1
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Alavizargar A, Gass M, Krahn MP, Heuer A. Elucidating the Membrane Binding Process of a Disordered Protein: Dynamic Interplay of Anionic Lipids and the Polybasic Region. ACS Phys Chem Au 2024; 4:167-179. [PMID: 38560754 PMCID: PMC10979486 DOI: 10.1021/acsphyschemau.3c00051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 12/06/2023] [Accepted: 12/06/2023] [Indexed: 04/04/2024]
Abstract
Intrinsically disordered regions of proteins are responsible for many biological processes such as in the case of liver kinase B1 (LKB1)-a serine/threonine kinase relevant for cell proliferation and cell polarity. LKB1 becomes fully activated upon recruitment to the plasma membrane by binding of its disordered C-terminal polybasic motif consisting of eight lysines/arginines to phospholipids. Here, we present extensive molecular dynamics (MD) simulations of the polybasic motif interacting with a model membrane composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and 1-palmitoyl-2-oleyl phosphatidic acid (PA) and cell culture experiments. Protein-membrane binding effects are due to the electrostatic interactions between the polybasic amino acids and PAs. For significant binding, the first three lysines turn out to be dispensable, which was also recapitulated in cell culture using transfected GFP-LKB1 variants. LKB1-membrane binding results in nonmonotonous changes in the structure of the protein as well as the membrane, in particular, accumulation of PAs and reduced thickness at the protein-membrane contact area. The protein-lipid binding turns out to be highly dynamic due to an interplay of PA-PA repulsion and protein-PA attraction. The thermodynamics of this interplay is captured by a statistical fluctuation model, which allows the estimation of both energies. Quantification of the significance of each polar amino acid in the polybasic provides detailed insights into the molecular mechanism of protein-membrane binding of LKB1. These results can likely be transferred to other proteins, which interact by intrinsically disordered polybasic regions with anionic membranes.
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Affiliation(s)
- Azadeh Alavizargar
- Institute
of Physical Chemistry, University of Münster, Corrensstr. 28/30, 48149 Münster, Germany
| | - Maximilian Gass
- Medical
Cell Biology, Medical Clinic D, University
Hospital of Münster, Albert-Schweitzer Campus 1-A14, 48149 Münster, Germany
| | - Michael P. Krahn
- Medical
Cell Biology, Medical Clinic D, University
Hospital of Münster, Albert-Schweitzer Campus 1-A14, 48149 Münster, Germany
| | - Andreas Heuer
- Institute
of Physical Chemistry, University of Münster, Corrensstr. 28/30, 48149 Münster, Germany
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2
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Crnjar A, Griñen A, Kamerlin SCL, Ramírez-Sarmiento CA. Conformational Selection of a Tryptophan Side Chain Drives the Generalized Increase in Activity of PET Hydrolases through a Ser/Ile Double Mutation. ACS Org Inorg Au 2023; 3:109-119. [PMID: 37035283 PMCID: PMC10080609 DOI: 10.1021/acsorginorgau.2c00054] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/15/2022] [Accepted: 12/15/2022] [Indexed: 04/12/2023]
Abstract
Poly(ethylene terephthalate) (PET) is the most common polyester plastic in the packaging industry and a major source of environmental pollution due to its single use. Several enzymes, termed PET hydrolases, have been found to hydrolyze this polymer at different temperatures, with the enzyme from Ideonella sakaiensis (IsPETase) having optimal catalytic activity at 30-35 °C. Crystal structures of IsPETase have revealed that the side chain of a conserved tryptophan residue within an active site loop (W185) shifts between three conformations to enable substrate binding and product release. This is facilitated by two residues unique to IsPETase, S214 and I218. When these residues are inserted into other PET hydrolases in place of the otherwise strictly conserved histidine and phenylalanine residues found at their respective positions, they enhance activity and decrease T opt. Herein, we combine molecular dynamics and well-tempered metadynamics simulations to investigate dynamic changes of the S214/I218 and H214/F218 variants of IsPETase, as well as three other mesophilic and thermophilic PET hydrolases, at their respective temperature and pH optima. Our simulations show that the S214/I218 insertion both increases the flexibility of active site loop regions harboring key catalytic residues and the conserved tryptophan and expands the conformational plasticity of this tryptophan side chain, enabling the conformational transitions that allow for substrate binding and product release in IsPETase. The observed catalytic enhancement caused by this substitution in other PET hydrolases appears to be due to conformational selection, by capturing the conformational ensemble observed in IsPETase.
