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Xue JW, Xu CH, Zhao W, Chen HY, Xu JJ. Unveiling the Dynamic Electrocatalytic Activity of Online Synthesized Bimetallic Nanocatalysts via Electrochemiluminescence Microscopy. NANO LETTERS 2024; 24:4665-4671. [PMID: 38587938 DOI: 10.1021/acs.nanolett.4c01026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
Effective bimetallic nanoelectrocatalysis demands precise control of composition, structure, and understanding catalytic mechanisms. To address these challenges, we employ a two-in-one approach, integrating online synthesis with real-time imaging of bimetallic Au@Metal core-shell nanoparticles (Au@M NPs) via electrochemiluminescence microscopy (ECLM). Within 120 s, online electrodeposition and in situ catalytic activity screening alternate. ECLM captures transient faradaic processes during potential switches, visualizes electrochemical processes in real-time, and tracks catalytic activity dynamics at the single-particle level. Analysis using ECL photon flux density eliminates size effects and yields quantitative electrocatalytic activity results. Notably, a nonlinear activity trend corresponding to the shell metal to Au surface atomic ratio is discerned, quantifying the optimal surface component ratio of Au@M NPs. This approach offers a comprehensive understanding of catalytic behavior during the deposition process with high spatiotemporal resolution, which is crucial for tailoring efficient bimetallic nanocatalysts for diverse applications.
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Affiliation(s)
- Jing-Wei Xue
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Cong-Hui Xu
- Institute of Nanochemistry and Nanobiology, School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, P. R. China
| | - Wei Zhao
- Institute of Nanochemistry and Nanobiology, School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, P. R. China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Jing-Juan Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
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2
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Tavakol M, Liu J, Hoff SE, Zhu C, Heinz H. Osteocalcin: Promoter or Inhibitor of Hydroxyapatite Growth? LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:1747-1760. [PMID: 38181199 DOI: 10.1021/acs.langmuir.3c02948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2024]
Abstract
Osteocalcin is the most abundant noncollagenous bone protein and the functions in bone remineralization as well as in inhibition of bone growth have remained unclear. In this contribution, we explain the dual role of osteocalcin in the nucleation of new calcium phosphate during bone remodeling and in the inhibition of hydroxyapatite crystal growth at the molecular scale. The mechanism was derived using pH-resolved all-atom models for the protein, phosphate species, and hydroxyapatite, along with molecular dynamics simulations and experimental and clinical observations. Osteocalcin binds to (hkl) hydroxyapatite surfaces through multiple residues, identified in this work, and the fingerprint of binding residues varies as a function of the (hkl) crystal facet and pH value. On balance, the affinity of osteocalcin to hydroxyapatite slows down crystal growth. The unique tricalcium γ-carboxylglutamic acid (Gla) domain hereby rarely adsorbs to hydroxyapatite surfaces and faces instead toward the solution. The Gla domain enables prenucleation of calcium phosphate for new bone formation at a slightly acidic pH of 5. The growth of prenucleation clusters of calcium phosphate continues upon increase in pH value from 5 to 7 and is much less favorable, or not observed, on the native osteocalcin structure at and above neutral pH values of 7. The results provide mechanistic insight into the early stages of bone remodeling from the molecular scale, help inform mutations of osteocalcin to modify binding to apatites, support drug design, and guide toward potential cures for osteoporosis and hyperosteogeny.
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Affiliation(s)
- Mahdi Tavakol
- Department of Chemical and Biological Engineering, University of Colorado Boulder, 3415 Colorado Ave, Boulder, Colorado 80301, United States
- Department of Mechanical Engineering, Sharif University of Technology, PO Box 11365-11155, Tehran, Iran
| | - Juan Liu
- Department of Chemical and Biological Engineering, University of Colorado Boulder, 3415 Colorado Ave, Boulder, Colorado 80301, United States
| | - Samuel E Hoff
- Department of Chemical and Biological Engineering, University of Colorado Boulder, 3415 Colorado Ave, Boulder, Colorado 80301, United States
| | - Cheng Zhu
- Department of Chemical and Biological Engineering, University of Colorado Boulder, 3415 Colorado Ave, Boulder, Colorado 80301, United States
| | - Hendrik Heinz
- Department of Chemical and Biological Engineering, University of Colorado Boulder, 3415 Colorado Ave, Boulder, Colorado 80301, United States
- Materials Science and Engineering Program, University of Colorado Boulder, 3415 Colorado Ave, Boulder, Colorado 80301, United States
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3
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Lachowski K, Chiang HT, Torkelson K, Zhou W, Zhang S, Pfaendtner J, Pozzo LD. Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:15878-15888. [PMID: 37910774 PMCID: PMC10653084 DOI: 10.1021/acs.langmuir.3c01577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 09/01/2023] [Accepted: 10/18/2023] [Indexed: 11/03/2023]
Abstract
Thin metal particles with two-dimensional (2D) symmetry are attractive for multiple applications but are difficult to synthesize in a reproducible manner. Although molecules that selectively adsorb to facets have been used to control nanoparticle shape, there is still limited research into the temporal control of growth processes to control these structural outcomes. Moreover, much of the current research into the growth of thin 2D particles lacks mechanistic details. In this work, we study why the substitution of isoleucine for methionine in a gold-binding peptide (Z2, RMRMKMK) results in an increase in gold nanoparticle anisotropy. Nanoplatelet growth in the presence of Z2M246I (RIRIKIK) is characterized using in situ small-angle X-ray scattering (SAXS) and UV-vis spectroscopy. Fitting time-resolved SAXS profiles reveal that 10 nm-thick particles with 2D symmetry are formed within the first few minutes of the reaction. Next, through a combination of electron diffraction and molecular dynamics simulations, we show that substitution of methionine for isoleucine increases the (111) facet selectivity in Z2M246I, and we conclude that this is key to the growth of nanoplatelets. However, the potential application of nanoplatelets formed using Z2M246I is limited due to their uncontrolled lateral growth, aggregation, and rapid sedimentation. Therefore, we use a liquid-handling robot to perform temporally controlled synthesis and dynamic intervention through the addition of Z2 to nanoplatelets grown in the presence of Z2M246I at different times. UV-vis spectroscopy, dynamic light scattering, and electron microscopy show that dynamic intervention results in control over the mean size and stability of plate-like particles. Finally, we use in situ UV-vis spectroscopy to study plate-like particle growth at different times of intervention. Our results demonstrate that both the selectivity and magnitude of binding free energy toward lattices are important for controlling nanoparticle growth pathways.
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Affiliation(s)
- Kacper
J. Lachowski
- Department
of Chemical Engineering, University of Washington, Seattle, Washington 98105, United States
- Molecular
Engineering and Sciences Institute, University
of Washington, Seattle, Washington 98105, United States
| | - Huat Thart Chiang
- Department
of Chemical Engineering, University of Washington, Seattle, Washington 98105, United States
| | - Kaylyn Torkelson
- Department
of Chemical Engineering, University of Washington, Seattle, Washington 98105, United States
| | - Wenhao Zhou
- Department
of Material Science and Engineering, University
of Washington, Seattle, Washington 98105, United States
- Physical
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Shuai Zhang
- Molecular
Engineering and Sciences Institute, University
of Washington, Seattle, Washington 98105, United States
- Department
of Material Science and Engineering, University
of Washington, Seattle, Washington 98105, United States
- Physical
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Jim Pfaendtner
- Department
of Chemical Engineering, University of Washington, Seattle, Washington 98105, United States
| | - Lilo D. Pozzo
- Department
of Chemical Engineering, University of Washington, Seattle, Washington 98105, United States
- Molecular
Engineering and Sciences Institute, University
of Washington, Seattle, Washington 98105, United States
- Department
of Material Science and Engineering, University
of Washington, Seattle, Washington 98105, United States
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4
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Janitra RS, Destiarani W, Hardianto A, Baroroh U, Rohmatulloh FG, Rustaman, Subroto T, Rukiah, Yusuf M. Multilayer Model of Gold Nanoparticles (AuNPs) and Its Application in the Classical Molecular Dynamics Simulation of Citrate-Capped AuNPs. J Phys Chem B 2023; 127:7103-7110. [PMID: 37540714 DOI: 10.1021/acs.jpcb.3c00771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/06/2023]
Abstract
Studies on the interaction between gold nanoparticles (AuNPs) and functional proteins have been useful in developing diagnostic and therapeutic agents. Such studies require a realistic computational model of AuNPs for successful molecular design works. This study offers a new multilayer model of AuNPs to address the inconsistency between its molecular mechanics' interpretation and AuNP's plasmonic nature. We performed partial charge quantum calculation of AuNPs using Au13 and Au55 models. The result showed that it has partial negative charges on the surface and partial positive charges on the inner part, indicating that the AuNP model should be composed of multiatom types. We tested the partial charge parameters of these gold (Au) atoms in classical molecular dynamics simulation (CMD) of AuNPs. The result showed that our parameters performed better in simulating the adsorption of Na+ and dicarboxy acetone in terms of consistency with surface charge density than the zero charges Au in the interface force field (IFF). We proposed that the multiple-charged AuNP model can be developed further into a simpler four-atom type of Au in a larger AuNP size.
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Affiliation(s)
- Regaputra S Janitra
- Biotechnology Master Program, Postgraduate School, Universitas Padjadjaran, Jl. Dipatiukur 35, Bandung 40132, West Java, Indonesia
| | - Wanda Destiarani
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Jl. Singaperbangsa 2, Bandung 40132, West Java, Indonesia
| | - Ari Hardianto
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jl. Raya Bandung-Sumedang KM 21, Jatinangor 45363, West Java, Indonesia
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Jl. Singaperbangsa 2, Bandung 40132, West Java, Indonesia
| | - Umi Baroroh
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Jl. Singaperbangsa 2, Bandung 40132, West Java, Indonesia
- Department of Biotechnology, Indonesian School of Pharmacy, Jl. Soekarno Hatta No. 354, Bandung 40266, West Java, Indonesia
| | - Fauzian G Rohmatulloh
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Jl. Singaperbangsa 2, Bandung 40132, West Java, Indonesia
| | - Rustaman
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jl. Raya Bandung-Sumedang KM 21, Jatinangor 45363, West Java, Indonesia
| | - Toto Subroto
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jl. Raya Bandung-Sumedang KM 21, Jatinangor 45363, West Java, Indonesia
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Jl. Singaperbangsa 2, Bandung 40132, West Java, Indonesia
| | - Rukiah
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jl. Raya Bandung-Sumedang KM 21, Jatinangor 45363, West Java, Indonesia
| | - Muhammad Yusuf
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jl. Raya Bandung-Sumedang KM 21, Jatinangor 45363, West Java, Indonesia
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Jl. Singaperbangsa 2, Bandung 40132, West Java, Indonesia
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5
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Ihlenburg RBJ, Petracek D, Schrank P, Davari MD, Taubert A, Rothenstein D. Identification of the First Sulfobetaine Hydrogel-Binding Peptides via Phage Display Assay. Macromol Rapid Commun 2023; 44:e2200896. [PMID: 36703485 DOI: 10.1002/marc.202200896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/11/2023] [Indexed: 01/28/2023]
Abstract
Using the M13 phage display, a series of 7- and 12-mer peptides which interact with new sulfobetaine hydrogels are identified. Two peptides each from the 7- and 12-mer peptide libraries bind to the new sulfobetaine hydrogels with high affinity compared to the wild-type phage lacking a dedicated hydrogel binding peptide. This is the first report of peptides binding to zwitterionic sulfobetaine hydrogels and the study therefore opens up the pathway toward new phage or peptide/hydrogel hybrids with high application potential.
