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Zhao Z, Yu W, Yang W, Zhang G, Huang C, Han J, Narain R, Zeng H. Dual-Protection Inorganic-Protein Coating on Mg-Based Biomaterials through Tooth-Enamel-Inspired Biomineralization. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2313211. [PMID: 38339916 DOI: 10.1002/adma.202313211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/06/2024] [Indexed: 02/12/2024]
Abstract
Biocompatible magnesium alloys represent revolutionary implantable materials in dentistry and orthopedics but face challenges due to rapid biocorrosion, necessitating protective coatings to mitigate dysfunction. Directly integrating durable protective coatings onto Mg surfaces is challenging because of intrinsic low coating compactness. Herein, inspired by tooth enamel, a novel highly compact dual-protection inorganic-protein (inorganicPro) coating is in situ constructed on Mg surfaces through bovine serum albumin (BSA) protein-boosted reaction between sodium fluoride (NaF) and Mg substrates. The association of Mg ions and BSA establishes a local hydrophobic domain that lowers the formation enthalpy of NaMgF3 nanoparticles. This process generates finer nanoparticles that function as "bricks," facilitating denser packing, consequently reducing voidage inside coatings by over 50% and reinforcing mechanical durability. Moreover, the incorporation of BSA in and on the coatings plays two synergistic roles: 1) acting as "mortar" to seal residual cracks within coatings, thereby promoting coating compactness and tripling anticorrosion performance, and 2) mitigating fouling-accelerated biocorrosion in complex biosystems via tenfold resistance against biofoulant attachments, including biofluids, proteins, and metabolites. This innovative strategy, leveraging proteins to alter inorganic reactions, benefits the future coating design for Mg-based and other metallic materials with tailored anticorrosion and antifouling performances.
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Affiliation(s)
- Ziqian Zhao
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta, T6G 1H9, Canada
| | - Wenting Yu
- Department of Orthodontics, Beijing Stomatological Hospital and School of Stomatology, Capital Medical University, Beijing, 100050, China
| | - Wenshuai Yang
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta, T6G 1H9, Canada
| | - Guohao Zhang
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, National Center of Stomatology, National Clinical Research Center for Oral Diseases, National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing Key Laboratory of Digital Stomatology, Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health, NMPA Key Laboratory for Dental Materials, Beijing, 100081, China
| | - Charley Huang
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta, T6G 1H9, Canada
| | - Jianmin Han
- Department of Dental Materials, Peking University School and Hospital of Stomatology, National Center of Stomatology, National Clinical Research Center for Oral Diseases, National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing Key Laboratory of Digital Stomatology, Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health, NMPA Key Laboratory for Dental Materials, Beijing, 100081, China
| | - Ravin Narain
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta, T6G 1H9, Canada
| | - Hongbo Zeng
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta, T6G 1H9, Canada
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2
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Armstrong Z, Jordahl D, MacRae A, Li Q, Lenertz M, Shen P, Botserovska A, Feng L, Ugrinov A, Yang Z. A Protocol for Custom Biomineralization of Enzymes in Metal-Organic Frameworks (MOFs). Bio Protoc 2024; 14:e4930. [PMID: 38379827 PMCID: PMC10875352 DOI: 10.21769/bioprotoc.4930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 11/16/2023] [Accepted: 01/04/2024] [Indexed: 02/22/2024] Open
Abstract
Enzyme immobilization offers a number of advantages that improve biocatalysis; however, finding a proper way to immobilize enzymes is often a challenging task. Implanting enzymes in metal-organic frameworks (MOFs) via co-crystallization, also known as biomineralization, provides enhanced reusability and stability with minimal perturbation and substrate selectivity to the enzyme. Currently, there are limited metal-ligand combinations with a proper protocol guiding the experimental procedures. We have recently explored 10 combinations that allow custom immobilization of enzymes according to enzyme stability and activity in different metals/ligands. Here, as a follow-up of that work, we present a protocol for how to carry out custom immobilization of enzymes using the available combinations of metal ions and ligands. Detailed procedures to prepare metal ions, ligands, and enzymes for their co-crystallization, together with characterization and assessment, are discussed. Precautions for each experimental step and result analysis are highlighted as well. This protocol is important for enzyme immobilization in various research and industrial fields. Key features • A wide selection of metal ions and ligands allows for the immobilization of enzymes in metal-organic frameworks (MOFs) via co-crystallization. • Step-by-step enzyme immobilization procedure via co-crystallization of metal ions, organic linkers, and enzymes. • Practical considerations and experimental conditions to synthesize the enzyme@MOF biocomposites are discussed. • The demonstrated method can be generalized to immobilize other enzymes and find other metal ion/ligand combinations to form MOFs in water and host enzymes.
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Affiliation(s)
- Zoe Armstrong
- Department of Chemistry and Biochemistry, North
Dakota State University, Fargo, ND, USA
| | - Drew Jordahl
- Department of Chemistry and Biochemistry, North
Dakota State University, Fargo, ND, USA
| | - Austin MacRae
- Department of Chemistry and Biochemistry, North
Dakota State University, Fargo, ND, USA
| | - Qiaobin Li
- Department of Chemistry and Biochemistry, North
Dakota State University, Fargo, ND, USA
| | - Mary Lenertz
- Department of Chemistry and Biochemistry, North
Dakota State University, Fargo, ND, USA
| | | | | | - Li Feng
- Department of Chemistry and Biochemistry, North
Dakota State University, Fargo, ND, USA
| | - Angel Ugrinov
- Department of Chemistry and Biochemistry, North
Dakota State University, Fargo, ND, USA
| | - Zhongyu Yang
- Department of Chemistry and Biochemistry, North
Dakota State University, Fargo, ND, USA
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3
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Knight BM, Edgar KJ, De Yoreo JJ, Dove PM. Chitosan as a Canvas for Studies of Macromolecular Controls on CaCO 3 Biological Crystallization. Biomacromolecules 2023; 24:1078-1102. [PMID: 36853173 DOI: 10.1021/acs.biomac.2c01394] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
A mechanistic understanding of how macromolecules, typically as an organic matrix, nucleate and grow crystals to produce functional biomineral structures remains elusive. Advances in structural biology indicate that polysaccharides (e.g., chitin) and negatively charged proteoglycans (due to carboxyl, sulfate, and phosphate groups) are ubiquitous in biocrystallization settings and play greater roles than currently recognized. This review highlights studies of CaCO3 crystallization onto chitinous materials and demonstrates that a broader understanding of macromolecular controls on mineralization has not emerged. With recent advances in biopolymer chemistry, it is now possible to prepare chitosan-based hydrogels with tailored functional group compositions. By deploying these characterized compounds in hypothesis-based studies of nucleation rate, quantitative relationships between energy barrier to crystallization, macromolecule composition, and solvent structuring can be determined. This foundational knowledge will help researchers understand composition-structure-function controls on mineralization in living systems and tune the designs of new materials for advanced applications.
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Affiliation(s)
- Brenna M Knight
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
- Department of Geosciences, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Kevin J Edgar
- Department of Sustainable Biomaterials, Virginia Tech, Blacksburg, Virginia 24061, United States
- Macromolecules Innovation Institute, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - James J De Yoreo
- Department of Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Patricia M Dove
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
- Macromolecules Innovation Institute, Virginia Tech, Blacksburg, Virginia 24061, United States
- Department of Geosciences, Virginia Tech, Blacksburg, Virginia 24061, United States
- Department of Materials Science and Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
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4
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Shao L, Ma J, Prelesnik JL, Zhou Y, Nguyen M, Zhao M, Jenekhe SA, Kalinin SV, Ferguson AL, Pfaendtner J, Mundy CJ, De Yoreo JJ, Baneyx F, Chen CL. Hierarchical Materials from High Information Content Macromolecular Building Blocks: Construction, Dynamic Interventions, and Prediction. Chem Rev 2022; 122:17397-17478. [PMID: 36260695 DOI: 10.1021/acs.chemrev.2c00220] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Hierarchical materials that exhibit order over multiple length scales are ubiquitous in nature. Because hierarchy gives rise to unique properties and functions, many have sought inspiration from nature when designing and fabricating hierarchical matter. More and more, however, nature's own high-information content building blocks, proteins, peptides, and peptidomimetics, are being coopted to build hierarchy because the information that determines structure, function, and interfacial interactions can be readily encoded in these versatile macromolecules. Here, we take stock of recent progress in the rational design and characterization of hierarchical materials produced from high-information content blocks with a focus on stimuli-responsive and "smart" architectures. We also review advances in the use of computational simulations and data-driven predictions to shed light on how the side chain chemistry and conformational flexibility of macromolecular blocks drive the emergence of order and the acquisition of hierarchy and also on how ionic, solvent, and surface effects influence the outcomes of assembly. Continued progress in the above areas will ultimately usher in an era where an understanding of designed interactions, surface effects, and solution conditions can be harnessed to achieve predictive materials synthesis across scale and drive emergent phenomena in the self-assembly and reconfiguration of high-information content building blocks.
