department of Ophthalmology, RWTH Aachen University, Aachen, Germany.
| | - Gernot Roessler
- Department of Ophthalmology, RWTH Aachen University, Aachen, Germany.
| | - Sandra Johnen
- Department of Ophthalmology, RWTH Aachen University, Aachen, Germany.
| | - Felix Jakob
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany.,DWI - Leibniz-Institute for Interactive Materials, Aachen, Germany
| | - Peter Walter
- Department of Ophthalmology, RWTH Aachen University, Aachen, Germany.
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany.,DWI - Leibniz-Institute for Interactive Materials, Aachen, Germany
| | - Tibor Lohmann
- Department of Ophthalmology, RWTH Aachen University, Aachen, Germany.
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17
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Lee RV, Zareie HM, Sarikaya M. Chimeric Peptide-Based Biomolecular Constructs for Versatile Nucleic Acid Biosensing. ACS APPLIED MATERIALS & INTERFACES 2022; 14:23164-23181. [PMID: 35543419 DOI: 10.1021/acsami.2c03341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Nucleic acid biomarkers hold great potential as key indicators for the diagnosis and monitoring of diseases. Herein we design and implement bifunctional chimeric biomolecules composed of a solid-binding peptide (SBP) domain that specifically adsorbs onto solid sensor surfaces and a peptide nucleic acid (PNA) moiety that facilitates anchoring of antisense oligonucleotide (ASO) probes for the detection of nucleic acid targets. A gold-binding peptide, AuBP1, previously selected by directed evolution to specifically bind to gold, served as the basis for immobilizing nucleic acid probes onto gold substrates. Using surface plasmon resonance (SPR) spectroscopy and quartz crystal microbalance (QCM) analyses, we demonstrate the sequential biomolecular assembly of the heterofunctional solid-binding peptide-antisense oligomer (SBP-ASO) construct onto a sensor surface and the subsequent detection of DNA in an aqueous environment. The effect of steric hindrance on optimal probe assembly is observed, establishing that less packing density results in greater target capture efficacy. In addition, an adsorbed layer of chimeric solid-binding peptide-peptide nucleic acid (SBP-PNA) undergoes viscoelastic changes at the solid-liquid interface upon probe immobilization and DNA target capture, whereby the rigid biofunctional layer becomes more flexible. The dual nature of the chimeric construct is highly amenable to a variety of platforms allowing for both specific recognition and probe immobilization on the sensor surface, while the modular design of the solid-binding peptide-antisense oligonucleotide provides facile functionalization of a wide diversity of solid substrates.
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Affiliation(s)
- Richard V Lee
- GEMSEC, Genetically Engineered Materials Science and Engineering Center, Department of Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Hadi M Zareie
- GEMSEC, Genetically Engineered Materials Science and Engineering Center, Department of Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Mehmet Sarikaya
- GEMSEC, Genetically Engineered Materials Science and Engineering Center, Department of Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
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18
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Janairo JIB. A Machine Learning Classification Model for Gold-Binding Peptides. ACS OMEGA 2022; 7:14069-14073. [PMID: 35559171 PMCID: PMC9089360 DOI: 10.1021/acsomega.2c00640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/31/2022] [Indexed: 06/15/2023]
Abstract
There has been growing interest in using peptides for the controlled synthesis of nanomaterials. Peptides play a crucial role not only in regulating the nanostructure formation process but also in influencing the resulting properties of the nanomaterials. Leveraging machine learning (ML) in the biomimetic workflow is anticipated to accelerate peptide discovery, make the process more resource-efficient, and unravel associations among attributes that may be useful in peptide design. In this study, a binary ML classifier is formulated that was trained and tested on 1720 peptide examples. The support vector machine classifier uses Kidera factors to categorize peptides into one of two groups based on their binding ability. The classifier exhibits satisfactory performance, as demonstrated by various performance metrics. In addition, key variables that bear a huge impact on the model were identified, such as peptide hydrophobicity. As these trends were derived from a large and diverse dataset, the insights drawn from the data are expected to be generalizable and robust. Thus, the presented ML model is an important step toward the rational and predictive peptide design.
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19
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Hughes ZE, Nguyen MA, Wang J, Liu Y, Swihart MT, Poloczek M, Frazier PI, Knecht MR, Walsh TR. Tuning Materials-Binding Peptide Sequences toward Gold- and Silver-Binding Selectivity with Bayesian Optimization. ACS NANO 2021; 15:18260-18269. [PMID: 34747170 DOI: 10.1021/acsnano.1c07298] [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: 06/13/2023]
Abstract
Peptide sequence engineering can potentially deliver materials-selective binding capabilities, which would be highly attractive in numerous biotic and abiotic nanomaterials applications. However, the number of known materials-selective peptide sequences is small, and identification of new sequences is laborious and haphazard. Previous attempts have sought to use machine learning and other informatics approaches that rely on existing data sets to accelerate the discovery of materials-selective peptides, but too few materials-selective sequences are known to enable reliable prediction. Moreover, this knowledge base is expensive to expand. Here, we combine a comprehensive and integrated experimental and modeling effort and introduce a Bayesian Effective Search for Optimal Sequences (BESOS) approach to address this challenge. Through this combined approach, we significantly expand the data set of Au-selective peptide sequences and identify an additional Ag-selective peptide sequence. Analysis of the binding motifs for the Ag-binders offers a roadmap for future prediction with machine learning, which should guide identification of further Ag-selective sequences. These discoveries will enable wider and more versatile integration of Ag nanoparticles in biological platforms.