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Affiliation(s)
- Alessandro Crnjar
- Department
of Chemistry—BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden
| | - Aransa Griñen
- Institute
for Biological and Medical Engineering, Schools of Engineering, Medicine
and Biological Sciences, Pontificia Universidad
Católica de Chile, Av. Vicuña Mackenna 4860, Santiago 7820436, Chile
- ANID—Millennium
Science Initiative Program—Millennium Institute for Integrative
Biology (iBio), Av. Libertador
Bernardo O’Higgins 340, Santiago 8331150, Chile
| | - Shina C. L. Kamerlin
- Department
of Chemistry—BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, 901 Atlantic
Drive NW, Atlanta, Georgia 30332-0400, United
States
| | - César A. Ramírez-Sarmiento
- Institute
for Biological and Medical Engineering, Schools of Engineering, Medicine
and Biological Sciences, Pontificia Universidad
Católica de Chile, Av. Vicuña Mackenna 4860, Santiago 7820436, Chile
- ANID—Millennium
Science Initiative Program—Millennium Institute for Integrative
Biology (iBio), Av. Libertador
Bernardo O’Higgins 340, Santiago 8331150, Chile
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3
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Rutz A, Das CK, Fasano A, Jaenecke J, Yadav S, Apfel UP, Engelbrecht V, Fourmond V, Léger C, Schäfer LV, Happe T. Increasing the O 2 Resistance of the [FeFe]-Hydrogenase CbA5H through Enhanced Protein Flexibility. ACS Catal 2022; 13:856-865. [PMID: 36733639 PMCID: PMC9886219 DOI: 10.1021/acscatal.2c04031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 12/08/2022] [Indexed: 12/29/2022]
Abstract
The high turnover rates of [FeFe]-hydrogenases under mild conditions and at low overpotentials provide a natural blueprint for the design of hydrogen catalysts. However, the unique active site (H-cluster) degrades upon contact with oxygen. The [FeFe]-hydrogenase fromClostridium beijerinckii (CbA5H) is characterized by the flexibility of its protein structure, which allows a conserved cysteine to coordinate to the active site under oxidative conditions. Thereby, intrinsic cofactor degradation induced by dioxygen is minimized. However, the protection from O2 is only partial, and the activity of the enzyme decreases upon each exposure to O2. By using site-directed mutagenesis in combination with electrochemistry, ATR-FTIR spectroscopy, and molecular dynamics simulations, we show that the kinetics of the conversion between the oxygen-protected inactive state (cysteine-bound) and the oxygen-sensitive active state can be accelerated by replacing a surface residue that is very distant from the active site. This sole exchange of methionine for a glutamate residue leads to an increased resistance of the hydrogenase to dioxygen. With our study, we aim to understand how local modifications of the protein structure can have a crucial impact on protein dynamics and how they can control the reactivity of inorganic active sites through outer sphere effects.
