1
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Rogers DM, Do H, Hirst JD. An Improved Diabatization Scheme for Computing the Electronic Circular Dichroism of Proteins. J Phys Chem B 2024. [PMID: 39034688 DOI: 10.1021/acs.jpcb.4c02582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
Abstract
We advance the quality of first-principles calculations of protein electronic circular dichroism (CD) through an amelioration of a key deficiency of a previous procedure that involved diabatization of electronic states on the amide chromophore (to obtain interamide couplings) in a β-strand conformation of a diamide. This yields substantially improved calculated far-ultraviolet (far-UV) electronic circular dichroism (CD) spectra for β-sheet conformations. The interamide couplings from the diabatization procedure for 13 secondary structural elements (13 diamide structures) are applied to compute the CD spectra for seven example proteins: myoglobin (α helix), jacalin (β strand), concanavalin A (β type I), elastase (β type II), papain (α + β), 310-helix bundle (310-helix) and snow flea antifreeze protein (polyproline). In all cases, except concanavalin A and papain, the CD spectra computed using the interamide couplings from the diabatization procedure yield improved agreement with experiment with respect to previous first-principles calculations.
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Affiliation(s)
- David M Rogers
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Hainam Do
- Department of Chemical and Environmental Engineering and Key Laboratory of Carbonaceous Waste Processing and Process Intensification Research of Zhejiang Province, University of Nottingham Ningbo China, Ningbo 315100, China
- New Materials Institute, University of Nottingham Ningbo China, Ningbo 315042, China
| | - Jonathan D Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
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2
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Michaelis M, Cupellini L, Mensch C, Perry CC, Delle Piane M, Colombi Ciacchi L. Tidying up the conformational ensemble of a disordered peptide by computational prediction of spectroscopic fingerprints. Chem Sci 2023; 14:8483-8496. [PMID: 37592980 PMCID: PMC10430726 DOI: 10.1039/d3sc02202a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 07/15/2023] [Indexed: 08/19/2023] Open
Abstract
The most advanced structure prediction methods are powerless in exploring the conformational ensemble of disordered peptides and proteins and for this reason the "protein folding problem" remains unsolved. We present a novel methodology that enables the accurate prediction of spectroscopic fingerprints (circular dichroism, infrared, Raman, and Raman optical activity), and by this allows for "tidying up" the conformational ensembles of disordered peptides and disordered regions in proteins. This concept is elaborated for and applied to a dodecapeptide, whose spectroscopic fingerprint is measured and theoretically predicted by means of enhanced-sampling molecular dynamics coupled with quantum mechanical calculations. Following this approach, we demonstrate that peptides lacking a clear propensity for ordered secondary-structure motifs are not randomly, but only conditionally disordered. This means that their conformational landscape, or phase-space, can be well represented by a basis-set of conformers including about 10 to 100 structures. The implications of this finding have profound consequences both for the interpretation of experimental electronic and vibrational spectral features of peptides in solution and for the theoretical prediction of these features using accurate and computationally expensive techniques. The here-derived methods and conclusions are expected to fundamentally impact the rationalization of so-far elusive structure-spectra relationships for disordered peptides and proteins, towards improved and versatile structure prediction methods.