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Affiliation(s)
- Zak E Hughes
- Institute for Frontier Materials, Deakin University, Geelong, 3216 VIC, Australia
| | | | - Jialei Wang
- School of Operations Research and Information Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Yang Liu
- Department of Chemical and Biological Engineering, University at Buffalo (SUNY), Buffalo, New York 14260, United States
| | - Mark T Swihart
- Department of Chemical and Biological Engineering, University at Buffalo (SUNY), Buffalo, New York 14260, United States
| | - Matthias Poloczek
- School of Operations Research and Information Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Peter I Frazier
- School of Operations Research and Information Engineering, Cornell University, Ithaca, New York 14853, United States
| | | | - Tiffany R Walsh
- Institute for Frontier Materials, Deakin University, Geelong, 3216 VIC, Australia
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20
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Yucesoy D, Akkineni S, Tamerler C, Hinds BJ, Sarikaya M. Solid-Binding Peptide-Guided Spatially Directed Immobilization of Kinetically Matched Enzyme Cascades in Membrane Nanoreactors. ACS OMEGA 2021; 6:27129-27139. [PMID: 34693133 PMCID: PMC8529655 DOI: 10.1021/acsomega.1c03774] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 09/20/2021] [Indexed: 05/08/2023]
Abstract
Biocatalysis is a useful strategy for sustainable green synthesis of fine chemicals due to its high catalytic rate, reaction specificity, and operation under ambient conditions. Addressable immobilization of enzymes onto solid supports for one-pot multistep biocatalysis, however, remains a major challenge. In natural pathways, enzymes are spatially coupled to prevent side reactions, eradicate inhibitory products, and channel metabolites sequentially from one enzyme to another. Construction of a modular immobilization platform enabling spatially directed assembly of multiple biocatalysts would, therefore, not only allow the development of high-efficiency bioreactors but also provide novel synthetic routes for chemical synthesis. In this study, we developed a modular cascade flow reactor using a generalizable solid-binding peptide-directed immobilization strategy that allows selective immobilization of fusion enzymes on anodic aluminum oxide (AAO) monoliths with high positional precision. Here, the lactate dehydrogenase and formate dehydrogenase enzymes were fused with substrate-specific peptides to facilitate their self-immobilization through the membrane channels in cascade geometry. Using this cascade model, two-step biocatalytic production of l-lactate is demonstrated with concomitant regeneration of soluble nicotinamide adenine dinucleotide (NADH). Both fusion enzymes retained their catalytic activity upon immobilization, suggesting their optimal display on the support surface. The 85% cascading reaction efficiency was achieved at a flow rate that kinetically matches the residence time of the slowest enzyme. In addition, 84% of initial catalytic activity was preserved after 10 days of continuous operation at room temperature. The peptide-directed modular approach described herein is a highly effective strategy to control surface orientation, spatial localization, and loading of multiple enzymes on solid supports. The implications of this work provide insight for the single-step construction of high-power cascadic devices by enabling co-expression, purification, and immobilization of a variety of engineered fusion enzymes on patterned surfaces.
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Affiliation(s)
- Deniz
T. Yucesoy
- Department
of Bioengineering, Izmir Institute of Technology, Urla, Izmir 35430, Turkey
| | - Susrut Akkineni
- Department
of Materials Science and Engineering, University
of Washington, Seattle, Washington 98195, United States
| | - Candan Tamerler
- Department
of Mechanical Engineering, Institute for Bioengineering Research, University of Kansas, Lawrence, Kansas 66045, United States
| | - Bruce J. Hinds
- Department
of Materials Science and Engineering, University
of Washington, Seattle, Washington 98195, United States
| | - Mehmet Sarikaya
- Department
of Materials Science and Engineering, University
of Washington, Seattle, Washington 98195, United States
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21
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Olagunju MO, Liu Y, Frenkel AI, Knecht MR. Atomically Resolved Characterization of Optically Driven Ligand Reconfiguration on Nanoparticle Catalyst Surfaces. ACS APPLIED MATERIALS & INTERFACES 2021; 13:44302-44311. [PMID: 34499467 DOI: 10.1021/acsami.1c11256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Dynamic ligand layers on nanoparticle surfaces could prove to be critically important to enhance the functionality of individual materials. Such capabilities could complement the properties of the inorganic component to provide multifunctionality or the ability to be remotely actuated. Peptide-based ligands have demonstrated the ability to be remotely responsive to structural changes when adsorbed to nanoparticle surfaces via incorporation of photoswitches into their molecular structure. In this contribution, direct spectroscopic evidence of the remote actuation of a photoswitchable peptide adsorbed onto Au nanoparticles is demonstrated using X-ray absorption fine structure spectroscopic methods. From this analysis, Au-X (X = C or N) coordination numbers confirm the changes before and after photoswitching in the surface ligand conformation, which was correlated directly to variations in the catalytic application of the materials for nitrophenol reduction processes. In addition, the catalytic application of the materials was demonstrated to be significantly sensitive to the structure of the nitrophenol substrate used in the reaction, suggesting that changes in the reactivity are likely based upon the peptide conformation and substrate structure. Such results confirm that surface ligands can be remotely reconfigured on nanoparticle surfaces, providing pathways to apply such capabilities to a variety of applications beyond catalysis ranging from drug delivery to sensing.
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Affiliation(s)
- Mary O Olagunju
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146, United States
| | - Yang Liu
- Department of Materials Science and Chemical Engineering, Stony Brook University, Stony Brook, New York 11794, United States
| | - Anatoly I Frenkel
- Department of Materials Science and Chemical Engineering, Stony Brook University, Stony Brook, New York 11794, United States
- Chemistry Division, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - 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 7th Avenue, Suite 475, Miami, Florida 33136, United States
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22
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Suyetin M, Bag S, Anand P, Borkowska-Panek M, Gußmann F, Brieg M, Fink K, Wenzel W. Modelling peptide adsorption energies on gold surfaces with an effective implicit solvent and surface model. J Colloid Interface Sci 2021; 605:493-499. [PMID: 34371421 DOI: 10.1016/j.jcis.2021.07.090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 07/15/2021] [Accepted: 07/16/2021] [Indexed: 01/23/2023]
Abstract
The interaction of proteins and peptides with inorganic surfaces is relevant in a wide array of technological applications. A rational approach to design peptides for specific surfaces would build on amino-acid and surface specific interaction models, which are difficult to characterize experimentally or by modeling. Even with such a model at hand, the large number of possible sequences and the large conformation space of peptides make comparative simulations challenging. Here we present a computational protocol, the effective implicit surface model (EISM), for efficient in silico evaluation of the binding affinity trends of peptides on parameterized surface, with a specific application to the widely studied gold surface. In EISM the peptide surface interactions are modeled with an amino-acid and surface specific implicit solvent model, which permits rapid exploration of the peptide conformational degrees of freedom. We demonstrate the parametrization of the model and compare the results with all-atom simulations and experimental results for specific peptides.
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Affiliation(s)
- Mikhail Suyetin
- Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Saientan Bag
- Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Priya Anand
- Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Monika Borkowska-Panek
- Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Florian Gußmann
- Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Martin Brieg
- Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Karin Fink
- Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Wolfgang Wenzel
- Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany.
