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Moon J, Hu G, Hayashi T. Application of Machine Learning in the Quantitative Analysis of the Surface Characteristics of Highly Abundant Cytoplasmic Proteins: Toward AI-Based Biomimetics. Biomimetics (Basel) 2024; 9:162. [PMID: 38534847 DOI: 10.3390/biomimetics9030162] [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: 12/14/2023] [Revised: 02/12/2024] [Accepted: 02/29/2024] [Indexed: 03/28/2024] Open
Abstract
Proteins in the crowded environment of human cells have often been studied regarding nonspecific interactions, misfolding, and aggregation, which may cause cellular malfunction and disease. Specifically, proteins with high abundance are more susceptible to these issues due to the law of mass action. Therefore, the surfaces of highly abundant cytoplasmic (HAC) proteins directly exposed to the environment can exhibit specific physicochemical, structural, and geometrical characteristics that reduce nonspecific interactions and adapt to the environment. However, the quantitative relationships between the overall surface descriptors still need clarification. Here, we used machine learning to identify HAC proteins using hydrophobicity, charge, roughness, secondary structures, and B-factor from the protein surfaces and quantified the contribution of each descriptor. First, several supervised learning algorithms were compared to solve binary classification problems for the surfaces of HAC and extracellular proteins. Then, logistic regression was used for the feature importance analysis of descriptors considering model performance (80.2% accuracy and 87.6% AUC) and interpretability. The HAC proteins showed positive correlations with negatively and positively charged areas but negative correlations with hydrophobicity, the B-factor, the proportion of beta structures, roughness, and the proportion of disordered regions. Finally, the details of each descriptor could be explained concerning adaptative surface strategies of HAC proteins to regulate nonspecific interactions, protein folding, flexibility, stability, and adsorption. This study presented a novel approach using various surface descriptors to identify HAC proteins and provided quantitative design rules for the surfaces well-suited to human cellular crowded environments.
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Affiliation(s)
- Jooa Moon
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Yokohama 226-8502, Japan
| | - Guanghao Hu
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Yokohama 226-8502, Japan
| | - Tomohiro Hayashi
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Yokohama 226-8502, Japan
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa 277-0882, Japan
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2
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Kawase O, Iwaya H, Asano Y, Inoue H, Kudo S, Sasahira M, Azuma N, Kondoh D, Ichikawa-Seki M, Xuan X, Sakamoto K, Okamoto H, Nakadate H, Inoue W, Saito I, Narita M, Sekii K, Kobayashi K. Identification of novel yolk ferritins unique to planarians: planarians supply aluminum rather than iron to vitellaria in egg capsules. Cell Tissue Res 2021; 386:391-413. [PMID: 34319433 DOI: 10.1007/s00441-021-03506-8] [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: 07/31/2020] [Accepted: 07/07/2021] [Indexed: 11/29/2022]
Abstract
All animals, other than Platyhelminthes, produce eggs containing yolk, referred to as "entolecithal" eggs. However, only Neoophora, in the phylum Platyhelminthes, produce "ectolecithal" eggs (egg capsules), in which yolk is stored in the vitelline cells surrounding oocytes. Vitelline cells are derived from vitellaria (yolk glands). Vitellaria are important reproductive organs that may be studied to elucidate unique mechanisms that have been evolutionarily conserved within Platyhelminthes. Currently, only limited molecular level information is available on vitellaria. The current study identified major vitellaria-specific proteins in a freshwater planarian, Dugesia ryukyuensis, using peptide mass fingerprinting (PMF) and expression analyses. Amino acid sequence analysis and orthology analysis via OrthoFinder ver.2.3.8 indicated that the identified major vitellaria-specific novel yolk ferritins were conserved in planarians (Tricladida). Because ferritins play an important role in Fe (iron) storage, we examined the metal elements contained in vitellaria and ectolecithal eggs, using non-heme iron histochemistry, elemental analysis based on inductively coupled plasma mass spectrometry and transmission electron microscopy- energy-dispersive X-ray spectroscopy analysis. Interestingly, vitellaria and egg capsules contained large amounts of aluminum (Al), but not Fe. The knockdown of the yolk ferritin genes caused a decrease in the volume of egg capsules, abnormality in juveniles, and increase in Al content in vitellaria. Yolk ferritins of D. ryukyuensis may regulate Al concentration in vitellaria via their pooling function of Al and protect the egg capsule production and normal embryogenesis from Al toxicity.
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Affiliation(s)
- Osamu Kawase
- Department of Biology, Premedical Sciences, Dokkyo Medical University, Mibu-machi, Shimotsuga-gun, Tochigi, 321-0293, Japan
| | - Hisashi Iwaya
- Department of Biology, Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori, 036-8561, Japan
| | - Yoshiya Asano
- Department of Neuroanatomy, Cell Biology and Histology, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki, Aomori, 036-8562, Japan
| | - Hiromoto Inoue
- Department of Biology, Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori, 036-8561, Japan
| | - Seiya Kudo
- Department of Biology, Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori, 036-8561, Japan
| | - Motoki Sasahira
- Department of Biology, Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori, 036-8561, Japan
| | - Nobuyuki Azuma
- Department of Biology, Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori, 036-8561, Japan
| | - Daisuke Kondoh
- Department of Basic Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine, Inaba-cho, Obihiro, Hokkaido, 080-8555, Japan
| | - Madoka Ichikawa-Seki
- Laboratory of Veterinary Parasitology, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, 020-8550, Japan
| | - Xuenan Xuan
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inaba-cho, Obihiro, Hokkaido, 080-8555, Japan
| | - Kimitoshi Sakamoto
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori, 036-8561, Japan
| | - Hikaru Okamoto
- Department of Biology, Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori, 036-8561, Japan
| | - Hinaki Nakadate
- Department of Biology, Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori, 036-8561, Japan
| | - Wataru Inoue
- Department of Biology, Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori, 036-8561, Japan
| | - Ikuma Saito
- Department of Biology, Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori, 036-8561, Japan
| | - Miyu Narita
- Department of Biology, Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori, 036-8561, Japan
| | - Kiyono Sekii
- Department of Biology, Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori, 036-8561, Japan
| | - Kazuya Kobayashi
- Department of Biology, Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori, 036-8561, Japan.