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Affiliation(s)
- Monika Michaelis
- Hybrid Materials Interfaces Group, Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), and MAPEX Center for Materials and Processes, University of Bremen Am Fallturm 1 Bremen 28359 Germany
- Biomolecular and Materials Interface Research Group, Interdisciplinary Biomedical Research Centre, School of Science and Technology, Nottingham Trent University Clifton Lane Nottingham NG11 8NS UK
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, University of Pisa Via G. Moruzzi 13 Pisa I-56124 Italy
| | - Carl Mensch
- Molecular Spectroscopy Research Group, Department of Chemistry, University of Antwerp Groenenborgerlaan 171 Antwerp 2020 Belgium
| | - 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
| | - Massimo Delle Piane
- Hybrid Materials Interfaces Group, Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), and MAPEX Center for Materials and Processes, University of Bremen Am Fallturm 1 Bremen 28359 Germany
- Department of Applied Science and Technology, Politecnico di Torino Corso Duca degli Abruzzi 24 Torino 10129 Italy
| | - Lucio Colombi Ciacchi
- Hybrid Materials Interfaces Group, Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), and MAPEX Center for Materials and Processes, University of Bremen Am Fallturm 1 Bremen 28359 Germany
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3
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Pavan C, Santalucia R, Escolano-Casado G, Ugliengo P, Mino L, Turci F. Physico-Chemical Approaches to Investigate Surface Hydroxyls as Determinants of Molecular Initiating Events in Oxide Particle Toxicity. Int J Mol Sci 2023; 24:11482. [PMID: 37511241 PMCID: PMC10380507 DOI: 10.3390/ijms241411482] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/04/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
The study of molecular recognition patterns is crucial for understanding the interactions between inorganic (nano)particles and biomolecules. In this review we focus on hydroxyls (OH) exposed at the surface of oxide particles (OxPs) which can play a key role in molecular initiating events leading to OxPs toxicity. We discuss here the main analytical methods available to characterize surface OH from a quantitative and qualitative point of view, covering thermogravimetry, titration, ζ potential measurements, and spectroscopic approaches (NMR, XPS). The importance of modelling techniques (MD, DFT) for an atomistic description of the interactions between membranes/proteins and OxPs surfaces is also discussed. From this background, we distilled a new approach methodology (NAM) based on the combination of IR spectroscopy and bioanalytical assays to investigate the molecular interactions of OxPs with biomolecules and membranes. This NAM has been already successfully applied to SiO2 particles to identify the OH patterns responsible for the OxPs' toxicity and can be conceivably extended to other surface-hydroxylated oxides.
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Affiliation(s)
- Cristina Pavan
- Department of Chemistry, University of Torino, Via Giuria 7, 10125 Torino, Italy
- "G. Scansetti" Interdepartmental Centre for Studies on Asbestos and Other Toxic Particulates, University of Torino, 10125 Torino, Italy
- Louvain Centre for Toxicology and Applied Pharmacology, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Rosangela Santalucia
- Department of Chemistry, University of Torino, Via Giuria 7, 10125 Torino, Italy
- Nanostructured Interfaces and Surfaces (NIS) Interdepartmental Centre, University of Torino, 10125 Torino, Italy
| | - Guillermo Escolano-Casado
- Department of Chemistry, University of Torino, Via Giuria 7, 10125 Torino, Italy
- Nanostructured Interfaces and Surfaces (NIS) Interdepartmental Centre, University of Torino, 10125 Torino, Italy
| | - Piero Ugliengo
- Department of Chemistry, University of Torino, Via Giuria 7, 10125 Torino, Italy
- Nanostructured Interfaces and Surfaces (NIS) Interdepartmental Centre, University of Torino, 10125 Torino, Italy
| | - Lorenzo Mino
- Department of Chemistry, University of Torino, Via Giuria 7, 10125 Torino, Italy
- Nanostructured Interfaces and Surfaces (NIS) Interdepartmental Centre, University of Torino, 10125 Torino, Italy
| | - Francesco Turci
- Department of Chemistry, University of Torino, Via Giuria 7, 10125 Torino, Italy
- "G. Scansetti" Interdepartmental Centre for Studies on Asbestos and Other Toxic Particulates, University of Torino, 10125 Torino, Italy
- Nanostructured Interfaces and Surfaces (NIS) Interdepartmental Centre, University of Torino, 10125 Torino, Italy
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4
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He P, Yang G, Zhu D, Kong H, Corrales-Ureña YR, Colombi Ciacchi L, Wei G. Biomolecule-mimetic nanomaterials for photothermal and photodynamic therapy of cancers: Bridging nanobiotechnology and biomedicine. J Nanobiotechnology 2022; 20:483. [PMID: 36384717 PMCID: PMC9670580 DOI: 10.1186/s12951-022-01691-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 10/27/2022] [Indexed: 11/17/2022] Open
Abstract
Nanomaterial-based phototherapy has become an important research direction for cancer therapy, but it still to face some obstacles, such as the toxic side effects and low target specificity. The biomimetic synthesis of nanomaterials using biomolecules is a potential strategy to improve photothermal therapy (PTT) and photodynamic therapy (PDT) techniques due to their endowed biocompatibility, degradability, low toxicity, and specific targeting. This review presents recent advances in the biomolecule-mimetic synthesis of functional nanomaterials for PTT and PDT of cancers. First, we introduce four biomimetic synthesis methods via some case studies and discuss the advantages of each method. Then, we introduce the synthesis of nanomaterials using some biomolecules such as DNA, RNA, protein, peptide, polydopamine, and others, and discuss in detail how to regulate the structure and functions of the obtained biomimetic nanomaterials. Finally, potential applications of biomimetic nanomaterials for both PTT and PDT of cancers are demonstrated and discussed. We believe that this work is valuable for readers to understand the mechanisms of biomimetic synthesis and nanomaterial-based phototherapy techniques, and will contribute to bridging nanotechnology and biomedicine to realize novel highly effective cancer therapies.