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23
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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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24
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Lee KZ, Basnayake Pussepitiyalage V, Lee YH, Loesch-Fries LS, Harris MT, Hemmati S, Solomon KV. Engineering Tobacco Mosaic Virus and Its Virus-Like-Particles for Synthesis of Biotemplated Nanomaterials. Biotechnol J 2021; 16:e2000311. [PMID: 33135368 DOI: 10.1002/biot.202000311] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/27/2020] [Indexed: 12/12/2022]
Abstract
Biomolecules are increasingly attractive templates for the synthesis of functional nanomaterials. Chief among them is the plant tobacco mosaic virus (TMV) due to its high aspect ratio, narrow size distribution, diverse biochemical functionalities presented on the surface, and compatibility with a number of chemical conjugations. These properties are also easily manipulated by genetic modification to enable the synthesis of a range of metallic and non-metallic nanomaterials for diverse applications. This article reviews the characteristics of TMV and related viruses, and their virus-like particle (VLP) derivatives, and how these may be manipulated to extend their use and function. A focus of recent efforts has been on greater understanding and control of the self-assembly processes that drive biotemplate formation. How these features have been exploited in engineering applications such as, sensing, catalysis, and energy storage are briefly outlined. While control of VLP surface features is well-established, fewer tools exist to control VLP self-assembly, which limits efforts to control template uniformity and synthesis of certain templated nanomaterials. However, emerging advances in synthetic biology, machine learning, and other fields promise to accelerate efforts to control template uniformity and nanomaterial synthesis enabling more widescale industrial use of VLP-based biotemplates.
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Affiliation(s)
- Kok Zhi Lee
- Agricultural & Biological Engineering, Purdue University, 225 S University St, West Lafayette, IN, 47907, USA
| | | | - Yu-Hsuan Lee
- School of Chemical Engineering, Purdue University, 480 W Stadium Ave, West Lafayette, IN, 47907, USA
| | - L Sue Loesch-Fries
- Department of Botany and Plant Pathology, Purdue University, 915 W State St, West Lafayette, IN, 47907, USA
| | - Michael T Harris
- School of Chemical Engineering, Purdue University, 480 W Stadium Ave, West Lafayette, IN, 47907, USA
| | - Shohreh Hemmati
- School of Chemical Engineering, Oklahoma State University, 420 Engineering North, Stillwater, OK, 74078, USA
| | - Kevin V Solomon
- Agricultural & Biological Engineering, Purdue University, 225 S University St, West Lafayette, IN, 47907, USA
- Laboratory of Renewable Resources Engineering (LORRE), Purdue University, 500 Central Drive, West Lafayette, IN, 47907, USA
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25
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Yuca E, Şahin Kehribar E, Şeker UÖŞ. Interaction of microbial functional amyloids with solid surfaces. Colloids Surf B Biointerfaces 2021; 199:111547. [PMID: 33385820 DOI: 10.1016/j.colsurfb.2020.111547] [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: 10/21/2020] [Revised: 12/16/2020] [Accepted: 12/18/2020] [Indexed: 10/22/2022]
Abstract
HYPOTHESIS Self-assembling protein subunits hold great potential as biomaterials with improved functions. Among the self-assembled protein structures functional amyloids are promising unique properties such as resistance to harsh physical and chemical conditions their mechanical strength, and ease of functionalization. Curli proteins, which are functional amyloids of bacterial biofilms can be programmed as intelligent biomaterials. EXPERIMENTS In order to obtain controllable curli based biomaterials for biomedical applications, and to understand role of each of the curli forming monomeric proteins (namely CsgA and CsgB from Escherichia coli) we characterized their binding kinetics to gold, hydroxyapatite, and silica surfaces. FINDINGS We demonstrated that CsgA, CsgB, and their equimolar mixture have different binding strengths for different surfaces. On hydroxyapatite and silica surfaces, CsgB is the crucial element that determines the final adhesiveness of the CsgA-CsgB mixture. On the gold surface, on the other hand, CsgA controls the behavior of the mixture. Those findings uncover the binding behavior of curli proteins CsgA and CsgB on different biomedically valuable surfaces to obtain a more precise control on their adhesion to a targeted surface.
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Affiliation(s)
- Esra Yuca
- Molecular Biology and Genetics Department, Yildiz Technical University, 34210 Istanbul, Turkey
| | - Ebru Şahin Kehribar
- UNAM-Institute of Materials Science and Nanotechnology, Bilkent University, TR-06800 Ankara, Turkey
| | - Urartu Özgür Şafak Şeker
- UNAM-Institute of Materials Science and Nanotechnology, Bilkent University, TR-06800 Ankara, Turkey.
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26
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Lawrence RL, Olagunju MO, Liu Y, Mahalingam K, Slocik JM, Naik RR, Frenkel AI, Knecht MR. Remote controlled optical manipulation of bimetallic nanoparticle catalysts using peptides. Catal Sci Technol 2021. [DOI: 10.1039/d1cy00189b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Remote optical manipulation of peptide ligands on bimetallic nanoparticle surfaces allows for tunable catalytic reactivity.
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Affiliation(s)
| | | | - Yang Liu
- Department of Materials Science and Chemical Engineering
- Stony Brook University
- Stony Brook
- USA
| | | | | | - Rajesh R. Naik
- Air Force Research Laboratory
- Wright-Patterson Air Force Base
- USA
| | - Anatoly I. Frenkel
- Department of Materials Science and Chemical Engineering
- Stony Brook University
- Stony Brook
- USA
- Chemistry Division
| | - Marc R. Knecht
- Department of Chemistry
- University of Miami
- Coral Gables
- USA
- Dr. J.T. Macdonald Foundation Biomedical Nanotechnology Institute
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27
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Kuang Z, Singh KM, Oliver DJ, Dennis PB, Perry CC, Naik RR. Gamma estimator of Jarzynski equality for recovering binding energies from noisy dynamic data sets. Nat Commun 2020; 11:5517. [PMID: 33139719 PMCID: PMC7606380 DOI: 10.1038/s41467-020-19233-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 09/28/2020] [Indexed: 11/26/2022] Open
Abstract
A fundamental problem in thermodynamics is the recovery of macroscopic equilibrated interaction energies from experimentally measured single-molecular interactions. The Jarzynski equality forms a theoretical basis in recovering the free energy difference between two states from exponentially averaged work performed to switch the states. In practice, the exponentially averaged work value is estimated as the mean of finite samples. Numerical simulations have shown that samples having thousands of measurements are not large enough for the mean to converge when the fluctuation of external work is above 4 kBT, which is easily observable in biomolecular interactions. We report the first example of a statistical gamma work distribution applied to single molecule pulling experiments. The Gibbs free energy of surface adsorption can be accurately evaluated even for a small sample size. The values obtained are comparable to those derived from multi-parametric surface plasmon resonance measurements and molecular dynamics simulations. Measuring interaction energies from experimentally measured single-molecular interactions is challenging. Here, the authors report a gamma work distribution applied to single molecule pulling events for estimating peptide absorption free energy.
