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Qiao Y, Wu G, Liu Z, He H, Tan W, Xu B. Assessment of the Enzymatic Dephosphorylation Kinetics in the Assemblies of a Phosphopentapeptide that Forms Intranuclear Nanoribbons. Biomacromolecules 2024; 25:1310-1318. [PMID: 38265878 PMCID: PMC11071069 DOI: 10.1021/acs.biomac.3c01288] [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] [Indexed: 01/26/2024]
Abstract
Although the formation of peptide assemblies catalyzed by alkaline phosphatase (ALP) has received increasing attention in inhibiting cancer cells, the detailed enzyme kinetics of the dephosphorylation of the corresponding phosphopeptide assemblies have yet to be determined. We recently discovered that assemblies from a phosphopentapeptide can form intracellular nanoribbons that kill induced pluripotent stem cells or osteosarcoma cells, but the kinetics of enzymatic dephosphorylation remain unknown. Thus, we chose to examine the enzyme kinetics of the dephosphorylation of the phosphopentapeptide [NBD-LLLLpY (1)] from concentrations below to above its critical micelle concentration (CMC). Our results show that the phosphopeptide exhibits a CMC of 75 μM in phosphate saline buffer, and the apparent Vmax and Km values of alkaline phosphatase catalyzed dephosphorylation are approximately 0.24 μM/s and 5.67 mM, respectively. Despite dephosphorylation remaining incomplete at 60 min in all the concentrations tested, dephosphorylation of the phosphopeptide at concentrations of 200 μM or above mainly results in nanoribbons, dephosphorylation at concentrations of CMC largely produces nanofibers, and dephosphorylation below the CMC largely generates nanoparticles. Moreover, the formation of nanoribbons correlates with the intranuclear accumulation of the pentapeptide. By providing the first examination of the enzymatic kinetics of phosphopeptide assemblies, this work further supports the notion that the assemblies of phosphopentapeptides can act as a new functional entity for controlling cell fates.
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Affiliation(s)
- Yuchen Qiao
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Grace Wu
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Zhiyu Liu
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Hongjian He
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Weiyi Tan
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Bing Xu
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
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2
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Sen S, Thaker A, Sirajudeen L, Williams D, Nannenga BL. Protein-Nanoparticle Complex Structure Determination by Cryo-Electron Microscopy. ACS APPLIED BIO MATERIALS 2022; 5:4696-4700. [PMID: 35587230 DOI: 10.1021/acsabm.2c00130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Methods that allow the study of the structure of proteins in complex with nanomaterials promise to enhance our understanding of how biological molecules interface with inorganic materials. We used single-particle cryo-electron microscopy (cryo-EM) to demonstrate the potential for cryo-EM analysis to reveal structural details of protein-nanoparticle complexes. Two protein-nanomaterial complexes, namely, GroEL bound to platinum nanoparticles (GroEL-PtNP) and ferritin bound to an iron oxide nanoparticle, were used as model samples. For the GroEL-PtNP complex, a final reconstruction was obtained to 3.93 Å, which allowed us to fit the atomic model of GroEL into the resulting map. This sets the stage for future work and improvements on the use of cryo-EM for the study of protein-nanomaterial complexes.
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Affiliation(s)
- Sagnik Sen
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe 85287, Arizona, United States
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe 85287, Arizona, United States
| | - Amar Thaker
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe 85287, Arizona, United States
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe 85287, Arizona, United States
| | - Luqmanal Sirajudeen
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe 85287, Arizona, United States
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe 85287, Arizona, United States
| | - Dewight Williams
- John M. Cowley Center for High Resolution Electron Microscopy, Arizona State University, Tempe 85281, Arizona, United States
| | - Brent L Nannenga
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe 85287, Arizona, United States
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe 85287, Arizona, United States
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3
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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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4
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Brljak N, Knecht MR, Walsh TR. Controlling the Orientation and Viscoelasticity of Materials-Binding Peptides on Hexagonal Boron Nitride Using Fatty Acids. J Phys Chem B 2021; 125:10621-10628. [PMID: 34505506 DOI: 10.1021/acs.jpcb.1c05446] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The adsorption of materials-binding peptides to technologically relevant 2D nanosheets of h-BN could be transformative for both property modulation and materials applications. To enhance binding, integration of non-natural functionalities into the biomolecule could prove to be important. However, very little is understood regarding the impact of these biomolecular structural alterations on the binding, which could influence the affinity and surface-adsorbed structures. Here, the effect of fatty acid incorporation site and carbon chain length is investigated using the BP7 peptide, previously identified with affinity for h-BN. The peptide was modified at either the N- or C-terminus with a fatty acid chain length of 6-12 carbons long. The binding affinity and bio-overlayer viscoelasticity are quantified using quartz crystal microbalance analysis. While fatty acid conjugation did not substantially affect the affinity of the resultant biomolecules, it did alter the viscoelasticity of the biomolecular overlayer on the h-BN surface based upon the carbon chain length and incorporation site. Molecular dynamics simulations demonstrate interplay between enthalpic and entropic effects in modifying the overlayer viscoelasticity. The simulations predict that C-terminal conjugation promotes the enhancement of upright adsorbed states, compared with the N-terminal case, with this effect most pronounced for the 10-carbon chain.