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Affiliation(s)
- Peng He
- College of Chemistry and Chemical Engineering, Qingdao University, Qingdao, 266071, People's Republic of China
| | - Guozheng Yang
- College of Chemistry and Chemical Engineering, Qingdao University, Qingdao, 266071, People's Republic of China
| | - Danzhu Zhu
- College of Chemistry and Chemical Engineering, Qingdao University, Qingdao, 266071, People's Republic of China
| | - Hao Kong
- College of Chemistry and Chemical Engineering, Qingdao University, Qingdao, 266071, People's Republic of China
| | - Yendry Regina Corrales-Ureña
- Hybrid Materials Interfaces Group, Faculty of Production Engineering, University of Bremen, 28359, Bremen, Germany.
| | - Lucio Colombi Ciacchi
- Hybrid Materials Interfaces Group, Faculty of Production Engineering, University of Bremen, 28359, Bremen, Germany
| | - Gang Wei
- College of Chemistry and Chemical Engineering, Qingdao University, Qingdao, 266071, People's Republic of China.
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5
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Rogers DM, Do H, Hirst JD. Electronic circular dichroism of proteins computed using a diabatisation scheme. Mol Phys 2022. [DOI: 10.1080/00268976.2022.2133748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Affiliation(s)
- David M. Rogers
- School of Chemistry, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Hainam Do
- Department of Chemical and Environmental Engineering and Key Laboratory of Carbonaceous Waste Processing and Process Intensification Research of Zhejiang Province, University of Nottingham Ningbo China, Ningbo, People’s Republic of China
- New Materials Institute, University of Nottingham Ningbo China, Ningbo, People’s Republic of China
| | - Jonathan D. Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham, United Kingdom
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6
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Wollborn T, Michaelis M, Ciacchi LC, Fritsching U. Protein conformational changes at the oil/water-interface induced by premix membrane emulsification. J Colloid Interface Sci 2022; 628:72-81. [PMID: 35908433 DOI: 10.1016/j.jcis.2022.07.132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 06/16/2022] [Accepted: 07/20/2022] [Indexed: 11/18/2022]
Abstract
We present combined experimental and modelling evidence that β-lactoglobulin proteins employed as stabilizers of oil/water emulsions undergo minor but significant conformational changes during premix membrane emulsification processes. Circular Dichroism spectroscopy and Molecular Dynamics simulations reveal that the native protein structure is preserved as a metastable state after adsorption at stress-free oil/water interfaces. However, the shear stress applied to the oil droplets during their fragmentation in narrow membrane pores causes a transition into a more stable, partially unfolded interfacial state. The protein's β-sheet content is reduced by up to 8% in a way that is largely independent of the pressure applied during emulsification, and is driven by an increase of contacts between the oil and hydrophobic residues at the expense of structural order within the protein core.