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Affiliation(s)
- Zhifeng Kuang
- Air Force Research Laboratory, Wright-Patterson Air Force Base, OH, 45433, USA
| | - Kristi M Singh
- Air Force Research Laboratory, Wright-Patterson Air Force Base, OH, 45433, USA
| | - Daniel J Oliver
- Biomolecular and Materials Interface Research Group, Interdisciplinary Biomedical Research Centre, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK
| | - Patrick B Dennis
- Air Force Research Laboratory, Wright-Patterson Air Force Base, OH, 45433, USA
| | - Carole C Perry
- Biomolecular and Materials Interface Research Group, Interdisciplinary Biomedical Research Centre, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK
| | - Rajesh R Naik
- Air Force Research Laboratory, Wright-Patterson Air Force Base, OH, 45433, USA.
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28
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Gao Y, Liu Y, Yan R, Zhou J, Dong H, Hua X, Wang P. Bifunctional Peptide-Conjugated Gold Nanoparticles for Precise and Efficient Nucleus-Targeting Bioimaging in Live Cells. Anal Chem 2020; 92:13595-13603. [PMID: 32940455 DOI: 10.1021/acs.analchem.0c03476] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Real-time in situ imaging of organelles is increasingly important in modern biomedical analysis and diseases diagnosis. To realize this goal, organelle-targeting nanoparticles as one of the most commonly used technologies in subcellular sensing and imaging has attracted a lot of interest. The biocompatibility, specificity, and binding efficiency are especially critical for efficient organelle-targeting bioimaging. Gold nanoparticles (AuNPs) fabricated with bifunctional peptides constructed with both Au-binding affinity and nucleus-targeting ability were designed and examined for efficient nucleus-targeting bioimaging. Such a design is expected to achieve an oriented assembling of peptides by the medium of the Au-binding peptides specifically assembled on the surface of AuNPs, with the nucleus-targeting end open for accessibility. The bifunctional peptides showed strong binding affinity toward AuNPs and led to a binding capability ∼1.5 times higher than that of the bare nucleus-targeting peptides, ensuring good surface coverage of the nanoparticles for enhanced nucleus-targeting ability. Such fabricated AuNPs demonstrated over 90% cell viability after incubation for 24 h with HepG2 cells, which were highly biocompatible. Precise and efficient bioimaging of the nucleus was achieved for HepG2 cells by using the fabricated AuNPs as observed with a confocal laser scanning microscope, a dark-field/fluorescence microscope, and a transmission electron microscope. The high surface coverage and oriented binding pattern appeared to be a promising strategy for construction of organelle-targeting agencies.
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Affiliation(s)
- Yingying Gao
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Yueling Liu
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Rui Yan
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Jinfeng Zhou
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Hao Dong
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Xin Hua
- Key Laboratory of Advanced Materials, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Ping Wang
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, Saint Paul, Minnesota 55108, United States
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29
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Palanikumar L, Al-Hosani S, Kalmouni M, Saleh HO, Magzoub M. Hexokinase II-Derived Cell-Penetrating Peptide Mediates Delivery of MicroRNA Mimic for Cancer-Selective Cytotoxicity. Biochemistry 2020; 59:2259-2273. [PMID: 32491855 DOI: 10.1021/acs.biochem.0c00141] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Cancer cells are often characterized by elevated levels of mitochondrion-bound hexokinase II (HKII), which facilitates their survival, proliferation, and metastasis. Here, we have designed a cancer-selective cell-penetrating peptide (CPP) by covalently coupling a short penetration-accelerating sequence (PAS) to the mitochondrial membrane-binding N-terminal 15 amino acids of HKII (pHK). PAS-pHK mediates efficient cellular uptake and cytosolic delivery of a synthetic mimic of miR-126, a tumor suppressor miRNA downregulated in many malignancies. Following uptake by breast cancer MCF-7 cells, the CPP-miRNA conjugate is distributed throughout the cytosol and shows strong colocalization with mitochondria, where PAS-pHK induces depolarization of mitochondrial membrane potential, inhibition of metabolic activities, depletion of intracellular ATP levels, release of cytochrome c, and, finally, apoptosis. Concomitantly, the miR-126 cargo synergistically enhances the anticancer effects of PAS-pHK. Importantly, the PAS-pHK-miR-126 conjugate is not toxic to noncancerous MCF-10A and HEK-93 cells. Our results demonstrate the potential of PAS-pHK-mediated delivery of miRNA mimics as a novel cancer-selective therapeutic strategy.
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Affiliation(s)
- L Palanikumar
- Biology Program, Division of Science, New York University Abu Dhabi, P.O. Box 129188, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| | - Sumaya Al-Hosani
- Biology Program, Division of Science, New York University Abu Dhabi, P.O. Box 129188, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| | - Mona Kalmouni
- Biology Program, Division of Science, New York University Abu Dhabi, P.O. Box 129188, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| | - Hadi Omar Saleh
- Biology Program, Division of Science, New York University Abu Dhabi, P.O. Box 129188, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| | - Mazin Magzoub
- Biology Program, Division of Science, New York University Abu Dhabi, P.O. Box 129188, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
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30
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Yucesoy DT, Khatayevich D, Tamerler C, Sarikaya M. Rationally designed chimeric solid‐binding peptides for tailoring solid interfaces. ACTA ACUST UNITED AC 2020. [DOI: 10.1002/mds3.10065] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Deniz T. Yucesoy
- GEMSEC Genetically Engineered Materials Science and Engineering Center University of Washington Seattle WA USA
- Department of Materials Science and Engineering University of Washington Seattle WA USA
| | - Dimitry Khatayevich
- GEMSEC Genetically Engineered Materials Science and Engineering Center University of Washington Seattle WA USA
- Department of Materials Science and Engineering University of Washington Seattle WA USA
| | - Candan Tamerler
- GEMSEC Genetically Engineered Materials Science and Engineering Center University of Washington Seattle WA USA
- Department of Materials Science and Engineering University of Washington Seattle WA USA
- Department of Mechanical Engineering Bioengineering Program Institute for Bioengineering Research University of Kansas Lawrence Lawrence KS USA
| | - Mehmet Sarikaya
- GEMSEC Genetically Engineered Materials Science and Engineering Center University of Washington Seattle WA USA
- Department of Materials Science and Engineering University of Washington Seattle WA USA
- Department of Chemical Engineering University of Washington Seattle WA USA
- Department of Oral Health Sciences University of Washington Seattle WA USA
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31
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Elucidating the Binding Mechanism of a Novel Silica-Binding Peptide. Biomolecules 2019; 10:biom10010004. [PMID: 31861313 PMCID: PMC7022404 DOI: 10.3390/biom10010004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 12/15/2019] [Accepted: 12/16/2019] [Indexed: 12/18/2022] Open
Abstract
Linker-protein G (LPG) is a bifunctional fusion protein composed of a solid-binding peptide (SBP, referred as the "linker") with high affinity to silica-based compounds and a Streptococcus protein G (PG), which binds antibodies. The binding mechanisms of LPG to silica-based materials was studied using different biophysical techniques and compared to that of PG without the linker. LPG displayed high binding affinity to a silica surface (KD = 34.77 ± 11.8 nM), with a vertical orientation, in comparison to parent PG, which exhibited no measurable binding affinity. Incorporation of the linker in the fusion protein, LPG, had no effect on the antibody-binding function of PG, which retained its secondary structure and displayed no alteration of its chemical stability. The LPG system provided a milder, easier, and faster affinity-driven immobilization of antibodies to inorganic surfaces when compared to traditional chemical coupling techniques.
