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Freitas AI, Domingues L, Aguiar TQ. Bare silica as an alternative matrix for affinity purification/immobilization of His-tagged proteins. Sep Purif Technol 2022. [DOI: 10.1016/j.seppur.2022.120448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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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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Ma J, Cai B, Zhang S, Jian T, De Yoreo JJ, Chen CL, Baneyx F. Nanoparticle-Mediated Assembly of Peptoid Nanosheets Functionalized with Solid-Binding Proteins: Designing Heterostructures for Hierarchy. NANO LETTERS 2021; 21:1636-1642. [PMID: 33555891 DOI: 10.1021/acs.nanolett.0c04285] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The fabrication of ordered architectures that intimately integrate polymer, protein, and inorganic components remains difficult. Two promising building blocks to tackle this challenge are peptoids, peptide mimics capable of self-assembly into well-defined structures, and solid-binding peptides, which offer a biological path to controlled inorganic assembly. Here, we report on the synthesis of 3.3-nm-thick thiol-reactive peptoid nanosheets from equimolar mixtures of unmodified and maleimide-derivatized versions of the Nbpe6Nce6 oligomer, optimize the location of engineered cysteine residues in silica-binding derivatives of superfolder green fluorescent protein for maleimide conjugation, and react the two components to form protein-peptoid hybrids exhibiting partial or uniform protein coverage on both of their sides. Using 10 nm silica nanoparticles, we trigger the stacking of these 2D structures into a multilayered material composed of alternating peptoid, protein, and organic layers. This simple and modular approach to hierarchical hybrid synthesis should prove useful in bioimaging and photocatalysis applications.
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Affiliation(s)
| | - Bin Cai
- Physical Sciences Division, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Shuai Zhang
- Physical Sciences Division, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Tengyue Jian
- Physical Sciences Division, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - James J De Yoreo
- Physical Sciences Division, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Chun-Long Chen
- Physical Sciences Division, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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Zhang X, Chen J, Li E, Hu C, Luo SZ, He C. Ultrahigh Adhesion Force Between Silica-Binding Peptide SB7 and Glass Substrate Studied by Single-Molecule Force Spectroscopy and Molecular Dynamic Simulation. Front Chem 2020; 8:600918. [PMID: 33330393 PMCID: PMC7729015 DOI: 10.3389/fchem.2020.600918] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/23/2020] [Indexed: 12/22/2022] Open
Abstract
Many proteins and peptides have been identified to effectively and specifically bind on certain surfaces such as silica, polystyrene and titanium dioxide. It is of great interest, in many areas such as enzyme immobilization, surface functionalization and nanotechnology, to understand how these proteins/peptides bind to solid surfaces. Here we use single-molecule force spectroscopy (SMFS) based on atomic force microscopy to directly measure the adhesion force between a silica-binding peptide SB7 and glass surface at single molecule level. SMFS results show that the adhesion force of a single SB7 detaching from the glass surface distributes in two populations at ~220 pN and 610 pN, which is higher than the unfolding forces of most mechanically stable proteins and the unbinding forces of most stable protein-protein interactions. Molecular dynamics simulation reveals that the electrostatic interactions between positively charged arginine residues and the silica surface dominates the binding of SB7 on silica. Our study provides experimental evidence and molecular mechanism at the single-molecule level for the SB7-based immobilization of proteins on silica-based surface, which is able to withstand high mechanical forces, making it an ideal fusion tag for silica surface immobilization or peptide-base adhesive materials.