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Affiliation(s)
- Tobias Wollborn
- Leibniz Institute for Materials Engineering - IWT, Badgasteiner Straße 3, 28359 Bremen, Germany.
| | - Monika Michaelis
- Hybrid Materials Interfaces Group, University of Bremen, Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), Am Fallturm 1, 28359 Bremen, Germany; Biomolecular and Materials Interface Research Group, Interdisciplinary Biomedical Research Centre, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, United Kingdom
| | - Lucio Colombi Ciacchi
- Hybrid Materials Interfaces Group, University of Bremen, Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), Am Fallturm 1, 28359 Bremen, Germany; MAPEX Center for Materials and Processes, Am Fallturm 1, 28359 Bremen, Germany
| | - Udo Fritsching
- Leibniz Institute for Materials Engineering - IWT, Badgasteiner Straße 3, 28359 Bremen, Germany; MAPEX Center for Materials and Processes, Am Fallturm 1, 28359 Bremen, Germany; Particles and Process Engineering, University of Bremen, Badgasteiner Straße 3, 28359 Bremen, Germany
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7
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Michaelis M, Delle Piane M, Rothenstein D, Perry CC, Colombi Ciacchi L. Lessons from a Challenging System: Accurate Adsorption Free Energies at the Amino Acid/ZnO Interface. J Chem Theory Comput 2021; 17:4420-4434. [PMID: 34191508 DOI: 10.1021/acs.jctc.1c00165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We undertake steps to overcome four challenges that have hindered the understanding of ZnO/biomolecule interfaces at the atomic scale: parametrization of a classical force field, ZnO surface termination and amino acid protonation state in methanol, and convergence of enhanced sampling molecular dynamics simulations. We predict adsorption free energies for histidine, serine, cysteine, and tryptophan in remarkable agreement with experimental measurements obtained via a novel indicator-displacement assay. Adsorption is driven by direct surface/amino-acid interactions mediated by terminal hydroxyl groups and stabilized by strongly structured methanol solvation shells.
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Affiliation(s)
- Monika Michaelis
- Hybrid Materials Interfaces Group, University of Bremen, Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), and MAPEX Center for Materials and Processes, Am Fallturm 1, Bremen 28359, Germany.,Biomolecular and Materials Interface Research Group, Interdisciplinary Biomedical Research Centre, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, United Kingdom
| | - Massimo Delle Piane
- Hybrid Materials Interfaces Group, University of Bremen, Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), and MAPEX Center for Materials and Processes, Am Fallturm 1, Bremen 28359, Germany.,Department of Applied Science and Technology, Politecnico di Torino, Torino 10129, Italy
| | - Dirk Rothenstein
- Institute for Materials Science, Department of Bioinspired Materials, University of Stuttgart, Heisenbergstrasse 3, Stuttgart 70569, Germany
| | - 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, United Kingdom
| | - Lucio Colombi Ciacchi
- Hybrid Materials Interfaces Group, University of Bremen, Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), and MAPEX Center for Materials and Processes, Am Fallturm 1, Bremen 28359, Germany
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8
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Casalini T. Not only in silico drug discovery: Molecular modeling towards in silico drug delivery formulations. J Control Release 2021; 332:390-417. [PMID: 33675875 DOI: 10.1016/j.jconrel.2021.03.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 02/28/2021] [Accepted: 03/02/2021] [Indexed: 12/18/2022]
Abstract
The use of methods at molecular scale for the discovery of new potential active ligands, as well as previously unknown binding sites for target proteins, is now an established reality. Literature offers many successful stories of active compounds developed starting from insights obtained in silico and approved by Food and Drug Administration (FDA). One of the most famous examples is raltegravir, a HIV integrase inhibitor, which was developed after the discovery of a previously unknown transient binding area thanks to molecular dynamics simulations. Molecular simulations have the potential to also improve the design and engineering of drug delivery devices, which are still largely based on fundamental conservation equations. Although they can highlight the dominant release mechanism and quantitatively link the release rate to design parameters (size, drug loading, et cetera), their spatial resolution does not allow to fully capture how phenomena at molecular scale influence system behavior. In this scenario, the "computational microscope" offered by simulations at atomic scale can shed light on the impact of molecular interactions on crucial parameters such as release rate and the response of the drug delivery device to external stimuli, providing insights that are difficult or impossible to obtain experimentally. Moreover, the new paradigm brought by nanomedicine further underlined the importance of such computational microscope to study the interactions between nanoparticles and biological components with an unprecedented level of detail. Such knowledge is a fundamental pillar to perform device engineering and to achieve efficient and safe formulations. After a brief theoretical background, this review aims at discussing the potential of molecular simulations for the rational design of drug delivery systems.