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3
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Watanabe M, Bhawal UK, Takemoto S, Nishiyama N, Nakahara Y, Tatematsu KI, Sezutsu H, Kuwabara N, Minamisawa T, Shiba K, Asakura T. Bio-functionalized titanium surfaces with modified silk fibroin carrying titanium binding motif to enhance the ossific differentiation of MC3T3-E1. Biotechnol Bioeng 2021; 118:2585-2596. [PMID: 33818762 DOI: 10.1002/bit.27777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 03/24/2021] [Accepted: 03/31/2021] [Indexed: 02/03/2023]
Abstract
Silk fibroin (SF) from Bombyx mori has superior properties as both a textile and a biomaterial, and has been used to functionalize the surfaces of various medical inorganic materials including titanium (Ti). In this study, we endowed SF with reversible binding ability to Ti by embedding a titanium binding motif (minTBP-1 and RKLPDA). Artificial SF proteins were first created by conjugating gene cassettes for SF motif (AGSGAG) and minTBP-1 motif with different ratios, which have been shown to bind reversibly to Ti surfaces in quartz crystal microbalance analyses. Based on these results, the functionalized SF (TiBP-SF) containing the designed peptide [TS[(AGSGAG)3 AS]2 RKLPDAS]8 was prepared from the cocoon of transgenic B. mori, which accelerates the ossific differentiation of MC3T3-E1 cells when coated on titanium substrates. Thus, TiBP-SF presents an alternative for endowing the surfaces of titanium materials with osseointegration functionality, which would allow the exploration of potential applications in the medical field.
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Affiliation(s)
- Mai Watanabe
- Division of Protein Engineering, Cancer Institute, Japanese Foundation for Cancer Research, Koto, Tokyo, Japan.,Department of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
| | - Ujjal K Bhawal
- Department of Biochemistry and Molecular Biology, Research Institute of Oral Science, Nihon University School of Dentistry at Matsudo, Matsudo, Chiba, Japan
| | - Shinji Takemoto
- Department of Biomedical Engineering, Iwate Medical University, Yahaba, Iwate, Japan
| | - Norihiro Nishiyama
- Department of Dental Biomaterials, Nihon University School of Dentistry at Matsudo, Matsudo, Chiba, Japan
| | - Yuichi Nakahara
- Transgenic Silkworm Research Unit, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Ken-Ichiro Tatematsu
- Transgenic Silkworm Research Unit, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Hideki Sezutsu
- Transgenic Silkworm Research Unit, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Nobuo Kuwabara
- Gunma Sericultural Technology Center, Maebashi, Gunma, Japan
| | - Tamiko Minamisawa
- Division of Protein Engineering, Cancer Institute, Japanese Foundation for Cancer Research, Koto, Tokyo, Japan
| | - Kiyotaka Shiba
- Division of Protein Engineering, Cancer Institute, Japanese Foundation for Cancer Research, Koto, Tokyo, Japan
| | - Tetsuo Asakura
- Department of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
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Tanaka M, Morita S, Hayashi T. Role of interfacial water in determining the interactions of proteins and cells with hydrated materials. Colloids Surf B Biointerfaces 2020; 198:111449. [PMID: 33310639 DOI: 10.1016/j.colsurfb.2020.111449] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 10/09/2020] [Accepted: 11/01/2020] [Indexed: 01/27/2023]
Abstract
Water molecules play a crucial role in biointerfacial interactions, including protein adsorption and desorption. To understand the role of water in the interaction of proteins and cells at biological interfaces, it is important to compare particular states of hydration water with various physicochemical properties of hydrated biomaterials. In this review, we discuss the fundamental concepts for determining the interactions of proteins and cells with hydrated materials along with selected examples corresponding to our recent studies, including poly(2-methoxyethyl acrylate) (PMEA), PMEA derivatives, and other biomaterials. The states of water were analyzed by differential scanning calorimetry, in situ attenuated total reflection infrared spectroscopy, and surface force measurements. We found that intermediate water which is loosely bound to a biomaterial, is a useful indicator of the bioinertness of material surfaces. This finding on intermediate water provides novel insights and helps develop novel experimental models for understanding protein adsorption in a wide range of materials, such as those used in biomedical applications.
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Affiliation(s)
- Masaru Tanaka
- Institute for Materials Chemistry and Engineering, Kyushu University, CE41 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan.
| | - Shigeaki Morita
- Department of Engineering Science, Osaka Electro-Communication University, 18-8 Hatsucho, Neyagawa, 572-8530, Japan
| | - Tomohiro Hayashi
- Department of Materials Science and Engineering, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8502, Japan; JST-PRESTO, 4-1-8 Hon-cho, Kawaguchi, Saitama, 332-0012, Japan
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5
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Li L, Liu W, Zhao Y, Ma P, Zha S, Chen P, Lu H, Jiang X, Wan S, Luo J, Dai Q, Hu J, Utomo YKS, Han X, Yang Z, Yang L, He Q. Dual-Peptide-Functionalized Nanofibrous Scaffolds Recruit Host Endothelial Progenitor Cells for Vasculogenesis to Repair Calvarial Defects. ACS APPLIED MATERIALS & INTERFACES 2020; 12:3474-3493. [PMID: 31874023 DOI: 10.1021/acsami.9b21434] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Vasculogenesis (de novo formation of vessels) induced by endothelial progenitor cells (EPCs) is requisite for vascularized bone regeneration. However, there exist few available options for promoting vasculogenesis within artificial bone grafts except for exogenous EPC transplantation, which suffers from the source of EPC, safety, cost, and time concerns in clinical applications. This study aimed at endogenous EPC recruitment for vascularized bone regeneration by using a bioinspired EPC-induced graft. The EPC-induced graft was created by immobilizing two bioactive peptides, WKYMVm and YIGSR, on the surface of poly(ε-caprolactone) (PCL)/poliglecaprone (PGC) nanofibrous scaffolds via a polyglycolic acid (PGA)-binding peptide sequence. Remarkable immobilization efficacy of WKYMVm and YIGSR peptides and their sustained release (over 14 days) from scaffolds were observed. In vivo and in vitro studies showed robust recruitment of EPCs, which subsequently contributed to early vasculogenesis and ultimate bone regeneration. The dual-peptide-functionalized nanofibrous scaffolds proposed in this study provide a promising therapeutic strategy for vasculogenesis in bone defect repair.