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32
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Dedisch S, Wiens A, Davari MD, Söder D, Rodriguez‐Emmenegger C, Jakob F, Schwaneberg U. Matter‐
tag
: A universal immobilization platform for enzymes on polymers, metals, and silicon‐based materials. Biotechnol Bioeng 2019; 117:49-61. [DOI: 10.1002/bit.27181] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 09/19/2019] [Accepted: 09/20/2019] [Indexed: 01/02/2023]
Affiliation(s)
- Sarah Dedisch
- DWI – Leibniz‐Institute for Interactive MaterialsAachen Germany
- Lehrstuhl für BiotechnologieRWTH Aachen UniversityAachen Germany
| | - Annika Wiens
- Lehrstuhl für BiotechnologieRWTH Aachen UniversityAachen Germany
| | - Mehdi D. Davari
- Lehrstuhl für BiotechnologieRWTH Aachen UniversityAachen Germany
| | - Dominik Söder
- DWI – Leibniz‐Institute for Interactive MaterialsAachen Germany
| | - Cesar Rodriguez‐Emmenegger
- DWI – Leibniz‐Institute for Interactive MaterialsAachen Germany
- Institute of Technical and Macromolecular ChemistryRWTH Aachen UniversityAachen Germany
| | - Felix Jakob
- DWI – Leibniz‐Institute for Interactive MaterialsAachen Germany
- Lehrstuhl für BiotechnologieRWTH Aachen UniversityAachen Germany
| | - Ulrich Schwaneberg
- DWI – Leibniz‐Institute for Interactive MaterialsAachen Germany
- Lehrstuhl für BiotechnologieRWTH Aachen UniversityAachen Germany
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33
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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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34
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Sokullu E, Soleymani Abyaneh H, Gauthier MA. Plant/Bacterial Virus-Based Drug Discovery, Drug Delivery, and Therapeutics. Pharmaceutics 2019; 11:E211. [PMID: 31058814 PMCID: PMC6572107 DOI: 10.3390/pharmaceutics11050211] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 04/23/2019] [Accepted: 04/25/2019] [Indexed: 02/06/2023] Open
Abstract
Viruses have recently emerged as promising nanomaterials for biotechnological applications. One of the most important applications of viruses is phage display, which has already been employed to identify a broad range of potential therapeutic peptides and antibodies, as well as other biotechnologically relevant polypeptides (including protease inhibitors, minimizing proteins, and cell/organ targeting peptides). Additionally, their high stability, easily modifiable surface, and enormous diversity in shape and size, distinguish viruses from synthetic nanocarriers used for drug delivery. Indeed, several plant and bacterial viruses (e.g., phages) have been investigated and applied as drug carriers. The ability to remove the genetic material within the capsids of some plant viruses and phages produces empty viral-like particles that are replication-deficient and can be loaded with therapeutic agents. This review summarizes the current applications of plant viruses and phages in drug discovery and as drug delivery systems and includes a discussion of the present status of virus-based materials in clinical research, alongside the observed challenges and opportunities.
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Affiliation(s)
- Esen Sokullu
- Institut National de la Recherche Scientifique (INRS), EMT Research Center, Varennes, QC J3X 1S2, Canada.
| | - Hoda Soleymani Abyaneh
- Institut National de la Recherche Scientifique (INRS), EMT Research Center, Varennes, QC J3X 1S2, Canada.
| | - Marc A Gauthier
- Institut National de la Recherche Scientifique (INRS), EMT Research Center, Varennes, QC J3X 1S2, Canada.
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35
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Mao CM, Sampath J, Sprenger KG, Drobny G, Pfaendtner J. Molecular Driving Forces in Peptide Adsorption to Metal Oxide Surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:5911-5920. [PMID: 30955325 DOI: 10.1021/acs.langmuir.8b01392] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Molecular recognition between peptides and metal oxide surfaces is a fundamental process in biomineralization, self-assembly, and biocompatibility. Yet, the underlying driving forces and dominant mechanisms remain unclear, bringing obstacles to understand and control this process. To elucidate the mechanism of peptide/surface recognition, specifically the role of serine phosphorylation, we employed molecular dynamics simulation and metadynamics-enhanced sampling to study five artificial peptides, DDD, DSS, DpSpS, DpSpSGKK, and DpSKGpSK, interacting with two surfaces: rutile TiO2 and quartz SiO2. On both surfaces, we observe that phosphorylation increases the binding energy. However, the interfacial peptide conformation reveals a distinct binding mechanism on each surface. We also study the impact of peptide sequence to binding free energy and interfacial conformation on both surfaces, specifically the impact on the behavior of phosphorylated serine. Finally, the results are discussed in context of prior studies investigating the role of serine phosphorylation in peptide binding to silica.