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Affiliation(s)
- Tommaso Casalini
- Department of Chemistry and Applied Bioscience, Institute for Chemical and Bioengineering, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, Zürich 8093, Switzerland; Polymer Engineering Laboratory, Institute for Mechanical Engineering and Materials Technology, University of Applied Sciences and Arts of Southern Switzerland (SUPSI), Via la Santa 1, Lugano 6962, Switzerland.
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9
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Abstract
We present an atomistic force field for the azo-moiety of the photoswitchable FK-11-X peptide. We use the parameters to study the unfolding of the peptide through molecular dynamics simulations. The unfolded ensemble contains many different structures, ranging from a partially unfolded peptide to a fully unfolded structure. The averaged computed far-ultraviolet circular dichroism (CD) spectrum of the set of structures, which was simulated using the newly developed force field, agrees well with experiment. The rate of the simulated unfolding process was estimated to have a time constant of 5.80 ± 0.03 ns from the time evolution of the CD spectrum of the peptide, computed from the backbone conformations sampled over 40 simulated trajectories. Our estimated time constant is faster than, but not inconsistent with, previous experimental estimates from time-resolved infrared and optical rotatory dispersion spectroscopy.
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Affiliation(s)
- Francois Auvray
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Jonathan D Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
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10
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Michaelis M, Fayyaz A, Parambath M, Koeppen S, Ciacchi LC, Hanley QS, Perry CC. Platform for Screening Abiotic/Biotic Interactions Using Indicator Displacement Assays. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:14230-14237. [PMID: 31609123 DOI: 10.1021/acs.langmuir.9b03085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
This paper describes novel adaptations of optically sectioned planar format assays to screen compounds for their affinities to materials surfaces. The novel platform, which we name optically sectioned indicator displacement assays (O-IDA), makes use of displaceable dyes in a format adaptable to high-throughput multiwell plate technologies. We describe two approaches: the first being where the dye exhibits fluorescence in both the surface bound and unbound state and the second, where fluorescence is lost upon displacement of the dye from the surface. Half maximal inhibitory concentration (IC50), binding affinity (Ki), and binding free energy (ΔGads) values can be extracted from the raw data. Representative biomolecules were tested for interactions with silica in an aqueous environment and ZnO(0001)-Zn and (10-10) facets in a nonaqueous environment. We provide the first experimental values for both the binding of small molecules to silica and the facet-dependent ZnO binding affinity of key amino acids associated with ZnO-specific oligopeptides. The specific data will be invaluable to those studying interactions at interfaces both experimentally and computationally. O-IDA provides a general framework for the high-throughput screening of molecule binding to materials surfaces, which has important applications in drug delivery, (bio-) catalysis, biosensing, and biomaterial engineering.