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Affiliation(s)
- Li Li
- Orthopedic Department, Southwest Hospital , The First Hospital Affiliated to Army Medical University (Southwest Hospital) , Chongqing 400038 , P.R. China
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College , Chongqing University , Chongqing 400044 , China
- Orthopedic Department , The First Affiliated Hospital of Zhengzhou University , Zhengzhou 450001 , P.R. China
- Institute for Clean Energy & Advanced Materials, Faculty of Materials and Energy , Southwest University , Chongqing 400715 , P.R. China
| | - Wanqian Liu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College , Chongqing University , Chongqing 400044 , China
| | - Yulan Zhao
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College , Chongqing University , Chongqing 400044 , China
| | - Pingping Ma
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College , Chongqing University , Chongqing 400044 , China
| | - Shenfang Zha
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College , Chongqing University , Chongqing 400044 , China
| | - Peixin Chen
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College , Chongqing University , Chongqing 400044 , China
| | - Hongwei Lu
- Orthopedic Department, Southwest Hospital , The First Hospital Affiliated to Army Medical University (Southwest Hospital) , Chongqing 400038 , P.R. China
| | - Xiaorui Jiang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College , Chongqing University , Chongqing 400044 , China
| | - Shuang Wan
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College , Chongqing University , Chongqing 400044 , China
| | - Jiangming Luo
- Center of Joint Surgery, Southwest Hospital , The First Hospital Affiliated to Army Medical University (Southwest Hospital) , Chongqing 400038 , P.R. China
| | - Qijie Dai
- Orthopedic Department, Southwest Hospital , The First Hospital Affiliated to Army Medical University (Southwest Hospital) , Chongqing 400038 , P.R. China
| | - Junxian Hu
- Orthopedic Department, Southwest Hospital , The First Hospital Affiliated to Army Medical University (Southwest Hospital) , Chongqing 400038 , P.R. China
| | - Yohanes Kristo Sugiarto Utomo
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College , Chongqing University , Chongqing 400044 , China
| | - Xinyun Han
- Orthopedic Department, Southwest Hospital , The First Hospital Affiliated to Army Medical University (Southwest Hospital) , Chongqing 400038 , P.R. China
- Institute for Clean Energy & Advanced Materials, Faculty of Materials and Energy , Southwest University , Chongqing 400715 , P.R. China
| | - Zhengwei Yang
- Orthopedic Department, Southwest Hospital , The First Hospital Affiliated to Army Medical University (Southwest Hospital) , Chongqing 400038 , P.R. China
| | - Li Yang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College , Chongqing University , Chongqing 400044 , China
| | - Qingyi He
- Orthopedic Department, Southwest Hospital , The First Hospital Affiliated to Army Medical University (Southwest Hospital) , Chongqing 400038 , P.R. China
- Orthopedic Department , The First Affiliated Hospital of Zhengzhou University , Zhengzhou 450001 , P.R. China
- Institute for Clean Energy & Advanced Materials, Faculty of Materials and Energy , Southwest University , Chongqing 400715 , P.R. China
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6
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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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7
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Limo MJ, Sola-Rabada A, Boix E, Thota V, Westcott ZC, Puddu V, Perry CC. Interactions between Metal Oxides and Biomolecules: from Fundamental Understanding to Applications. Chem Rev 2018; 118:11118-11193. [PMID: 30362737 DOI: 10.1021/acs.chemrev.7b00660] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Metallo-oxide (MO)-based bioinorganic nanocomposites promise unique structures, physicochemical properties, and novel biochemical functionalities, and within the past decade, investment in research on materials such as ZnO, TiO2, SiO2, and GeO2 has significantly increased. Besides traditional approaches, the synthesis, shaping, structural patterning, and postprocessing chemical functionalization of the materials surface is inspired by strategies which mimic processes in nature. Would such materials deliver new technologies? Answering this question requires the merging of historical knowledge and current research from different fields of science. Practically, we need an effective defragmentation of the research area. From our perspective, the superficial accounting of material properties, chemistry of the surfaces, and the behavior of biomolecules next to such surfaces is a problem. This is particularly of concern when we wish to bridge between technologies in vitro and biotechnologies in vivo. Further, besides the potential practical technological efficiency and advantages such materials might exhibit, we have to consider the wider long-term implications of material stability and toxicity. In this contribution, we present a critical review of recent advances in the chemistry and engineering of MO-based biocomposites, highlighting the role of interactions at the interface and the techniques by which these can be studied. At the end of the article, we outline the challenges which hamper progress in research and extrapolate to developing and promising directions including additive manufacturing and synthetic biology that could benefit from molecular level understanding of interactions occurring between inanimate (abiotic) and living (biotic) materials.