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Affiliation(s)
- Li Shao
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Jinrong Ma
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington 98195, United States
| | - Jesse L Prelesnik
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Yicheng Zhou
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Mary Nguyen
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States.,Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Mingfei Zhao
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Samson A Jenekhe
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States.,Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Sergei V Kalinin
- Department of Materials Science and Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Andrew L Ferguson
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Jim Pfaendtner
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.,Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Christopher J Mundy
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.,Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - James J De Yoreo
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.,Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - François Baneyx
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington 98195, United States.,Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Chun-Long Chen
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.,Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
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5
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Wu Z, Xiong W. Neumann's principle based eigenvector approach for deriving non-vanishing tensor elements for nonlinear optics. J Chem Phys 2022; 157:134702. [PMID: 36209027 PMCID: PMC9531997 DOI: 10.1063/5.0118711] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 09/05/2022] [Indexed: 11/14/2022] Open
Abstract
Physical properties are commonly represented by tensors, such as optical susceptibilities. The conventional approach of deriving non-vanishing tensor elements of symmetric systems relies on the intuitive consideration of positive/negative sign flipping after symmetry operations, which could be tedious and prone to miscalculation. Here, we present a matrix-based approach that gives a physical picture centered on Neumann's principle. The principle states that symmetries in geometric systems are adopted by their physical properties. We mathematically apply the principle to the tensor expressions and show a procedure with clear physical intuition to derive non-vanishing tensor elements based on eigensystems. The validity of the approach is demonstrated by examples of commonly known second and third-order nonlinear susceptibilities of chiral/achiral surfaces, together with complicated scenarios involving symmetries such as D6 and Oh symmetries. We then further applied this method to higher-rank tensors that are useful for 2D and high-order spectroscopy. We also extended our approach to derive nonlinear tensor elements with magnetization, which is critical for measuring spin polarization on surfaces for quantum information technologies. A Mathematica code based on this generalized approach is included that can be applied to any symmetry and higher order nonlinear processes.
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Affiliation(s)
- Zishan Wu
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, California 92093, USA
| | - Wei Xiong
- Authors to whom correspondence should be addressed: and
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6
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Wang K, Luo F, Wang L, Zhang B, Fan Y, Wang X, Xu D, Zhang X. Biomineralization from the Perspective of Ion Aggregation: Calcium Phosphate Nucleation in the Physiological Environment. ACS APPLIED MATERIALS & INTERFACES 2021; 13:49519-49534. [PMID: 34609125 DOI: 10.1021/acsami.1c15393] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Biomineralization is an important process of bone tissue generation. Calcium (Ca) and phosphate (P) ions aggregate and nucleate under the regulation of biomolecules at the initial mineralization stage. Due to the complexity of the physiological environment, the movement behavior and mineralization mechanism of calcium and phosphate ions, as well as the effect of biomolecules on them, are not clear. In this study, computer simulations and experimental verification were applied to investigate the characteristics of the initial biomineralization from the view of ion aggregation and nucleation. The results prove that P ions play a more important role in mineralization than Ca ions. The guanidyl group and surrounding carboxyl terminal groups are a potential excellent nucleation domain on proteins. The interval distribution of acidic/basic residues on protein is more conductive to the formation of large Ca and P ions clusters. The involvement of protein could increase the probability of hydroxyapatite phase precipitation, especially in the presence of a helical conformation. The detailed information on Ca and P ions behavior provided by the computer simulations is helpful for further understanding the mechanism of biomineralization, which will promote the development of bone repair materials to the biomimetic mineralized materials.
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Affiliation(s)
- Kefeng Wang
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, China
- Research Center for Material Genome Engineering, Sichuan University, Chengdu 610064, China
| | - Fengxiong Luo
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, China
| | - Ling Wang
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, China
| | - Boqing Zhang
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, China
| | - Yujiang Fan
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, China
| | - Xin Wang
- Research Center for Material Genome Engineering, Sichuan University, Chengdu 610064, China
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Dingguo Xu
- Research Center for Material Genome Engineering, Sichuan University, Chengdu 610064, China
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Xingdong Zhang
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, China
- Research Center for Material Genome Engineering, Sichuan University, Chengdu 610064, China
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7
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Metal-organic frameworks conjugated with biomolecules as efficient platforms for development of biosensors. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116285] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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8
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Sattar MA. Interface Structure and Dynamics in Polymer‐Nanoparticle Hybrids: A Review on Molecular Mechanisms Underlying the Improved Interfaces. ChemistrySelect 2021. [DOI: 10.1002/slct.202100831] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Mohammad Abdul Sattar
- R&D Centre MRF Limited Chennai 600019 India
- Colloid and Interface Chemistry Laboratory Department of Chemistry Indian Institute of Technology Madras Chennai 600036 India
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9
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Yamashita S, Sudo T, Kamiya H, Okada Y. Ligand Exchange Reactions between Phosphonic Acids at TiO
2
Nanoparticle Surfaces. ChemistrySelect 2021. [DOI: 10.1002/slct.202100541] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Shohei Yamashita
- Department of Chemical Engineering Tokyo University of Agriculture and Technology 2-24-16 Naka-cho, Koganei Tokyo 184-8588 Japan
| | - Tatsuya Sudo
- Department of Chemical Engineering Tokyo University of Agriculture and Technology 2-24-16 Naka-cho, Koganei Tokyo 184-8588 Japan
| | - Hidehiro Kamiya
- Department of Chemical Engineering Tokyo University of Agriculture and Technology 2-24-16 Naka-cho, Koganei Tokyo 184-8588 Japan
| | - Yohei Okada
- Department of Chemical Engineering Tokyo University of Agriculture and Technology 2-24-16 Naka-cho, Koganei Tokyo 184-8588 Japan
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10
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Tan W, Wei T, Huo J, Loubidi M, Liu T, Liang Y, Deng L. Electrostatic Interaction-Induced Formation of Enzyme-on-MOF as Chemo-Biocatalyst for Cascade Reaction with Unexpectedly Acid-Stable Catalytic Performance. ACS APPLIED MATERIALS & INTERFACES 2019; 11:36782-36788. [PMID: 31532179 DOI: 10.1021/acsami.9b13080] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Combining biocatalytic and chemocatalytic reactions in a one-pot reaction not only avoids the tedious isolation of intermediates during the reactions but also provides a desirable alternative to extend the range of catalytic reactions. Here, we report a facile strategy to immobilize an enzyme, glucose oxidase (GOx), on PCN-222(Fe) induced by electrostatic interaction in which PCN-222(Fe) serves as both a support and chemocatalyst. The immobilization was confirmed through ζ potential measurement, confocal laser scanning microscopy, Fourier transform infrared spectrometry, and UV-vis spectroscopy. This chemo-biocatalyst was applied to a cascade reaction to catalyze glucose oxidation and ABTS (ABTS = 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (or pyrogallol) oxidation. The catalytic kinetics studies show that these chemo-biocatalytic cascade reactions obey the Michaelis-Menten equation, which indicates that the cascade reactions follow the typical enzymatic dynamic regulation process. Interestingly, GOx/PCN-222(Fe) exhibits an exceptional acid-stable catalytic performance as evidenced by circular dichroism spectroscopy where no significant structure change was observed toward acidic solutions with different pH values. GOx/PCN-222(Fe) also displays desirable recyclability since no significant loss of conversion rates was found after six repeated reactions. This work presents a convenient strategy to construct metal-organic framework based chemo-biocatalysts, which may find potential applications in sensing and nanomachines.