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Affiliation(s)
- Xiaoxu Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijng, China
| | - Jialin Chen
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Enci Li
- State Key Laboratory of Precision Measuring Technology and Instrument, Tianjin University, Tianjin, China
| | - Chunguang Hu
- State Key Laboratory of Precision Measuring Technology and Instrument, Tianjin University, Tianjin, China
| | - Shi-Zhong Luo
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Chengzhi He
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijng, China
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Hellner B, Alamdari S, Pyles H, Zhang S, Prakash A, Sprenger KG, De Yoreo JJ, Baker D, Pfaendtner J, Baneyx F. Sequence–Structure–Binding Relationships Reveal Adhesion Behavior of the Car9 Solid-Binding Peptide: An Integrated Experimental and Simulation Study. J Am Chem Soc 2020; 142:2355-2363. [DOI: 10.1021/jacs.9b11617] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
| | | | | | - Shuai Zhang
- Physical Sciences Division, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | | | | | - James J. De Yoreo
- Physical Sciences Division, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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Carli S, Carneiro LABDC, Ward RJ, Meleiro LP. Immobilization of a β-glucosidase and an endoglucanase in ferromagnetic nanoparticles: A study of synergistic effects. Protein Expr Purif 2019; 160:28-35. [DOI: 10.1016/j.pep.2019.03.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 01/11/2019] [Accepted: 03/29/2019] [Indexed: 12/14/2022]
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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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Dunakey SJG, Coyle BL, Thomas A, Xu M, Swift BJF, Baneyx F. Selective Labeling and Decoration of the Ends and Sidewalls of Single-Walled Carbon Nanotubes Using Mono- and Bispecific Solid-Binding Fluorescent Proteins. Bioconjug Chem 2019; 30:959-965. [PMID: 30816696 DOI: 10.1021/acs.bioconjchem.9b00097] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Simple and robust strategies for the noncovalent functionalization of carbon nanostructures with proteins are of considerable interest in hybrid nanomaterials synthesis, part-to-part assembly, and biosensor development. Here, we show that fusion of the Car9 and Car15 carbon-binding peptides to the C-termini of the sfGFP and mCherry fluorescent proteins enables selective labeling of the ends or the sidewalls of single walled carbon nanotubes. By installing a gold-binding peptide or a single cysteine residue in carbon-binding variants of sfGFP, we further produce heterobifunctional solid-binding proteins that support the decoration of nanotubes sidewalls or termini with gold nanoparticles. The approach described here is generic and should prove useful for the controlled assembly of other hybrid materials.
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Affiliation(s)
- Sonja J G Dunakey
- Department of Chemical Engineering , University of Washington , Box 351750, Seattle , Washington 98195 , United States
| | - Brandon L Coyle
- Department of Chemical Engineering , University of Washington , Box 351750, Seattle , Washington 98195 , United States
| | - Alexander Thomas
- Department of Chemical Engineering , University of Washington , Box 351750, Seattle , Washington 98195 , United States
| | - Meng Xu
- Department of Chemical Engineering , University of Washington , Box 351750, Seattle , Washington 98195 , United States
| | - Brian J F Swift
- Department of Chemical Engineering , University of Washington , Box 351750, Seattle , Washington 98195 , United States
| | - François Baneyx
- Department of Chemical Engineering , University of Washington , Box 351750, Seattle , Washington 98195 , United States
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Imai K, Shimizu K, Kamimura M, Honda H. Interaction between porous silica gel microcarriers and peptides for oral administration of functional peptides. Sci Rep 2018; 8:10971. [PMID: 30030485 PMCID: PMC6054636 DOI: 10.1038/s41598-018-29345-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 07/05/2018] [Indexed: 11/26/2022] Open
Abstract
Functional peptides, peptides that have biological activities, have attracted attention as active ingredients of functional foods and health foods. In particular, for food applications, because orally ingested peptides are degraded by digestive enzymes in the stomach, novel oral administration methods that can prevent peptide degradation and successfully deliver them intestinally are desired. In the present study, we focused on porous silica gel, which has many useful characteristics, such as large surface area, pH responsive functional groups, size controllable pores, and approval as food additives. We investigated the possibility of using porous silica gel as a peptide degradation protective microcarrier. As a result, we found that heat treatment of the silica gel at 600 °C for 2 h remarkably enhanced the adsorbed amount of many peptides under acidic conditions, and negatively charged and highly hydrophobic peptides had suitable characteristics for oral intestinal delivery with silica gel. Finally, we demonstrated the degree of protection from pepsin degradation and found that the protection of DFELEDD peptide was 57.1 ± 3.9% when DFELEDD was mixed with the heat-treated silica gel. These results indicated that the heat-treated silica gel is promising for efficient oral intestinal delivery of hydrophobic negatively charged peptides.
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Affiliation(s)
- Kento Imai
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan
| | - Kazunori Shimizu
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan
| | - Mitsuhiro Kamimura
- Fuji Silysia Chemical Ltd., 1846, 2-Chome, Kozoji-Cho, Kasugai-Shi, Aichi, 487-0013, Japan
| | - Hiroyuki Honda
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan.
- Innovative Research Center for Preventive Medical Engineering, Nagoya University, Nagoya, 464-8601, Japan.
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Khoshnevisan K, Vakhshiteh F, Barkhi M, Baharifar H, Poor-Akbar E, Zari N, Stamatis H, Bordbar AK. Immobilization of cellulase enzyme onto magnetic nanoparticles: Applications and recent advances. MOLECULAR CATALYSIS 2017. [DOI: 10.1016/j.mcat.2017.09.006] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Affinity purification of Car9-tagged proteins on silica matrices: Optimization of a rapid and inexpensive protein purification technology. Protein Expr Purif 2017; 135:70-77. [DOI: 10.1016/j.pep.2017.05.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 05/11/2017] [Accepted: 05/11/2017] [Indexed: 11/21/2022]
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