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Affiliation(s)
- Ramona B J Ihlenburg
- Institute of Chemistry, University of Potsdam, Karl-Liebknecht-Straße 24-25, D-14476, Potsdam, Germany
| | - David Petracek
- Department Bioinspired Materials, Institute for Materials Science, University of Stuttgart, Heisenbergstraße 3, D-70569, Stuttgart, Germany
| | - Paul Schrank
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120, Halle, Germany
| | - Mehdi D Davari
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120, Halle, Germany
| | - Andreas Taubert
- Institute of Chemistry, University of Potsdam, Karl-Liebknecht-Straße 24-25, D-14476, Potsdam, Germany
| | - Dirk Rothenstein
- Department Bioinspired Materials, Institute for Materials Science, University of Stuttgart, Heisenbergstraße 3, D-70569, Stuttgart, Germany
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6
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Janairo JIB. Sequence rules for gold-binding peptides. RSC Adv 2023; 13:21146-21152. [PMID: 37449032 PMCID: PMC10337651 DOI: 10.1039/d3ra04269c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 07/06/2023] [Indexed: 07/18/2023] Open
Abstract
Metal-binding peptides play a central role in bionanotechnology, wherein they are responsible for directing growth and influencing the resulting properties of inorganic nanomaterials. One of the key advantages of using peptides to create nanomaterials is their versatility, wherein subtle changes in the sequence can have a dramatic effect on the structure and properties of the nanomaterial. However, precisely knowing which position and which amino acid should be modified within a given sequence to enhance a specific property can be a daunting challenge owing to combinatorial complexity. In this study, classification based on association rules was performed using 860 gold-binding peptides. Using a minimum support threshold of 0.035 and confidence of 0.9, 30 rules with confidence and lift values greater than 0.9 and 1, respectively, were extracted that can differentiate high-binding from low-binding peptides. The test performance of these rules for categorizing the peptides was found to be satisfactory, as characterized by accuracy = 0.942, F1 = 0.941, MCC = 0.884. What stands out from the extracted rules are the importance of tryptophan and arginine residues in differentiating peptides with high binding affinity from those with low affinity. In addition, the association rules revealed that positions 2 and 4 within a decapeptide are frequently involved in the rules, thus suggesting their importance in influencing peptide binding affinity to AuNPs. Collectively, this study identified sequence rules that may be used to design peptides with high binding affinity.
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7
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Alizadeh Sahraei A, Azizi D, Mokarizadeh AH, Boffito DC, Larachi F. Emerging Trends of Computational Chemistry and Molecular Modeling in Froth Flotation: A Review. ACS ENGINEERING AU 2023; 3:128-164. [PMID: 37362006 PMCID: PMC10288516 DOI: 10.1021/acsengineeringau.2c00053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 06/28/2023]
Abstract
Froth flotation is the most versatile process in mineral beneficiation, extensively used to concentrate a wide range of minerals. This process comprises mixtures of more or less liberated minerals, water, air, and various chemical reagents, involving a series of intermingled multiphase physical and chemical phenomena in the aqueous environment. Today's main challenge facing the froth flotation process is to gain atomic-level insights into the properties of its inherent phenomena governing the process performance. While it is often challenging to determine these phenomena via trial-and-error experimentations, molecular modeling approaches not only elicit a deeper understanding of froth flotation but can also assist experimental studies in saving time and budget. Thanks to the rapid development of computer science and advances in high-performance computing (HPC) infrastructures, theoretical/computational chemistry has now matured enough to successfully and gainfully apply to tackle the challenges of complex systems. In mineral processing, however, advanced applications of computational chemistry are increasingly gaining ground and demonstrating merit in addressing these challenges. Accordingly, this contribution aims to encourage mineral scientists, especially those interested in rational reagent design, to become familiarized with the necessary concepts of molecular modeling and to apply similar strategies when studying and tailoring properties at the molecular level. This review also strives to deliver the state-of-the-art integration and application of molecular modeling in froth flotation studies to assist either active researchers in this field to disclose new directions for future research or newcomers to the field to initiate innovative works.
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Affiliation(s)
- Abolfazl Alizadeh Sahraei
- Department
of Chemical Engineering, Université
Laval, 1065 Avenue de la Médecine, Québec, Québec G1V 0A6, Canada
| | - Dariush Azizi
- Department
of Chemical Engineering, École Polytechnique
de Montréal, 2900 Boulevard Édouard-Montpetit, Montréal H3T 1J4, Canada
| | - Abdol Hadi Mokarizadeh
- School
of Polymer Science and Polymer Engineering, University of Akron, Akron, Ohio 44325, United States
| | - Daria Camilla Boffito
- Department
of Chemical Engineering, École Polytechnique
de Montréal, 2900 Boulevard Édouard-Montpetit, Montréal H3T 1J4, Canada
| | - Faïçal Larachi
- Department
of Chemical Engineering, Université
Laval, 1065 Avenue de la Médecine, Québec, Québec G1V 0A6, Canada
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8
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Yamada Y, Anderson CF, Schneider JP. De Novo Design of a Versatile Peptide-Based Coating to Impart Targeted Functionality at the Surface of Native Polystyrene. ACS APPLIED MATERIALS & INTERFACES 2023. [PMID: 37276244 DOI: 10.1021/acsami.3c02606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Peptide sequence periodicity is a simple design tool that can be used to generate functional peptide-based surface coatings. De novo-designed peptide N3-PEG-VK16 is characterized by a hydrophobic periodicity of two that avidly binds to native polystyrene priming its surface for subsequent targeted functionalization via chemical ligation. The peptidic portion of N3-PEG-VK16 is responsible for surface binding, converting polystyrene's hydrophobic surface into a wettable and electrostatically charged environment that facilitates cell attachment. Native polystyrene surfaces are coated by simple peptide adsorption from an aqueous buffered solution, and the resulting primed surface is easily functionalized by cycloaddition chemistry. Herein, we show that ligating a vitronectin-derived peptide to primed polystyrene surfaces enables adhesion, expansion, long-term culture, and phenotype maintenance of human induced pluripotent stem cells. To demonstrate scope, we also show that additional functional ligands can be used, for example, nerve growth factor protein, to control neurite outgrowth.
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Affiliation(s)
- Yuji Yamada
- Department of Clinical Biochemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Caleb F Anderson
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute-Frederick, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Joel P Schneider
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute-Frederick, National Institutes of Health, Frederick, Maryland 21702, United States
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9
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Yokoyama K, Thomas J, Ardner W, Kieft M, Neuwirth LS, Liu W. An Approach for In-Situ Detection of Gold Colloid Aggregates Amyloid Formations Within The Hippocampus of The Cohen's Alzheimer's Disease Rat Model By Surface Enhanced Raman Scattering Methods. J Neurosci Methods 2023; 393:109892. [PMID: 37230258 DOI: 10.1016/j.jneumeth.2023.109892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 04/25/2023] [Accepted: 05/19/2023] [Indexed: 05/27/2023]
Abstract
BACKGROUND Amyloid beta (Aβ) peptides, such as Aβ1-40 or Aβ1-42 are regarded as hallmark neuropathological biomarkers associated with Alzheimer's disease (AD). The formation of an aggregates by Aβ1-40 or Aβ1-42-coated gold nano-particles are hypothesized to contain conformation of Aβ oligomers, which could exist only at an initial stage of fibrillogenesis. NEW METHOD The attempt of in-situ detection of externally initiated gold colloid (ca. 80nm diameter) aggregates in the middle section of the hippocampus of the Long Evans Cohen's Alzheimer's disease rat model was conducted through the Surface Enhanced Raman Scattering (SERS) method. RESULTS The SERS spectral features contained modes associated with β-sheet interactions and a significant number of modes that were previously reported in SERS shifts for Alzheimer diseased rodent and human brain tissues; thereby, strongly implying a containment of amyloid fibrils. The spectral patterns were further examined and compared with those collected from in-vitro gold colloid aggregates which were formed from Aβ1-40 - or Aβ1-42 -coated 80nm gold colloid under pH ~4, pH ~7, and pH ~10, and the best matched datasets were found with that of the aggregates of Aβ1-42 -coated 80nm gold colloid at ~pH 4.0. The morphology and physical size of this specific gold colloid aggregate was clearly different from those found in-vitro. COMPARISON WITH EXISTING METHOD(S) The amyloid fibril with a β-sheet conformation identified in previously reported in AD mouse/human brain tissues was involved in a formation of the gold colloid aggregates. However, to our surprise, best explanation for the observed SERS spectral features was possible with those in vitro Aβ1-42 -coated 80nm gold colloid under pH ~4. CONCLUSIONS A formation of gold colloid aggregates was confirmed in the AD rat hippocampal brain section with unique physical morphology compared to those observed in in-vitro Aβ1-42 or Aβ1-40 mediated gold colloid aggregates. It was concluded that a β-sheet conformation identified in previously reported in AD mouse/human brain tissues was in volved in a formation of the gold colloid aggregates.
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Affiliation(s)
- Kazushige Yokoyama
- Department of Chemistry, The State University of New York Geneseo College, Geneseo, NY, USA
| | - Joshua Thomas
- Department of Chemistry, The State University of New York Geneseo College, Geneseo, NY, USA
| | - Windsor Ardner
- Department of Chemistry, The State University of New York Geneseo College, Geneseo, NY, USA
| | - Madison Kieft
- Department of Chemistry, The State University of New York Geneseo College, Geneseo, NY, USA
| | - Lorenz S Neuwirth
- Department of Psychology, The State University of New York Old Westbury, Old Westbury, NY, USA; SUNY Neuroscience Research Institute, The State University of New York Old Westbury, Old Westbury, NY, USA
| | - Wei Liu
- WITec Instruments Corp, Knoxville, TN, USA
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10
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Construction of catalyst layer network structure for proton exchange membrane fuel cell derived from polymeric dispersion. J Colloid Interface Sci 2023; 638:184-192. [PMID: 36738543 DOI: 10.1016/j.jcis.2023.01.132] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/24/2023] [Accepted: 01/27/2023] [Indexed: 02/04/2023]
Abstract
A rational design of the structure of catalyst layer (CL) is required for proton exchange membrane fuel cells to attain outstanding performance and excellent stability. It is crucial to have a profound comprehension of the correlations existing between the properties (catalyst ink), network structures of CL and proton exchange membrane fuel cells' performance for the rational design of the structure of CL. This study deeply investigates the effects of a series of alcohol solvents on the properties and network structure of CL. The results demonstrate that the CL aggregates in higher ε solution show smaller particle sizes, and the sulfonic acid groups (∼SO3H) tend to extend more outward due to the strong dissociation. A more continuous and homogeneous ionomer distribution around Pt/C aggregates is observed in the CL, which improves the electrochemically active surface area (ECSA) and performance of the electrode. But, the electrode has a poor performance at high current density regions due to the mass transfer resistance. Based on this, a two-step solvent control strategy is proposed to maintain uniform ionomer and aggerates distribution and optimize the mass transfer for CL. The performance of the cell improves from 0.555 V to 0.615 V at 2000 mA·cm-2.
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11
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Brooks SC, Jin R, Zerbach VC, Zhang Y, Walsh TR, Rosi NL. Single Amino Acid Modifications for Controlling the Helicity of Peptide-Based Chiral Gold Nanoparticle Superstructures. J Am Chem Soc 2023; 145:6546-6553. [PMID: 36912863 PMCID: PMC10037318 DOI: 10.1021/jacs.3c00827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Abstract
Assembling nanoparticles (NPs) into well-defined superstructures can lead to emergent collective properties that depend on their 3-D structural arrangement. Peptide conjugate molecules designed to both bind to NP surfaces and direct NP assembly have proven useful for constructing NP superstructures, and atomic- and molecular-level alterations to these conjugates have been shown to manifest in observable changes to nanoscale structure and properties. The divalent peptide conjugate, C16-(PEPAu)2 (PEPAu = AYSSGAPPMPPF), directs the formation of one-dimensional helical Au NP superstructures. This study examines how variation of the ninth amino acid residue (M), which is known to be a key Au anchoring residue, affects the structure of the helical assemblies. A series of conjugates of differential Au binding affinities based on variation of the ninth residue were designed, and Replica Exchange with Solute Tempering (REST) Molecular Dynamics simulations of the peptides on an Au(111) surface were performed to determine the approximate surface contact and to assign a binding score for each new peptide. A helical structure transition from double helices to single helices is observed as the peptide binding affinity to the Au(111) surface decreases. Accompanying this distinct structural transition is the emergence of a plasmonic chiroptical signal. REST-MD simulations were also used to predict new peptide conjugate molecules that would preferentially direct the formation of single-helical AuNP superstructures. Significantly, these findings demonstrate how small modifications to peptide precursors can be leveraged to precisely direct inorganic NP structure and assembly at the nano- and microscale, further expanding and enriching the peptide-based molecular toolkit for controlling NP superstructure assembly and properties.