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Affiliation(s)
- Monika Michaelis
- Hybrid Materials Interfaces Group, Faculty of Production Engineering, Bremen Center for Computational Material Science (BCCMS), Center for Environmental Research and Sustainable Technology (UFT) and MAPEX Centre for Materials and Processes , University of Bremen , D-28359 Bremen , Germany
| | | | | | - Susan Koeppen
- Hybrid Materials Interfaces Group, Faculty of Production Engineering, Bremen Center for Computational Material Science (BCCMS), Center for Environmental Research and Sustainable Technology (UFT) and MAPEX Centre for Materials and Processes , University of Bremen , D-28359 Bremen , Germany
| | - Lucio Colombi Ciacchi
- Hybrid Materials Interfaces Group, Faculty of Production Engineering, Bremen Center for Computational Material Science (BCCMS), Center for Environmental Research and Sustainable Technology (UFT) and MAPEX Centre for Materials and Processes , University of Bremen , D-28359 Bremen , Germany
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11
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Casalini T, Limongelli V, Schmutz M, Som C, Jordan O, Wick P, Borchard G, Perale G. Molecular Modeling for Nanomaterial-Biology Interactions: Opportunities, Challenges, and Perspectives. Front Bioeng Biotechnol 2019; 7:268. [PMID: 31681746 PMCID: PMC6811494 DOI: 10.3389/fbioe.2019.00268] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 09/27/2019] [Indexed: 12/17/2022] Open
Abstract
Injection of nanoparticles (NP) into the bloodstream leads to the formation of a so-called "nano-bio" interface where dynamic interactions between nanoparticle surfaces and blood components take place. A common consequence is the formation of the protein corona, that is, a network of adsorbed proteins that can strongly alter the surface properties of the nanoparticle. The protein corona and the resulting structural changes experienced by adsorbed proteins can lead to substantial deviations from the expected cellular uptake as well as biological responses such as NP aggregation and NP-induced protein fibrillation, NP interference with enzymatic activity, or the exposure of new antigenic epitopes. Achieving a detailed understanding of the nano-bio interface is still challenging due to the synergistic effects of several influencing factors like pH, ionic strength, and hydrophobic effects, to name just a few. Because of the multiscale complexity of the system, modeling approaches at a molecular level represent the ideal choice for a detailed understanding of the driving forces and, in particular, the early events at the nano-bio interface. This review aims at exploring and discussing the opportunities and perspectives offered by molecular modeling in this field through selected examples from literature.
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Affiliation(s)
- Tommaso Casalini
- Polymer Engineering Laboratory, Department of Innovative Technologies, Institute for Mechanical Engineering and Materials Technology, University of Applied Sciences and Arts of Southern Switzerland (SUPSI), Manno, Switzerland
| | - Vittorio Limongelli
- Faculty of Biomedical Sciences, Center for Computational Medicine in Cardiology, Institute of Computational Science, Università della Svizzera italiana (USI), Lugano, Switzerland
- Department of Pharmacy, University of Naples “Federico II”, Naples, Italy
| | - Mélanie Schmutz
- Technology and Society Laboratory, Swiss Federal Laboratories for Materials Science and Technology (Empa), St. Gallen, Switzerland
| | - Claudia Som
- Technology and Society Laboratory, Swiss Federal Laboratories for Materials Science and Technology (Empa), St. Gallen, Switzerland
| | - Olivier Jordan
- School of Pharmaceutical Sciences, University of Geneva, Genève, Switzerland
| | - Peter Wick
- Laboratory for Particles – Biology Interactions, Swiss Federal Laboratories for Materials Science and Technology (Empa), St. Gallen, Switzerland
| | - Gerrit Borchard
- School of Pharmaceutical Sciences, University of Geneva, Genève, Switzerland
| | - Giuseppe Perale
- Polymer Engineering Laboratory, Department of Innovative Technologies, Institute for Mechanical Engineering and Materials Technology, University of Applied Sciences and Arts of Southern Switzerland (SUPSI), Manno, Switzerland
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, Wien, Austria
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12
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Stapelfeldt K, Stamboroski S, Walter I, Suter N, Kowalik T, Michaelis M, Brüggemann D. Controlling the Multiscale Structure of Nanofibrous Fibrinogen Scaffolds for Wound Healing. NANO LETTERS 2019; 19:6554-6563. [PMID: 31418579 DOI: 10.1021/acs.nanolett.9b02798] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
As a key player in blood coagulation and tissue repair, fibrinogen has gained increasing attention to develop nanofibrous biomaterial scaffolds for wound healing. Current techniques to prepare protein nanofibers, like electrospinning or extrusion, are known to induce lasting changes in the protein conformation. Often, such secondary changes are associated with amyloid transitions, which can evoke unwanted disease mechanisms. Starting from our recently introduced technique to self-assemble fibrinogen scaffolds in physiological salt buffers, we here investigated the morphology and secondary structure of our novel fibrinogen nanofibers. Aiming at optimum self-assembly conditions for wound healing scaffolds, we studied the influence of fibrinogen concentration and pH on the protein conformation. Using circular dichroism and Fourier-transform infrared spectroscopy, we observed partial transitions from α-helical structures to β-strands upon fiber formation. Interestingly, a staining with thioflavin T revealed that this conformational transition was not associated with any amyloid formation. Toward novel scaffolds for wound healing, which are stable in aqueous environment, we also introduced cross-linking of fibrinogen scaffolds in formaldehyde vapor. This treatment allowed us to maintain the nanofibrous morphology while the conformation of fibrinogen nanofibers was redeveloped toward a more native state after rehydration. Altogether, self-assembled fibrinogen scaffolds are excellent candidates for novel wound healing systems since their multiscale structures can be well controlled without inducing any pathogenic amyloid transitions.