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Affiliation(s)
- Nermina Brljak
- 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.,Dr. J.T. Macdonald Foundation Biomedical Nanotechnology Institute, University of Miami, UM Life Science Technology Building, 1951 NW Seventh Avenue, Suite 475, Miami, Florida 33136, United States
| | - Tiffany R Walsh
- Institute for Frontier Materials, Deakin University, Waurn Ponds, 3216 Victoria, Australia
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5
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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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6
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Ozaki M, Yoshida S, Tsuruoka T, Usui K. Intracellular mineralization of gold nanoparticles using gold ion-binding peptides with cell-penetrating ability. Chem Commun (Camb) 2021; 57:725-728. [PMID: 33411858 DOI: 10.1039/d0cc06117d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We developed a system to directly produce gold nanoparticles in cells by intracellular mineralization in lower concentration than conventional methods using a peptide consisting of a cell-penetrating sequence and a gold ion-binding sequence. Furthermore, we could control the uniquely shaped gold nanostructures that were produced by changing peptide structures.
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Affiliation(s)
- Makoto Ozaki
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 6500047, Kobe, Japan.
| | - Shuhei Yoshida
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 6500047, Kobe, Japan.
| | - Takaaki Tsuruoka
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 6500047, Kobe, Japan.
| | - Kenji Usui
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 6500047, Kobe, Japan.
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7
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The Effect of Oligomerization on A Solid-Binding Peptide Binding to Silica-Based Materials. NANOMATERIALS 2020; 10:nano10061070. [PMID: 32486317 PMCID: PMC7353425 DOI: 10.3390/nano10061070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/11/2020] [Accepted: 05/12/2020] [Indexed: 12/22/2022]
Abstract
The bifunctional linker-protein G (LPG) fusion protein comprises a peptide (linker) sequence and a truncated form of Streptococcus strain G148 protein G (protein G). The linker represents a multimeric solid-binding peptide (SBP) comprising 4 × 21-amino acid sequence repeats that display high binding affinity towards silica-based materials. In this study, several truncated derivatives were investigated to determine the effect of the SBP oligomerization on the silica binding function of LPG (for the sake of clarity, LPG will be referred from here on as 4 × LPG). Various biophysical characterization techniques were used to quantify and compare the truncated derivatives against 4 × LPG and protein G without linker (PG). The derivative containing two sequence repeats (2 × LPG) showed minimal binding to silica, while the truncated derivative with only a single sequence (1 × LPG) displayed no binding. The derivative containing three sequence repeats (3 × LPG) was able to bind to silica with a binding affinity of KD = 53.23 ± 4.5 nM, which is 1.5 times lower than that obtained for 4 × LPG under similar experimental conditions. Circular dichroism (CD) spectroscopy and fluorescence spectroscopy studies indicated that the SBP degree of oligomerization has only a small effect on the secondary structure (the linker unravels the beginning of the protein G sequence) and chemical stability of the parent protein G. However, based on quartz crystal microbalance with dissipation monitoring (QCM-D), oligomerization is an important parameter for a strong and stable binding to silica. The replacement of three sequence repeats by a (GGGGS)12 glycine-rich spacer indicated that the overall length rather than the SBP oligomerization mediated the effective binding to silica.