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Affiliation(s)
- Andreas Rutz
- Photobiotechnology,
Department of Plant Biochemistry, Ruhr-Universität
Bochum, 44801 Bochum, Germany
| | - Chandan K. Das
- Theoretical
Chemistry, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Andrea Fasano
- Laboratoire
de Bioénergétique et Ingénierie des Protéines, CNRS, Aix-Marseille Université, Institut de
Microbiologie de la Méditerranée, 13009 Marseille, France
| | - Jan Jaenecke
- Photobiotechnology,
Department of Plant Biochemistry, Ruhr-Universität
Bochum, 44801 Bochum, Germany
| | - Shanika Yadav
- Inorganic
Chemistry Ι, Department of Chemistry and Biochemistry, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Ulf-Peter Apfel
- Inorganic
Chemistry Ι, Department of Chemistry and Biochemistry, Ruhr-Universität Bochum, 44801 Bochum, Germany,Fraunhofer
UMSICHT, 46047 Oberhausen, Germany
| | - Vera Engelbrecht
- Photobiotechnology,
Department of Plant Biochemistry, Ruhr-Universität
Bochum, 44801 Bochum, Germany
| | - Vincent Fourmond
- Laboratoire
de Bioénergétique et Ingénierie des Protéines, CNRS, Aix-Marseille Université, Institut de
Microbiologie de la Méditerranée, 13009 Marseille, France
| | - Christophe Léger
- Laboratoire
de Bioénergétique et Ingénierie des Protéines, CNRS, Aix-Marseille Université, Institut de
Microbiologie de la Méditerranée, 13009 Marseille, France
| | - Lars V. Schäfer
- Theoretical
Chemistry, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Thomas Happe
- Photobiotechnology,
Department of Plant Biochemistry, Ruhr-Universität
Bochum, 44801 Bochum, Germany,
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4
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Kundu A, Mamatkulov SI, Brünig FN, Bonthuis DJ, Netz RR, Elsaesser T, Fingerhut BP. Short-Range Cooperative Slow-down of Water Solvation Dynamics Around SO 4 2--Mg 2+ Ion Pairs. ACS Phys Chem Au 2022; 2:506-514. [PMID: 36465835 PMCID: PMC9706802 DOI: 10.1021/acsphyschemau.2c00034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/15/2022] [Accepted: 09/15/2022] [Indexed: 06/17/2023]
Abstract
The presence of ions affects the structure and dynamics of water on a multitude of length and time scales. In this context, pairs of Mg2+ and SO4 2- ions in water constitute a prototypical system for which conflicting pictures of hydration geometries and dynamics have been reported. Key issues are the molecular pair and solvation shell geometries, the spatial range of electric interactions, and their impact on solvation dynamics. Here, we introduce asymmetric SO4 2- stretching vibrations as new and most specific local probes of solvation dynamics that allow to access ion hydration dynamics at the dilute concentration (0.2 M) of a native electrolyte environment. Highly sensitive heterodyne 2D-IR spectroscopy in the fingerprint region of the SO4 2- ions around 1100 cm-1 reveals a specific slow-down of solvation dynamics for hydrated MgSO4 and for Na2SO4 in the presence of Mg2+ ions, which manifests as a retardation of spectral diffusion compared to aqueous Na2SO4 solutions in the absence of Mg2+ ions. Extensive molecular dynamics and density functional theory QM/MM simulations provide a microscopic view of the observed ultrafast dephasing and hydration dynamics. They suggest a molecular picture where the slow-down of hydration dynamics arises from the structural peculiarities of solvent-shared SO4 2--Mg2+ ion pairs.
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Affiliation(s)
- Achintya Kundu
- Max-Born-Institut
Für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin12489, Germany
| | - Shavkat I. Mamatkulov
- Institute
of Material Sciences of Uzbekistan Academy of Sciences, Tashkent100084, Uzbekistan
| | | | - Douwe Jan Bonthuis
- Institute
of Theoretical and Computational Physics, Graz University of Technology, Graz8010, Austria
| | - Roland R. Netz
- Fachbereich
Physik, Freie Universität Berlin, Berlin14195, Germany
| | - Thomas Elsaesser
- Max-Born-Institut
Für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin12489, Germany
| | - Benjamin P. Fingerhut
- Max-Born-Institut
Für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin12489, Germany
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5
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Monteiro H, Paiva A, Duarte ARC, Galamba N. Structure and Dynamic Properties of a Glycerol-Betaine Deep Eutectic Solvent: When Does a DES Become an Aqueous Solution? ACS Sustain Chem Eng 2022; 10:3501-3512. [PMID: 35371624 PMCID: PMC8941986 DOI: 10.1021/acssuschemeng.1c07461] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/27/2021] [Indexed: 05/25/2023]
Abstract
Deep eutectic solvents (DESs) are an emerging class of green solvents with a wide spectrum of potential applications whose properties may be further tailored through the addition of water. Here, we study, through molecular dynamics, the influence of water on the properties of a betaine-glycerol-water (B:G:W) DES (1:2:ζ; ζ = 0 to 100), aiming at getting insight into the structural and dynamic crossover between a DES and an aqueous solution. The density, shear viscosity, and diffusion coefficients are found to exhibit a non-linear dependence of ζ, similar to that observed for the solvation layers' composition. Each Gly and Bet are replaced, respectively, by ∼3 and ∼5 water molecules, with the highest rates of depletion being found for Gly around Bet and Gly around Gly. Above ζ = 7 (70 mol %; 29.5 wt %), a major structural transformation occurs, with the complete disruption of the second Bet-Gly solvation layer and the formation of a new second layer at a shorter distance, accompanied by a sudden change in the rate of increase of the components' diffusion. Nonetheless, opposite to other DES, our results indicate a smooth crossover between a DES and an aqueous solution.
