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Optimized Silica-Binding Peptide-Mediated Delivery of Bactericidal Lysin Efficiently Prevents Staphylococcus aureus from Adhering to Device Surfaces. Int J Mol Sci 2021; 22:ijms222212544. [PMID: 34830425 PMCID: PMC8619460 DOI: 10.3390/ijms222212544] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/07/2021] [Accepted: 11/16/2021] [Indexed: 01/18/2023] Open
Abstract
Staphylococcal-associated device-related infections (DRIs) represent a significant clinical challenge causing major medical and economic sequelae. Bacterial colonization, proliferation, and biofilm formation after adherence to surfaces of the indwelling device are probably the primary cause of DRIs. To address this issue, we incorporated constructs of silica-binding peptide (SiBP) with ClyF, an anti-staphylococcal lysin, into functionalized coatings to impart bactericidal activity against planktonic and sessile Staphylococcus aureus. An optimized construct, SiBP1-ClyF, exhibited improved thermostability and staphylolytic activity compared to its parental lysin ClyF. SiBP1-ClyF-functionalized coatings were efficient in killing MRSA strain N315 (>99.999% within 1 h) and preventing the growth of static and dynamic S. aureus biofilms on various surfaces, including siliconized glass, silicone-coated latex catheter, and silicone catheter. Additionally, SiBP1-ClyF-immobilized surfaces supported normal attachment and growth of mammalian cells. Although the recycling potential and long-term stability of lysin-immobilized surfaces are still affected by the fragility of biological protein molecules, the present study provides a generic strategy for efficient delivery of bactericidal lysin to solid surfaces, which serves as a new approach to prevent the growth of antibiotic-resistant microorganisms on surfaces in hospital settings and could be adapted for other target pathogens as well.
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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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Kamathewatta NJB, Nguyen TM, Lietz R, Hughes T, Taktak Karaca B, Deay DO, Richter ML, Tamerler C, Berrie CL. Probing Selective Self-Assembly of Putrescine Oxidase with Controlled Orientation Using a Genetically Engineered Peptide Tag. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:7536-7547. [PMID: 34102059 DOI: 10.1021/acs.langmuir.1c01033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Controlling enzyme orientation and location on surfaces is a critical step for their successful deployment in diverse applications from biosensors to lab-on-a-chip devices. Functional activity of the enzymes on the surface will largely depend on the spatial arrangement and orientation. Solid binding peptides have been proven to offer versatility for immobilization of biomolecules on inorganic materials including metals, oxides, and minerals. Previously, we demonstrated the utility of a gold binding peptide genetically incorporated into the enzyme putrescine oxidase (PutOx-AuBP), enabling self-enzyme assembly on gold substrates. PutOx is an attractive biocatalyst among flavin oxidases, using molecular oxygen as an electron acceptor without requiring a dissociable coenzyme. Here, we explore the selective self-assembly of this enzyme on a range of surfaces using atomic force microscopy (AFM) along with the assessment of functional activity. This work probes the differences in surface coverage, distribution, size, shape, and activity of PutOx-AuBP in comparison to those of native putrescine oxidase (PutOx) on multiple surfaces to provide insight for material-selective enzymatic assembly. Surfaces investigated include metal (templated-stripped gold (TSG)), oxide (native SiO2 on Si(111)), minerals (mica and graphite), and self-assembled monolayers (SAMs) with a range of hydrophobicity and charge. Supported by both the coverage and the dimensions of immobilized enzymes, our results indicate that of the surfaces investigated, material-selective binding takes place with orientation control only for PutOx-AuBP onto the TSG substrate. These differences are consistent with the measurements of surface-bound enzymatic activities. Substrate-dependent differences observed indicate significant variations in enzyme-surface interactions ranging from peptide-directed self-assembly to enzyme aggregation. The implications of this study provide insight for the fabrication of enzymatic patterns directed by self-assembling peptide tags onto localized surface regions. Enabling functional enzyme-based nanoscale materials offers a fascinating path for utilization of sustainable biocatalysts integrated into multiscale devices.