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8
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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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9
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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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10
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Lee DJ, Park HS, Koo K, Lee JY, Nam YS, Lee W, Yang MY. Gold Binding Peptide Identified from Microfluidic Biopanning: An Experimental and Molecular Dynamics Study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:522-528. [PMID: 30592604 DOI: 10.1021/acs.langmuir.8b02563] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Biopanning refers to the processes of screening peptides with a high affinity to a target material. Microfluidic biopanning has advantages compared to conventional biopanning which requires large amounts of the target material and involves inefficient multiple pipetting steps to remove nonspecific or low-affinity peptides. Here, we fabricate a microfluidic biopanning system to identify a new gold-binding peptide (GBP). A polydimethylsiloxane microfluidic device is fabricated and bonded to a glass slide with a gold pattern that is deposited by electron-beam evaporation. The microfluidic biopanning system can provide high adjustability in the washing step during the biopanning process because the liquid flow rate and the resulting shear stress can be precisely controlled. The surface plasmon resonance analysis shows that the binding affinity of the identified GBP is comparable to previously reported GBPs. Moreover, molecular dynamics simulations are performed to understand its binding affinity against the gold surface in detail. Theoretical calculations suggest that the association and dissociation rates of the GBPs depend on their sequence-dependent conformations and interactions with the gold surface. These findings provide insight into designing efficient biopanning tools and peptides with a high affinity for various target materials.
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Affiliation(s)
| | | | - Kunmo Koo
- Center for Nanomaterials and Chemical Reactions , Institute for Basic Science (IBS) , 291 Daehak-ro, Yuseong-gu , Daejeon 34141 , Republic of Korea
| | - Jeong Yong Lee
- Center for Nanomaterials and Chemical Reactions , Institute for Basic Science (IBS) , 291 Daehak-ro, Yuseong-gu , Daejeon 34141 , Republic of Korea
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11
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Dong H, Sarkes DA, Rice JJ, Hurley MM, Fu AJ, Stratis-Cullum DN. Living Bacteria-Nanoparticle Hybrids Mediated through Surface-Displayed Peptides. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:5837-5848. [PMID: 29692178 DOI: 10.1021/acs.langmuir.8b00114] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In this study, we investigated the preparation of living bacteria-nanoparticle hybrids mediated by surface-displayed peptides. The assembly of metallic nanoparticles on living bacteria has been achieved under mild conditions utilizing metal-peptide interactions, whereas the viability of the bacterial cells was greatly preserved. Escherichia coli was engineered with inducible gene circuits to control the display of peptides with desired sequences. Several designed peptide sequences as well as known gold-binding peptides were expressed on the cell surface using enhanced circularly permuted outer membrane protein X (eCPX) scaffolds. Driven by metal-peptide affinity, "biofriendly" citrate-stabilized gold nanoparticles were self-assembled onto the surface of bacteria with displayed peptides, which required overcoming the repulsive force between negatively charged nanoparticles and negatively charged cells. The bacteria/Au nanoparticle hybrids were highly viable and maintained the ability to grow and divide, which is a crucial step toward the creation of living material systems. Further activity and preservation of the bacterial hybrid assembly was demonstrated. The method described herein enables the conjugation of bacterial surfaces with diverse metal-rich nanoparticles in an inducible, and therefore easily controlled, manner. The expressed peptide sequences can be easily modified to alter the binding affinity and specificity for a wide variety of materials to form on-demand, high-density living biohybrids.