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Affiliation(s)
- Karsten Stapelfeldt
- Institute for Biophysics , University of Bremen , Otto-Hahn-Allee 1 , 28359 Bremen , Germany
| | - Stephani Stamboroski
- Fraunhofer Institute for Manufacturing Technology and Advanced Materials , Wiener Strasse 12 , 28359 Bremen , Germany
| | - Irina Walter
- Institute for Biophysics , University of Bremen , Otto-Hahn-Allee 1 , 28359 Bremen , Germany
| | - Naiana Suter
- Institute for Biophysics , University of Bremen , Otto-Hahn-Allee 1 , 28359 Bremen , Germany
| | - Thomas Kowalik
- Fraunhofer Institute for Manufacturing Technology and Advanced Materials , Wiener Strasse 12 , 28359 Bremen , Germany
| | - Monika Michaelis
- Interdisciplinary Biomedical Research Centre , Nottingham Trent University , Clifton Lane , Nottingham NG11 8NS , U.K
- Hybrid Materials Interfaces Group , University of Bremen , Am Fallturm 1 , 28359 Bremen , Germany
| | - Dorothea Brüggemann
- Institute for Biophysics , University of Bremen , Otto-Hahn-Allee 1 , 28359 Bremen , Germany
- MAPEX Center for Materials and Processes , University of Bremen , 28359 Bremen , Germany
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13
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Michaelis M, Hildebrand N, Meißner RH, Wurzler N, Li Z, Hirst JD, Micsonai A, Kardos J, Delle Piane M, Colombi Ciacchi L. Impact of the Conformational Variability of Oligopeptides on the Computational Prediction of Their CD Spectra. J Phys Chem B 2019; 123:6694-6704. [DOI: 10.1021/acs.jpcb.9b03932] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- M. Michaelis
- Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), and MAPEX Center for Materials and Processes, Hybrid Materials Interfaces Group, University of Bremen, Am Fallturm 1, Bremen 28359, Germany
- Biomolecular and Materials Interface Research Group, Interdisciplinary Biomedical Research Centre, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, United Kingdom
| | - N. Hildebrand
- Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), and MAPEX Center for Materials and Processes, Hybrid Materials Interfaces Group, University of Bremen, Am Fallturm 1, Bremen 28359, Germany
| | - R. H. Meißner
- Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), and MAPEX Center for Materials and Processes, Hybrid Materials Interfaces Group, University of Bremen, Am Fallturm 1, Bremen 28359, Germany
| | - N. Wurzler
- Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), and MAPEX Center for Materials and Processes, Hybrid Materials Interfaces Group, University of Bremen, Am Fallturm 1, Bremen 28359, Germany
| | - Z. Li
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - J. D. Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - A. Micsonai
- Department of Biochemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest H-1117, Hungary
| | - J. Kardos
- Department of Biochemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest H-1117, Hungary
| | - M. Delle Piane
- Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), and MAPEX Center for Materials and Processes, Hybrid Materials Interfaces Group, University of Bremen, Am Fallturm 1, Bremen 28359, Germany
| | - L. Colombi Ciacchi
- Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), and MAPEX Center for Materials and Processes, Hybrid Materials Interfaces Group, University of Bremen, Am Fallturm 1, Bremen 28359, Germany
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