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Affiliation(s)
- Marion J Limo
- Interdisciplinary Biomedical Research Centre, School of Science and Technology , Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS , United Kingdom.,Interface and Surface Analysis Centre, School of Pharmacy , University of Nottingham , University Park, Nottingham NG7 2RD , United Kingdom
| | - Anna Sola-Rabada
- Interdisciplinary Biomedical Research Centre, School of Science and Technology , Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS , United Kingdom
| | - Estefania Boix
- Interdisciplinary Biomedical Research Centre, School of Science and Technology , Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS , United Kingdom.,Department of Bioproducts and Biosystems , Aalto University , P.O. Box 16100, FI-00076 Aalto , Finland
| | - Veeranjaneyulu Thota
- Interdisciplinary Biomedical Research Centre, School of Science and Technology , Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS , United Kingdom
| | - Zayd C Westcott
- Interdisciplinary Biomedical Research Centre, School of Science and Technology , Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS , United Kingdom
| | - Valeria Puddu
- Interdisciplinary Biomedical Research Centre, School of Science and Technology , Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS , United Kingdom
| | - Carole C Perry
- Interdisciplinary Biomedical Research Centre, School of Science and Technology , Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS , United Kingdom
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8
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Agosta L, Brandt EG, Lyubartsev AP. Diffusion and reaction pathways of water near fully hydrated TiO 2 surfaces from ab initio molecular dynamics. J Chem Phys 2018; 147:024704. [PMID: 28711052 DOI: 10.1063/1.4991381] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Ab initio molecular dynamics simulations are reported for water-embedded TiO2 surfaces to determine the diffusive and reactive behavior at full hydration. A three-domain model is developed for six surfaces [rutile (110), (100), and (001), and anatase (101), (100), and (001)] which describes waters as "hard" (irreversibly bound to the surface), "soft" (with reduced mobility but orientation freedom near the surface), or "bulk." The model explains previous experimental data and provides a detailed picture of water diffusion near TiO2 surfaces. Water reactivity is analyzed with a graph-theoretic approach that reveals a number of reaction pathways on TiO2 which occur at full hydration, in addition to direct water splitting. Hydronium (H3O+) is identified to be a key intermediate state, which facilitates water dissociation by proton hopping between intact and dissociated waters near the surfaces. These discoveries significantly improve the understanding of nanoscale water dynamics and reactivity at TiO2 interfaces under ambient conditions.
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Affiliation(s)
- Lorenzo Agosta
- Department of Materials and Environmental Chemistry, Stockholm University, 10691 Stockholm, Sweden
| | - Erik G Brandt
- Department of Materials and Environmental Chemistry, Stockholm University, 10691 Stockholm, Sweden
| | - Alexander P Lyubartsev
- Department of Materials and Environmental Chemistry, Stockholm University, 10691 Stockholm, Sweden
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9
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Suzuki Y, Shindo H. Binding sites and structure of peptides bound to SiO2 nanoparticles studied by solution NMR spectroscopy. Polym J 2018. [DOI: 10.1038/s41428-018-0084-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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10
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Buckle EL, Lum JS, Roehrich AM, Stote RE, Vandermoon B, Dracinsky M, Filocamo SF, Drobny GP. Serine-Lysine Peptides as Mediators for the Production of Titanium Dioxide: Investigating the Effects of Primary and Secondary Structures Using Solid-State NMR Spectroscopy and DFT Calculations. J Phys Chem B 2018; 122:4708-4718. [PMID: 29595262 DOI: 10.1021/acs.jpcb.8b00745] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A biomimetic approach to the formation of titania (TiO2) nanostructures is desirable because of the mild conditions required in this form of production. We have identified a series of serine-lysine peptides as candidates for the biomimetic production of TiO2 nanostructures. We have assayed these peptides for TiO2-precipitating activity upon exposure to titanium bis(ammonium lactato)dihydroxide and have characterized the resulting coprecipitates using scanning electron microscopy. A subset of these assayed peptides efficiently facilitates the production of TiO2 nanospheres. Here, we investigate the process of TiO2 nanosphere formation mediated by the S-K peptides KSSKK- and SKSK3SKS using one-dimensional and two-dimensional solid-state NMR (ssNMR) on peptide samples with uniformly 13C-enriched residues. ssNMR is used to assign 13C chemical shifts (CSs) site-specifically in each free peptide and TiO2-embedded peptide, which are used to derive secondary structures in the neat and TiO2 coprecipitated states. The backbone 13C CSs are used to assess secondary structural changes undergone during the coprecipitation process. Side-chain 13C CS changes are analyzed with density functional theory calculations and used to determine side-chain conformational changes that occur upon coprecipitation with TiO2 and to determine surface orientation of lysine side chains in TiO2-peptide composites.
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Affiliation(s)
- Erika L Buckle
- Department of Chemistry , University of Washington , Box 351700 , Seattle , Washington 98195 , United States
| | - June S Lum
- Biological Sciences and Technology Team , US Army Natick Soldier Research, Development and Engineering Center , Natick , Massachusetts 01760 , United States
| | - Adrienne M Roehrich
- Department of Chemistry , University of Washington , Box 351700 , Seattle , Washington 98195 , United States
| | - Robert E Stote
- Biological Sciences and Technology Team , US Army Natick Soldier Research, Development and Engineering Center , Natick , Massachusetts 01760 , United States
| | - Branden Vandermoon
- Department of Chemistry , University of Washington , Box 351700 , Seattle , Washington 98195 , United States
| | - Martin Dracinsky
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo 2 , 16610 Prague , Czech Republic
| | - Shaun F Filocamo
- Biological Sciences and Technology Team , US Army Natick Soldier Research, Development and Engineering Center , Natick , Massachusetts 01760 , United States
| | - Gary P Drobny
- Department of Chemistry , University of Washington , Box 351700 , Seattle , Washington 98195 , United States
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11
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Kokubun K, Matsumura S, Yudasaka M, Iijima S, Shiba K. Immobilization of a carbon nanomaterial-based localized drug-release system using a bispecific material-binding peptide. Int J Nanomedicine 2018; 13:1643-1652. [PMID: 29588591 PMCID: PMC5862015 DOI: 10.2147/ijn.s155913] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Introduction Inorganic materials are widely used in medical devices, such as artificial hearts, vessels, and joints, in stents, and as nanocarriers for drug-delivery systems. Carbon nanomaterials are of particular interest due to their biological inertness and their capability to accommodate molecules. Several attempts have been proposed, in which carbon nanomaterials are used as nanocarriers for the systemic delivery of drugs. Materials and methods We developed a drug-delivery system in which oxidized single-walled carbon nanohorns (oxSWNHs) were immobilized on a titanium (Ti) surface using material-binding peptides to enable localized drug delivery. For this purpose, we utilized a bispecific peptidic aptamer comprising a core sequence of a Ti-binding peptide and a SWNH-binding peptide to immobilize oxSWNHs on Ti. Results Scanning electron microscopy was used to confirm the presence of oxSWNHs adsorbed onto the Ti surface, and a quartz crystal microbalance was used to evaluate the binding process during oxSWNH adsorption. The oxSWNHs-ornamented Ti substrate was nontoxic to cells and released biologically active dexamethasone over a sustained period. Conclusion This oxSWNHs-immobilized system can be used to modify the surface of Ti in implants and be loaded with drugs that stimulate osteogenesis and bone regeneration.