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Affiliation(s)
- Sydney C Brooks
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Ruitao Jin
- Institute for Frontier Materials, Deakin University, Geelong, Victoria 3216, Australia
| | - Victoria C Zerbach
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Yuyu Zhang
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Tiffany R Walsh
- Institute for Frontier Materials, Deakin University, Geelong, Victoria 3216, Australia
| | - Nathaniel L Rosi
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pennsylvania 15260, United States
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12
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Winton AJ, Allen MA. Rational Design of a Bifunctional Peptide Exhibiting Lithium Titanate Oxide and Carbon Nanotube Affinities for Lithium-Ion Battery Applications. ACS APPLIED MATERIALS & INTERFACES 2023; 15:8579-8589. [PMID: 36729082 DOI: 10.1021/acsami.2c18018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Phage display is employed as a method for identifying polypeptides that bind to lithium-ion battery materials, specifically lithium titanate oxide (LTO) and multiwalled carbon nanotubes (MWCNTs). Output/input assays are used as a quantitative measure to narrow down the strongest binding polypeptides from several peptides selected through biopanning. Negatively stained transmission electron microscopy is used to verify that a phage presenting a particular LTO or MWCNT binding peptide sequence colocalizes with the respective material. Heterologous expression allows for ample polypeptides to be grown and purified using a peptide expression vector. Isothermal titration calorimetry in conjunction with alanine scanning enables determination of the pertinent residues involved in LTO binding and yields a dissociation constant of 3.41 μM. A rationally designed bifunctional peptide exhibiting LTO and MWCNT binding domains is subsequently validated to exhibit both LTO and MWCNT affinities and is incorporated as a binding agent in LTO coin-type electrochemical cells where the bifunctional peptide demonstrates stability at high cycle rates and potential as an alternative to non-specific binding agents for aqueous slurry processing of lithium-ion battery electrodes.
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Affiliation(s)
- Alexander J Winton
- Department of Chemistry & Biochemistry, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
| | - Mark A Allen
- Department of Chemistry & Biochemistry, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
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13
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Biomedical applications of solid-binding peptides and proteins. Mater Today Bio 2023; 19:100580. [PMID: 36846310 PMCID: PMC9950531 DOI: 10.1016/j.mtbio.2023.100580] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/06/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
Over the past decades, solid-binding peptides (SBPs) have found multiple applications in materials science. In non-covalent surface modification strategies, solid-binding peptides are a simple and versatile tool for the immobilization of biomolecules on a vast variety of solid surfaces. Especially in physiological environments, SBPs can increase the biocompatibility of hybrid materials and offer tunable properties for the display of biomolecules with minimal impact on their functionality. All these features make SBPs attractive for the manufacturing of bioinspired materials in diagnostic and therapeutic applications. In particular, biomedical applications such as drug delivery, biosensing, and regenerative therapies have benefited from the introduction of SBPs. Here, we review recent literature on the use of solid-binding peptides and solid-binding proteins in biomedical applications. We focus on applications where modulating the interactions between solid materials and biomolecules is crucial. In this review, we describe solid-binding peptides and proteins, providing background on sequence design and binding mechanism. We then discuss their application on materials relevant for biomedicine (calcium phosphates, silicates, ice crystals, metals, plastics, and graphene). Although the limited characterization of SBPs still represents a challenge for their design and widespread application, our review shows that SBP-mediated bioconjugation can be easily introduced into complex designs and on nanomaterials with very different surface chemistries.
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14
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Solvation Structure and Dynamics of Aqueous Solutions of Au+ Ions: A Molecular Dynamics Simulation Study. J SOLUTION CHEM 2023. [DOI: 10.1007/s10953-022-01234-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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15
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Surface modification of nanoparticles to improve oil recovery Mechanisms: A critical review of the methods, influencing Parameters, advances and prospects. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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Kanhaiya K, Heinz H. Adsorption and Diffusion of Oxygen on Pure and Partially Oxidized Metal Surfaces in Ultrahigh Resolution. NANO LETTERS 2022; 22:5392-5400. [PMID: 35730668 DOI: 10.1021/acs.nanolett.2c00490] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The interaction of gas molecules with metal and oxide surfaces plays a critical role in corrosion, catalysis, sensing, and heterogeneous materials. However, insights into the dynamics of O2 from picoseconds to microseconds have remained unavailable to date. We obtained 3D potential energy surfaces for adsorption of O2 on 11 common pristine and partially oxidized (hkl) surfaces of Ni and Al in picometer resolution and high accuracy of 0.1 kcal/mol, identified binding sites, and surface mobility from 25 to 300 °C. We explain relative oxidation rates and parameters for oxide growth. We employed over 150 000 molecular mechanics and molecular dynamics simulations with the interface force field (IFF) using structural data from X-ray diffraction (XRD) and low-energy electron diffraction (LEED). The methods reach 10 to 50 times higher accuracy than possible before and are suited to analyze gas interactions with metals up to the micrometer scale including defects and irregular nanostructures.
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Affiliation(s)
- Krishan Kanhaiya
- Department of Chemical and Biological Engineering, University of Colorado at Boulder, Boulder, Colorado 80309, United States
| | - Hendrik Heinz
- Department of Chemical and Biological Engineering, University of Colorado at Boulder, Boulder, Colorado 80309, United States
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17
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Sokolová M, Šestáková H, Truksa M, Šafařík M, Hadravová R, Bouř P, Šebestík J. Photochemical synthesis of pink silver and its use for monitoring peptide nitration via surface enhanced Raman spectroscopy (SERS). Amino Acids 2022; 54:1261-1274. [PMID: 35731286 DOI: 10.1007/s00726-022-03178-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 05/31/2022] [Indexed: 12/01/2022]
Abstract
Oxidative stress may cause extended tyrosine posttranslational modifications of peptides and proteins. The 3-nitro-L-tyrosine (Nit), which is typically formed, affects protein behavior during neurodegenerative processes, such as Alzheimer's and Parkinson's diseases. Such metabolic products may be conveniently detected at very low concentrations by surface enhanced Raman spectroscopy (SERS). Previously, we have explored the SERS detection of the Nit NO2 bending vibrational bands in a presence of hydrogen chloride (Niederhafner et al., Amino Acids 53:517-532, 2021, ibid). In this article, we describe performance of a new SERS substrate, "pink silver", synthesized photochemically. It provides SERS even without the HCl induction, and the acid further decreases the detection limit about 9 times. Strong SERS bands were observed in the asymmetric (1550-1475 cm-1) and symmetric (1360-1290 cm-1) NO stretching in the NO2 group. The bending vibration was relatively weak, but appeared stronger when HCl was added. The band assignments were supported by density functional theory modeling.
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Affiliation(s)
- Marina Sokolová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic
| | - Hana Šestáková
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic
| | - Martin Truksa
- Mensa Gymnázium O.P.S., Španielova 1111/19, 163 00, Prague 6, Czech Republic
| | - Martin Šafařík
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic
| | - Romana Hadravová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic
| | - Jaroslav Šebestík
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic. .,Mensa Gymnázium O.P.S., Španielova 1111/19, 163 00, Prague 6, Czech Republic.
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18
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Sen S, Thaker A, Sirajudeen L, Williams D, Nannenga BL. Protein-Nanoparticle Complex Structure Determination by Cryo-Electron Microscopy. ACS APPLIED BIO MATERIALS 2022; 5:4696-4700. [PMID: 35587230 DOI: 10.1021/acsabm.2c00130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Methods that allow the study of the structure of proteins in complex with nanomaterials promise to enhance our understanding of how biological molecules interface with inorganic materials. We used single-particle cryo-electron microscopy (cryo-EM) to demonstrate the potential for cryo-EM analysis to reveal structural details of protein-nanoparticle complexes. Two protein-nanomaterial complexes, namely, GroEL bound to platinum nanoparticles (GroEL-PtNP) and ferritin bound to an iron oxide nanoparticle, were used as model samples. For the GroEL-PtNP complex, a final reconstruction was obtained to 3.93 Å, which allowed us to fit the atomic model of GroEL into the resulting map. This sets the stage for future work and improvements on the use of cryo-EM for the study of protein-nanomaterial complexes.
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Affiliation(s)
- Sagnik Sen
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe 85287, Arizona, United States
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe 85287, Arizona, United States
| | - Amar Thaker
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe 85287, Arizona, United States
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe 85287, Arizona, United States
| | - Luqmanal Sirajudeen
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe 85287, Arizona, United States
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe 85287, Arizona, United States
| | - Dewight Williams
- John M. Cowley Center for High Resolution Electron Microscopy, Arizona State University, Tempe 85281, Arizona, United States
| | - Brent L Nannenga
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe 85287, Arizona, United States
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe 85287, Arizona, United States
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19
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Farouq MAH, Kubiak-Ossowska K, Al Qaraghuli MM, Ferro VA, Mulheran PA. Functionalisation of Inorganic Material Surfaces with Staphylococcus Protein A: A Molecular Dynamics Study. Int J Mol Sci 2022; 23:ijms23094832. [PMID: 35563221 PMCID: PMC9103475 DOI: 10.3390/ijms23094832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/21/2022] [Accepted: 04/25/2022] [Indexed: 12/07/2022] Open
Abstract
Staphylococcus protein A (SpA) is found in the cell wall of Staphylococcus aureus bacteria. Its ability to bind to the constant Fc regions of antibodies means it is useful for antibody extraction, and further integration with inorganic materials can lead to the development of diagnostics and therapeutics. We have investigated the adsorption of SpA on inorganic surface models such as experimentally relevant negatively charged silica, as well as positively charged and neutral surfaces, by use of fully atomistic molecular dynamics simulations. We have found that SpA, which is itself negatively charged at pH7, is able to adsorb on all our surface models. However, adsorption on charged surfaces is more specific in terms of protein orientation compared to a neutral Au (111) surface, while the protein structure is generally well maintained in all cases. The results indicate that SpA adsorption is optimal on the siloxide-rich silica surface, which is negative at pH7 since this keeps the Fc binding regions free to interact with other species in solution. Due to the dominant role of electrostatics, the results are transferable to other inorganic materials and pave the way for new diagnostic and therapeutic designs where SpA might be used to conjugate antibodies to nanoparticles.
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Affiliation(s)
- Mohammed A. H. Farouq
- Department of Chemical and Process Engineering, University of Strathclyde, 75 Montrose Street, Glasgow G1 1XJ, UK; (M.M.A.Q.); (P.A.M.)
- Correspondence: ; Tel.: +44-01-4155-24400
| | - Karina Kubiak-Ossowska
- Department of Physics/Archie-West HPC, University of Strathclyde, 107 Rottenrow East, Glasgow G4 0NG, UK;
| | - Mohammed M. Al Qaraghuli
- Department of Chemical and Process Engineering, University of Strathclyde, 75 Montrose Street, Glasgow G1 1XJ, UK; (M.M.A.Q.); (P.A.M.)