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Affiliation(s)
- Hong Dong
- Biotechnology Branch , US Army Research Laboratory , 2800 Powder Mill Road , Adelphi , Maryland 20783 , United States
- General Technical Services , 1451 Route 34 South , Wall Township , New Jersey 07727 , United States
| | - Deborah A Sarkes
- Biotechnology Branch , US Army Research Laboratory , 2800 Powder Mill Road , Adelphi , Maryland 20783 , United States
| | - Jeffrey J Rice
- Department of Chemical Engineering , Auburn University , 212 Ross Hall , Auburn , Alabama 36849 , United States
- Oak Ridge Associated Universities , 4692 Millennium Drive, Suite 101 , Belcamp , Maryland 21017 , United States
| | - Margaret M Hurley
- Biotechnology Branch , US Army Research Laboratory , 2800 Powder Mill Road , Adelphi , Maryland 20783 , United States
| | - Adele J Fu
- Biotechnology Branch , US Army Research Laboratory , 2800 Powder Mill Road , Adelphi , Maryland 20783 , United States
- Oak Ridge Associated Universities , 4692 Millennium Drive, Suite 101 , Belcamp , Maryland 21017 , United States
| | - Dimitra N Stratis-Cullum
- Biotechnology Branch , US Army Research Laboratory , 2800 Powder Mill Road , Adelphi , Maryland 20783 , United States
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12
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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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13
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Tanaka M, Hikiba S, Yamashita K, Muto M, Okochi M. Array-based functional peptide screening and characterization of gold nanoparticle synthesis. Acta Biomater 2017; 49:495-506. [PMID: 27865964 DOI: 10.1016/j.actbio.2016.11.037] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 11/11/2016] [Accepted: 11/16/2016] [Indexed: 01/20/2023]
Abstract
Based on inorganic material production through biomineralization in organisms, the use of biological molecules in nanomaterial production has received increasing attention as a vehicle to synthesize inorganic materials with selected properties in ambient conditions. Among various biological molecules that interact with metallic surfaces, short peptides are putative ligand molecules as they exhibit potential to control the synthesis of nanoscale materials with tailored functions. Herein, using a spot synthesis-based peptide array, the gold nanoparticle (AuNP) binding activities of approximately 1800 peptides were evaluated and revealed various activities ranging from positive (high-affinity binding peptides) to negative (weak- or null-affinity binding peptides). Among 50 peptides showing the highest AuNP binding activity, 46 sequences showed the presence of tryptophan-based motifs including W[Xn]W, H[Xn]W, and W[Xn]H (W: tryptophan, X: any amino acid, n: 1-8 amino acid residues), whereas none of these motifs was found in the WORST50 peptides. Notably, three peptides showing the highest binding affinities possessed bi-functionality in AuNP binding and Au(III) reduction in solution and on solid surfaces. In addition, the characterization of truncated peptide derivatives revealed unique peptide motifs for their function expressions that also supported the importance of tryptophan-based motifs for peptide-AuNP binding. These findings open the door for peptide-mediated precise regulation of AuNP synthesis in ambient condition and for site dependent controlled AuNP integration onto nanotechnological devices. STATEMENT OF SIGNIFICANCE The development of a technique for functionally regulated nanosized material production in ambient condition is broadly required according to the expansion of nanomaterial based applications. Short peptides, which bind to metallic surfaces, have great potential for the technique development, but the realization remains a difficult challenge due to the lack of metal binding peptide varieties. Herein, approximately 1800 peptides with the gold nanoparticle (AuNP) binding activity are reported and characterized. Furthermore, by three highest binding peptides, the expression of bi-functionality in AuNP binding and Au(III) reduction was serendipitously discovered in solution and on solid surfaces. These findings will be attributed to new technique development of functional nanoparticle synthesis in mild condition, and for site-dependent AuNP integration in various nanotechnological devices.
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Affiliation(s)
- Masayoshi Tanaka
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 2-12-1, O-okayama, Meguro-ku, Tokyo 152-8552, Japan; JST ImPACT, Japan
| | - Shun Hikiba
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 2-12-1, O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Kiyoto Yamashita
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 2-12-1, O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Masaki Muto
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 2-12-1, O-okayama, Meguro-ku, Tokyo 152-8552, Japan; JST ImPACT, Japan
| | - Mina Okochi
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 2-12-1, O-okayama, Meguro-ku, Tokyo 152-8552, Japan; JST ImPACT, Japan.
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14
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Peptide engineered microcantilevers for selective chemical force microscopy and monitoring of nanoparticle capture. Biointerphases 2016; 11:04B312. [PMID: 28010112 DOI: 10.1116/1.4972417] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Engineered peptides capable of binding to silica have been used to provide contrast in chemical force microscopy and tested for their capacity to selectively capture silica nanoparticles (NPs). Gold coated atomic force microscopy (AFM) microcantilevers with integrated tips and colloidal probes were functionalized with engineered peptides through a thiol group of a terminal cysteine which was linked via a glycine trimer to a 12-mer binding sequence. The functionalized probes demonstrated a significantly increased binding force on silicon oxide areas of a gold-patterned silicon wafer, whereas plain gold probes, and those functionalized with a random permutation of the silica binding peptide motif or an all-histidine sequence displayed similar adhesion forces to gold and silicon oxide. As the functionalized probes also allowed contact mode imaging subsequently to the adhesion mapping, also the associated friction contrast was measured and found to be similar to the adhesion contrast. Furthermore, the adsorption of silica NPs onto planar gold surfaces functionalized in the same manner was observed to be selective. Notably, the surface coverage with silica NPs was found to decrease with increasing pH, implying the importance of electrostatic interactions between the peptide and the NPs. Finally, the adsorption of silica NPs was monitored via the decrease in fundamental resonance frequency of an AFM microcantilever functionalized with silica binding peptides.