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Affiliation(s)
- Wenlong Tan
- State Key Laboratory of Chem/Bio-Sensing and Chemometrics, Provincial Hunan Key Laboratory for Graphene Materials and Devices, College of Chemistry and Chemical Engineering , Hunan University , Changsha 410082 , Hunan , China
| | - Ting Wei
- State Key Laboratory of Chem/Bio-Sensing and Chemometrics, Provincial Hunan Key Laboratory for Graphene Materials and Devices, College of Chemistry and Chemical Engineering , Hunan University , Changsha 410082 , Hunan , China
| | - Jia Huo
- State Key Laboratory of Chem/Bio-Sensing and Chemometrics, Provincial Hunan Key Laboratory for Graphene Materials and Devices, College of Chemistry and Chemical Engineering , Hunan University , Changsha 410082 , Hunan , China
- Shenzhen Research Institute of Hunan University , Shenzhen 518057 , Guangdong , China
| | - Mohammed Loubidi
- State Key Laboratory of Chem/Bio-Sensing and Chemometrics, Provincial Hunan Key Laboratory for Graphene Materials and Devices, College of Chemistry and Chemical Engineering , Hunan University , Changsha 410082 , Hunan , China
| | - Tingting Liu
- State Key Laboratory of Chem/Bio-Sensing and Chemometrics, Provincial Hunan Key Laboratory for Graphene Materials and Devices, College of Chemistry and Chemical Engineering , Hunan University , Changsha 410082 , Hunan , China
| | - Yu Liang
- State Key Laboratory of Chem/Bio-Sensing and Chemometrics, Provincial Hunan Key Laboratory for Graphene Materials and Devices, College of Chemistry and Chemical Engineering , Hunan University , Changsha 410082 , Hunan , China
| | - Libo Deng
- Shenzhen University , Shenzhen 518057 , Guangdong , China
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11
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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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12
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Neupane S, Patnode K, Li H, Baryeh K, Liu G, Hu J, Chen B, Pan Y, Yang Z. Enhancing Enzyme Immobilization on Carbon Nanotubes via Metal-Organic Frameworks for Large-Substrate Biocatalysis. ACS APPLIED MATERIALS & INTERFACES 2019; 11:12133-12141. [PMID: 30839195 DOI: 10.1021/acsami.9b01077] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Biocatalysis of large-sized substrates finds wide applications. Immobilizing the involved enzymes on solid supports improves biocatalysis yet faces challenges such as enzyme structural perturbation, leaching, and low cost-efficiencies, depending on immobilization strategies/matrices. Carbon nanotubes (CNTs) are attractive matrices but challenged by enzyme leaching (physical adsorption) or perturbation (covalent linking). Zeolitic imidazolate frameworks (ZIFs) overcome these issues. However, our recent study [ J. Am. Chem. Soc., 2018, 140, 16032-16036] showed reduced cost-efficiency as enzymes trapped below the ZIF surfaces cannot participate in biocatalysis; the enzyme-ZIF composites are also unstable under acidic conditions. In this work, we demonstrate the feasibility of using ZIFs to immobilize enzymes on CNT surfaces on two model enzymes, T4 lysozyme and amylase, both of which showed negligible leaching and retained catalytic activity under neutral and acidic conditions. To better understand the behavior of enzymes on CNTs and CNT-ZIF, we characterized enzyme orientation on both matrices using site-directed spin-labeling (SDSL)-electron paramagnetic resonance (EPR), which is immune to the complexities caused by CNT and ZIF background signals and enzyme-matrix interactions. Our structural investigations showed enhanced enzyme exposure to the solvent compared to enzymes in ZIFs alone; orientation of enzymes in matrices itself is directly related to substrate accessibility and, therefore, essential for understanding and improving catalytic efficiency. To the best of our knowledge, this is the first time ZIFs and one-pot synthesis are employed to anchor large-substrate enzymes on CNT surfaces for biocatalysis. This is also the first report of enzyme orientation on the CNT surface and upon trapping in CNT-ZIF composites. Our results are essential for guiding the rational design of CNT-ZIF combinations to improve enzyme stabilization, loading capacity, and catalytic efficiency.
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Affiliation(s)
| | | | | | | | | | - Jinlian Hu
- Institute of Textiles and Clothing , The Hong Kong Polytechnic University , Kowloon 999077 , Hong Kong , China
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13
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Drout RJ, Robison L, Farha OK. Catalytic applications of enzymes encapsulated in metal–organic frameworks. Coord Chem Rev 2019. [DOI: 10.1016/j.ccr.2018.11.009] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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14
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Lukasheva NV, Tolmachev DA, Karttunen M. Mineralization of phosphorylated cellulose: crucial role of surface structure and monovalent ions for optimizing calcium content. Phys Chem Chem Phys 2019; 21:1067-1077. [PMID: 30511059 DOI: 10.1039/c8cp05767b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cellulose can be phosphorylated to produce organic matrices with highly adsorptive properties for, e.g., biocompatible materials for biomedical applications. We focus on the effects of phosphorylation of surfaces of crystalline nanocellulose and, in particular, on the competitive adsorption of mono- and divalent cations (Na+ and Ca2+) typically contained in mineralizing salt mixtures using all-atom molecular dynamics (MD) simulations. Phosphorylation was applied at 12% and 25% both in water and CaCl2 solutions. Our main result shows that Na+ and Ca2+ cations are concentrated in different interfacial layers with Na+ ions penetrating much closer to the surface. This behavior cannot be described by the Poisson-Boltzmann theory or implicit solvent simulations. Our analysis shows that the physical origin of this observation is due to a balance between the electrostatic interactions and hydration free energy associated with the ions. Adsorption levels of the different ions also respond differently to changes in the degree of phosphorylation. We show that the number of adsorbed Na+ ions per phosphate group increases whereas the number of adsorbed Ca2+ ions decreases with an increasing degree of phosphorylation (or when the number of binding sites increases). The decrease in the number of adsorbed Ca2+ ions can be explained by an increasing "charge-charge" repulsion between the Ca2+ ions attracted by the charged surface. Importantly, our results demonstrate the existence of an optimum degree of phosphorylation in terms of adsorbed Ca2+ ions and can be used as a guideline in materials design, for example, when choosing the cellulose matrix or with other similarly structured biomolecular and polymer surfaces.
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Affiliation(s)
- Natalia V Lukasheva
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoj pr. V.O., 31, 199004 St. Petersburg, Russia.
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15
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Kirchon A, Feng L, Drake HF, Joseph EA, Zhou HC. From fundamentals to applications: a toolbox for robust and multifunctional MOF materials. Chem Soc Rev 2018; 47:8611-8638. [PMID: 30234863 DOI: 10.1039/c8cs00688a] [Citation(s) in RCA: 637] [Impact Index Per Article: 106.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
In recent years, metal-organic frameworks (MOFs) have been regarded as one of the most important classes of materials. The combination of various metal clusters and ligands, arranged in a vast array of geometries has led to an ever-expanding MOF family. Each year, new and novel MOF structures are discovered. The structural diversity present in MOFs has significantly expanded the application of these new materials. MOFs show great potential for a variety of applications, including but not limited to: gas storage and separation, catalysis, biomedicine delivery, and chemical sensing. This review intends to offer a short summary of some of the most important topics and recent development in MOFs. The scope of this review shall cover the fundamental aspects concerning the design and synthesis of MOFs and range to the practical applications regarding their stability and derivative structures. Emerging trends of MOF development will also be discussed. These trends shall include multicomponent MOFs, defect development in MOFs, and MOF composites. The ever important structure-property-application relationship for MOFs will also be investigated. Overall, this review provides insight into both existing structures and emerging aspects of MOFs.
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Affiliation(s)
- Angelo Kirchon
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255, USA.
| | - Liang Feng
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255, USA.
| | - Hannah F Drake
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255, USA.
| | - Elizabeth A Joseph
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255, USA.
| | - Hong-Cai Zhou
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255, USA. and Department of Material Science and Engineering, Texas A&M University, College Station, Texas 77843-3003, USA
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16
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Cui J, Ren S, Sun B, Jia S. Optimization protocols and improved strategies for metal-organic frameworks for immobilizing enzymes: Current development and future challenges. Coord Chem Rev 2018. [DOI: 10.1016/j.ccr.2018.05.004] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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17
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Cai C, Lin J, Lu Y, Zhang Q, Wang L. Polypeptide self-assemblies: nanostructures and bioapplications. Chem Soc Rev 2018; 45:5985-6012. [PMID: 27722321 DOI: 10.1039/c6cs00013d] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Polypeptide copolymers can self-assemble into diverse aggregates. The morphology and structure of aggregates can be varied by changing molecular architectures, self-assembling conditions, and introducing secondary components such as polymers and nanoparticles. Polypeptide self-assemblies have gained significant attention because of their potential applications as delivery vehicles for therapeutic payloads and as additives in the biomimetic mineralization of inorganics. This review article provides an overview of recent advances in nanostructures and bioapplications related to polypeptide self-assemblies. We highlight recent contributions to developing strategies for the construction of polypeptide assemblies with increasing complexity and novel functionality that are suitable for bioapplications. The relationship between the structure and properties of the polypeptide aggregates is emphasized. Finally, we briefly outline our perspectives and discuss the challenges in the field.