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK;
- EPSRC Future Manufacturing Research Hub for Continuous Manufacturing and Advanced Crystallisation (CMAC), University of Strathclyde, 99 George Street, Glasgow G1 1RD, UK
| | - Valerie A. Ferro
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK;
| | - Paul A. Mulheran
- Department of Chemical and Process Engineering, University of Strathclyde, 75 Montrose Street, Glasgow G1 1XJ, UK; (M.M.A.Q.); (P.A.M.)
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20
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Odegard GM, Patil SU, Deshpande PP, Kanhaiya K, Winetrout JJ, Heinz H, Shah SP, Maiaru M. Molecular Dynamics Modeling of Epoxy Resins Using the Reactive Interface Force Field. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c01813] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gregory M. Odegard
- Michigan Technological University, Houghton, Michigan 49931, United States
| | - Sagar U. Patil
- Michigan Technological University, Houghton, Michigan 49931, United States
| | | | - Krishan Kanhaiya
- University of Colorado at Boulder, Boulder, Colorado 80309, United States
| | | | - Hendrik Heinz
- University of Colorado at Boulder, Boulder, Colorado 80309, United States
| | - Sagar P. Shah
- University of Massachusetts at Lowell, Lowell, Massachusetts 01854, United States
| | - Marianna Maiaru
- University of Massachusetts at Lowell, Lowell, Massachusetts 01854, United States
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21
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Meena SK, Lerouge F, Baldeck P, Andraud C, Garavelli M, Parola S, Sulpizi M, Rivalta I. On the origin of controlled anisotropic growth of monodisperse gold nanobipyramids. NANOSCALE 2021; 13:15292-15300. [PMID: 34486622 DOI: 10.1039/d1nr01768c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We elucidate the crucial role of the cetyl trimethylammonium bromide (CTAB) surfactant in the anisotropic growth mechanism of gold nano-bipyramids, nano-objects with remarkable optical properties and high tunability. Atomistic molecular dynamics simulations predict different surface coverages of the CTAB (positively charged) heads and their (bromide) counterions as function of the gold exposed surfaces. High concentration of CTAB surfactant promotes formation of gold nanograins in solution that work as precursors for the smooth anisotropic growth of more elongated nano-bipyramidal objects. Nanobipyramids feature higher index facets with respect to nanorods, allowing higher CTAB coverages that stabilize their formation and leading to narrower inter-micelles channels that smooth down their anisotropic growth. Absorption spectroscopy and scanning electron microscopy confirmed the formation of nanograins and demonstrated the importance of surfactant concentration on driving the growth towards nano-bipyramids rather than nanorods. The outcome explains the formation of the monodisperse bipyramidal nano-objects, the origin of their controlled shapes and sizes along with their remarkable stability.
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Affiliation(s)
- Santosh Kumar Meena
- Chemical Engineering and Process Development Division, CSIR-National Chemical Laboratory (NCL), Dr. HomiBhabha Road, Pune-411008, India.
| | - Frederic Lerouge
- Univ Lyon, Ens de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France
| | - Patrice Baldeck
- Univ Lyon, Ens de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France
| | - Chantal Andraud
- Univ Lyon, Ens de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France
| | - Marco Garavelli
- Dipartimento di Chimica Industriale "Toso Montanari", Universitá degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy.
| | - Stephane Parola
- Univ Lyon, Ens de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France
| | - Marialore Sulpizi
- Institute of Physics, Johannes Gutenberg University Mainz, Staudingerweg 7, 55099 Mainz, Germany.
| | - Ivan Rivalta
- Dipartimento di Chimica Industriale "Toso Montanari", Universitá degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy.
- Univ Lyon, Ens de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France
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22
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Farhadian A, Assar Kashani S, Rahimi A, Oguzie EE, Javidparvar AA, Nwanonenyi SC, Yousefzadeh S, Nabid MR. Modified hydroxyethyl cellulose as a highly efficient eco-friendly inhibitor for suppression of mild steel corrosion in a 15% HCl solution at elevated temperatures. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116607] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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23
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Thaker A, Sirajudeen L, Simmons CR, Nannenga BL. Structure-guided identification of a peptide for bio-enabled gold nanoparticle synthesis. Biotechnol Bioeng 2021; 118:4867-4873. [PMID: 34436761 DOI: 10.1002/bit.27927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/02/2021] [Accepted: 08/22/2021] [Indexed: 12/11/2022]
Abstract
In this study, we show that maltose-binding protein (MBP) is capable of facilitating stable gold nanoparticle synthesis, and a structure of MBP in the presence of gold ions was determined by X-ray crystallography. Using this high-resolution structure of gold ion bound MBP, a peptide (AT1) was selected and synthesized and was shown to also aid in the synthesis of stable gold nanoparticles under similar experimental conditions to those used for protein facilitated synthesis. This structure-based approach represents a new potential method for the selection of peptides capable of facilitating stable nanoparticle synthesis.
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Affiliation(s)
- Amar Thaker
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, Arizona, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Luqmanal Sirajudeen
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, Arizona, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Chad R Simmons
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Brent L Nannenga
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, Arizona, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
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24
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Adiram-Filiba N, Ohaion E, Verner G, Schremer A, Nadav-Tsubery M, Lublin-Tennenbaum T, Keinan-Adamsky K, Lucci M, Luchinat C, Ravera E, Goobes G. Structure and Dynamics Perturbations in Ubiquitin Adsorbed or Entrapped in Silica Materials Are Related to Disparate Surface Chemistries Resolved by Solid-State NMR Spectroscopy. Biomacromolecules 2021; 22:3718-3730. [PMID: 34333966 DOI: 10.1021/acs.biomac.1c00495] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Protein immobilization on material surfaces is emerging as a powerful tool in the design of devices and active materials for biomedical and pharmaceutical applications as well as for catalysis. Preservation of the protein's biological functionality is crucial to the design process and is dependent on the ability to maintain its structural and dynamical integrity while removed from the natural surroundings. The scientific techniques to validate the structure of immobilized proteins are scarce and usually provide limited information as a result of poor resolution. In this work, we benchmarked the ability of standard solid-state NMR techniques to resolve the effects of binding to dissimilar silica materials on a model protein. In particular, the interactions between ubiquitin and the surfaces of MCM41, SBA15, and silica formed in situ were tested for their influence on the structure and dynamics of the protein. It is shown that the protein's globular fold in the free state is only slightly perturbed in the three silica materials. Local motions on a residue level that are quenched by immobilization or, conversely, that arise from the process are also detailed. NMR measurements show that these perturbations are unique to each silica material and can serve as reporters of the characteristic surface chemistry.
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Affiliation(s)
| | - Eli Ohaion
- Department of Chemistry, Bar Ilan University, Ramat Gan 5290002, Israel
| | - Gilit Verner
- Department of Chemistry, Bar Ilan University, Ramat Gan 5290002, Israel
| | - Avital Schremer
- Department of Chemistry, Bar Ilan University, Ramat Gan 5290002, Israel
| | | | | | | | - Massimo Lucci
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Enrico Ravera
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Gil Goobes
- Department of Chemistry, Bar Ilan University, Ramat Gan 5290002, Israel
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25
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Barry E, Burns R, Chen W, De Hoe GX, De Oca JMM, de Pablo JJ, Dombrowski J, Elam JW, Felts AM, Galli G, Hack J, He Q, He X, Hoenig E, Iscen A, Kash B, Kung HH, Lewis NHC, Liu C, Ma X, Mane A, Martinson ABF, Mulfort KL, Murphy J, Mølhave K, Nealey P, Qiao Y, Rozyyev V, Schatz GC, Sibener SJ, Talapin D, Tiede DM, Tirrell MV, Tokmakoff A, Voth GA, Wang Z, Ye Z, Yesibolati M, Zaluzec NJ, Darling SB. Advanced Materials for Energy-Water Systems: The Central Role of Water/Solid Interfaces in Adsorption, Reactivity, and Transport. Chem Rev 2021; 121:9450-9501. [PMID: 34213328 DOI: 10.1021/acs.chemrev.1c00069] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The structure, chemistry, and charge of interfaces between materials and aqueous fluids play a central role in determining properties and performance of numerous water systems. Sensors, membranes, sorbents, and heterogeneous catalysts almost uniformly rely on specific interactions between their surfaces and components dissolved or suspended in the water-and often the water molecules themselves-to detect and mitigate contaminants. Deleterious processes in these systems such as fouling, scaling (inorganic deposits), and corrosion are also governed by interfacial phenomena. Despite the importance of these interfaces, much remains to be learned about their multiscale interactions. Developing a deeper understanding of the molecular- and mesoscale phenomena at water/solid interfaces will be essential to driving innovation to address grand challenges in supplying sufficient fit-for-purpose water in the future. In this Review, we examine the current state of knowledge surrounding adsorption, reactivity, and transport in several key classes of water/solid interfaces, drawing on a synergistic combination of theory, simulation, and experiments, and provide an outlook for prioritizing strategic research directions.
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Affiliation(s)
- Edward Barry
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Applied Materials Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Center for Molecular Engineering, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States
| | - Raelyn Burns
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Applied Materials Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States
| | - Wei Chen
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Materials Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Center for Molecular Engineering, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637 United States
| | - Guilhem X De Hoe
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Materials Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Center for Molecular Engineering, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637 United States
| | - Joan Manuel Montes De Oca
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637 United States
| | - Juan J de Pablo
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Materials Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637 United States
| | - James Dombrowski
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208 United States
| | - Jeffrey W Elam
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Applied Materials Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Center for Molecular Engineering, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States
| | - Alanna M Felts
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208 United States
| | - Giulia Galli
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Materials Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637 United States
| | - John Hack
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637 United States
| | - Qiming He
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Materials Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Center for Molecular Engineering, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637 United States
| | - Xiang He
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Chemical Sciences and Engineering Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States
| | - Eli Hoenig
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637 United States
| | - Aysenur Iscen
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208 United States
| | - Benjamin Kash
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637 United States
| | - Harold H Kung
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208 United States
| | - Nicholas H C Lewis
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637 United States
| | - Chong Liu
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637 United States
| | - Xinyou Ma
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637 United States
| | - Anil Mane
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Applied Materials Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States
| | - Alex B F Martinson
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Materials Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Center for Molecular Engineering, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States
| | - Karen L Mulfort
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Chemical Sciences and Engineering Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States
| | - Julia Murphy
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637 United States
| | - Kristian Mølhave
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Technical University of Denmark, Anker Engelunds Vej 1 Bygning 101A, Kgs. Lyngby, Lyngby, Hovedstaden 2800, DK Denmark
| | - Paul Nealey
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Materials Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637 United States
| | - Yijun Qiao
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Materials Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Center for Molecular Engineering, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States
| | - Vepa Rozyyev
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Applied Materials Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States
| | - George C Schatz
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208 United States
| | - Steven J Sibener
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637 United States
| | - Dmitri Talapin
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637 United States
| | - David M Tiede
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Chemical Sciences and Engineering Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States
| | - Matthew V Tirrell
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Materials Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Center for Molecular Engineering, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637 United States
| | - Andrei Tokmakoff
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637 United States
| | - Gregory A Voth
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637 United States
| | - Zhongyang Wang
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637 United States
| | - Zifan Ye
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637 United States
| | - Murat Yesibolati
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Technical University of Denmark, Anker Engelunds Vej 1 Bygning 101A, Kgs. Lyngby, Lyngby, Hovedstaden 2800, DK Denmark
| | - Nestor J Zaluzec
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Photon Sciences Directorate, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States
| | - Seth B Darling
- Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Center for Molecular Engineering, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Chemical Sciences and Engineering Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.,Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637 United States
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26
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Kasprzhitskii A, Lazorenko G. Corrosion inhibition properties of small peptides: DFT and Monte Carlo simulation studies. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115782] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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27
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Wang S, Zhu E, Huang Y, Heinz H. Direct correlation of oxygen adsorption on platinum-electrolyte interfaces with the activity in the oxygen reduction reaction. SCIENCE ADVANCES 2021; 7:eabb1435. [PMID: 34108201 PMCID: PMC8189588 DOI: 10.1126/sciadv.abb1435] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 04/22/2021] [Indexed: 05/24/2023]
Abstract
The oxygen reduction reaction (ORR) on platinum catalysts is essential in fuel cells. Quantitative predictions of the relative ORR activity in experiments, in the range of 1 to 50 times, have remained challenging because of incomplete mechanistic understanding and lack of computational tools to account for the associated small differences in activation energies (<2.3 kilocalories per mole). Using highly accurate molecular dynamics (MD) simulation with the Interface force field (0.1 kilocalories per mole), we elucidated the mechanism of adsorption of molecular oxygen on regular and irregular platinum surfaces and nanostructures, followed by local density functional theory (DFT) calculations. The relative ORR activity is determined by oxygen access to platinum surfaces, which greatly depends on specific water adlayers, while electron transfer occurs at a similar slow rate. The MD methods facilitate quantitative predictions of relative ORR activities of any platinum nanostructures, are applicable to other catalysts, and enable effective MD/DFT approaches.