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Affiliation(s)
- Hugo Monteiro
- LAQV,
REQUIMTE, Departamento de Química, Nova School of Science and Technology, 2829-516 Caparica, Portugal
| | - Alexandre Paiva
- LAQV,
REQUIMTE, Departamento de Química, Nova School of Science and Technology, 2829-516 Caparica, Portugal
| | - Ana Rita C. Duarte
- LAQV,
REQUIMTE, Departamento de Química, Nova School of Science and Technology, 2829-516 Caparica, Portugal
| | - Nuno Galamba
- Biosystems
and Integrative Sciences Institute, Faculty
of Sciences of the University of Lisbon, C8, Campo Grande, 1749-016 Lisbon, Portugal
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6
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Konrad J, Meißner RH, Bitzek E, Zahn D. A Molecular Simulation Approach to Bond Reorganization in Epoxy Resins: From Curing to Deformation and Fracture. ACS Polym Au 2021; 1:165-174. [PMID: 36855655 PMCID: PMC9954341 DOI: 10.1021/acspolymersau.1c00016] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We model bond formation and dissociation processes in thermosetting polymer networks from molecular dynamics simulations. For this, a coarsened molecular mechanics model is derived from quantum calculations to provide effective interaction potentials that enable million-atoms scale simulations. The importance of bond (re)organization is demonstrated for (i) simulating epoxy resin formation-for which our approach leads to realistic network models which can now account for degrees of curing up to 98%. Moreover, (ii) we elucidate the competition of bond dissociation and bond reformation during plastic deformation and fracture. On this basis, we rationalize the molecular mechanisms that account for the irreversible nature of damaging epoxy polymers by mechanical load.
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Affiliation(s)
- Julian Konrad
- Department
of Chemistry and Pharmacy, Computer Chemistry Center, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, 91052, Germany
| | - Robert H. Meißner
- Institute
of Polymers and Composites, Hamburg University
of Technology, Hamburg, 21073, Germany,Helmholtz-Zentrum
Hereon, Institute of Surface Science, Geesthacht, 21502, Germany
| | - Erik Bitzek
- Department
of Materials Science and Engineering, Institute I, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, 91052, Germany
| | - Dirk Zahn
- Department
of Chemistry and Pharmacy, Computer Chemistry Center, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, 91052, Germany,
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7
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Tabassum T, Azeem SM, Muwonge AN, Frey KM. Application of Structure-based Methods to Analyze Resistance Mutations for Chemically Diverse Non-Nucleoside Reverse Transcriptase Inhibitors. Curr HIV Res 2021; 18:283-291. [PMID: 32493197 DOI: 10.2174/1570162x18666200603141209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 04/17/2020] [Accepted: 05/12/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Non-nucleoside reverse transcriptase inhibitors (NNRTIs) are used in combination with antiretroviral therapy to suppress viral loads in HIV patients. The chemical design of NNRTIs has changed in recent years in response to resistance-associated mutations (RAMs) and resistance. NNRTIs are chemically diverse compounds that bind an allosteric site of HIV RT. Resistance- associated mutations (RAMs) identified in HIV patients are associated with NNRTI resistance. RAMs confer amino acid changes that alter both structural and physiochemical properties of the allosteric site. Ultimately, these changes reduce NNRTI affinity. Previously, we