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Affiliation(s)
- Chunhua Cai
- Shanghai Key Laboratory of Advanced Polymeric Materials, State Key Laboratory of Bioreactor Engineering, Key Laboratory for Ultrafine Materials of Ministry of Education, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Jiaping Lin
- Shanghai Key Laboratory of Advanced Polymeric Materials, State Key Laboratory of Bioreactor Engineering, Key Laboratory for Ultrafine Materials of Ministry of Education, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Yingqing Lu
- Shanghai Key Laboratory of Advanced Polymeric Materials, State Key Laboratory of Bioreactor Engineering, Key Laboratory for Ultrafine Materials of Ministry of Education, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Qian Zhang
- Shanghai Key Laboratory of Advanced Polymeric Materials, State Key Laboratory of Bioreactor Engineering, Key Laboratory for Ultrafine Materials of Ministry of Education, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Liquan Wang
- Shanghai Key Laboratory of Advanced Polymeric Materials, State Key Laboratory of Bioreactor Engineering, Key Laboratory for Ultrafine Materials of Ministry of Education, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, China.
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18
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Ghatee MH, Koleini MM. Bonding, structural and thermodynamic analysis of dissociative adsorption of H 3O + ion onto calcite (101⁻4) surface: CPMD and DFT calculations. J Mol Model 2017; 23:331. [PMID: 29105032 DOI: 10.1007/s00894-017-3499-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Accepted: 10/09/2017] [Indexed: 11/26/2022]
Abstract
We used density functional theory (DFT) and Car-Parrinello molecular dynamics (CPMD) simulation to investigate the adsorption and bond formation of hydronium ion (H3O+) onto a [Formula: see text] calcite surface. For surface coverage of 25% to 100%, the nature of H3O+ interaction was explored through electron density and energetics in the context of bond critical points. The adsorbate-adsorbent structure was studied by simulation of pair correlation function. The results revealed that dissociation into water molecule(s) and proton(s) complements H3O+ ion(s) adsorbtion. The H2O molecule adsorbs onto the surface via its O atom, and interacts with surface calcium in a closed-shell mode; the H+ ion makes a covalent bond to the surface oxygen while maintaining H-bonding with water. Adsorption energies were diminished by 70-90 kJ mol-1 when Obridge-bonded H+ ions transferred to the Oterminal manually. While dissociative adsorption of H3O+ ions is spontaneous at all surface coverages tested, the free energy was lowest at 75% coverage. Also, protonation of a completely pre-hydrated calcite surface leads to stronger interaction of water molecules with the surface. This unique outlook on hydrating calcite provides specific insights into biomineralization of this mineral, and helps depict further pH consequences in the field of biomaterial adsorption. Graphical abstract Dissociative adsorption of hydronium ion onto the surface of calcite.
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Affiliation(s)
- Mohammad Hadi Ghatee
- Department of Chemistry, Shiraz University, Shiraz, 71946, Iran.
- Sharif Upstream Petroleum Research Institute, School of Chemical and Petroleum Engineering, Sharif University of Technology, Tehran, Iran.
- Department of Chemistry, University of Houston, Houston, TX, 77204-5003, USA.
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19
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Yang X, Rees RJ, Conway W, Puxty G, Yang Q, Winkler DA. Computational Modeling and Simulation of CO2 Capture by Aqueous Amines. Chem Rev 2017; 117:9524-9593. [PMID: 28517929 DOI: 10.1021/acs.chemrev.6b00662] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Xin Yang
- CSIRO Manufacturing, Bayview Avenue, Clayton 3169, Australia
- College
of Chemistry, Key Lab of Green Chemistry and Technology in Ministry
of Education, Sichuan University, Chengdu 610064, People’s Republic of China
| | - Robert J. Rees
- Data61
- CSIRO, Door 34 Goods
Shed, Village Street, Docklands VIC 3008, Australia
| | | | | | - Qi Yang
- CSIRO Manufacturing, Bayview Avenue, Clayton 3169, Australia
| | - David A. Winkler
- CSIRO Manufacturing, Bayview Avenue, Clayton 3169, Australia
- Monash Institute of Pharmaceutical Sciences, 392 Royal Parade, Parkville 3052, Australia
- Latrobe Institute for Molecular Science, Bundoora 3046, Australia
- School
of
Chemical and Physical Science, Flinders University, Bedford Park 5042, Australia
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20
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Zadpoor AA. Biomaterials and Tissue Biomechanics: A Match Made in Heaven? MATERIALS 2017; 10:ma10050528. [PMID: 28772890 PMCID: PMC5459088 DOI: 10.3390/ma10050528] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 05/09/2017] [Accepted: 05/09/2017] [Indexed: 01/20/2023]
Abstract
Biomaterials and tissue biomechanics have been traditionally separate areas of research with relatively little overlap in terms of methodological approaches. Recent advances in both fields on the one hand and developments in fabrication techniques and design approaches on the other have prepared the ground for joint research efforts by both communities. Additive manufacturing and rational design are examples of the revolutionary fabrication techniques and design methodologies that could facilitate more intimate collaboration between biomaterial scientists and biomechanists. This editorial article highlights the various ways in which the research on tissue biomechanics and biomaterials are related to each other and could benefit from each other’s results and methodologies.
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Affiliation(s)
- Amir A Zadpoor
- Department of Biomechanical Engineering, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology (TU Delft), Mekelweg 2, Delft 2628 CD, The Netherlands.
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21
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Hu H, Rey AD. Multi-step modeling of liquid crystals using ab initio molecular packing and hybrid quantum mechanics/molecular mechanics simulations. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2017. [DOI: 10.1142/s0219633617500122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A density functional theory (DFT) based multi-step simulation method is used to characterize the detailed molecular structure and inter/intra- molecular interactions of two benchmark liquid crystals (LC) 5CB, 8CB and a novel tri-biphenyl ring bent core LC material. The method uses hybrid DFT at the B3LYP/6-31G* level to obtain molecular structure and Raman data. These results are fed to a crystal packing simulation to find possible crystal structures. A pico-second quantum mechanics/molecular mechanics (QM/MM) simulation model is built for the selected structures with lower overall energy as well as optimal density. The stabilized crystal structures are then extended into a super cell, heated and simulated using a mixed force field and nano-second molecular dynamics (MD). The described simulation process sequence provides predictions of molecular Raman spectrum, LC density, isotropic depolarization ratio, ratio of differential polarizability, order parameters, molecular structures, and rotating Raman spectrum of the different mesophases. The Raman spectra, order parameters and depolarization ratios all agree well with existing experimental and previous simulation results. The study of the novel tri-biphenyl ring bent core LC system shows that the ratio of differential polarizability depends on intra-molecular interactions. The findings presented in this manuscript contribute to the on-going efforts to establish links between LC molecular structures and their properties, including optical behavior.
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Affiliation(s)
- Hang Hu
- Department of Chemical Engineering, McGill University, H3A 0G4, Montreal, Canada
| | - Alejandro D. Rey
- Department of Chemical Engineering, McGill University, H3A 0G4, Montreal, Canada
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22
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Butler KT, Hendon CH, Walsh A. Designing porous electronic thin-film devices: band offsets and heteroepitaxy. Faraday Discuss 2017. [DOI: 10.1039/c7fd00019g] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Increasing numbers of electrically active porous framework materials are being reported, with conductivities that make them attractive for technological applications. As design strategies for efficient carrier transport emerge, the next challenge is to incorporate the materials into a functioning device. In thin-film devices interface effects are of critical importance to overall function. In this article we present a method to identify compatible materials combinations to achieve mechanically robust, electronically optimal pairings. The computational screening is based on a two-step procedure: (i) matching of lattice constants to ensure interfaces with minimal epitaxial strain and therefore maximal mechanical and chemical stability; (ii) matching of absolute electron energies to construct energy-band-alignment diagrams, which can be used to screen for particular electronic applications. We apply the methodology to search for zeolitic imidazolate framework (ZIF) type materials that are compatible with native metal electrodes. The procedure allows us to predict simple routes for electrochemical deposition of ZIFs for application as conductive porous electrodes.
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Affiliation(s)
| | | | - Aron Walsh
- Department of Materials
- Imperial College London
- London
- UK
- Department of Materials Science and Engineering
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23
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Lian X, Fang Y, Joseph E, Wang Q, Li J, Banerjee S, Lollar C, Wang X, Zhou HC. Enzyme–MOF (metal–organic framework) composites. Chem Soc Rev 2017; 46:3386-3401. [DOI: 10.1039/c7cs00058h] [Citation(s) in RCA: 791] [Impact Index Per Article: 113.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
This review summarizes the syntheses and applications of metal–organic framework (MOF)–enzyme composites with specific emphasis on the merits MOFs bring to the immobilized enzymes.