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Affiliation(s)
- Shiyi Wang
- Department of Chemical and Biological Engineering, University of Colorado at Boulder, Boulder, CO 80309, USA
| | - Enbo Zhu
- Department of Materials Science and Engineering, University of California, Los Angeles, CA 90095, USA
| | - Yu Huang
- Department of Materials Science and Engineering, University of California, Los Angeles, CA 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA
| | - Hendrik Heinz
- Department of Chemical and Biological Engineering, University of Colorado at Boulder, Boulder, CO 80309, USA.
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28
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Osella S. Artificial Photosynthesis: Is Computation Ready for the Challenge Ahead? NANOMATERIALS 2021; 11:nano11020299. [PMID: 33498961 PMCID: PMC7911014 DOI: 10.3390/nano11020299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 12/13/2022]
Abstract
A tremendous effort is currently devoted to the generation of novel hybrid materials with enhanced electronic properties for the creation of artificial photosynthetic systems. This compelling and challenging problem is well-defined from an experimental point of view, as the design of such materials relies on combining organic materials or metals with biological systems like light harvesting and redox-active proteins. Such hybrid systems can be used, e.g., as bio-sensors, bio-fuel cells, biohybrid photoelectrochemical cells, and nanostructured photoelectronic devices. Despite these efforts, the main bottleneck is the formation of efficient interfaces between the biological and the organic/metal counterparts for efficient electron transfer (ET). It is within this aspect that computation can make the difference and improve the current understanding of the mechanisms underneath the interface formation and the charge transfer efficiency. Yet, the systems considered (i.e., light harvesting protein, self-assembly monolayer and surface assembly) are more and more complex, reaching (and often passing) the limit of current computation power. In this review, recent developments in computational methods for studying complex interfaces for artificial photosynthesis will be provided and selected cases discussed, to assess the inherent ability of computation to leave a mark in this field of research.
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Affiliation(s)
- Silvio Osella
- Chemical and Biological Systems Simulation Lab, Center of New Technologies, University of Warsaw, Banacha 2C, 02-097 Warsaw, Poland
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29
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Deguchi S, Yokoyama R, Maki T, Tomita K, Osugi R, Hakamada M, Mabuchi M. A new mechanism for reduced cell adhesion: Adsorption dynamics of collagen on a nanoporous gold surface. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2020; 119:111461. [PMID: 33321592 DOI: 10.1016/j.msec.2020.111461] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/14/2020] [Accepted: 08/25/2020] [Indexed: 11/24/2022]
Abstract
Nanostructured materials such as nanoparticles and nanoporous materials strongly affect cell behaviors such as cell viability. Because cellular uptake of nanoporous materials does not occur, mechanisms for the effects of nanoporous materials on cells are different from those of nanoparticles. The effects of nanoporous materials on cells are thought to result from large conformational changes in the extracellular matrix (ECM) induced by the nanoporous materials, although the mechanotransduction and the critical focal adhesion cluster size also have an effect on the cell response. However, we show that the adhesion of mesenchymal stem cells to a gold surface is reduced for nanoporous gold (NPG), despite the conformational changes in collagen induced by NPG being below the detection limits of the experimental analyses. The adsorption dynamics of collagen on NPG are investigated by molecular dynamics simulations to determine the origin of the reduced cell adhesion to NPG. The adsorption energy of collagen on NPG is lower than that on flat gold (FG) despite there being little difference between the global conformation of collagen segments adsorbed on NPG compared with FG. This finding is related to the surface strain of NPG and the limited movement of collagen amino acids owing to interchain hydrogen bonds. The results obtained in this study provide new insight into the interactions between nanostructured materials and the ECM.
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Affiliation(s)
- Soichiro Deguchi
- Graduate School of Energy Science, Kyoto University, Yoshidahonmachi, Sakyo, 606-8501, Kyoto, Japan.
| | - Ryo Yokoyama
- Graduate School of Energy Science, Kyoto University, Yoshidahonmachi, Sakyo, 606-8501, Kyoto, Japan
| | - Takuya Maki
- Graduate School of Energy Science, Kyoto University, Yoshidahonmachi, Sakyo, 606-8501, Kyoto, Japan
| | - Kazuki Tomita
- Graduate School of Energy Science, Kyoto University, Yoshidahonmachi, Sakyo, 606-8501, Kyoto, Japan
| | - Ryosuke Osugi
- Graduate School of Energy Science, Kyoto University, Yoshidahonmachi, Sakyo, 606-8501, Kyoto, Japan
| | - Masataka Hakamada
- Graduate School of Energy Science, Kyoto University, Yoshidahonmachi, Sakyo, 606-8501, Kyoto, Japan
| | - Mamoru Mabuchi
- Graduate School of Energy Science, Kyoto University, Yoshidahonmachi, Sakyo, 606-8501, Kyoto, Japan
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30
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Wei Y, Nie Y, Han Z, Huang H, Liao X, Wang X, Fan Z, Zheng Y. Au@polydopamine nanoparticles/tocilizumab composite as efficient scavengers of oxygen free radicals for improving the treatment of rheumatoid arthritis. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2020; 118:111434. [PMID: 33255028 DOI: 10.1016/j.msec.2020.111434] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 08/12/2020] [Accepted: 08/20/2020] [Indexed: 12/18/2022]
Abstract
Rheumatoid arthritis (RA) is the most common chronic autoimmune disorder associated with high-cost, side effects, and low therapeutic effects. To improve the treatment of RA, we originally developed a novel anti-RA Au@polydopamine nanoparticles (PDANPs)/TCZ composite using PDANPs as the binding sites of gold nanoparticles (AuNPs) and the drug carries of tocilizumab (TCZ) through a facile and environmentally-friend method, aiming to effectively scavenge oxygen free radicals (OFR) and inhibit the formation of related inflammatory factors. Characterizations showed that AuNPs with the size of 11.4 ± 2.9 nm randomly distributed onto the surface of PDANPs (145.8 ± 31.9 nm), meanwhile TCZ was chemically cross-linked to PDANPs through Schiff base linkage. The synthesized composite had good biocompatibility that can promote the proliferation and growth of chondrocytes and fibroblasts. More importantly, Au@PDANPs/TCZ composite showed more excellent abilities to scavenge OFR and inhibit the related inflammatory factors in vitro and in vivo than that of AuNPs and PDANPs owing to the synergistic scavenging effect, ensuring its best therapeutic effect in RA therapy. This new composite will have application potential in the treatment of RA related disease.
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Affiliation(s)
- Yuan Wei
- School of Stomatology, Lanzhou University, Lanzhou 730000, PR China
| | - Yingying Nie
- Institute of Sensing Technology, Gansu Academy of Sciences, Lanzhou 730000, PR China
| | - Zongpu Han
- School of Stomatology, Lanzhou University, Lanzhou 730000, PR China
| | - Haofei Huang
- School of Stomatology, Lanzhou University, Lanzhou 730000, PR China
| | - Xiaozhu Liao
- School of Stomatology, Lanzhou University, Lanzhou 730000, PR China
| | - Xusen Wang
- School of Stomatology, Lanzhou University, Lanzhou 730000, PR China
| | - Zengjie Fan
- School of Stomatology, Lanzhou University, Lanzhou 730000, PR China.
| | - Yan Zheng
- School of Stomatology, Lanzhou University, Lanzhou 730000, PR China.
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31
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Jahan Sajib MS, Sarker P, Wei Y, Tao X, Wei T. Protein Corona on Gold Nanoparticles Studied with Coarse-Grained Simulations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:13356-13363. [PMID: 33124831 DOI: 10.1021/acs.langmuir.0c02767] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Understanding protein corona formation in an aqueous environment at the molecular and atomistic levels is critical to applications such as biomolecule-detection and drug delivery. In this work, we employed mesoscopic coarse-grained simulations to study ovispirin-1 and lysozyme protein coronas on bare gold nanoparticles. Our study showed that protein corona formation is governed by protein-surface and protein-protein interactions, as well as the surface hydrophobic effect. The corona structure was found to be dependent on protein types and the size of nanoparticles. Ovispirin proteins form homogeneous single-layered adsorption in comparison with the lysozyme's inhomogeneous multilayered aggregates on gold NP surfaces. The decrease in nanoparticle size leads to more angular degrees of freedom for protein adsorption orientation. Subsequent atomistic molecular dynamics simulations further demonstrate the loss of secondary structure of ovispirin upon adsorption and the heterogeneity of its local structure.
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Affiliation(s)
- Md Symon Jahan Sajib
- Department of Chemical Engineering, Howard University, Washington, D.C. 20059, United States
| | - Pranab Sarker
- Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, United States
| | - Yong Wei
- Department of Computer Science and Information Systems, University of North Georgia, Dahlonega, Georgia 30597, United States
| | - Xiuping Tao
- Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, United States
| | - Tao Wei
- Department of Chemical Engineering, Howard University, Washington, D.C. 20059, United States
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32
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Raj A, Dhandia N, Balani K. Adhesin Protein Interaction of Staphylococcus Aureus Bacteria with Various Biomaterial Surfaces. ACS Biomater Sci Eng 2020; 6:6161-6172. [PMID: 33449661 DOI: 10.1021/acsbiomaterials.0c01285] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The primary stage of adhesion during implant infection is dominated by interactions of the surface proteins of the bacteria with the substrate atoms. In the current work, molecular dynamics (MD) simulations have been utilized to investigate the mechanics of the associated adhesion forces of bacteria on different surfaces. The unfolding of these adhesion proteins is investigated in order to map these events to earlier experiments on bacterial de-adhesion (using single cell force spectroscopy) with real-life substrates (i.e., ultrahigh molecular weight polyethylene, hydroxyapatite, Ti alloy, and stainless steel). The adhesion of Staphylococcus aureus adhesin (i.e., SpA) is observed by altering their orientation on the silica substrate through MD simulations, followed by capturing unfolding events of three adhesins (SpA, ClfA, and SraP) of variable lengths possessing different secondary structures. The output long-range and short-range interaction forces and consequent visualization of changes in the secondary structure of protein segments are presented during the de-adhesion process. Simulation results are correlated with extracted short-range forces (using Poisson regression) from real-life bacterial de-adhesion experiments. Insights into such protein-substrate interactions may allow for engineering of biomaterials and designing of nonbiofouling surfaces.