used a combination of computational and experimental methods to analyze and validate RAMs for 3 diarylpyrimidine (DAPY) NNRTIs. OBJECTIVE The objective of this study is to apply these methods to other chemically diverse, non- DAPY NNRTIs. MATERIALS AND METHODS We selected MIV-150 (experimental microbicide) and doravirine for this study. A computational and molecular modeling strategy was used to evaluate the effects of RAMs. Calculated changes in drug affinity and stability (ΔS + ΔA) were used to determine overall resistance levels: susceptible, low, intermediate, and high. The ΔS + ΔA values for K101P suggest that this mutation confers intermediate/high-level resistance to MIV-150, but remains susceptible to doravirine. Based on the determined resistance levels, we analyzed the models and used Molecular Dynamics (MD) to compare the interactions of MIV-150/doravirine with RT wild-type (WT) and RT (K101P). From MD, we found that key interactions were lost with RT (K101P), but were retained with doravirine. To experimentally validate our findings, we conducted a fluorescence-based reverse transcription assay for MIV-150 with RT (WT) and RT (K101P). IC50 values determined in assays showed a 101-fold change in potency for MIV-150, but essentially no change for doravirine. RESULTS Our computational and experimental results are also consistent with antiviral data reported in the literature. CONCLUSION We believe that this approach is effective for analyzing mutations to determine resistance profiles for chemically diverse NNRTIs in development.
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Affiliation(s)
- Tasnim Tabassum
- Long Island University, Arnold & Marie Schwartz College of Pharmacy and Health Sciences, Brooklyn, NY 11201, United States
| | - Syeda M Azeem
- Long Island University, Arnold & Marie Schwartz College of Pharmacy and Health Sciences, Brooklyn, NY 11201, United States
| | - Alecia N Muwonge
- Long Island University, Arnold & Marie Schwartz College of Pharmacy and Health Sciences, Brooklyn, NY 11201, United States
| | - Kathleen M Frey
- Fairleigh Dickinson University, School of Pharmacy and Health Sciences, Florham Park, NJ, United States
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8
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Li JX, Wang SQ, Du QS, Wei H, Li XM, Meng JZ, Wang QY, Xie NZ, Huang RB, Chou KC. Simulated Protein Thermal Detection (SPTD) for Enzyme Thermostability Study and an Application Example for Pullulanase from Bacillus deramificans. Curr Pharm Des 2019; 24:4023-4033. [PMID: 30421671 DOI: 10.2174/1381612824666181113120948] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 11/01/2018] [Accepted: 11/07/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND The relationship between protein structure and its bioactivity is one of the fundamental problems for protein engineering and pharmaceutical design. METHOD A new method, called SPTD (Simulated Protein Thermal Detection), was proposed for studying and improving the thermal stability of enzymes. The method was based on the evidence observed by conducting the MD (Molecular Dynamics) simulation for all the atoms of an enzyme vibrating from the velocity at a room temperature (e.g., 25°C) to the desired working temperature (e.g., 65°C). According to the recorded MD trajectories and the coordinate deviations of the constituent residues under the two different temperatures, some new strategies have been found that are useful for both drug delivery and starch industry. CONCLUSION The SPTD technique presented in this paper may become a very useful tool for pharmaceutical design and protein engineering.