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Affiliation(s)
- Xizhen Lian
- Department of Chemistry
- Texas A&M University
- College Station
- USA
| | - Yu Fang
- Department of Chemistry
- Texas A&M University
- College Station
- USA
| | | | - Qi Wang
- Department of Chemistry
- Texas A&M University
- College Station
- USA
| | - Jialuo Li
- Department of Chemistry
- Texas A&M University
- College Station
- USA
| | - Sayan Banerjee
- Department of Chemistry
- Texas A&M University
- College Station
- USA
| | | | - Xuan Wang
- Department of Chemistry
- Texas A&M University
- College Station
- USA
| | - Hong-Cai Zhou
- Department of Chemistry
- Texas A&M University
- College Station
- USA
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24
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Lifanov Y, Vorselaars B, Quigley D. Nucleation barrier reconstruction via the seeding method in a lattice model with competing nucleation pathways. J Chem Phys 2016; 145:211912. [DOI: 10.1063/1.4962216] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Yuri Lifanov
- Centre for Complexity Science, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Bart Vorselaars
- School of Mathematics and Physics, University of Lincoln, Lincolnshire LN6 7TS, United Kingdom
| | - David Quigley
- Department of Physics and Centre for Scientific Computing, University of Warwick, Coventry CV4 7AL, United Kingdom
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25
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Rubinstein AI, Sabirianov RF, Namavar F. Effects of the dielectric properties of the ceramic-solvent interface on the binding of proteins to oxide ceramics: a non-local electrostatic approach. NANOTECHNOLOGY 2016; 27:415703. [PMID: 27585807 DOI: 10.1088/0957-4484/27/41/415703] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The rapid development of nanoscience and nanotechnology has raised many fundamental questions that significantly impede progress in these fields. In particular, understanding the physicochemical processes at the interface in aqueous solvents requires the development and application of efficient and accurate methods. In the present work we evaluate the electrostatic contribution to the energy of model protein-ceramic complex formation in an aqueous solvent. We apply a non-local (NL) electrostatic approach that accounts for the effects of the short-range structure of the solvent on the electrostatic interactions of the interfacial systems. In this approach the aqueous solvent is considered as a non-ionic liquid, with the rigid and strongly correlated dipoles of the water molecules. We have found that an ordered interfacial aqueous solvent layer at the protein- and ceramic-solvent interfaces reduces the charging energy of both the ceramic and the protein in the solvent, and significantly increases the electrostatic contribution to their association into a complex. This contribution in the presented NL approach was found to be significantly shifted with respect to the classical model at any dielectric constant value of the ceramics. This implies a significant increase of the adsorption energy in the protein-ceramic complex formation for any ceramic material. We show that for several biocompatible ceramics (for example HfO2, ZrO2, and Ta2O5) the above effect predicts electrostatically induced protein-ceramic complex formation. However, in the framework of the classical continuum electrostatic model (the aqueous solvent as a uniform dielectric medium with a high dielectric constant ∼80) the above ceramics cannot be considered as suitable for electrostatically induced complex formation. Our results also show that the protein-ceramic electrostatic interactions can be strong enough to compensate for the unfavorable desolvation effect in the process of protein-ceramic complex formation.
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Affiliation(s)
- Alexander I Rubinstein
- Department of Physics, Laboratory of Applied Spectroscopy, Ariel University, Ariel 40700, West Bank. Department of Physics, University of Nebraska at Omaha, Omaha, NE 68182, USA
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26
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Intercalated water layers promote thermal dissipation at bio-nano interfaces. Nat Commun 2016; 7:12854. [PMID: 27659484 PMCID: PMC5036148 DOI: 10.1038/ncomms12854] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Accepted: 08/09/2016] [Indexed: 01/18/2023] Open
Abstract
The increasing interest in developing nanodevices for biophysical and biomedical applications results in concerns about thermal management at interfaces between tissues and electronic devices. However, there is neither sufficient knowledge nor suitable tools for the characterization of thermal properties at interfaces between materials of contrasting mechanics, which are essential for design with reliability. Here we use computational simulations to quantify thermal transfer across the cell membrane–graphene interface. We find that the intercalated water displays a layered order below a critical value of ∼1 nm nanoconfinement, mediating the interfacial thermal coupling, and efficiently enhancing the thermal dissipation. We thereafter develop an analytical model to evaluate the critical value for power generation in graphene before significant heat is accumulated to disturb living tissues. These findings may provide a basis for the rational design of wearable and implantable nanodevices in biosensing and thermotherapic treatments where thermal dissipation and transport processes are crucial. Thermal management is important for designing bio-nano interfaces for biosensing and thermotherapic applications. Here the authors perform simulations showing that nm-thick water layers between graphene and cell membranes display layered ordering, promoting interfacial thermal coupling and thermal dissipation.
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27
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Heinz H, Ramezani-Dakhel H. Simulations of inorganic-bioorganic interfaces to discover new materials: insights, comparisons to experiment, challenges, and opportunities. Chem Soc Rev 2016; 45:412-48. [PMID: 26750724 DOI: 10.1039/c5cs00890e] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Natural and man-made materials often rely on functional interfaces between inorganic and organic compounds. Examples include skeletal tissues and biominerals, drug delivery systems, catalysts, sensors, separation media, energy conversion devices, and polymer nanocomposites. Current laboratory techniques are limited to monitor and manipulate assembly on the 1 to 100 nm scale, time-consuming, and costly. Computational methods have become increasingly reliable to understand materials assembly and performance. This review explores the merit of simulations in comparison to experiment at the 1 to 100 nm scale, including connections to smaller length scales of quantum mechanics and larger length scales of coarse-grain models. First, current simulation methods, advances in the understanding of chemical bonding, in the development of force fields, and in the development of chemically realistic models are described. Then, the recognition mechanisms of biomolecules on nanostructured metals, semimetals, oxides, phosphates, carbonates, sulfides, and other inorganic materials are explained, including extensive comparisons between modeling and laboratory measurements. Depending on the substrate, the role of soft epitaxial binding mechanisms, ion pairing, hydrogen bonds, hydrophobic interactions, and conformation effects is described. Applications of the knowledge from simulation to predict binding of ligands and drug molecules to the inorganic surfaces, crystal growth and shape development, catalyst performance, as well as electrical properties at interfaces are examined. The quality of estimates from molecular dynamics and Monte Carlo simulations is validated in comparison to measurements and design rules described where available. The review further describes applications of simulation methods to polymer composite materials, surface modification of nanofillers, and interfacial interactions in building materials. The complexity of functional multiphase materials creates opportunities to further develop accurate force fields, including reactive force fields, and chemically realistic surface models, to enable materials discovery at a million times lower computational cost compared to quantum mechanical methods. The impact of modeling and simulation could further be increased by the advancement of a uniform simulation platform for organic and inorganic compounds across the periodic table and new simulation methods to evaluate system performance in silico.
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Affiliation(s)
- Hendrik Heinz
- Department of Chemical and Biological Engineering, University of Colorado-Boulder, Boulder, CO 80309, USA.
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28
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Abstract
The interface between collagen and the mineral reinforcement phase, carbonated hydroxyapatite (cAp), is essential for bone's remarkable functionality as a biological composite material. The very small dimensions of the cAp phase and the disparate natures of the reinforcement and matrix are essential to the material's performance but also complicate study of this interface. This article summarizes what is known about the cAp-collagen interface in bone and begins with descriptions of the matrix and reinforcement roles in composites, of the phases bounding the interface, of growth of cAp growing within the collagen matrix, and of the effect of intra- and extrafibrilar mineral on determinations of interfacial properties. Different observed interfacial interactions with cAp (collagen, water, non-collagenous proteins) are reviewed; experimental results on interface interactions during loading are reported as are their influence on macroscopic mechanical properties; conclusions of numerical modeling of interfacial interactions are also presented. The data suggest interfacial interlocking (bending of collagen molecules around cAp nanoplatelets) and water-mediated bonding between collagen and cAp are essential to load transfer. The review concludes with descriptions of areas where new research is needed to improve understanding of how the interface functions.