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Affiliation(s)
- Arindam Raj
- Materials Science and Engineering, Indian Institute of Technology Kanpur, Kanpur208016, India.,Mechanical Engineering and Materials Science, Yale University, New Haven06520-8292, Connecticut, United States
| | - Neeraj Dhandia
- Materials Science and Engineering, Indian Institute of Technology Kanpur, Kanpur208016, India
| | - Kantesh Balani
- Materials Science and Engineering, Indian Institute of Technology Kanpur, Kanpur208016, India
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33
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Kuang Z, Singh KM, Oliver DJ, Dennis PB, Perry CC, Naik RR. Gamma estimator of Jarzynski equality for recovering binding energies from noisy dynamic data sets. Nat Commun 2020; 11:5517. [PMID: 33139719 PMCID: PMC7606380 DOI: 10.1038/s41467-020-19233-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 09/28/2020] [Indexed: 11/26/2022] Open
Abstract
A fundamental problem in thermodynamics is the recovery of macroscopic equilibrated interaction energies from experimentally measured single-molecular interactions. The Jarzynski equality forms a theoretical basis in recovering the free energy difference between two states from exponentially averaged work performed to switch the states. In practice, the exponentially averaged work value is estimated as the mean of finite samples. Numerical simulations have shown that samples having thousands of measurements are not large enough for the mean to converge when the fluctuation of external work is above 4 kBT, which is easily observable in biomolecular interactions. We report the first example of a statistical gamma work distribution applied to single molecule pulling experiments. The Gibbs free energy of surface adsorption can be accurately evaluated even for a small sample size. The values obtained are comparable to those derived from multi-parametric surface plasmon resonance measurements and molecular dynamics simulations. Measuring interaction energies from experimentally measured single-molecular interactions is challenging. Here, the authors report a gamma work distribution applied to single molecule pulling events for estimating peptide absorption free energy.
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Affiliation(s)
- Zhifeng Kuang
- Air Force Research Laboratory, Wright-Patterson Air Force Base, OH, 45433, USA
| | - Kristi M Singh
- Air Force Research Laboratory, Wright-Patterson Air Force Base, OH, 45433, USA
| | - Daniel J Oliver
- Biomolecular and Materials Interface Research Group, Interdisciplinary Biomedical Research Centre, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK
| | - Patrick B Dennis
- Air Force Research Laboratory, Wright-Patterson Air Force Base, OH, 45433, USA
| | - Carole C Perry
- Biomolecular and Materials Interface Research Group, Interdisciplinary Biomedical Research Centre, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK
| | - Rajesh R Naik
- Air Force Research Laboratory, Wright-Patterson Air Force Base, OH, 45433, USA.
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34
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Ou X, Xue B, Lao Y, Wutthinitikornkit Y, Tian R, Zou A, Yang L, Wang W, Cao Y, Li J. Structure and sequence features of mussel adhesive protein lead to its salt-tolerant adhesion ability. SCIENCE ADVANCES 2020; 6:6/39/eabb7620. [PMID: 32978166 PMCID: PMC7518861 DOI: 10.1126/sciadv.abb7620] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 08/12/2020] [Indexed: 05/11/2023]
Abstract
Mussels can strongly adhere to hydrophilic minerals in sea habitats by secreting adhesive proteins. The adhesion ability of these proteins is often attributed to the presence of Dopa derived from posttranslational modification of Tyr, whereas the contribution of structural feature is overlooked. It remains largely unknown how adhesive proteins overcome the surface-bound water layer to establish underwater adhesion. Here, we use molecular dynamics simulations to probe the conformations of adhesive protein Pvfp-5β and its salt-tolerant underwater adhesion on superhydrophilic mica. Dopa and positively charged basic residues form pairs, in this intrinsically disordered protein, and these residue pairs can lead to firm surface binding. Our simulations further suggest that the unmodified Tyr shows similar functions on surface adhesion by forming pairing structure with a positively charged residue. We confirm the presence of these residue pairs and verify the strong binding ability of unmodified proteins using nuclear magnetic resonance spectroscopy and lap shear tests.
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Affiliation(s)
- Xinwen Ou
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
| | - Bin Xue
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
| | - Yichong Lao
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
| | - Yanee Wutthinitikornkit
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
| | - Ranran Tian
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
| | - Aodong Zou
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
| | - Lingyun Yang
- iHuman Institute, Shanghai Tech University, 393 Hua Xia Zhong Road, Shanghai 201210, China
| | - Wei Wang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
| | - Yi Cao
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China.
| | - Jingyuan Li
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Zheda Road 38, Hangzhou 310027, China.
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35
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Wen X, Ou Y, Zarick HF, Zhang X, Hmelo AB, Victor QJ, Paul EP, Slocik JM, Naik RR, Bellan LM, Lin EC, Bardhan R. PRADA: Portable Reusable Accurate Diagnostics with nanostar Antennas for multiplexed biomarker screening. Bioeng Transl Med 2020; 5:e10165. [PMID: 33005736 PMCID: PMC7510456 DOI: 10.1002/btm2.10165] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/23/2020] [Accepted: 05/03/2020] [Indexed: 02/06/2023] Open
Abstract
Precise monitoring of specific biomarkers in biological fluids with accurate biodiagnostic sensors is critical for early diagnosis of diseases and subsequent treatment planning. In this work, we demonstrated an innovative biodiagnostic sensor, portable reusable accurate diagnostics with nanostar antennas (PRADA), for multiplexed biomarker detection in small volumes (~50 μl) enabled in a microfluidic platform. Here, PRADA simultaneously detected two biomarkers of myocardial infarction, cardiac troponin I (cTnI), which is well accepted for cardiac disorders, and neuropeptide Y (NPY), which controls cardiac sympathetic drive. In PRADA immunoassay, magnetic beads captured the biomarkers in human serum samples, and gold nanostars (GNSs) "antennas" labeled with peptide biorecognition elements and Raman tags detected the biomarkers via surface-enhanced Raman spectroscopy (SERS). The peptide-conjugated GNS-SERS barcodes were leveraged to achieve high sensitivity, with a limit of detection (LOD) of 0.0055 ng/ml of cTnI, and a LOD of 0.12 ng/ml of NPY comparable with commercially available test kits. The innovation of PRADA was also in the regeneration and reuse of the same sensor chip for ~14 cycles. We validated PRADA by testing cTnI in 11 de-identified cardiac patient samples of various demographics within a 95% confidence interval and high precision profile. We envision low-cost PRADA will have tremendous translational impact and be amenable to resource-limited settings for accurate treatment planning in patients.
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Affiliation(s)
- Xiaona Wen
- Department of Chemical and Biomolecular EngineeringVanderbilt UniversityNashvilleTennesseeUSA
| | - Yu‐Chuan Ou
- Department of Chemical and Biomolecular EngineeringVanderbilt UniversityNashvilleTennesseeUSA
| | - Holly F. Zarick
- Department of Chemical and Biomolecular EngineeringVanderbilt UniversityNashvilleTennesseeUSA
| | - Xin Zhang
- Department of Mechanical EngineeringVanderbilt UniversityNashvilleTennesseeUSA
| | - Anthony B. Hmelo
- Department of Physics and AstronomyVanderbilt UniversityNashvilleTennesseeUSA
| | - Quinton J. Victor
- Department of Chemical and Biomolecular EngineeringVanderbilt UniversityNashvilleTennesseeUSA
| | - Eden P. Paul
- Department of Chemical and Biomolecular EngineeringVanderbilt UniversityNashvilleTennesseeUSA
| | - Joseph M. Slocik
- Materials and Manufacturing Directorate and 711th Human Performance Wing, Air Force Research LaboratoryWright‐Patterson Air Force BaseDaytonOhioUSA
| | - Rajesh R. Naik
- Materials and Manufacturing Directorate and 711th Human Performance Wing, Air Force Research LaboratoryWright‐Patterson Air Force BaseDaytonOhioUSA
| | - Leon M. Bellan
- Department of Mechanical EngineeringVanderbilt UniversityNashvilleTennesseeUSA
| | - Eugene C. Lin
- Department of Chemistry and BiochemistryNational Chung Cheng UniversityChiayiTaiwan
| | - Rizia Bardhan
- Department of Chemical and Biological EngineeringIowa State UniversityAmesIowaUSA
- Nanovaccine InstituteIowa State UniversityAmesIowaUSA
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36
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Azizi D, Larachi F, Garnier A, Lagüe P, Levasseur B. Sorption of aqueous amino acid species on sulphidic mineral surfaces—DFT study and insights on biosourced‐reagent mineral flotation. CAN J CHEM ENG 2020. [DOI: 10.1002/cjce.23841] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Dariush Azizi
- Department of Chemical Engineering Université Laval Québec Québec Canada
| | - Faïçal Larachi
- Department of Chemical Engineering Université Laval Québec Québec Canada
| | - Alain Garnier
- Department of Chemical Engineering Université Laval Québec Québec Canada
| | - Patrick Lagüe
- Department of Biochemistry, Microbiology & Bioinformatics Université Laval Québec Québec Canada
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37
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Yadav S, Springborg M, Singhal S, Molayem M, Goel N. Mechanistic Details and Conformational Behavior of Selective Peptide Linkage Facilitated by Au nClusters. ChemistrySelect 2020. [DOI: 10.1002/slct.202001564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Sarita Yadav
- Theoretical and Computational Chemistry Group Department of Chemistry Centre of Advanced Studies in Chemistry Panjab University Chandigarh 160014 India
| | - Michael Springborg
- Physical and Theoretical Chemistry University of Saarland Saarbrücken Germany
- School of Materials Science and Engineering Tianjin University Tianjin 300072 China
| | - Sonal Singhal
- Theoretical and Computational Chemistry Group Department of Chemistry Centre of Advanced Studies in Chemistry Panjab University Chandigarh 160014 India
| | - Mohammad Molayem
- Physical and Theoretical Chemistry University of Saarland Saarbrücken Germany
| | - Neetu Goel
- Theoretical and Computational Chemistry Group Department of Chemistry Centre of Advanced Studies in Chemistry Panjab University Chandigarh 160014 India
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38
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Liu J, Zeng J, Zhu C, Miao J, Huang Y, Heinz H. Interpretable molecular models for molybdenum disulfide and insight into selective peptide recognition. Chem Sci 2020; 11:8708-8722. [PMID: 34094188 PMCID: PMC8162032 DOI: 10.1039/d0sc01443e] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 07/16/2020] [Indexed: 12/14/2022] Open
Abstract
Molybdenum disulfide (MoS2) is a layered material with outstanding electrical and optical properties. Numerous studies evaluate the performance in sensors, catalysts, batteries, and composites that can benefit from guidance by simulations in all-atom resolution. However, molecular simulations remain difficult due to lack of reliable models. We introduce an interpretable force field for MoS2 with record performance that reproduces structural, interfacial, and mechanical properties in 0.1% to 5% agreement with experiments. The model overcomes structural instability, deviations in interfacial and mechanical properties by several 100%, and empirical fitting protocols in earlier models. It is compatible with several force fields for molecular dynamics simulation, including the interface force field (IFF), CVFF, DREIDING, PCFF, COMPASS, CHARMM, AMBER, and OPLS-AA. The parameters capture polar covalent bonding, X-ray structure, cleavage energy, infrared spectra, bending stability, bulk modulus, Young's modulus, and contact angles with polar and nonpolar solvents. We utilized the models to uncover the binding mechanism of peptides to the MoS2 basal plane. The binding strength of several 7mer and 8mer peptides scales linearly with surface contact and replacement of surface-bound water molecules, and is tunable in a wide range from -86 to -6 kcal mol-1. The binding selectivity is multifactorial, including major contributions by van-der-Waals coordination and charge matching of certain side groups, orientation of hydrophilic side chains towards water, and conformation flexibility. We explain the relative attraction and role of the 20 amino acids using computational and experimental data. The force field can be used to screen and interpret the assembly of MoS2-based nanomaterials and electrolyte interfaces up to a billion atoms with high accuracy, including multiscale simulations from the quantum scale to the microscale.