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Affiliation(s)
- Katsutoshi Kokubun
- Division of Protein Engineering, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan.,Department of Clinical Pathophysiology, Tokyo Dental College, Tokyo, Japan
| | - Sachiko Matsumura
- Division of Protein Engineering, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Masako Yudasaka
- Nanomaterials Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan.,Graduate School of Science and Technology, Meijo University, Nagoya, Japan
| | - Sumio Iijima
- Nanomaterials Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan.,Graduate School of Science and Technology, Meijo University, Nagoya, Japan
| | - Kiyotaka Shiba
- Division of Protein Engineering, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
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12
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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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13
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Buckle EL, Roehrich A, Vandermoon B, Drobny GP. Comparative Study of Secondary Structure and Interactions of the R5 Peptide in Silicon Oxide and Titanium Oxide Coprecipitates Using Solid-State NMR Spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:10517-10524. [PMID: 28898103 PMCID: PMC6786483 DOI: 10.1021/acs.langmuir.7b01048] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A biomimetic, peptide-mediated approach to inorganic nanostructure formation is of great interest as an alternative to industrial production methods. To investigate the role of peptide structure on silica (SiO2) and titania (TiO2) morphologies, we use the R5 peptide domain derived from the silaffin protein to produce uniform SiO2 and TiO2 nanostructures from the precursor silicic acid and titanium bis(ammonium lactato)dihydroxide, respectively. The resulting biosilica and biotitania nanostructures are characterized using scanning electron microscopy. To investigate the process of R5-mediated SiO2 and TiO2 formation, we carry out 1D and 2D solid-state NMR (ssNMR) studies on R5 samples with uniformly 13C- and 15N-labeled residues to determine the backbone and side-chain chemical shifts. 13C chemical shift data are in turn used to determine peptide backbone torsion angles and secondary structure for the R5 peptide neat, in silica, and in titania. We are thus able to assess the impact of the different mineral environments on peptide structure, and we can further elucidate from 13C chemical shifts change the degree to which various side chains are in close proximity to the mineral phases. These comparisons add to the understanding of the role of R5 and its structure in both SiO2 and TiO2 formation.
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Affiliation(s)
- Erika L Buckle
- Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195, United States
| | - Adrienne Roehrich
- Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195, United States
| | - Branden Vandermoon
- Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195, United States
| | - Gary P Drobny
- Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195, United States
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14
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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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15
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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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16
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Identification and binding mechanism of phage displayed peptides with specific affinity to acidalkali treated titanium. Colloids Surf B Biointerfaces 2016; 146:307-17. [DOI: 10.1016/j.colsurfb.2016.06.032] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 05/27/2016] [Accepted: 06/18/2016] [Indexed: 11/20/2022]
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17
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Sultan AM, Westcott ZC, Hughes ZE, Palafox-Hernandez JP, Giesa T, Puddu V, Buehler MJ, Perry CC, Walsh TR. Aqueous Peptide-TiO2 Interfaces: Isoenergetic Binding via Either Entropically or Enthalpically Driven Mechanisms. ACS APPLIED MATERIALS & INTERFACES 2016; 8:18620-18630. [PMID: 27355097 DOI: 10.1021/acsami.6b05200] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A major barrier to the systematic improvement of biomimetic peptide-mediated strategies for the controlled growth of inorganic nanomaterials in environmentally benign conditions lies in the lack of clear conceptual connections between the sequence of the peptide and its surface binding affinity, with binding being facilitated by noncovalent interactions. Peptide conformation, both in the adsorbed and in the nonadsorbed state, is the key relationship that connects peptide-materials binding with peptide sequence. Here, we combine experimental peptide-titania binding characterization with state-of-the-art conformational sampling via molecular simulations to elucidate these structure/binding relationships for two very different titania-binding peptide sequences. The two sequences (Ti-1, QPYLFATDSLIK; Ti-2, GHTHYHAVRTQT) differ in their overall hydropathy, yet via quartz-crystal microbalance measurements and predictions from molecular simulations, we show these sequences both support very similar, strong titania-binding affinities. Our molecular simulations reveal that the two sequences exhibit profoundly different modes of surface binding, with Ti-1 acting as an entropically driven binder while Ti-2 behaves as an enthalpically driven binder. The integrated approach presented here provides a rational basis for peptide sequence engineering to achieve the in situ growth and organization of titania nanostructures in aqueous media and for the design of sequences suitable for a range of technological applications that involve the interface between titania and biomolecules.
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Affiliation(s)
- Anas M Sultan
- Institute for Frontier Materials, Deakin University , Geelong, Victoria 3216, Australia
| | - Zayd C Westcott
- Interdisciplinary Biomedical Research Centre, School of Science and Technology, Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS, United Kingdom
| | - Zak E Hughes
- Institute for Frontier Materials, Deakin University , Geelong, Victoria 3216, Australia
| | | | - Tristan Giesa
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Department of Civil and Environmental Engineering, Massachusetts Institute of Technology , 77 Massachusetts Ave, Cambridge, Massachusetts 02139, United States
| | - Valeria Puddu
- Interdisciplinary Biomedical Research Centre, School of Science and Technology, Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS, United Kingdom
| | - Markus J Buehler
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Department of Civil and Environmental Engineering, Massachusetts Institute of Technology , 77 Massachusetts Ave, Cambridge, Massachusetts 02139, United States
| | - Carole C Perry
- Interdisciplinary Biomedical Research Centre, School of Science and Technology, Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS, United Kingdom
| | - Tiffany R Walsh
- Institute for Frontier Materials, Deakin University , Geelong, Victoria 3216, Australia
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18
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Kim SO, Jackman JA, Mochizuki M, Yoon BK, Hayashi T, Cho NJ. Correlating single-molecule and ensemble-average measurements of peptide adsorption onto different inorganic materials. Phys Chem Chem Phys 2016; 18:14454-9. [PMID: 27174015 DOI: 10.1039/c6cp01168c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The coating of solid-binding peptides (SBPs) on inorganic material surfaces holds significant potential for improved surface functionalization at nano-bio interfaces. In most related studies, the goal has been to engineer peptides with selective and high binding affinity for a target material. The role of the material substrate itself in modulating the adsorption behavior of a peptide molecule remains less explored and there are few studies that compare the interaction of one peptide with different inorganic substrates. Herein, using a combination of two experimental techniques, we investigated the adsorption of a 16 amino acid-long random coil peptide to various inorganic substrates - gold, silicon oxide, titanium oxide and aluminum oxide. Quartz crystal microbalance-dissipation (QCM-D) experiments were performed in order to measure the peptide binding affinity for inorganic solid supports at the ensemble average level, and atomic force microscopy (AFM) experiments were conducted in order to determine the adhesion force of a single peptide molecule. A positive trend was observed between the total mass uptake of attached peptide and the single-molecule adhesion force on each substrate. Peptide affinity for gold was appreciably greater than for the oxide substrates. Collectively, the results obtained in this study offer insight into the ways in which inorganic materials can differentially influence and modulate the adhesion of SBPs.