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Affiliation(s)
| | - Tyler M Nguyen
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Rachel Lietz
- Institute for Bioengineering Research, University of Kansas, Lawrence, Kansas 66045, United States
| | - Talisa Hughes
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Banu Taktak Karaca
- Institute for Bioengineering Research, University of Kansas, Lawrence, Kansas 66045, United States
- Department of Electrical and Electronics Engineering, Istanbul Technical University, Istanbul 34469, Turkey
| | - Dwight O Deay
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, United States
| | - Mark L Richter
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, United States
| | - Candan Tamerler
- Institute for Bioengineering Research, University of Kansas, Lawrence, Kansas 66045, United States
- Bioengineering Program, University of Kansas, Lawrence, Kansas 66045, United States
- Department of Mechanical Engineering, University of Kansas, Lawrence, Kansas 66045, United States
| | - Cindy L Berrie
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
- Institute for Bioengineering Research, University of Kansas, Lawrence, Kansas 66045, United States
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Sarikaya R, Song L, Yuca E, Xie SX, Boone K, Misra A, Spencer P, Tamerler C. Bioinspired multifunctional adhesive system for next generation bio-additively designed dental restorations. J Mech Behav Biomed Mater 2021; 113:104135. [PMID: 33160267 PMCID: PMC8101502 DOI: 10.1016/j.jmbbm.2020.104135] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 07/17/2020] [Accepted: 10/07/2020] [Indexed: 12/16/2022]
Abstract
Resin-based composite has overtaken dental amalgam as the most popular material for the repair of lost or damaged tooth structure. In spite of the popularity, the average composite lifetime is about half that of amalgam restorations. The leading cause of composite-restoration failure is decay at the margin where the adhesive is applied. The adhesive is intended to seal the composite/tooth interface, but the adhesive seal to dentin is fragile and readily degraded by acids, enzymes and other oral fluids. The inherent weakness of this material system is attributable to several factors including the lack of antimicrobial properties, remineralization capabilities and durable mechanical performance - elements that are central to the integrity of the adhesive/dentin (a/d) interfacial seal. Our approach to this problem offers a transition from a hybrid to a biohybrid structure. Discrete peptides are tethered to polymers to provide multi-bio-functional adhesive formulations that simultaneously achieve antimicrobial and remineralization properties. The bio-additive materials design combines several functional properties with the goal of providing an adhesive that will serve as a durable barrier to recurrent decay at the composite/tooth interface. This article provides an overview of our multi-faceted approach which uses peptides tethered to polymers and new polymer chemistries to achieve the next generation adhesive system - an adhesive that provides antimicrobial properties, repair of defective dentin and enhanced mechanical performance.
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Affiliation(s)
- Rizacan Sarikaya
- Institute for Bioengineering Research (IBER), University of Kansas (KU), 1530 W. 15th St, Lawrence, KS, 66045, USA; Department of Mechanical Engineering, University of Kansas (KU), 1530 W. 15th St, Lawrence, KS, 66045, USA
| | - Linyong Song
- Institute for Bioengineering Research (IBER), University of Kansas (KU), 1530 W. 15th St, Lawrence, KS, 66045, USA
| | - Esra Yuca
- Institute for Bioengineering Research (IBER), University of Kansas (KU), 1530 W. 15th St, Lawrence, KS, 66045, USA; Department of Molecular Biology and Genetics, Yildiz Technical University, Istanbul, 34210, Turkey
| | - Sheng-Xue Xie
- Institute for Bioengineering Research (IBER), University of Kansas (KU), 1530 W. 15th St, Lawrence, KS, 66045, USA
| | - Kyle Boone
- Institute for Bioengineering Research (IBER), University of Kansas (KU), 1530 W. 15th St, Lawrence, KS, 66045, USA; Bioengineering Program, University of Kansas, 1530 W. 15th St, University of Kansas (KU), Lawrence, KS, 66045, USA
| | - Anil Misra
- Institute for Bioengineering Research (IBER), University of Kansas (KU), 1530 W. 15th St, Lawrence, KS, 66045, USA; Civil, Environmental and Architectural Engineering Department, University of Kansas (KU), 1530 W. 15th St, Lawrence, KS, 66045, USA
| | - Paulette Spencer
- Institute for Bioengineering Research (IBER), University of Kansas (KU), 1530 W. 15th St, Lawrence, KS, 66045, USA; Department of Mechanical Engineering, University of Kansas (KU), 1530 W. 15th St, Lawrence, KS, 66045, USA; Bioengineering Program, University of Kansas, 1530 W. 15th St, University of Kansas (KU), Lawrence, KS, 66045, USA
| | - Candan Tamerler
- Institute for Bioengineering Research (IBER), University of Kansas (KU), 1530 W. 15th St, Lawrence, KS, 66045, USA; Department of Mechanical Engineering, University of Kansas (KU), 1530 W. 15th St, Lawrence, KS, 66045, USA; Bioengineering Program, University of Kansas, 1530 W. 15th St, University of Kansas (KU), Lawrence, KS, 66045, USA.
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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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Care A, Petroll K, Gibson ESY, Bergquist PL, Sunna A. Solid-binding peptides for immobilisation of thermostable enzymes to hydrolyse biomass polysaccharides. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:29. [PMID: 28184244 PMCID: PMC5289021 DOI: 10.1186/s13068-017-0715-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 01/19/2017] [Indexed: 05/04/2023]
Abstract
BACKGROUND Solid-binding peptides (SBPs) bind strongly to a diverse range of solid materials without the need for any chemical reactions. They have been used mainly for the functionalisation of nanomaterials but little is known about their use for the immobilisation of thermostable enzymes and their feasibility in industrial-scale biocatalysis. RESULTS A silica-binding SBP sequence was fused genetically to three thermostable hemicellulases. The resulting enzymes were active after fusion and exhibited identical pH and temperature optima but differing thermostabilities when compared to their corresponding unmodified enzymes. The silica-binding peptide mediated the efficient immobilisation of each enzyme onto zeolite, demonstrating the construction of single enzyme biocatalytic modules. Cross-linked enzyme aggregates (CLEAs) of enzyme preparations either with or without zeolite immobilisation displayed greater activity retention during enzyme recycling than those of free enzymes (without silica-binding peptide) or zeolite-bound enzymes without any crosslinking. CLEA preparations comprising all three enzymes simultaneously immobilised onto zeolite enabled the formation of multiple enzyme biocatalytic modules which were shown to degrade several hemicellulosic substrates. CONCLUSIONS The current work introduced the construction of functional biocatalytic modules for the hydrolysis of simple and complex polysaccharides. This technology exploited a silica-binding SBP to mediate effectively the rapid and simple immobilisation of thermostable enzymes onto readily-available and inexpensive silica-based matrices. A conceptual application of biocatalytic modules consisting of single or multiple enzymes was validated by hydrolysing various hemicellulosic polysaccharides.
