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Pantaleone S, Rimola A, Ugliengo P, Sodupe M. First-Principles Modeling of Protein/Surface Interactions. Polyglycine Secondary Structure Adsorption on the TiO 2 (101) Anatase Surface Adopting a Full Periodic Approach. J Chem Inf Model 2021; 61:5484-5498. [PMID: 34752107 DOI: 10.1021/acs.jcim.1c00689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Computational modeling of protein/surface systems is challenging since the conformational variations of the protein and its interactions with the surface need to be considered at once. Adoption of first-principles methods to this purpose is overwhelming and computationally extremely expensive so that, in many cases, dramatically simplified systems (e.g., small peptides or amino acids) are used at the expenses of modeling nonrealistic systems. In this work, we propose a cost-effective strategy for the modeling of peptide/surface interactions at a full quantum mechanical level, taking the adsorption of polyglycine on the TiO2 (101) anatase surface as a test case. Our approach is based on applying the periodic boundary conditions for both the surface model and the polyglycine peptide, giving rise to full periodic polyglycine/TiO2 surface systems. By proceeding this way, the considered complexes are modeled with a drastically reduced number of atoms compared with the finite-analogous systems, modeling the polypeptide structures at the same time in a realistic way. Within our modeling approach, full periodic density functional theory calculations (including implicit solvation effects) and ab initio molecular dynamics (AIMD) simulations at the PBE-D2* theory level have been carried out to investigate the adsorption and relative stability of the different polyglycine structures (i.e., extended primary, β-sheet, and α-helix) on the TiO2 surface. It has been found that, upon adsorption, secondary structures become partially denatured because the peptide C═O groups form Ti-O═C dative bonds. AIMD simulations have been fundamental to identify these phenomena because thermal and entropic effects are of paramount importance. Irrespective of the simulated environments (gas phase and implicit solvent), adsorption of the α-helix is more favorable than that of the β-sheet because in the former, more Ti-O═C bonds are formed and the adsorbed secondary structure results less distorted with respect to the isolated state. Under the implicit water solvent, additionally, adsorbed β-sheet structures weaken with respect to their isolated states as the H-bonds between the strands are longer due to solvation effects. Accordingly, the results indicate that the preferred conformation upon adsorption is the α-helix over the β-sheet.
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Affiliation(s)
- Stefano Pantaleone
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193, Catalonia, Spain.,Dipartimento di Chimica and Nanostructured Interfaces and Surfaces (NIS) Inter-Departmental Centre, Università degli Studi di Torino, Via P. Giuria 7, Torino 10125, Italy.,Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Via Elce di Sotto 8, Perugia I-06123, Italy
| | - Albert Rimola
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193, Catalonia, Spain
| | - Piero Ugliengo
- Dipartimento di Chimica and Nanostructured Interfaces and Surfaces (NIS) Inter-Departmental Centre, Università degli Studi di Torino, Via P. Giuria 7, Torino 10125, Italy
| | - Mariona Sodupe
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193, Catalonia, Spain
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Giussani L, Tabacchi G, Coluccia S, Fois E. Confining a Protein-Containing Water Nanodroplet inside Silica Nanochannels. Int J Mol Sci 2019; 20:E2965. [PMID: 31216631 PMCID: PMC6627703 DOI: 10.3390/ijms20122965] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 06/10/2019] [Accepted: 06/14/2019] [Indexed: 02/01/2023] Open
Abstract
Incorporation of biological systems in water nanodroplets has recently emerged as a new frontier to investigate structural changes of biomolecules, with perspective applications in ultra-fast drug delivery. We report on the molecular dynamics of the digestive protein Pepsin subjected to a double confinement. The double confinement stemmed from embedding the protein inside a water nanodroplet, which in turn was caged in a nanochannel mimicking the mesoporous silica SBA-15. The nano-bio-droplet, whose size fits with the pore diameter, behaved differently depending on the protonation state of the pore surface silanols. Neutral channel sections allowed for the droplet to flow, while deprotonated sections acted as anchoring piers for the droplet. Inside the droplet, the protein, not directly bonded to the surface, showed a behavior similar to that reported for bulk water solutions, indicating that double confinement should not alter its catalytic activity. Our results suggest that nanobiodroplets, recently fabricated in volatile environments, can be encapsulated and stored in mesoporous silicas.
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Affiliation(s)
- Lara Giussani
- Dipartimento di Scienza e Alta Tecnologia and INSTM udr Como, Insubria University, Via Valleggio 9, I-22100 Como, Italy.
| | - Gloria Tabacchi
- Dipartimento di Scienza e Alta Tecnologia and INSTM udr Como, Insubria University, Via Valleggio 9, I-22100 Como, Italy.
| | - Salvatore Coluccia
- Dipartimento di Chimica, Turin University, Via P. Giuria 7, I-10125 Turin, Italy.
| | - Ettore Fois
- Dipartimento di Scienza e Alta Tecnologia and INSTM udr Como, Insubria University, Via Valleggio 9, I-22100 Como, Italy.