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Affiliation(s)
- Seong-Oh Kim
- School of Materials Science and Engineering and Centre for Biomimetic Sensor Science, Nanyang Technological University, 50 Nanyang Drive 637553, Singapore.
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19
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Suzuki Y, Shindo H, Asakura T. Structure and Dynamic Properties of a Ti-Binding Peptide Bound to TiO2 Nanoparticles As Accessed by 1H NMR Spectroscopy. J Phys Chem B 2016; 120:4600-7. [DOI: 10.1021/acs.jpcb.6b03260] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Yu Suzuki
- Tenure-Track
Program for Innovative Research, University of Fukui, 3-9-1, Bunkyo, Fukui-shi, Fukui 910-8507, Japan
| | - Heisaburo Shindo
- Department
of Biotechnology, Tokyo University of Agriculture and Technology, 2-24-16,
Nakacho, Koganei, Tokyo 184-8588, Japan
| | - Tetsuo Asakura
- Department
of Biotechnology, Tokyo University of Agriculture and Technology, 2-24-16,
Nakacho, Koganei, Tokyo 184-8588, Japan
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20
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Self-assembly and photocatalytic activity of branched silicatein/silintaphin filaments decorated with silicatein-synthesized TiO2 nanoparticles. Bioprocess Biosyst Eng 2016; 39:1477-86. [DOI: 10.1007/s00449-016-1619-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 04/26/2016] [Indexed: 12/18/2022]
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21
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Yazici H, O'Neill MB, Kacar T, Wilson BR, Oren EE, Sarikaya M, Tamerler C. Engineered Chimeric Peptides as Antimicrobial Surface Coating Agents toward Infection-Free Implants. ACS APPLIED MATERIALS & INTERFACES 2016; 8:5070-81. [PMID: 26795060 PMCID: PMC5310947 DOI: 10.1021/acsami.5b03697] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Prevention of bacterial colonization and consequent biofilm formation remains a major challenge in implantable medical devices. Implant-associated infections are not only a major cause of implant failures but also their conventional treatment with antibiotics brings further complications due to the escalation in multidrug resistance to a variety of bacterial species. Owing to their unique properties, antimicrobial peptides (AMPs) have gained significant attention as effective agents to combat colonization of microorganisms. These peptides have been shown to exhibit a wide spectrum of activities with specificity to a target cell while having a low tendency for developing bacterial resistance. Engineering biomaterial surfaces that feature AMP properties, therefore, offer a promising approach to prevent implant infections. Here, we engineered a chimeric peptide with bifunctionality that both forms a robust solid-surface coating while presenting antimicrobial property. The individual domains of the chimeric peptides were evaluated for their solid-binding kinetics to titanium substrate as well as for their antimicrobial properties in solution. The antimicrobial efficacy of the chimeric peptide on the implant material was evaluated in vitro against infection by a variety of bacteria, including Streptococcus mutans, Staphylococcus. epidermidis, and Escherichia coli, which are commonly found in oral and orthopedic implant related surgeries. Our results demonstrate significant improvement in reducing bacterial colonization onto titanium surfaces below the detectable limit. Engineered chimeric peptides with freely displayed antimicrobial domains could be a potential solution for developing infection-free surfaces by engineering implant interfaces with highly reduced bacterial colonization property.
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Affiliation(s)
- Hilal Yazici
- Genetically Engineered Materials Science and Engineering Center, Department of Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
- Department of Molecular Biology and Genetics, Molecular Biology, Biotechnology and Genetic Center, Istanbul Technical University, Istanbul 34469, Turkey
| | - Mary B. O'Neill
- Genetically Engineered Materials Science and Engineering Center, Department of Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Turgay Kacar
- Genetically Engineered Materials Science and Engineering Center, Department of Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
- Department of Molecular Biology and Genetics, Molecular Biology, Biotechnology and Genetic Center, Istanbul Technical University, Istanbul 34469, Turkey
| | - Brandon R. Wilson
- Genetically Engineered Materials Science and Engineering Center, Department of Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - E. Emre Oren
- Genetically Engineered Materials Science and Engineering Center, Department of Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
- Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
| | - Mehmet Sarikaya
- Genetically Engineered Materials Science and Engineering Center, Department of Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Candan Tamerler
- Genetically Engineered Materials Science and Engineering Center, Department of Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
- Department of Mechanical Engineering, Bioengineering Research Center, University of Kansas, Lawrence, Kansas 66045, United States
- Corresponding Author Phone: 785-864-2984. . Corresponding author address: Bioengineering Research Center, Department of Mechanical Engineering, 1530 W, 15th St, Learned Hall, Lawrence, KS 66047
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22
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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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23
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Jutz G, van Rijn P, Santos Miranda B, Böker A. Ferritin: a versatile building block for bionanotechnology. Chem Rev 2015; 115:1653-701. [PMID: 25683244 DOI: 10.1021/cr400011b] [Citation(s) in RCA: 284] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Günther Jutz
- DWI - Leibniz-Institut für Interaktive Materialien e.V., Lehrstuhl für Makromolekulare Materialien und Oberflächen, RWTH Aachen University , Forckenbeckstrasse 50, D-52056 Aachen, Germany
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24
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Agosta L, Zollo G, Arcangeli C, Buonocore F, Gala F, Celino M. Water driven adsorption of amino acids on the (101) anatase TiO2 surface: an ab initio study. Phys Chem Chem Phys 2015; 17:1556-61. [DOI: 10.1039/c4cp03056g] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Arginine and lysine are stably adsorbed onto the (101) anatase TiO2 surface in water solution.