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Affiliation(s)
- Andrew Care
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), Macquarie University, Sydney, Australia
| | - Kerstin Petroll
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia
| | - Emily S. Y. Gibson
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia
| | - Peter L. Bergquist
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia
- Department of Molecular Medicine & Pathology, Medical School, University of Auckland, Auckland, New Zealand
- Biomolecular Discovery and Design Research Centre, Macquarie University, Sydney, Australia
| | - Anwar Sunna
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia
- Biomolecular Discovery and Design Research Centre, Macquarie University, Sydney, Australia
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Wright LB, Palafox-Hernandez JP, Rodger PM, Corni S, Walsh TR. Facet selectivity in gold binding peptides: exploiting interfacial water structure. Chem Sci 2015; 6:5204-5214. [PMID: 29449926 PMCID: PMC5669244 DOI: 10.1039/c5sc00399g] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 06/20/2015] [Indexed: 11/21/2022] Open
Abstract
Peptide sequences that can discriminate between gold facets under aqueous conditions offer a promising route to control the growth and organisation of biomimetically-synthesised gold nanoparticles. Knowledge of the interplay between sequence, conformations and interfacial properties is essential for predictable manipulation of these biointerfaces, but the structural connections between a given peptide sequence and its binding affinity remain unclear, impeding practical advances in the field. These structural insights, at atomic-scale resolution, are not easily accessed with experimental approaches, but can be delivered via molecular simulation. A current unmet challenge lies in forging links between predicted adsorption free energies derived from enhanced sampling simulations with the conformational ensemble of the peptide and the water structure at the surface. To meet this challenge, here we use an in situ combination of Replica Exchange with Solute Tempering with Metadynamics simulations to predict the adsorption free energy of a gold-binding peptide sequence, AuBP1, at the aqueous Au(111), Au(100)(1 × 1) and Au(100)(5 × 1) interfaces. We find adsorption to the Au(111) surface is stronger than to Au(100), irrespective of the reconstruction status of the latter. Our predicted free energies agree with experiment, and correlate with trends in interfacial water structuring. For gold, surface hydration is predicted as a chief determining factor in peptide-surface recognition. Our findings can be used to suggest how shaped seed-nanocrystals of Au, in partnership with AuBP1, could be used to control AuNP nanoparticle morphology.
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Affiliation(s)
- Louise B Wright
- Dept. of Chemistry , University of Warwick , Coventry , CV4 7AL , UK
| | | | - P Mark Rodger
- Dept. of Chemistry , University of Warwick , Coventry , CV4 7AL , UK
- Centre for Scientific Computing , University of Warwick , Coventry , CV4 7AL , UK .
| | - Stefano Corni
- Centro S3 CNR Istituto Nanoscienze , Modena , Italy .
| | - Tiffany R Walsh
- Institute for Frontier Materials , Deakin University , Geelong , 3216 , VIC , Australia .
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Solid-binding peptides: smart tools for nanobiotechnology. Trends Biotechnol 2015; 33:259-68. [PMID: 25796487 DOI: 10.1016/j.tibtech.2015.02.005] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 02/15/2015] [Accepted: 02/23/2015] [Indexed: 12/12/2022]
Abstract
Over the past decade, solid-binding peptides (SBPs) have been used increasingly as molecular building blocks in nanobiotechnology. These peptides show selectivity and bind with high affinity to the surfaces of a diverse range of solid materials including metals, metal oxides, metal compounds, magnetic materials, semiconductors, carbon materials, polymers, and minerals. They can direct the assembly and functionalisation of materials, and have the ability to mediate the synthesis and construction of nanoparticles and complex nanostructures. As the availability of newly synthesised nanomaterials expands rapidly, so too do the potential applications for SBPs.
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Yucesoy DT, Karaca BT, Cetinel S, Caliskan HB, Adali E, Gul-Karaguler N, Tamerler C. Direct bioelectrocatalysis at the interfaces by genetically engineered dehydrogenase. BIOINSPIRED BIOMIMETIC AND NANOBIOMATERIALS 2015. [DOI: 10.1680/bbn.14.00022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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10
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Abstract
Nanobio versus Bionano--what's in a name? This special Issue of Biotechnology Journal includes two sections, one featuring articles on nanobio, the other articles on bionano. The editors of the issue, François Baneyx and Je-Kyun Park, discuss the similarities and differences between the two in their editorial.
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