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Affiliation(s)
- Juan Liu
- Department of Chemical and Biological Engineering, University of Colorado- Boulder Boulder CO 80309 USA
| | - Jin Zeng
- Department of Chemical and Biological Engineering, University of Colorado- Boulder Boulder CO 80309 USA
| | - Cheng Zhu
- Department of Chemical and Biological Engineering, University of Colorado- Boulder Boulder CO 80309 USA
| | - Jianwei Miao
- Department of Physics and Astronomy, University of California Los Angeles California 90095 USA
- California NanoSystems Institute, University of California, Los Angeles CA 90095 USA
| | - Yu Huang
- California NanoSystems Institute, University of California, Los Angeles CA 90095 USA
- Department of Materials Science and Engineering, University of California, Los Angeles 90095 USA
| | - Hendrik Heinz
- Department of Chemical and Biological Engineering, University of Colorado- Boulder Boulder CO 80309 USA
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39
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González-Rubio G, Mosquera J, Kumar V, Pedrazo-Tardajos A, Llombart P, Solís DM, Lobato I, Noya EG, Guerrero-Martínez A, Taboada JM, Obelleiro F, MacDowell LG, Bals S, Liz-Marzán LM. Micelle-directed chiral seeded growth on anisotropic gold nanocrystals. Science 2020; 368:1472-1477. [DOI: 10.1126/science.aba0980] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 01/22/2020] [Accepted: 05/01/2020] [Indexed: 12/25/2022]
Affiliation(s)
- Guillermo González-Rubio
- CIC biomaGUNE, Basque Research and Technology Alliance (BRTA), 20014 Donostia-San Sebastián, Spain
| | - Jesús Mosquera
- CIC biomaGUNE, Basque Research and Technology Alliance (BRTA), 20014 Donostia-San Sebastián, Spain
| | - Vished Kumar
- CIC biomaGUNE, Basque Research and Technology Alliance (BRTA), 20014 Donostia-San Sebastián, Spain
| | - Adrián Pedrazo-Tardajos
- Electron Microscopy for Materials Research (EMAT), University of Antwerp, 2020 Antwerp, Belgium
| | - Pablo Llombart
- Departamento de Química Física, Universidad Complutense de Madrid, 28040 Madrid, Spain
- Instituto de Química Física Rocasolano, CSIC, E-28006 Madrid, Spain
| | - Diego M. Solís
- Department of Electrical and Systems Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ivan Lobato
- Electron Microscopy for Materials Research (EMAT), University of Antwerp, 2020 Antwerp, Belgium
| | - Eva G. Noya
- Instituto de Química Física Rocasolano, CSIC, E-28006 Madrid, Spain
| | | | - José M. Taboada
- Departamento de Tecnología de los Computadores y de las Comunicaciones, University of Extremadura, 10003 Cáceres, Spain
| | - Fernando Obelleiro
- Departamento de Teoría de la Se ñal y Comunicaciones, University of Vigo, 36310 Vigo, Spain
| | - Luis G. MacDowell
- Departamento de Química Física, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Sara Bals
- Electron Microscopy for Materials Research (EMAT), University of Antwerp, 2020 Antwerp, Belgium
| | - Luis M. Liz-Marzán
- CIC biomaGUNE, Basque Research and Technology Alliance (BRTA), 20014 Donostia-San Sebastián, Spain
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), 20014 Donostia-San Sebastián, Spain
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40
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Mokashi-Punekar S, Brooks SC, Hogan CD, Rosi NL. Leveraging Peptide Sequence Modification to Promote Assembly of Chiral Helical Gold Nanoparticle Superstructures. Biochemistry 2020; 60:1044-1049. [PMID: 32510207 DOI: 10.1021/acs.biochem.0c00361] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptide conjugate molecules comprising a gold-binding peptide (e.g., AYSSGAPPMPPF) attached to an aliphatic tail have proven to be powerful agents for directing the synthesis and assembly of gold nanoparticle superstructures, in particular chiral helices having interesting plasmonic chiroptical properties. The composition and structure of these molecular agents can be tailored to carefully tune the structure and properties of gold nanoparticle single and double helices. To date, modifications to the β-sheet region (AYSSGA) of the peptide sequence have not been exploited to control the metrics and assembly of such superstructures. We report here that systematic peptide sequence variation in a series of gold-binding peptide conjugate molecules can be leveraged not only to affect the assembly of peptide conjugates but also to control the synthesis, assembly, and optical properties of gold nanoparticle superstructures. Depending upon the hydrophobicity of a single-amino acid variant, the conjugates yield either dispersed gold nanoparticles or helical superstructures. These results provide evidence that subtle changes to peptide sequence, via single-amino acid variation in the β-sheet region, can be leveraged to program structural control in chiral gold nanoparticle superstructures.
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Affiliation(s)
- Soumitra Mokashi-Punekar
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Sydney C Brooks
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Camera D Hogan
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Nathaniel L Rosi
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States.,Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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41
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The Effect of Oligomerization on A Solid-Binding Peptide Binding to Silica-Based Materials. NANOMATERIALS 2020; 10:nano10061070. [PMID: 32486317 PMCID: PMC7353425 DOI: 10.3390/nano10061070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/11/2020] [Accepted: 05/12/2020] [Indexed: 12/22/2022]
Abstract
The bifunctional linker-protein G (LPG) fusion protein comprises a peptide (linker) sequence and a truncated form of Streptococcus strain G148 protein G (protein G). The linker represents a multimeric solid-binding peptide (SBP) comprising 4 × 21-amino acid sequence repeats that display high binding affinity towards silica-based materials. In this study, several truncated derivatives were investigated to determine the effect of the SBP oligomerization on the silica binding function of LPG (for the sake of clarity, LPG will be referred from here on as 4 × LPG). Various biophysical characterization techniques were used to quantify and compare the truncated derivatives against 4 × LPG and protein G without linker (PG). The derivative containing two sequence repeats (2 × LPG) showed minimal binding to silica, while the truncated derivative with only a single sequence (1 × LPG) displayed no binding. The derivative containing three sequence repeats (3 × LPG) was able to bind to silica with a binding affinity of KD = 53.23 ± 4.5 nM, which is 1.5 times lower than that obtained for 4 × LPG under similar experimental conditions. Circular dichroism (CD) spectroscopy and fluorescence spectroscopy studies indicated that the SBP degree of oligomerization has only a small effect on the secondary structure (the linker unravels the beginning of the protein G sequence) and chemical stability of the parent protein G. However, based on quartz crystal microbalance with dissipation monitoring (QCM-D), oligomerization is an important parameter for a strong and stable binding to silica. The replacement of three sequence repeats by a (GGGGS)12 glycine-rich spacer indicated that the overall length rather than the SBP oligomerization mediated the effective binding to silica.
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42
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Mark LO, Zhu C, Medlin JW, Heinz H. Understanding the Surface Reactivity of Ligand-Protected Metal Nanoparticles for Biomass Upgrading. ACS Catal 2020. [DOI: 10.1021/acscatal.9b04772] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lesli O. Mark
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80303, United States
| | - Cheng Zhu
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80303, United States
| | - J. Will Medlin
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80303, United States
| | - Hendrik Heinz
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80303, United States
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43
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He H, Chen R, Zhang L, Williams T, Fang X, Shen W. Fabrication of single-crystalline gold nanowires on cellulose nanofibers. J Colloid Interface Sci 2020; 562:333-341. [PMID: 31855796 DOI: 10.1016/j.jcis.2019.11.093] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 11/12/2019] [Accepted: 11/23/2019] [Indexed: 11/16/2022]
Abstract
Cellulose nanofibers (CNF) are promising nanomaterials for functional inks and printed sensors, although the potential applications are currently limited by the available functionalization methods. This work outlines a convenient method to grow a novel and highly conductive network of single-crystalline gold nanowires (AuNW) on CNF for use in conductive inks and printed sensors. The CNF are able to reduce Au (III) precursors to Au (0) monomers and generate nucleation sites for the subsequent monomer-by-monomer growth of Au nanocrystals; sodium citrate is used to control the reduction kinetics and the crystal growth. The growth of these AuNW/CNF materials is a three-step process of redox reaction, isotropic nucleation and anisotropic crystallization: the morphology and crystal structure of Au nanocrystals on CNF can be controlled by adjusting the reaction temperature and concentrations of citrate and CNF. The AuNW/CNF materials obtained have been formulated into highly conductive and atmospherically stable inks for use in either directly writing or screen printing. We have demonstrated AuNW/CNF-printed sensors with highly controllable electrical conductivity as well as excellent stability against rinsing and immersion by water and ethanol.
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Affiliation(s)
- Hui He
- Department of Chemical Engineering, Monash University, Clayton, VIC 3800, Australia.
| | - Ruoyang Chen
- Department of Chemical Engineering, Monash University, Clayton, VIC 3800, Australia.
| | - Liyuan Zhang
- Department of Chemical Engineering, Monash University, Clayton, VIC 3800, Australia; National Local Joint Engineering Laboratory for Advanced Textile Processing and Clean Production, Science & Technology Institute, Wuhan Textile University, Jiangxia, Hubei 430200, PR China.
| | - Timothy Williams
- Monash Centre for Electron Microscopy, Monash University, Clayton, VIC 3800, Australia
| | - Xiya Fang
- Monash Centre for Electron Microscopy, Monash University, Clayton, VIC 3800, Australia
| | - Wei Shen
- Department of Chemical Engineering, Monash University, Clayton, VIC 3800, Australia.
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44
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Taha M, Lee MJ. Influence of the alanine side-chain methyl group on the peptide-gold nanoparticles interactions. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.112528] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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45
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Lin CH, Ju SP, Su JW, Li DE. Peptide Capping Agent Design for Gold (111) Facet by Molecular Simulation and Experimental Approaches. Sci Rep 2020; 10:2090. [PMID: 32034260 PMCID: PMC7005706 DOI: 10.1038/s41598-020-59144-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 01/23/2020] [Indexed: 11/21/2022] Open
Abstract
The stochastic tunneling-basin hopping method (STUN-BH) was utilized to obtain the most stable peptide S7 configuration (Ac-Ser-Ser-Phe-Pro-Gln-Pro-Asn-CONH2) adsorbed on Au(111) facet. After the most stable S7 configuration was found, molecular dynamics (MD) simulation was conducted to investigate the thermal stability between S7 and Au facet at 300 K in both vacuum and water environment. Moreover, further design sets of peptide sequences on Au(111) facet were used to compare with S7. All molecular simulations were carried out by the large-scale atomic/molecular massively parallel simulator (LAMMPS). The Amber99sb-ILDN force field was employed for modeling the interatomic interaction of peptides, and the TIP3P water was used for the water environment. The CHARMM-METAL force field was introduced to model the S7, PF8 (Ac-Pro-Phe-Ser-Pro-Phe-Ser-Pro-Phe-CONH2) and FS8 (Ac-Phe-Ser-Phe-Ser-Phe-Ser-Phe-Ser-CONH2) interactions with Au(111). The MD simulation results demonstrate that the morphology of Pro affects the adsorption stability of Phe. Therefore, we designed two sequences, PF8 and FS8, to confirm our simulation result through experiment. The present study also develops a novel low-temperature plasma synthesis method to evaluate the facet selecting performance of the designed peptide sequences of S7, PF8, and FS8. The experimental results suggest that the reduced Au atom seed is captured with the designed peptide sequences and slowing growing under room temperature for 72 hours. The experimental results are in the excellent agreement with the simulation finding that the Pro in the designed peptide sequences plays a critical role in the facet selection for Au atom stacking.
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Affiliation(s)
- Che-Hsin Lin
- Department of Mechanical and Electro-Mechanical Engineering, National Sun Yat-sen University, Kaohsiung, 804, Taiwan
| | - Shin-Pon Ju
- Department of Mechanical and Electro-Mechanical Engineering, National Sun Yat-sen University, Kaohsiung, 804, Taiwan.