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Affiliation(s)
- Lorenzo Agosta
- Dipartimento di Scienze di Base e Applicate per l'Ingegneria (Sezione di Fisica)
- Università di Roma “La Sapienza”
- 00161 Rome
- Italy
- NAST Centre c/o Università degli Studi di Roma Tor Vergata
| | - Giuseppe Zollo
- Dipartimento di Scienze di Base e Applicate per l'Ingegneria (Sezione di Fisica)
- Università di Roma “La Sapienza”
- 00161 Rome
- Italy
| | - Caterina Arcangeli
- NAST Centre c/o Università degli Studi di Roma Tor Vergata
- Department of Physics
- 00133 Rome
- Italy
- ENEA Italian National Agency for New Technologies
| | - Francesco Buonocore
- NAST Centre c/o Università degli Studi di Roma Tor Vergata
- Department of Physics
- 00133 Rome
- Italy
- Center for Nanophase Materials Sciences Oak Ridge National Laboratory
| | - Fabrizio Gala
- Dipartimento di Scienze di Base e Applicate per l'Ingegneria (Sezione di Fisica)
- Università di Roma “La Sapienza”
- 00161 Rome
- Italy
| | - Massimo Celino
- NAST Centre c/o Università degli Studi di Roma Tor Vergata
- Department of Physics
- 00133 Rome
- Italy
- ENEA Italian National Agency for New Technologies
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25
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Sultan AM, Hughes ZE, Walsh TR. Binding affinities of amino acid analogues at the charged aqueous titania interface: implications for titania-binding peptides. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:13321-13329. [PMID: 25317483 DOI: 10.1021/la503312d] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Despite the extensive utilization of biomolecule-titania interfaces, biomolecular recognition and interactions at the aqueous titania interface remain far from being fully understood. Here, atomistic molecular dynamics simulations, in partnership with metadynamics, are used to calculate the free energy of adsorption of different amino acid side chain analogues at the negatively-charged aqueous rutile TiO2 (110) interface, under conditions corresponding with neutral pH. Our calculations predict that charged amino acid analogues have a relatively high affinity to the titania surface, with the arginine analogue predicted to be the strongest binder. Interactions between uncharged amino acid analogues and titania are found to be repulsive or weak at best. All of the residues that bound to the negatively-charged interface show a relatively stronger adsorption compared with the charge-neutral interface, including the negatively-charged analogue. Of the analogues that are found to bind to the titania surface, the rank ordering of the binding affinities is predicted to be "arginine" > "lysine" ≈ aspartic acid > "serine". This is the same ordering as was found previously for the charge-neutral aqueous titania interface. Our results show very good agreement with available experimental data and can provide a baseline for the interpretation of peptide-TiO2 adsorption data.
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Affiliation(s)
- Anas M Sultan
- Institute for Frontier Materials, Deakin University , Geelong, VIC 3216, Australia
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26
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Fukuta M, Zheng B, Uenuma M, Okamoto N, Uraoka Y, Yamashita I, Watanabe H. Controlled charged amino acids of Ti-binding peptide for surfactant-free selective adsorption. Colloids Surf B Biointerfaces 2014; 118:25-30. [PMID: 24727527 DOI: 10.1016/j.colsurfb.2014.03.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 03/15/2014] [Accepted: 03/15/2014] [Indexed: 11/17/2022]
Abstract
The adsorption mechanism of titanium-binding peptide (TBP) on metal oxide substrates was investigated by evaluating the adsorption behavior of ferritins with various alanine-substituted TBPs. Results revealed that (a) a positively charged amino acid, lysine (K) or arginine (R), in TBP can anchor ferritin to negative zeta-potential substrates, (b) the adsorption force of K is stronger than R, and (c) local electrostatic interactions and flexibility of TBP directly affect adsorption. Based on these findings, selective ferritin adsorption on SiO2 with TiOX patterned surfaces in a surfactant-free condition was demonstrated. Alanine-substituted TBP with one positively charged amino acid (K) and one negatively charged amino acid (D), achieved ferritin-selective adsorption without a surfactant. The importance of controlled electrostatic forces between TBP and a substrate for selective adsorption without a surfactant was clearly demonstrated.
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Affiliation(s)
- Megumi Fukuta
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Japan Science and Technology Agency, CREST, 5 Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan.
| | - Bin Zheng
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan; Japan Science and Technology Agency, CREST, 5 Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Mutsunori Uenuma
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan; Japan Science and Technology Agency, CREST, 5 Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Naofumi Okamoto
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Yukiharu Uraoka
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan; Japan Science and Technology Agency, CREST, 5 Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Ichiro Yamashita
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan; Japan Science and Technology Agency, CREST, 5 Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Heiji Watanabe
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Japan Science and Technology Agency, CREST, 5 Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
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27
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Hughes ZE, Wright LB, Walsh TR. Biomolecular adsorption at aqueous silver interfaces: first-principles calculations, polarizable force-field simulations, and comparisons with gold. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:13217-13229. [PMID: 24079907 DOI: 10.1021/la402839q] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The molecular simulation of biomolecules adsorbed at noble metal interfaces can assist in the development of bionanotechnology applications. In line with advances in polarizable force fields for adsorption at aqueous gold interfaces, there is scope for developing a similar force field for silver. One way to accomplish this is via the generation of in vacuo adsorption energies calculated using first-principles approaches for a wide range of different but biologically relevant small molecules, including water. Here, we present such first-principles data for a comprehensive range of bio-organic molecules obtained from plane-wave density functional theory calculations using the vdW-DF functional. As reported previously for the gold force field, GolP-CHARMM (Wright, L. B.; Rodger, P. M.; Corni, S.; Walsh, T. R. GolP-CHARMM: first-principles based force-fields for the interaction of proteins with Au(111) and Au(100). J. Chem. Theory Comput. 2013, 9, 1616-1630), we have used these data to construct a a new force field, AgP-CHARMM, suitable for the simulation of biomolecules at the aqueous Ag(111) and Ag(100) interfaces. This force field is derived to be consistent with GolP-CHARMM such that adsorption on Ag and Au can be compared on an equal footing. Our force fields are used to evaluate the water overlayer stability on both silver and gold, finding good agreement with known behaviors. We also calculate and compare the structuring (spatial and orientational) of liquid water adsorbed at both silver and gold. Finally, we report the adsorption free energy of a range of amino acids at both the Au(111) and Ag(111) aqueous interfaces, calculated using metadynamics. Stronger adsorption on gold was noted in most cases, with the exception being the carboxylate group present in aspartic acid. Our findings also indicate differences in the binding free energy profile between silver and gold for some amino acids, notably for His and Arg. Our analysis suggests that the relatively stronger structuring of the first water layer on silver, relative to gold, could give rise to these differences.