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Affiliation(s)
- S R Stock
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, 303 E. Chicago Ave., Chicago, IL, 60611-3008, USA,
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29
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Ahmad M, Abdul Aziz A. Elemental distribution and porosity enhancement in advanced nano bimetallic catalyst. POWDER TECHNOL 2015. [DOI: 10.1016/j.powtec.2015.03.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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30
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Liang K, Ricco R, Doherty CM, Styles MJ, Bell S, Kirby N, Mudie S, Haylock D, Hill AJ, Doonan CJ, Falcaro P. Biomimetic mineralization of metal-organic frameworks as protective coatings for biomacromolecules. Nat Commun 2015; 6:7240. [PMID: 26041070 PMCID: PMC4468859 DOI: 10.1038/ncomms8240] [Citation(s) in RCA: 811] [Impact Index Per Article: 90.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 04/20/2015] [Indexed: 12/22/2022] Open
Abstract
Enhancing the robustness of functional biomacromolecules is a critical challenge in biotechnology, which if addressed would enhance their use in pharmaceuticals, chemical processing and biostorage. Here we report a novel method, inspired by natural biomineralization processes, which provides unprecedented protection of biomacromolecules by encapsulating them within a class of porous materials termed metal-organic frameworks. We show that proteins, enzymes and DNA rapidly induce the formation of protective metal-organic framework coatings under physiological conditions by concentrating the framework building blocks and facilitating crystallization around the biomacromolecules. The resulting biocomposite is stable under conditions that would normally decompose many biological macromolecules. For example, urease and horseradish peroxidase protected within a metal-organic framework shell are found to retain bioactivity after being treated at 80 °C and boiled in dimethylformamide (153 °C), respectively. This rapid, low-cost biomimetic mineralization process gives rise to new possibilities for the exploitation of biomacromolecules.
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Affiliation(s)
- Kang Liang
- CSIRO Manufacturing Flagship, Private Bag 10, Clayton South, Victoria 3169, Australia
| | - Raffaele Ricco
- CSIRO Manufacturing Flagship, Private Bag 10, Clayton South, Victoria 3169, Australia
| | - Cara M. Doherty
- CSIRO Manufacturing Flagship, Private Bag 10, Clayton South, Victoria 3169, Australia
| | - Mark J. Styles
- CSIRO Manufacturing Flagship, Private Bag 10, Clayton South, Victoria 3169, Australia
| | - Stephen Bell
- Department of Chemistry, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Nigel Kirby
- Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3169, Australia
| | - Stephen Mudie
- Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3169, Australia
| | - David Haylock
- CSIRO Manufacturing Flagship, Private Bag 10, Clayton South, Victoria 3169, Australia
- The Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, Victoria 3800, Australia
| | - Anita J. Hill
- CSIRO Manufacturing Flagship, Private Bag 10, Clayton South, Victoria 3169, Australia
| | - Christian J. Doonan
- Department of Chemistry, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Paolo Falcaro
- CSIRO Manufacturing Flagship, Private Bag 10, Clayton South, Victoria 3169, Australia
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31
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Keller KS, Olsson MHM, Yang M, Stipp SLS. Adsorption of ethanol and water on calcite: dependence on surface geometry and effect on surface behavior. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:3847-3853. [PMID: 25790337 DOI: 10.1021/la504319z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Molecular dynamics (MD) simulations were used to explore adsorption on calcite, from a 1:1 mixture of ethanol and water, on planar {10.4} and stepped, i.e. vicinal, surfaces. Varying the surface geometry resulted in different adsorption patterns, which would directly influence the ability of ethanol to control calcite crystal growth, dissolution, and adsorption/desorption of other ions and molecules. Ethanol forms a well-ordered adsorbed layer on planar faces and on larger terraces, such as between steps and defects, providing little chance for water, with its weaker attachment, to displace it. However, on surfaces with steps, adsorption affinity depends on the length of the terraces between the steps. Long terraces allow ethanol to form a well-ordered, hydrophobic layer, but when step density is high, ethanol adsorption is less ordered, allowing water to associate at and near the steps and even displacing pre-existing ethanol. Water adsorbed at steps forms mass transport pathways between the bulk solution and the solid surface. Our simulations confirm the growth inhibiting properties of ethanol, also explaining how certain crystal faces are more stabilized because of their surface geometry. The -O(H) functional group on ethanol forms tight bonds with calcite; the nonpolar, -CH3 ends, which point away from the surface, create a hydrophobic layer that changes surface charge, thus wettability, and partly protects calcite from precipitation and dissolution. These tricks could easily be adopted by biomineralizing organisms, allowing them to turn on and off crystal growth. They undoubtedly also play a role in the wetting properties of mineral surfaces in commercial CaCO3 manufacture, oil production, and contamination remediation.
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Affiliation(s)
- K S Keller
- †Nano-Science Center, Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - M H M Olsson
- †Nano-Science Center, Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - M Yang
- ‡School of Material Science and Engineering, Southwest Petroleum University, Sichuan, China
| | - S L S Stipp
- †Nano-Science Center, Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
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32
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Swadling JB, Wright DW, Suter JL, Coveney PV. Structure, dynamics, and function of the hammerhead ribozyme in bulk water and at a clay mineral surface from replica exchange molecular dynamics. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:2493-2501. [PMID: 25647546 DOI: 10.1021/la503685t] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Compared with proteins, the relationship between structure, dynamics, and function of RNA enzymes (known as ribozymes) is far less well understood, despite the fact that ribozymes are found in many organisms and are often conceived as "molecular fossils" of the first self-replicating molecules to have arisen on Earth. To investigate how ribozymal function is governed by structure and dynamics, we study the full hammerhead ribozyme in bulk water and in an aqueous clay mineral environment by computer simulation using replica-exchange molecular dynamics. Through extensive sampling of the major conformational states of the hammerhead ribozyme, we are able to show that the hammerhead manifests a free-energy landscape reminiscent of that which is well known in proteins, exhibiting a "funnel" topology that guides the ribozyme into its globally most stable conformation. The active-site geometry is found to be closely correlated to the tertiary structure of the ribozyme, thereby reconciling conflicts between previously proposed mechanisms for the self-scission of the hammerhead. The conformational analysis also accounts for the differences reported experimentally in the catalytic activity of the hammerhead ribozyme, which is reduced when interacting with clay minerals as compared with bulk water.
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Affiliation(s)
- Jacob B Swadling
- Centre for Computational Science, Department of Chemistry, University College London , 20 Gordon Street, London WC1H 0AJ, United Kingdom
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Jain A, Jochum M, Peter C. Molecular dynamics simulations of peptides at the air-water interface: influencing factors on peptide-templated mineralization. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:15486-15495. [PMID: 25470652 DOI: 10.1021/la503549q] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Biomineralization is the intricate, biomedically highly relevant process by which living organisms deposit minerals on biological matrices to stiffen tissues and build skeletal structures and shells. Rapaport and coworkers ( J. Am. Chem. Soc. 2000 , 122 , 12523 ; Adv. Funct. Mater. 2008 , 18 , 2889 ; Acta Biomater. 2012 , 8 , 2466 ) have designed a class of self-assembling amphiphilic peptides that are capable of forming hydrogels and attracting ions from the environment, generating structures akin to the extracellular matrix and promoting bone regeneration. The air-water interface serves both in experiment and in simulations as a model hydrophobic surface to mimic the cell's organic-aqueous interface and to investigate the organization of the peptide matrix into ordered β-pleated monolayers and the subsequent onset of biomineral formation. To obtain insight into the underlying molecular mechanism, we have used molecular dynamics simulations to study the effect of peptide sequence on aggregate stability and ion-peptide interactions. We find-in excellent agreement with experimental observations-that the nature of the peptide termini (proline vs phenylalanine) affect the aggregate order, while the nature of the acidic side chains (aspartic vs glutamic acid) affect the aggregate's stability in the presence of ions. These simulations provide valuable microscopic insight into the way ions and peptide templates mutually affect each other during the early stages of biomineralization preceding nucleation.