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36
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YUCA ESRA, TAMERLER CANDAN. Self Assembled Recombinant Proteins on Metallic Nanoparticles As Bimodal Imaging Probes. JOM (WARRENDALE, PA. : 1989) 2019; 71:1281-1290. [PMID: 34149269 PMCID: PMC8211090 DOI: 10.1007/s11837-018-03325-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 12/28/2018] [Indexed: 05/12/2023]
Abstract
Combining multiple modalities is at the center of developing new methods for sensing and imaging that are required for comprehensive understanding of events at the molecular level. Various imaging modalities have been developed using metallic nanoparticles owning to their exceptional physical and chemical properties. Due to their localized surface plasmon resonance characteristics, gold and silver nanoparticles exhibit unique optoelectronic properties commonly used in biomedical sciences and engineering. Self assembled monolayers or physical adsorption have previously been adapted to functionalize the surfaces of nanoparticles with biomolecules for targeted imaging. However, depending on differences among the functional groups used on the nanoparticle surface, wide variation in the displayed biomolecular property to recognize its target may result. In the last decade, the properties of inorganic binding peptides have been proven advantageous to assemble selective functional nano-entities or proteins onto nanoparticles surfaces. Herein we explored formation of self-assembled hybrid metallic nano-architectures that are composed of gold and silver nanoparticles with fluorescent proteins, for use as bimodal imaging probes. We employed metal binding peptide-based assembly to self assemble green fluorescence protein onto metallic substrates of various geometries. Assembly of the green fluorescent proteins, genetically engineered to incorporate gold- or silver-binding peptides onto metallic nanoparticles, resulted in the generation of hybrid-, biomodal-imaging probes in a single step. Green fluorescent activity on gold and silver surfaces can be been monitored using both plasmonic and fluorescent signatures. Our results demonstrate a novel bimodal imaging system that can be finely tuned with respect to nanoparticle size and protein concentration. Resulting hybrid probes may mitigate the limitation of depth penetration into biological tissues as well as providing high signal-to-noise ratio and sensitivity.
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Affiliation(s)
- ESRA YUCA
- Institute for Bioengineering Research, University of Kansas, Lawrence-KS, 66045, USA
- Molecular Biology and Genetics, Yildiz Technical University, Istanbul 34210, Turkey
| | - CANDAN TAMERLER
- Institute for Bioengineering Research, University of Kansas, Lawrence-KS, 66045, USA
- Bioengineering Program, University of Kansas, Lawrence-KS, 66045, USA
- Mechanical Engineering, University of Kansas, Lawrence, KS 66045, USA
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37
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Hellner B, Lee SB, Subramaniam A, Subramanian VR, Baneyx F. Modeling the Cooperative Adsorption of Solid-Binding Proteins on Silica: Molecular Insights from Surface Plasmon Resonance Measurements. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:5013-5020. [PMID: 30869906 DOI: 10.1021/acs.langmuir.9b00283] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Combinatorially selected solid-binding peptides (SBPs) provide a versatile route for synthesizing advanced materials and devices, especially when they are installed within structurally or functionally useful protein scaffolds. However, their promise has not been fully realized because we lack a predictive understanding of SBP-material interactions. Thermodynamic and kinetic binding parameters obtained by fitting quartz crystal microbalance and surface plasmon resonance (SPR) data with the Langmuir model whose assumptions are rarely satisfied provide limited information on underpinning molecular interactions. Using SPR, we show here that a technologically useful SBP called Car9 confers proteins to which is fused a sigmoidal adsorption behavior modulated by partner identity, quaternary structure, and ionic strength. We develop a two-step cooperative model that accurately captures the kinetics of silica binding and provides insights into how SBP-SBP interactions, fused scaffold, and solution conditions modulate adsorption. Because cooperative binding can be converted to Langmuir adhesion by mutagenesis, our approach offers a path to identify and to better understand and design practically useful SBPs.
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Affiliation(s)
- Brittney Hellner
- Department of Chemical Engineering , University of Washington , Box 351750 Seattle , 98195 Washington , United States
| | - Seong Beom Lee
- Department of Chemical Engineering , University of Washington , Box 351750 Seattle , 98195 Washington , United States
| | - Akshay Subramaniam
- Department of Chemical Engineering , University of Washington , Box 351750 Seattle , 98195 Washington , United States
| | - Venkat R Subramanian
- Department of Chemical Engineering , University of Washington , Box 351750 Seattle , 98195 Washington , United States
| | - François Baneyx
- Department of Chemical Engineering , University of Washington , Box 351750 Seattle , 98195 Washington , United States
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38
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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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39
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Tang M, Gandhi NS, Burrage K, Gu Y. Adsorption of Collagen-like Peptides onto Gold Nanosurfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:4435-4444. [PMID: 30864812 DOI: 10.1021/acs.langmuir.8b03680] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The molecular behavior of proteins in the presence of inorganic surfaces is of fundamental biological significance. Examples include extracellular matrix proteins interacting with gold nanoparticles and metallic implant biomaterials, such as titanium and stainless steels. Uncharged inorganic surfaces that interact strongly with the solution phase (hydrophilic surfaces) have been commonly used in disease treatments. A deep understanding of the molecular behavior of body proteins in the presence of hydrophilic surfaces is important in terms of clinical applications. However, the adsorption mechanism of proteins onto hydrophilic surfaces remains not fully understood. Here, comprehensive molecular dynamics simulations are carried out to study the molecular response of a human collagen molecule segment (CMS) to the presence of a planar gold surface (AuNS) in explicit solvent, aiming to unravel the adsorption mechanism of proteins onto hydrophilic surfaces. The results demonstrate that in the presence of AuNS, the CMS first biasedly diffuses toward AuNS, followed by anchoring to the gold surface, and finally adsorbs stepwise onto AuNS, where the protein adjusts its structure to maximize the interaction with AuNS. We conclude that adsorption of proteins onto hydrophilic surfaces adheres to three steps, namely, biased diffusion, anchoring, and stepwise adsorption accompanied by structural adaptation. The obtained adsorption mechanism provides insights into the development of inorganic surfaces for biomedical and therapeutic applications.