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Affiliation(s)
- Zak E Hughes
- Institute for Frontier Materials, Deakin University , Geelong, Victoria 3216, Australia
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28
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Mori T, Hamers RJ, Pedersen JA, Cui Q. An Explicit Consideration of Desolvation is Critical to Binding Free Energy Calculations of Charged Molecules at Ionic Surfaces. J Chem Theory Comput 2013; 9:5059-69. [DOI: 10.1021/ct400487e] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Toshifumi Mori
- Department
of Chemistry and Theoretical Chemistry Institute, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Robert J. Hamers
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Joel A. Pedersen
- Department of Soil Science, Civil & Environmental Engineering, and Chemistry, University of Wisconsin—Madison, 1525 Observatory Drive, Madison, Wisconsin 53706, United States
| | - Qiang Cui
- Department
of Chemistry and Theoretical Chemistry Institute, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
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29
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Fukuta M, Zettsu N, Yamashita I, Uraoka Y, Watanabe H. The adsorption mechanism of titanium-binding ferritin to amphoteric oxide. Colloids Surf B Biointerfaces 2013; 102:435-40. [DOI: 10.1016/j.colsurfb.2012.07.042] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Revised: 07/11/2012] [Accepted: 07/12/2012] [Indexed: 10/28/2022]
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30
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Schneider J, Colombi Ciacchi L. Specific Material Recognition by Small Peptides Mediated by the Interfacial Solvent Structure. J Am Chem Soc 2012; 134:2407-13. [DOI: 10.1021/ja210744g] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Julian Schneider
- Hybrid Materials
Interfaces
Group, Faculty of Production Engineering and Bremen Center for Computational
Materials Science, University of Bremen, D-28359 Bremen, Germany
| | - Lucio Colombi Ciacchi
- Hybrid Materials
Interfaces
Group, Faculty of Production Engineering and Bremen Center for Computational
Materials Science, University of Bremen, D-28359 Bremen, Germany
- Fraunhofer Institute for Manufacturing Technology and Applied Materials Research IFAM, D-28359 Bremen, Germany
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31
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Arai Y, Okabe KI, Sekiguchi H, Hayashi T, Hara M. Nanoscale chemical composition analysis using peptides targeting inorganic materials. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:2478-2483. [PMID: 21284389 DOI: 10.1021/la104178h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Chemical composition analysis by scanning probe microscopy (SPM) in water is a method whose introduction has been long-awaited. Here we propose a simple method for performing chemical composition analyses of solid surfaces in water using atomic force microscopes (AFMs) with probes functionalized with peptides targeting inorganic materials. In this work, bicompositional surfaces of gold and titanium oxide were scanned with AFM probes modified with the titanium-binding peptide (TBP). We found that surface chemical composition clearly appeared as contrast in the mapping images of adhesion forces with nanometer-scale resolution. In this Article, we further discuss appropriate designs of the AFM probes and appropriate imaging conditions for the chemical composition analysis based on the results of force measurements of the single TBP-titanium bond.
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Affiliation(s)
- Yuki Arai
- 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
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32
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Material binding peptides for nanotechnology. Molecules 2011; 16:1426-51. [PMID: 21307821 PMCID: PMC6259601 DOI: 10.3390/molecules16021426] [Citation(s) in RCA: 122] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Revised: 02/06/2011] [Accepted: 02/08/2011] [Indexed: 12/20/2022] Open
Abstract
Remarkable progress has been made to date in the discovery of material binding peptides and their utilization in nanotechnology, which has brought new challenges and opportunities. Nowadays phage display is a versatile tool, important for the selection of ligands for proteins and peptides. This combinatorial approach has also been adapted over the past decade to select material-specific peptides. Screening and selection of such phage displayed material binding peptides has attracted great interest, in particular because of their use in nanotechnology. Phage display selected peptides are either synthesized independently or expressed on phage coat protein. Selected phage particles are subsequently utilized in the synthesis of nanoparticles, in the assembly of nanostructures on inorganic surfaces, and oriented protein immobilization as fusion partners of proteins. In this paper, we present an overview on the research conducted on this area. In this review we not only focus on the selection process, but also on molecular binding characterization and utilization of peptides as molecular linkers, molecular assemblers and material synthesizers.
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33
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Exploitation of peptide motif sequences and their use in nanobiotechnology. Curr Opin Biotechnol 2010; 21:412-25. [DOI: 10.1016/j.copbio.2010.07.008] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Revised: 07/13/2010] [Accepted: 07/15/2010] [Indexed: 12/18/2022]
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Ikeda T, Ninomiya KI, Hirota R, Kuroda A. Single-step affinity purification of recombinant proteins using the silica-binding Si-tag as a fusion partner. Protein Expr Purif 2010; 71:91-5. [DOI: 10.1016/j.pep.2009.12.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2009] [Revised: 12/16/2009] [Accepted: 12/16/2009] [Indexed: 10/20/2022]
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