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Affiliation(s)
- Jian-Xiu Li
- College of Life Science and Technology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, University Road, Nanning, Guangxi, 530004, China.,State Key Laboratory of Biomass Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi 530007, China
| | - Shu-Qing Wang
- School of Pharmacy, Tianjin Medical University, Tianjin 300070, China.,Gordon Life Science Institute, Boston, MA 02478, United States
| | - Qi-Shi Du
- State Key Laboratory of Biomass Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi 530007, China.,Gordon Life Science Institute, Boston, MA 02478, United States
| | - Hang Wei
- College of Life Science and Technology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, University Road, Nanning, Guangxi, 530004, China.,Nanning Bioclone Biotechnology Co., Lid., No.62 , Gaoxin Avenue, Nanning, Guangxi 530007, China
| | - Xiao-Ming Li
- Nanning Bioclone Biotechnology Co., Lid., No.62 , Gaoxin Avenue, Nanning, Guangxi 530007, China
| | - Jian-Zong Meng
- College of Life Science and Technology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, University Road, Nanning, Guangxi, 530004, China.,Nanning Bioclone Biotechnology Co., Lid., No.62 , Gaoxin Avenue, Nanning, Guangxi 530007, China
| | - Qing-Yan Wang
- State Key Laboratory of Biomass Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi 530007, China
| | - Neng-Zhong Xie
- State Key Laboratory of Biomass Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi 530007, China
| | - Ri-Bo Huang
- College of Life Science and Technology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, University Road, Nanning, Guangxi, 530004, China.,State Key Laboratory of Biomass Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi 530007, China
| | - Kuo-Chen Chou
- Gordon Life Science Institute, Boston, MA 02478, United States
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9
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Yalcin AO, Fan Z, Goris B, Li WF, Koster RS, Fang CM, van Blaaderen A, Casavola M, Tichelaar FD, Bals S, Van Tendeloo G, Vlugt TJH, Vanmaekelbergh D, Zandbergen H, van
Huis MA. Atomic resolution monitoring of cation exchange in CdSe-PbSe heteronanocrystals during epitaxial solid-solid-vapor growth. Nano Lett 2014; 14:3661-7. [PMID: 24844280 PMCID: PMC4055051 DOI: 10.1021/nl501441w] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Revised: 05/15/2014] [Indexed: 05/25/2023]
Abstract
Here, we show a novel solid-solid-vapor (SSV) growth mechanism whereby epitaxial growth of heterogeneous semiconductor nanowires takes place by evaporation-induced cation exchange. During heating of PbSe-CdSe nanodumbbells inside a transmission electron microscope (TEM), we observed that PbSe nanocrystals grew epitaxially at the expense of CdSe nanodomains driven by evaporation of Cd. Analysis of atomic-resolution TEM observations and detailed atomistic simulations reveals that the growth process is mediated by vacancies.
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Affiliation(s)
- Anil O. Yalcin
- Kavli
Institute of Nanoscience, Delft University
of Technology, Lorentzweg
1, 2628 CJ Delft, The Netherlands
| | - Zhaochuan Fan
- Process
and Energy Laboratory, Delft University
of Technology, Leeghwaterstraat
39, 2628 CB Delft, The Netherlands
| | - Bart Goris
- Electron
Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Wun-Fan Li
- Soft
Condensed Matter, Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 5, 3584 CC Utrecht, The Netherlands
| | - Rik S. Koster
- Soft
Condensed Matter, Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 5, 3584 CC Utrecht, The Netherlands
| | - Chang-Ming Fang
- Soft
Condensed Matter, Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 5, 3584 CC Utrecht, The Netherlands
| | - Alfons van Blaaderen
- Soft
Condensed Matter, Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 5, 3584 CC Utrecht, The Netherlands
| | - Marianna Casavola
- Condensed
Matter and Interfaces, Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 5, 3584 CC Utrecht, The Netherlands
| | - Frans D. Tichelaar
- Kavli
Institute of Nanoscience, Delft University
of Technology, Lorentzweg
1, 2628 CJ Delft, The Netherlands
| | - Sara Bals
- Electron
Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Gustaaf Van Tendeloo
- Electron
Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Thijs J. H. Vlugt
- Process
and Energy Laboratory, Delft University
of Technology, Leeghwaterstraat
39, 2628 CB Delft, The Netherlands
| | - Daniël Vanmaekelbergh
- Condensed
Matter and Interfaces, Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 5, 3584 CC Utrecht, The Netherlands
| | - Henny
W. Zandbergen
- Kavli
Institute of Nanoscience, Delft University
of Technology, Lorentzweg
1, 2628 CJ Delft, The Netherlands
| | - Marijn A. van
Huis
- Kavli
Institute of Nanoscience, Delft University
of Technology, Lorentzweg
1, 2628 CJ Delft, The Netherlands
- Soft
Condensed Matter, Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 5, 3584 CC Utrecht, The Netherlands
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