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Affiliation(s)
- Alok Jain
- Max Planck Institute for Polymer Research , Ackermannweg 10, 55128 Mainz, Germany
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Bertran O, Valle LJD, Revilla-López G, Rivas M, Chaves G, Casas MT, Casanovas J, Turon P, Puiggalí J, Alemán C. Synergistic Approach to Elucidate the Incorporation of Magnesium Ions into Hydroxyapatite. Chemistry 2014; 21:2537-46. [DOI: 10.1002/chem.201405428] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Indexed: 12/31/2022]
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Bevilaqua RCA, Rigo VA, Veríssimo-Alves M, Miranda CR. NMR characterization of hydrocarbon adsorption on calcite surfaces: a first principles study. J Chem Phys 2014; 141:204705. [PMID: 25429955 DOI: 10.1063/1.4902251] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The electronic and coordination environment of minerals surfaces, as calcite, are very difficult to characterize experimentally. This is mainly due to the fact that there are relatively few spectroscopic techniques able to detect Ca(2+). Since calcite is a major constituent of sedimentary rocks in oil reservoir, a more detailed characterization of the interaction between hydrocarbon molecules and mineral surfaces is highly desirable. Here we perform a first principles study on the adsorption of hydrocarbon molecules on calcite surface (CaCO3 (101¯4)). The simulations were based on Density Functional Theory with Solid State Nuclear Magnetic Resonance (SS-NMR) calculations. The Gauge-Including Projector Augmented Wave method was used to compute mainly SS-NMR parameters for (43)Ca, (13)C, and (17)O in calcite surface. It was possible to assign the peaks in the theoretical NMR spectra for all structures studied. Besides showing different chemical shifts for atoms located on different environments (bulk and surface) for calcite, the results also display changes on the chemical shift, mainly for Ca sites, when the hydrocarbon molecules are present. Even though the interaction of the benzene molecule with the calcite surface is weak, there is a clearly distinguishable displacement of the signal of the Ca sites over which the hydrocarbon molecule is located. A similar effect is also observed for hexane adsorption. Through NMR spectroscopy, we show that aromatic and alkane hydrocarbon molecules adsorbed on carbonate surfaces can be differentiated.
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Affiliation(s)
- Rochele C A Bevilaqua
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, UFABC, Santo André, SP, Brazil
| | - Vagner A Rigo
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, UFABC, Santo André, SP, Brazil
| | - Marcos Veríssimo-Alves
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, UFABC, Santo André, SP, Brazil
| | - Caetano R Miranda
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, UFABC, Santo André, SP, Brazil
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36
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Bano AM, Rodger PM, Quigley D. New insight into the stability of CaCO3 surfaces and nanoparticles via molecular simulation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:7513-21. [PMID: 24915605 DOI: 10.1021/la501409j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Using updated and improved atomistic models for the polymorphs of calcium carbonate and their constituent ions in solution, we revisit the question of surface energetics and nanoparticle stability. Using a simple lattice-based Monte Carlo scheme, we generate nanoparticle configurations in vacuum for all three biologically relevant polymorphs of calcium carbonate and establish that the bulk energetic ordering of polymorphs persists to the nanoscale. In aqueous environments, results based on surface enthalpy alone indicate that formation of mineral-water interfaces is marginally favorable in many cases. Including an estimate of lost entropy due to formation of structured water layers is sufficient to reverse this observation, implying a delicate balance of enthalpy and entropy at crystalline CaCO3. In contradiction to some previous studies, we find that small calcite nanoparticles with diameters in the range of 1.8-4.1 nm do not retain an ordered structure on nanosecond time scales. The consequences of these results for simulation studies of biomineralization are discussed.
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Affiliation(s)
- A Matthew Bano
- Department of Chemistry and Centre for Scientific Computing, University of Warwick , Coventry CV4 7AL, U.K
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Kahlen J, Salimi L, Sulpizi M, Peter C, Donadio D. Interaction of Charged Amino-Acid Side Chains with Ions: An Optimization Strategy for Classical Force Fields. J Phys Chem B 2014; 118:3960-72. [DOI: 10.1021/jp412490c] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jens Kahlen
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Leila Salimi
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Johannes Gutenberg University Mainz, Staudinger Weg 7, 55099 Mainz, Germany
| | - Marialore Sulpizi
- Johannes Gutenberg University Mainz, Staudinger Weg 7, 55099 Mainz, Germany
| | - Christine Peter
- University of Konstanz, P.O. Box 718, 78547 Konstanz, Germany
| | - Davide Donadio
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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Zhang Z, Wu T, Wang Q, Pan H, Tang R. Impact of interfacial high-density water layer on accurate estimation of adsorption free energy by Jarzynski's equality. J Chem Phys 2014; 140:034706. [DOI: 10.1063/1.4858428] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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Javaheri N, Cronemberger CM, Kaandorp JA. Modeling biosilicification at subcellular scales. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2014; 54:117-41. [PMID: 24420712 DOI: 10.1007/978-3-642-41004-8_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Biosilicification occurs in many organisms. Sponges and diatoms are major examples of them. In this chapter, we introduce a modeling approach that describes several biological mechanisms controlling silicification. Modeling biosilicification is a typical multiscale problem where processes at very different temporal and spatial scales need to be coupled: processes at the molecular level, physiological processes at the subcellular and cellular level, etc. In biosilicification morphology plays a fundamental role, and a spatiotemporal model is required. In the case of sponges, a particle simulation based on diffusion-limited aggregation is presented here. This model can describe fractal properties of silica aggregates in first steps of deposition on an organic template. In the case of diatoms, a reaction-diffusion model is introduced which can describe the concentrations of chemical components and has the possibility to include polymerization chain of reactions.
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Affiliation(s)
- Narjes Javaheri
- Section Computational Science, Faculty of Science, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
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Bertran O, del Valle LJ, Revilla-López G, Chaves G, Cardús L, Casas MT, Casanovas J, Turon P, Puiggalí J, Alemán C. Mineralization of DNA into nanoparticles of hydroxyapatite. Dalton Trans 2014; 43:317-27. [DOI: 10.1039/c3dt52112e] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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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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Hunter GK. Role of osteopontin in modulation of hydroxyapatite formation. Calcif Tissue Int 2013; 93:348-54. [PMID: 23334303 DOI: 10.1007/s00223-013-9698-6] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 11/28/2012] [Indexed: 10/27/2022]
Abstract
The presence of osteopontin (OPN) at high levels in both mineralized tissues such as bone and ectopic calcifications such as atherosclerotic plaque presents a conundrum: is OPN a promoter or inhibitor of hydroxyapatite (HA) formation? In vitro studies show that OPN adsorbs tightly to HA and is a potent inhibitor of crystal growth. Although the mechanism of the OPN-HA interaction is not fully understood, it is probably electrostatic in nature. Phosphorylation enhances OPN's ability to adsorb to and inhibit the growth of HA crystals, although other anionic groups also contribute to these properties. Recent findings suggest that OPN is an intrinsically unordered protein and that its lack of folded structure facilitates the protein's adsorption by allowing multiple binding geometries and the sequential formation of ionic bonds with Ca(2+) ions of the crystal surface. By analogy with other biominerals, it is likely that adsorption of OPN to HA results in "pinning" of growth steps. The abundance of OPN at sites of ectopic calcification reflects upregulation of the protein in response to crystal formation or even in response to elevated phosphate levels. Therefore, it appears that OPN is one of a group of proteins that function to prevent crystal formation in soft tissues. The role of OPN in bone mineralization, if any, is less clear. However, it is possible that it modulates HA formation, either by preventing crystal growth in "inappropriate" areas such as the osteoid seam or by regulating crystal growth habit (size and shape).
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Affiliation(s)
- Graeme K Hunter
- Schulich School of Medicine & Dentistry, University of Western Ontario, London, ON, N6A 5C1, Canada,
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Okhrimenko DV, Nissenbaum J, Andersson MP, Olsson MHM, Stipp SLS. Energies of the adsorption of functional groups to calcium carbonate polymorphs: the importance of -OH and -COOH groups. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:11062-73. [PMID: 23919655 DOI: 10.1021/la402305x] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The adsorption behavior of calcium carbonate is an important factor in many processes in nature, industry, and biological systems. We determined and compared the adsorption energies for a series of small molecules of different sizes and polarities (i.e., water, several alcohols, and acetic acid) on three synthetic CaCO3 polymorphs (calcite, aragonite, and vaterite). We measured isosteric heats of adsorption from vapor adsorption isotherms for 273 < T < 293 K, and we used XRD and SEM to confirm that samples did not change phase during the experiments. Density functional calculations and molecular dynamics simulations complemented the experimental results and aided interpretation. Alcohols with molecular mass greater than that of methanol bind more strongly to the calcium carbonate polymorphs than water and acetic acid. The adsorption energies for the alcohols are typical of chemisorption and indicate alcohol displacement of water from calcium carbonate surfaces. This explains why organisms favor biomolecules that contain alcohol functional groups (-OH) to control which polymorph they use, the crystal face and orientation, and the particle shape and size in biomineralization processes. This new insight is also very useful in understanding organic molecule adsorption mechanisms in soils, sediments, and rocks, which is important for predicting the behavior of mineral-fluid interactions when the challenge is to remediate contaminated groundwater aquifers or to produce oil and gas from reservoirs.
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Affiliation(s)
- D V Okhrimenko
- Nano-Science Center, Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark.