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Trachta M, Bludský O, Rubeš M. The interaction of proteins with silica surfaces. Part II: Free energies of capped amino acids. COMPUT THEOR CHEM 2019. [DOI: 10.1016/j.comptc.2018.12.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Heard CJ, Čejka J, Opanasenko M, Nachtigall P, Centi G, Perathoner S. 2D Oxide Nanomaterials to Address the Energy Transition and Catalysis. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1801712. [PMID: 30132995 DOI: 10.1002/adma.201801712] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 05/18/2018] [Indexed: 05/24/2023]
Abstract
2D oxide nanomaterials constitute a broad range of materials, with a wide array of current and potential applications, particularly in the fields of energy storage and catalysis for sustainable energy production. Despite the many similarities in structure, composition, and synthetic methods and uses, the current literature on layered oxides is diverse and disconnected. A number of reviews can be found in the literature, but they are mostly focused on one of the particular subclasses of 2D oxides. This review attempts to bridge the knowledge gap between individual layered oxide types by summarizing recent developments in all important 2D oxide systems including supported ultrathin oxide films, layered clays and double hydroxides, layered perovskites, and novel 2D-zeolite-based materials. Particular attention is paid to the underlying similarities and differences between the various materials, and the subsequent challenges faced by each research community. The potential of layered oxides toward future applications is critically evaluated, especially in the areas of electrocatalysis and photocatalysis, biomass conversion, and fine chemical synthesis. Attention is also paid to corresponding novel 3D materials that can be obtained via sophisticated engineering of 2D oxides.
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Affiliation(s)
- Christopher J Heard
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 128 43, Prague 2, Czech Republic
| | - Jiří Čejka
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 128 43, Prague 2, Czech Republic
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Science, Dolejškova 3, 182 23, Prague 8, Czech Republic
| | - Maksym Opanasenko
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 128 43, Prague 2, Czech Republic
| | - Petr Nachtigall
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 128 43, Prague 2, Czech Republic
| | - Gabriele Centi
- Dept.s MIFT and ChiBioFarAm-Industrial Chemistry, University of Messina, ERIC aisbl and CASPE/INSTM, V.le F. Stagno S'Alcontres 31, 98166, Messina, Italy
| | - Siglinda Perathoner
- Dept.s MIFT and ChiBioFarAm-Industrial Chemistry, University of Messina, ERIC aisbl and CASPE/INSTM, V.le F. Stagno S'Alcontres 31, 98166, Messina, Italy
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Abstract
Empty spaces are abhorred by nature, which immediately rushes in to fill the void. Humans have learnt pretty well how to make ordered empty nanocontainers, and to get useful products out of them. When such an order is imparted to molecules, new properties may appear, often yielding advanced applications. This review illustrates how the organized void space inherently present in various materials: zeolites, clathrates, mesoporous silica/organosilica, and metal organic frameworks (MOF), for example, can be exploited to create confined, organized, and self-assembled supramolecular structures of low dimensionality. Features of the confining matrices relevant to organization are presented with special focus on molecular-level aspects. Selected examples of confined supramolecular assemblies - from small molecules to quantum dots or luminescent species - are aimed to show the complexity and potential of this approach. Natural confinement (minerals) and hyperconfinement (high pressure) provide further opportunities to understand and master the atomistic-level interactions governing supramolecular organization under nanospace restrictions.
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Affiliation(s)
- Gloria Tabacchi
- Department of Science and High Technology, University of Insubria, Via Valleggio, 9 I-22100, Como, Italy
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Covell AD, Zeng Z, Mabe T, Wei J, Adamson A, LaJeunesse DR. Alternative SiO 2 Surface Direct MDCK Epithelial Behavior. ACS Biomater Sci Eng 2017; 3:3307-3317. [PMID: 33445372 DOI: 10.1021/acsbiomaterials.7b00645] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The mechanical interactions of cells are mediated through adhesive interactions. In this study, we examined the growth, cellular behavior, and adhesion of MDCK epithelial cells on three different SiO2 substrates: amorphous glass coverslips and the silicon oxide layers that grow on ⟨111⟩ and ⟨100⟩ wafers. While compositionally all three substrates are almost similar, differences in surface energy result in dramatic differences in epithelial cell morphology, cell-cell adhesion, cell-substrate adhesion, actin organization, and extracellular matrix (ECM) protein expression. We also observe striking differences in ECM protein binding to the various substrates due to the hydrogen bond interactions. Our results demonstrate that MDCK cells have a robust response to differences in substrates that is not obviated by nanotopography or surface composition and that a cell's response may manifest through subtle differences in surface energies of the materials. This work strongly suggests that other properties of a material other than composition and topology should be considered when interpreting and controlling interactions of cells with a substrate, whether it is synthetic or natural.
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Affiliation(s)
- Alan D Covell
- Department of Nanoscience, Joint School of Nanoscience and Nanoengineering, The University of North Carolina at Greensboro, 2907 East Gate City Blvd., Greensboro, North Carolina 27401, United States
| | - Zheng Zeng
- Department of Nanoscience, Joint School of Nanoscience and Nanoengineering, The University of North Carolina at Greensboro, 2907 East Gate City Blvd., Greensboro, North Carolina 27401, United States
| | - Taylor Mabe
- Department of Nanoscience, Joint School of Nanoscience and Nanoengineering, The University of North Carolina at Greensboro, 2907 East Gate City Blvd., Greensboro, North Carolina 27401, United States
| | - Jianjun Wei
- Department of Nanoscience, Joint School of Nanoscience and Nanoengineering, The University of North Carolina at Greensboro, 2907 East Gate City Blvd., Greensboro, North Carolina 27401, United States
| | - Amy Adamson
- Department of Biology, The University of North Carolina at Greensboro, 201 Eberhart Building, Greensboro, North Carolina 27402, United States
| | - Dennis R LaJeunesse
- Department of Nanoscience, Joint School of Nanoscience and Nanoengineering, The University of North Carolina at Greensboro, 2907 East Gate City Blvd., Greensboro, North Carolina 27401, United States
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