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40
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Conformational rearrangements in n-alkanes encapsulated within capsular self-assembly of capped carbon nanotubes. Chem Phys 2019. [DOI: 10.1016/j.chemphys.2018.10.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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41
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Lee N, Lee DW, Lee SM. Gold Nanoparticle-Stabilized, Tyrosine-Rich Peptide Self-Assemblies and Their Catalytic Activities in the Reduction of 4-Nitrophenol. Biomacromolecules 2018; 19:4534-4541. [DOI: 10.1021/acs.biomac.8b01221] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Namhun Lee
- Super Ultra Low Energy and Emission Vehicle (SULEEV) Center, Korea University, Anam-ro 145, Seongbuk-gu, Seoul 02841, Republic of Korea
- Department of Chemical Engineering, Division of Chemical and Biological Engineering, Kangwon National University, Gangwon-Do 24341, Republic of Korea
| | - Dae-Won Lee
- Department of Chemical Engineering, Division of Chemical and Biological Engineering, Kangwon National University, Gangwon-Do 24341, Republic of Korea
| | - Sang-Myung Lee
- Department of Chemical Engineering, Division of Chemical and Biological Engineering, Kangwon National University, Gangwon-Do 24341, Republic of Korea
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42
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43
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Lawrence RL, Hughes ZE, Cendan VJ, Liu Y, Lim CK, Prasad PN, Swihart MT, Walsh TR, Knecht MR. Optical Control of Nanoparticle Catalysis Influenced by Photoswitch Positioning in Hybrid Peptide Capping Ligands. ACS APPLIED MATERIALS & INTERFACES 2018; 10:33640-33651. [PMID: 30185023 DOI: 10.1021/acsami.8b10582] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Here, we present an in-depth analysis of structural factors that modulate peptide-capped nanoparticle catalytic activity via optically driven structural reconfiguration of the biointerface present at the particle surface. Six different sets of peptide-capped Au nanoparticles were prepared, in which an azobenzene photoswitch was incorporated into one of two well-studied peptide sequences with known affinity for Au, each at one of three different positions: the N- or C-terminus or mid-sequence. Changes in the photoswitch isomerization state induce a reversible structural change in the surface-bound peptide, which modulates the catalytic activity of the material. This control of reactivity is attributed to changes in the amount of accessible metallic surface area available to drive the reaction. This research specifically focuses on the effect of the peptide sequence and photoswitch position in the biomolecule, from which potential target systems for on/off reactivity have been identified. Additionally, trends associated with photoswitch position for a peptide sequence (Pd4) have been identified. Integrating the azobenzene at the N-terminus or central region results in nanocatalysts with greater reactivity in the trans and cis conformations, respectively, however, positioning the photoswitch at the C-terminus gives rise to a unique system that is reactive in the trans conformation and partially deactivated in the cis conformation. These results provide a fundamental basis for new directions in nanoparticle catalyst development to control activity in real time, which could have significant implications in the design of catalysts for multistep reactions using a single catalyst. Additionally, such a fine level of interfacial structural control could prove to be important for applications beyond catalysis, including biosensing, photonics, and energy technologies that are highly dependent on particle surface structures.
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Affiliation(s)
- Randy L Lawrence
- Department of Chemistry , University of Miami , 1301 Memorial Drive , Coral Gables , Florida 33146 , United States
| | - Zak E Hughes
- Institute for Frontier Materials , Deakin University , Geelong , Victoria 3216 , Australia
| | - Vincent J Cendan
- Department of Chemistry , University of Miami , 1301 Memorial Drive , Coral Gables , Florida 33146 , United States
| | | | | | | | | | - 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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44
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Abstract
Redox enzymes, which catalyze reactions involving electron transfers in living organisms, are very promising components of biotechnological devices, and can be envisioned for sensing applications as well as for energy conversion. In this context, one of the most significant challenges is to achieve efficient direct electron transfer by tunneling between enzymes and conductive surfaces. Based on various examples of bioelectrochemical studies described in the recent literature, this review discusses the issue of enzyme immobilization at planar electrode interfaces. The fundamental importance of controlling enzyme orientation, how to obtain such orientation, and how it can be verified experimentally or by modeling are the three main directions explored. Since redox enzymes are sizable proteins with anisotropic properties, achieving their functional immobilization requires a specific and controlled orientation on the electrode surface. All the factors influenced by this orientation are described, ranging from electronic conductivity to efficiency of substrate supply. The specificities of the enzymatic molecule, surface properties, and dipole moment, which in turn influence the orientation, are introduced. Various ways of ensuring functional immobilization through tuning of both the enzyme and the electrode surface are then described. Finally, the review deals with analytical techniques that have enabled characterization and quantification of successful achievement of the desired orientation. The rich contributions of electrochemistry, spectroscopy (especially infrared spectroscopy), modeling, and microscopy are featured, along with their limitations.
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Rübsam K, Davari MD, Jakob F, Schwaneberg U. KnowVolution of the Polymer-Binding Peptide LCI for Improved Polypropylene Binding. Polymers (Basel) 2018; 10:E423. [PMID: 30966458 PMCID: PMC6415234 DOI: 10.3390/polym10040423] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 04/04/2018] [Accepted: 04/07/2018] [Indexed: 12/02/2022] Open
Abstract
The functionalization of polymer surfaces by polymer-binding peptides offers tremendous opportunities for directed immobilization of enzymes, bioactive peptides, and antigens. The application of polymer-binding peptides as adhesion promoters requires reliable and stable binding under process conditions. Molecular modes of interactions between material surfaces, peptides, and solvent are often not understood to an extent that enables (semi-) rational design of polymer-binding peptides, hindering the full exploitation of their potential. Knowledge-gaining directed evolution (KnowVolution) is an efficient protein engineering strategy that facilitates tailoring protein properties to application demands through a combination of directed evolution and computational guided protein design. A single round of KnowVolution was performed to gain molecular insights into liquid chromatography peak I peptide, 47 aa (LCI)-binding to polypropylene (PP) in the presence of the competing surfactant Triton X-100. KnowVolution yielded a total of 8 key positions (D19, S27, Y29, D31, G35, I40, E42, and D45), which govern PP-binding in the presence of Triton X-100. The recombination of two of the identified amino acid substitutions (Y29R and G35R; variant KR-2) yielded a 5.4 ± 0.5-fold stronger PP-binding peptide compared to LCI WT in the presence of Triton X-100 (1 mM). The LCI variant KR-2 shows a maximum binding capacity of 8.8 ± 0.1 pmol/cm² on PP in the presence of Triton X-100 (up to 1 mM). The KnowVolution approach enables the development of polymer-binding peptides, which efficiently coat and functionalize PP surfaces and withstand surfactant concentrations that are commonly used, such as in household detergents.
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Affiliation(s)
- Kristin Rübsam
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, D-52074 Aachen, Germany.
- DWI-Leibniz-Institute for Interactive Materials, Forckenbeckstrasse 50, D-52074 Aachen, Germany.
| | - Mehdi D Davari
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, D-52074 Aachen, Germany.
| | - Felix Jakob
- DWI-Leibniz-Institute for Interactive Materials, Forckenbeckstrasse 50, D-52074 Aachen, Germany.
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, D-52074 Aachen, Germany.
- DWI-Leibniz-Institute for Interactive Materials, Forckenbeckstrasse 50, D-52074 Aachen, Germany.