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Bleek K, Taubert A. New developments in polymer-controlled, bioinspired calcium phosphate mineralization from aqueous solution. Acta Biomater 2013; 9:6283-321. [PMID: 23291492 DOI: 10.1016/j.actbio.2012.12.027] [Citation(s) in RCA: 143] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Revised: 11/13/2012] [Accepted: 12/21/2012] [Indexed: 11/19/2022]
Abstract
The polymer-controlled and bioinspired precipitation of inorganic minerals from aqueous solution at near-ambient or physiological conditions avoiding high temperatures or organic solvents is a key research area in materials science. Polymer-controlled mineralization has been studied as a model for biomineralization and for the synthesis of (bioinspired and biocompatible) hybrid materials for a virtually unlimited number of applications. Calcium phosphate mineralization is of particular interest for bone and dental repair. Numerous studies have therefore addressed the mineralization of calcium phosphate using a wide variety of low- and high-molecular-weight additives. In spite of the growing interest and increasing number of experimental and theoretical data, the mechanisms of polymer-controlled calcium phosphate mineralization are not entirely clear to date, although the field has made significant progress in the last years. A set of elegant experiments and calculations has shed light on some details of mineral formation, but it is currently not possible to preprogram a mineralization reaction to yield a desired product for a specific application. The current article therefore summarizes and discusses the influence of (macro)molecular entities such as polymers, peptides, proteins and gels on biomimetic calcium phosphate mineralization from aqueous solution. It focuses on strategies to tune the kinetics, morphologies, final dimensions and crystal phases of calcium phosphate, as well as on mechanistic considerations.
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Affiliation(s)
- Katrin Bleek
- Institute of Chemistry, University of Potsdam, D-14476 Potsdam, Germany
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45
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Herbers CR, Li C, van der Vegt NFA. Grand challenges in quantum-classical modeling of molecule-surface interactions. J Comput Chem 2013; 34:1177-88. [DOI: 10.1002/jcc.23247] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Revised: 11/27/2012] [Accepted: 01/03/2013] [Indexed: 11/11/2022]
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46
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Swadling JB, Suter JL, Greenwell HC, Coveney PV. Influence of surface chemistry and charge on mineral-RNA interactions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:1573-1583. [PMID: 23302032 DOI: 10.1021/la303352g] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We present the results of large-scale molecular simulations, run over several tens of nanoseconds, of 25-mer sequences of single-stranded ribonucleic acid (RNA) in bulk water and at the surface of three hydrated positively charged MgAl layered double hydroxide (LDH) minerals. The three LDHs differ in surface charge density, through varying the number of isomorphic Al substitutions. Over the course of the simulations, RNA adsorbs tightly to the LDH surface through electrostatic interactions between the charged RNA phosphate groups and the alumina charge sites present in the LDH sheet. The RNA strands arrange parallel to the surface with the base groups aligning normal to the surface and exposed to the bulk aqueous region. This templating effect makes LDH a candidate for amplifying the population of a known RNA sequence from a small number of RNAs. The structure and interactions of RNA at a positively charged, hydroxylated LDH surface were compared with those of RNA at a positively charged calcium montmorillonite surface, allowing us to establish the comparative effect of complexation and water structure at hydroxide and silicate surfaces. The systems were studied by computing radial distribution functions, atom density plots, and radii of gyration, as well as visualization. An observation pertinent to the role of these minerals in prebiotic chemistry is that, for a given charge density on the mineral surface, different genetic sequences of RNA adopt different configurations.
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Affiliation(s)
- Jacob B Swadling
- The Centre for Computational Science, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, United Kingdom
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Abstract
Abstract
The size, morphology and species-specific texture of mollusc shell biominerals is one of the unresolved questions in nature. In search of molecular control principles, chitin has been identified by Weiner and Traub (FEBS Lett. 1980, 111:311–316) as one of the organic compounds with a defined co-organization with mineral phases. Chitin fibers can be aligned with certain mineralogical axes of crystalline calcium carbonate in a species-specific manner. These original observations motivated the functional characterization of chitin forming enzymes in molluscs. The full-length cDNA cloning of mollusc chitin synthases identified unique myosin domains as part of the biological control system. The potential impact of molecular motors and other conserved domains of these complex transmembrane enzymes on the evolution of shell biomineralization is investigated and discussed in this article.
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Weber E, Guth C, Weiss IM. GFP facilitates native purification of recombinant perlucin derivatives and delays the precipitation of calcium carbonate. PLoS One 2012; 7:e46653. [PMID: 23056388 PMCID: PMC3463529 DOI: 10.1371/journal.pone.0046653] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 09/03/2012] [Indexed: 12/02/2022] Open
Abstract
Insolubility is one of the possible functions of proteins involved in biomineralization, which often limits their native purification. This becomes a major problem especially when recombinant expression systems are required to obtain larger amounts. For example, the mollusc shell provides a rich source of unconventional proteins, which can interfere in manifold ways with different mineral phases and interfaces. Therefore, the relevance of such proteins for biotechnological processes is still in its infancy. Here we report a simple and reproducible purification procedure for a GFP-tagged lectin involved in biomineralization, originally isolated from mother-of-pearl in abalone shells. An optimization of E. coli host cell culture conditions was the key to obtain reasonable yields and high degrees of purity by using simple one-step affinity chromatography. We identified a dual functional role for the GFP domain when it became part of a mineralizing system in vitro. First, the GFP domain improved the solubility of an otherwise insoluble protein, in this case recombinant perlucin derivatives. Second, GFP inhibited calcium carbonate precipitation in a concentration dependent manner. This was demonstrated here using a simple bulk assay over a time period of 400 seconds. At concentrations of 2 µg/ml and higher, the inhibitory effect was observed predominantly for HCO(3) (-) as the first ionic interaction partner, but not necessarily for Ca(2+). The interference of GFP-tagged perlucin derivatives with the precipitation of calcium carbonate generated different types of GFP-fluorescent composite calcite crystals. GFP-tagging offers therefore a genetically tunable tool to gently modify mechanical and optical properties of synthetic biocomposite minerals.
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Affiliation(s)
- Eva Weber
- INM – Leibniz Institute for New Materials gGmbH, Saarbruecken, Germany
| | - Christina Guth
- INM – Leibniz Institute for New Materials gGmbH, Saarbruecken, Germany
| | - Ingrid M. Weiss
- INM – Leibniz Institute for New Materials gGmbH, Saarbruecken, Germany
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Costa D, Garrain PA, Baaden M. Understanding small biomolecule-biomaterial interactions: A review of fundamental theoretical and experimental approaches for biomolecule interactions with inorganic surfaces. J Biomed Mater Res A 2012; 101:1210-22. [DOI: 10.1002/jbm.a.34416] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2012] [Revised: 08/07/2012] [Accepted: 08/12/2012] [Indexed: 12/13/2022]
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O'Young J, Liao Y, Xiao Y, Jalkanen J, Lajoie G, Karttunen M, Goldberg HA, Hunter GK. Matrix Gla protein inhibits ectopic calcification by a direct interaction with hydroxyapatite crystals. J Am Chem Soc 2011; 133:18406-12. [PMID: 21961692 DOI: 10.1021/ja207628k] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Mice lacking the gene encoding matrix gla protein (MGP) exhibit massive mineral deposition in blood vessels and die soon after birth. We hypothesize that MGP prevents arterial calcification by adsorbing to growing hydroxyapatite (HA) crystals. To test this, we have used a combined experimental-computational approach. We synthesized peptides covering the entire sequence of human MGP, which contains three sites of serine phosphorylation and five sites of γ-carboxylation, and studied their effects on HA crystal growth using a constant-composition autotitration assay. In parallel studies, the interactions of these sequences with the {100} and {001} faces of HA were analyzed using atomistic molecular dynamics (MD) simulations. YGlapS (amino acids 1-14 of human MGP) and SK-Gla (MGP43-56) adsorbed rapidly to the {100} and {001} faces and strongly inhibited HA growth (IC(50) = 2.96 μg/mL and 4.96 μg/mL, respectively). QR-Gla (MGP29-42) adsorbed more slowly and was a moderate growth inhibitor, while the remaining three (nonpost-translationally modified) peptides had little or no effect in either analysis. Substitution of gla with glutamic acid reduced the adsorption and inhibition activities of SK-Gla and (to a lesser extent) QR-Gla but not YGlapS; substitution of phosphoserine with serine reduced the inhibitory potency of YGlapS. These studies suggest that MGP prevents arterial calcification by a direct interaction with HA crystals that involves both phosphate groups and gla residues of the protein. The strong correlation between simulated adsorption and measured growth inhibition indicates that MD provides a powerful tool to predict the effects of proteins and peptides on crystal formation.
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Affiliation(s)
- Jason O'Young
- School of Dentistry, University of Western Ontario, London, Canada
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