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung, 807, Taiwan.
| | - Jia-Wei Su
- Department of Mechanical and Electro-Mechanical Engineering, National Sun Yat-sen University, Kaohsiung, 804, Taiwan
| | - Dai-En Li
- Department of Mechanical and Electro-Mechanical Engineering, National Sun Yat-sen University, Kaohsiung, 804, Taiwan
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46
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Zhang C, Li X, Wang Z, Huang X, Ge Z, Hu B. Influence of Structured Water Layers on Protein Adsorption Process: A Case Study of Cytochrome c and Carbon Nanotube Interactions and Its Implications. J Phys Chem B 2020; 124:684-694. [PMID: 31880460 DOI: 10.1021/acs.jpcb.9b10192] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cytochrome c, an essential protein of the electron transport chain, is known to be capable of amplifying the toxicity of carbon nanomaterials via free-radical generation. To understand their interaction, as well as the more general protein-nanoparticle interaction at molecular levels, we investigate the adsorptions between cytochrome c and carbon nanotubes (CNTs) in dynamic and thermodynamic ways using molecular dynamics simulations. The results reveal a well-defined three-phase process separated by two transition points: the diffusion phase where the protein diffuses in the water box, the lockdown phase I where the protein inserts into the surface-bound water layers and rearranges its conformation to fit to the surface of the CNT, and the lockdown phase II where cytochrome c repels the water molecules standing in its way to the surface of CNT and reaches stable adsorption states. The structured water layers affect the movement of atoms by electrostatic forces. In lockdown phase I, the conformation adjustment of the protein dominates the adsorption process. The most thermally favorable adsorption conformation is determined. It shows that except for the deformation of short β sheets and some portions of α helixes, most of the secondary structures of cytochrome c remain unchanged, implying that most of the functions of cytochrome c are preserved. During these processes, the energy contributions of the hydrophilic residues of cytochrome c are much larger than those of hydrophobic residues. Interestingly, the structured water layers at the CNT surface allow more hydrophilic residues such as Lys to get into close contact with the CNT, which plays a significant role during the anchoring process of adsorption. Our results demonstrate that the heme group is in close contact with the CNT in some of the adsorbed states, which hence provides a way for electron transfer from cytochrome c to the CNT surface.
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Affiliation(s)
- Chi Zhang
- Center of Materials Science and Optoelectronics Engineering, College of Materials Science and Opto-Electronic Technology , University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Xiaoyi Li
- Center of Materials Science and Optoelectronics Engineering, College of Materials Science and Opto-Electronic Technology , University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Zichen Wang
- Center of Materials Science and Optoelectronics Engineering, College of Materials Science and Opto-Electronic Technology , University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Xuqi Huang
- Center of Materials Science and Optoelectronics Engineering, College of Materials Science and Opto-Electronic Technology , University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Zhenpeng Ge
- Center of Materials Science and Optoelectronics Engineering, College of Materials Science and Opto-Electronic Technology , University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Benfeng Hu
- Center of Materials Science and Optoelectronics Engineering, College of Materials Science and Opto-Electronic Technology , University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
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47
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Scherb S, Hinaut A, Pawlak R, Vilhena JG, Liu Y, Freund S, Liu Z, Feng X, Müllen K, Glatzel T, Narita A, Meyer E. Giant thermal expansion of a two-dimensional supramolecular network triggered by alkyl chain motion. COMMUNICATIONS MATERIALS 2020; 1:8. [PMID: 32259137 PMCID: PMC7099928 DOI: 10.1038/s43246-020-0009-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 01/05/2020] [Indexed: 05/14/2023]
Abstract
Thermal expansion, the response in shape, area or volume of a solid with heat, is usually large in molecular materials compared to their inorganic counterparts. Resulting from the intrinsic molecule flexibility, conformational changes or variable intermolecular interactions, the exact interplay between these mechanisms is however poorly understood down to the molecular level. Here, we investigate the structural variations of a two-dimensional supramolecular network on Au(111) consisting of shape persistent polyphenylene molecules equipped with peripheral dodecyl chains. By comparing high-resolution scanning probe microscopy and molecular dynamics simulations obtained at 5 and 300 K, we determine the thermal expansion coefficient of the assembly of 980 ± 110 × 10-6 K-1, twice larger than other molecular systems hitherto reported in the literature, and two orders of magnitude larger than conventional materials. This giant positive expansion originates from the increased mobility of the dodecyl chains with temperature that determine the intermolecular interactions and the network spacing.
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Affiliation(s)
- Sebastian Scherb
- Department of Physics, University of Basel, Klingelbergstrasse 82, 4056 Basel, Switzerland
| | - Antoine Hinaut
- Department of Physics, University of Basel, Klingelbergstrasse 82, 4056 Basel, Switzerland
| | - Rémy Pawlak
- Department of Physics, University of Basel, Klingelbergstrasse 82, 4056 Basel, Switzerland
| | - J. G. Vilhena
- Department of Physics, University of Basel, Klingelbergstrasse 82, 4056 Basel, Switzerland
| | - Yi Liu
- Max Plank Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Sara Freund
- Department of Physics, University of Basel, Klingelbergstrasse 82, 4056 Basel, Switzerland
| | - Zhao Liu
- Department of Physics, University of Basel, Klingelbergstrasse 82, 4056 Basel, Switzerland
| | - Xinliang Feng
- Faculty of Chemistry and Food Chemistry, TU Dresden, Mommsenstrasse 4, 01069 Dresden, Germany
| | - Klaus Müllen
- Max Plank Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Thilo Glatzel
- Department of Physics, University of Basel, Klingelbergstrasse 82, 4056 Basel, Switzerland
| | - Akimitsu Narita
- Max Plank Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Ernst Meyer
- Department of Physics, University of Basel, Klingelbergstrasse 82, 4056 Basel, Switzerland
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48
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Ching WY, Poudel L, San S, Baral K. Interfacial Interaction between Suolunite Crystal and Silica Binding Peptide for Novel Bioinspired Cement. ACS COMBINATORIAL SCIENCE 2019; 21:794-804. [PMID: 31710806 DOI: 10.1021/acscombsci.9b00131] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Cement and concrete have been important construction materials throughout human history. There is an urgent need to explore novel and untraditional cementitious materials to enhance the durability of building materials and structures in response to increased infrastructure demand worldwide. We report an exploratory study on a biocomposite cement based on a large-scale computational study using density functional theory. An explicitly solvated mixture of a mineral calcium silicate hydrate (C-S-H) crystal suolunite (Ca2Si2O5(OH)2·H2O) and a silicon binding peptide with amino acid sequence PRO-PRO-PRO-TRP-LEU-PRO-TYR-MET-PRO-PRO-TRP-SER is constructed using ab initio molecular dynamics (AIMD). Detailed analysis on the interface structure, interatomic bonding, mechanical properties, and solvent effect of this model reveals a complex interplay of different types of covalent and ionic bonding, including ubiquitous hydrogen bonding which plays a crucial role in their properties. The use of the total bond order density (TBOD), a single quantum mechanical metric, for assessing the interfacial cohesion for this composite biocement is proposed. We find that the solvated model has a slightly larger TBOD than the dried one. These results could lead to a systematic search and rational design for different types of bioinspired and hybrid functional materials with other inorganic minerals and organic peptides.
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Affiliation(s)
- Wai-Yim Ching
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, Missouri 64110, United States
| | - Lokendra Poudel
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, Missouri 64110, United States
| | - Saro San
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, Missouri 64110, United States
| | - Khagendra Baral
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, Missouri 64110, United States
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Slocik JM, Dennis PB, Govorov AO, Bedford NM, Ren Y, Naik RR. Chiral Restructuring of Peptide Enantiomers on Gold Nanomaterials. ACS Biomater Sci Eng 2019; 6:2612-2620. [PMID: 33463283 DOI: 10.1021/acsbiomaterials.9b00933] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The use of biomolecules has been invaluable at generating and controlling optical chirality in nanomaterials; however, the structure and properties of the chiral biotemplate are not well understood due to the complexity of peptide-nanoparticle interactions. In this study, we show that the complex interactions between d-peptides and gold nanomaterials led to a chiral restructuring of peptides as demonstrated by circular dichroism and proteolytic cleavage of d-peptides via gold-mediated inversion of peptide chirality. The gold nanoparticles synthesized using d-peptide produce a highly ordered atomic surface and restructured peptide bonds for enzyme cleavage. Differences in gold nanoparticle catalyzed reduction of 4-nitrophenol were observed on the basis of the chiral peptide used in nanoparticle synthesis. Notably, the proteolytic cleavage of d-peptides on gold provides an opportunity for designing nanoparticle based therapeutics to treat peptide venoms, access new chemistries, or modulate the catalytic activity of nanomaterials.
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Affiliation(s)
- Joseph M Slocik
- Soft Matter Materials Branch, Materials and Manufacturing Directorate, Air Force Research Lab, Wright Patterson Air Force Base, Ohio 45433-7750, United States
| | - Patrick B Dennis
- Soft Matter Materials Branch, Materials and Manufacturing Directorate, Air Force Research Lab, Wright Patterson Air Force Base, Ohio 45433-7750, United States
| | - Alexander O Govorov
- Department of Physics and Astronomy, Ohio University, Athens, Ohio 45701, United States
| | - Nicholas M Bedford
- School of Engineering, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Yang Ren
- X-Ray Science Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Rajesh R Naik
- 711th Human Performance Wing, Air Force Research Lab, Wright Patterson Air Force Base, Ohio 45433-7750, United States
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Liu S, Yin X, Zhou H, Zhou B, Shao Q, Yang Z, Zhou R. Different platinum crystal surfaces show very distinct protein denaturation capabilities. NANOSCALE 2019; 11:19352-19361. [PMID: 31620747 DOI: 10.1039/c9nr03682b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Different platinum (Pt) surfaces of nanocrystals usually exhibit significant distinctions with regard to various biological, physical, and chemical characteristics, such as bio-recognition, surface wetting, and catalytic activities. In this study, we report for the first time that two shape-controlled Pt nanocrystals with the most common low-index surfaces, Pt(100) and Pt(111), show very dissimilar protein denaturation capabilities based on all-atom molecular dynamics simulations employing the widely used model protein, villin headpiece (HP35). We demonstrate that HP35 is well preserved on the Pt(100) crystal surface, whereas it is severely disrupted on the Pt(111) crystal surface. This surprising difference originates from the distinct water behavior in the first solvation shell (FSS) of the two Pt crystal surfaces. Within the FSS of the Pt(100) crystal surface, water molecules form a very compact and stable monolayer through a highly uniform rhombic hydrogen-bond network. This water monolayer prefers the adsorption of acidic residues (such as Glu and Asp) and acts as a shield to prevent other residues from directly coming into contact with the metal surface. On the other hand, the hydrogen bond network in the water monolayer in the FSS of the Pt(111) crystal surface is very sparse and quite defective, which makes it more vulnerable to the penetration of various residues, particularly those with planar side chains such as Phe, Trp and Arg due to strong dispersion interactions, leading to subsequent protein unfolding. The binding free energy calculations for some key amino acids on the two different crystal surfaces further uncover the molecular origin behind their distinct protein denaturation capability. Our study reveals the vital importance of interfacial water in determining the structure of proteins when binding to different metal crystal surfaces. The discovered molecular mechanisms may be helpful for the future development of a bio-assisted programmable synthetic strategy of sophisticated Pt nanostructures for biomedical applications.
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Affiliation(s)
- Shengtang Liu
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China.
| | - Xiuhua Yin
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China.
| | - Hong Zhou
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China.
| | - Bo Zhou
- School of Electronic Engineering, Chengdu Technological University, Chengdu 611730, China
| | - Qiwen Shao
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China.
| | - Zaixing Yang
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China.
| | - Ruhong Zhou
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China. and IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA and Department of Chemistry, Columbia University, New York, NY 10027, USA
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