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46
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Schwaminger S, Blank‐Shim SA, Borkowska‐Panek M, Anand P, Fraga‐García P, Fink K, Wenzel W, Berensmeier S. Experimental characterization and simulation of amino acid and peptide interactions with inorganic materials. Eng Life Sci 2018; 18:84-100. [PMID: 32624891 PMCID: PMC6999452 DOI: 10.1002/elsc.201700019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 06/02/2017] [Accepted: 07/03/2017] [Indexed: 02/06/2023] Open
Abstract
Inspired by nature, many applications and new materials benefit from the interplay of inorganic materials and biomolecules. A fundamental understanding of complex organic-inorganic interactions would improve the controlled production of nanomaterials and biosensors to the development of biocompatible implants for the human body. Although widely exploited in applications, the interaction of amino acids and peptides with most inorganic surfaces is not fully understood. To date, precisely characterizing complex surfaces of inorganic materials and analyzing surface-biomolecule interactions remain challenging both experimentally and computationally. This article reviews several approaches to characterizing biomolecule-surface interactions and illustrates the advantages and disadvantages of the methods presented. First, we explain how the adsorption mechanism of amino acids/peptides to inorganic surfaces can be determined and how thermodynamic and kinetic process constants can be obtained. Second, we demonstrate how this data can be used to develop models for peptide-surface interactions. The understanding and simulation of such interactions constitute a basis for developing molecules with high affinity binding domains in proteins for bioprocess engineering and future biomedical technologies.
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Affiliation(s)
| | | | | | - Priya Anand
- Institute of NanotechnologyKarlsruhe Institute of TechnologyKarlsruheGermany
| | - Paula Fraga‐García
- Bioseparation Engineering GroupTechnical University of MunichMünchenGermany
| | - Karin Fink
- Institute of NanotechnologyKarlsruhe Institute of TechnologyKarlsruheGermany
| | - Wolfgang Wenzel
- Institute of NanotechnologyKarlsruhe Institute of TechnologyKarlsruheGermany
| | - Sonja Berensmeier
- Bioseparation Engineering GroupTechnical University of MunichMünchenGermany
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47
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Leader A, Mandler D, Reches M. The role of hydrophobic, aromatic and electrostatic interactions between amino acid residues and a titanium dioxide surface. Phys Chem Chem Phys 2018; 20:29811-29816. [DOI: 10.1039/c8cp05775c] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Understanding the nature of interactions between inorganic surfaces and biomolecules, such as amino acids and peptides, can enhance the development of new materials.
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Affiliation(s)
- Avia Leader
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology
- The Hebrew University of Jerusalem
- Edmond Safra Campus
- Jerusalem 919041
- Israel
| | - Daniel Mandler
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology
- The Hebrew University of Jerusalem
- Edmond Safra Campus
- Jerusalem 919041
- Israel
| | - Meital Reches
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology
- The Hebrew University of Jerusalem
- Edmond Safra Campus
- Jerusalem 919041
- Israel
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48
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Munro CJ, Knecht MR. Solution Effects on Peptide-Mediated Reduction and Stabilization of Au Nanoparticles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:13757-13765. [PMID: 29091728 DOI: 10.1021/acs.langmuir.7b01896] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Biomimetic methods for the preparation and application of inorganic nanomaterials represent a unique avenue to sustainably generating functional materials with long-term activity. Typically, for the fabrication of these structures, the peptide is mixed with metal ions in solution prior to the addition of an exogenous reductant such as NaBH4, leading to nanoparticle nucleation and growth. In biological systems, strong reductants such as NaBH4 are not available, thus different metal ion reduction methods must be exploited. Recent work has shown that the AuBP1 peptide (WAGAKRLVLRRE), a Au binding peptide with an N-terminal tryptophan, can spontaneously reduce Au3+ without an exogenous reductant. Remarkably, this system initially demonstrated the formation of large Au aggregates that disassemble to form individual Au nanoparticles, stabilized by the peptide bound to the inorganic surface. In this contribution, we demonstrate the significant effects of aqueous solvent-processing conditions (pH, ionic strength, and ion composition) on the rate of particle evolution. Understanding how such effects alter the metal ion reduction process and subsequent nanoparticle fabrication is important in controlling the final structure/function relationship of the resultant peptide-capped materials. This work identifies conditions that may enhance nanoparticle synthesis using biomimetic approaches where the peptide has complete control over the complexation, reduction, nucleation, and growth of nanomaterials.
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Affiliation(s)
- Catherine J Munro
- Department of Chemistry, University of Miami , 1301 Memorial Drive, Coral Gables, Florida 33146, United States
| | - Marc R Knecht
- Department of Chemistry, University of Miami , 1301 Memorial Drive, Coral Gables, Florida 33146, United States
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49
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Yagi S, Akanuma S, Kaji A, Niiro H, Akiyama H, Uchida T, Yamagishi A. Selection of a platinum-binding sequence in a loop of a four-helix bundle protein. J Biosci Bioeng 2017; 125:192-198. [PMID: 29050803 DOI: 10.1016/j.jbiosc.2017.09.006] [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: 04/07/2017] [Revised: 09/01/2017] [Accepted: 09/20/2017] [Indexed: 10/18/2022]
Abstract
Protein-metal hybrids are functional materials with various industrial applications. For example, a redox enzyme immobilized on a platinum electrode is a key component of some biofuel cells and biosensors. To create these hybrid materials, protein molecules are bound to metal surfaces. Here, we report the selection of a novel platinum-binding sequence in a loop of a four-helix bundle protein, the Lac repressor four-helix protein (LARFH), an artificial protein in which four identical α-helices are connected via three identical loops. We created a genetic library in which the Ser-Gly-Gln-Gly-Gly-Ser sequence within the first inter-helical loop of LARFH was semi-randomly mutated. The library was then subjected to selection for platinum-binding affinity by using the T7 phage display method. The majority of the selected variants contained the Tyr-Lys-Arg-Gly-Tyr-Lys (YKRGYK) sequence in their randomized segment. We characterized the platinum-binding properties of mutant LARFH by using quartz crystal microbalance analysis. Mutant LARFH seemed to interact with platinum through its loop containing the YKRGYK sequence, as judged by the estimated exclusive area occupied by a single molecule. Furthermore, a 10-residue peptide containing the YKRGYK sequence bound to platinum with reasonably high affinity and basic side chains in the peptide were crucial in mediating this interaction. In conclusion, we have identified an amino acid sequence, YKRGYK, in the loop of a helix-loop-helix motif that shows high platinum-binding affinity. This sequence could be grafted into loops of other polypeptides as an approach to immobilize proteins on platinum electrodes for use as biosensors among other applications.
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Affiliation(s)
- Sota Yagi
- Department of Applied Life Science, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Satoshi Akanuma
- Faculty of Human Sciences, Waseda University, 2-579-15 Mikajima, Tokorozawa, Saitama 359-1192, Japan
| | - Asumi Kaji
- Department of Applied Life Science, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Hiroya Niiro
- Department of Applied Life Science, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Hayato Akiyama
- Department of Applied Life Science, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Tatsuya Uchida
- Department of Applied Life Science, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Akihiko Yamagishi
- Department of Applied Life Science, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan.
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50
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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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