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15
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Wang J, Liu K, Xing R, Yan X. Peptide self-assembly: thermodynamics and kinetics. Chem Soc Rev 2016; 45:5589-5604. [PMID: 27487936 DOI: 10.1039/c6cs00176a] [Citation(s) in RCA: 615] [Impact Index Per Article: 76.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Self-assembling systems play a significant role in physiological functions and have therefore attracted tremendous attention due to their great potential for applications in energy, biomedicine and nanotechnology. Peptides, consisting of amino acids, are among the most popular building blocks and programmable molecular motifs. Nanostructures and materials assembled using peptides exhibit important potential for green-life new technology and biomedical applications mostly because of their bio-friendliness and reversibility. The formation of these ordered nanostructures pertains to the synergistic effect of various intermolecular non-covalent interactions, including hydrogen-bonding, π-π stacking, electrostatic, hydrophobic, and van der Waals interactions. Therefore, the self-assembly process is mainly driven by thermodynamics; however, kinetics is also a critical factor in structural modulation and function integration. In this review, we focus on the influence of thermodynamic and kinetic factors on structural assembly and regulation based on different types of peptide building blocks, including aromatic dipeptides, amphiphilic peptides, polypeptides, and amyloid-relevant peptides.
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Affiliation(s)
- Juan Wang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
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Baumann V, Habeeb Muhammed MA, Blanch AJ, Dey P, Rodríguez-Fernández J. Biomolecules in Metal and Semiconductor Nanoparticle Growth. Isr J Chem 2015. [DOI: 10.1002/ijch.201500031] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Mochizuki M, Oguchi M, Kim SO, Jackman JA, Ogawa T, Lkhamsuren G, Cho NJ, Hayashi T. Quantitative Evaluation of Peptide-Material Interactions by a Force Mapping Method: Guidelines for Surface Modification. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:8006-8012. [PMID: 26125092 DOI: 10.1021/acs.langmuir.5b01691] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Peptide coatings on material surfaces have demonstrated wide application across materials science and biotechnology, facilitating the development of nanobio interfaces through surface modification. A guiding motivation in the field is to engineer peptides with a high and selective binding affinity to target materials. Herein, we introduce a quantitative force mapping method in order to evaluate the binding affinity of peptides to various hydrophilic oxide materials by atomic force microscopy (AFM). Statistical analysis of adhesion forces and probabilities obtained on substrates with a materials contrast enabled us to simultaneously compare the peptide binding affinity to different materials. On the basis of the experimental results and corresponding theoretical analysis, we discuss the role of various interfacial forces in modulating the strength of peptide attachment to hydrophilic oxide solid supports as well as to gold. The results emphasize the precision and robustness of our approach to evaluating the adhesion strength of peptides to solid supports, thereby offering guidelines to improve the design and fabrication of peptide-coated materials.
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Affiliation(s)
- Masahito Mochizuki
- †Department of Electronic Chemistry, Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8502, Japan
| | - Masahiro Oguchi
- †Department of Electronic Chemistry, Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8502, Japan
| | - Seong-Oh Kim
- ‡School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798 Singapore
- §School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, 637459 Singapore
| | - Joshua A Jackman
- ‡School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798 Singapore
- §School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, 637459 Singapore
| | - Tetsu Ogawa
- †Department of Electronic Chemistry, Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8502, Japan
| | - Ganchimeg Lkhamsuren
- †Department of Electronic Chemistry, Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8502, Japan
| | - Nam-Joon Cho
- ‡School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798 Singapore
- §School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, 637459 Singapore
- ∥Centre for Biomimetic Sensor Science, Nanyang Technological University, 50 Nanyang Drive, 637553 Singapore
| | - Tomohiro Hayashi
- †Department of Electronic Chemistry, Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8502, Japan
- ⊥Surface and Interface Science Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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