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Somarathne RP, Misra SK, Kariyawasam CS, Kessl JJ, Sharp JS, Fitzkee NC. Exploring Residue-Level Interactions between the Biofilm-Driving R2ab Protein and Polystyrene Nanoparticles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:1213-1222. [PMID: 38174900 PMCID: PMC10843815 DOI: 10.1021/acs.langmuir.3c02609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
In biological systems, proteins can bind to nanoparticles to form a "corona" of adsorbed molecules. The nanoparticle corona is of significant interest because it impacts an organism's response to a nanomaterial. Understanding the corona requires knowledge of protein structure, orientation, and dynamics at the surface. A residue-level mapping of protein behavior on nanoparticle surfaces is needed, but this mapping is difficult to obtain with traditional approaches. Here, we have investigated the interaction between R2ab and polystyrene nanoparticles (PSNPs) at the level of individual residues. R2ab is a bacterial surface protein from Staphylococcus epidermidis and is known to interact strongly with polystyrene, leading to biofilm formation. We have used mass spectrometry after lysine methylation and hydrogen-deuterium exchange (HDX) NMR spectroscopy to understand how the R2ab protein interacts with PSNPs of different sizes. Lysine methylation experiments reveal subtle but statistically significant changes in methylation patterns in the presence of PSNPs, indicating altered protein surface accessibility. HDX rates become slower overall in the presence of PSNPs. However, some regions of the R2ab protein exhibit faster than average exchange rates in the presence of PSNPs, while others are slower than the average behavior, suggesting conformational changes upon binding. HDX rates and methylation ratios support a recently proposed "adsorbotope" model for PSNPs, wherein adsorbed proteins consist of unfolded anchor points interspersed with partially structured regions. Our data also highlight the challenges of characterizing complex protein-nanoparticle interactions using these techniques, such as fast exchange rates. While providing insights into how R2ab adsorbs onto PSNP surfaces, this research emphasizes the need for advanced methods to comprehend residue-level interactions in the nanoparticle corona.
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Affiliation(s)
- Radha P Somarathne
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Sandeep K Misra
- Department of BioMolecular Sciences, University of Mississippi, University, Mississippi 38677, United States
| | - Chathuri S Kariyawasam
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Jacques J Kessl
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, Mississippi 39406, United States
| | - Joshua S Sharp
- Department of BioMolecular Sciences, University of Mississippi, University, Mississippi 38677, United States
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
| | - Nicholas C Fitzkee
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
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2
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Lima AF, Guido VS, Mina N, Torquato RJS, Sousa AA. Time Evolution of Ultrasmall Gold Nanoparticle-Protein Interactions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:6823-6836. [PMID: 37129569 DOI: 10.1021/acs.langmuir.3c00402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
To date, much effort has been devoted toward the study of protein corona formation onto large gold nanoparticles (GNPs). However, the protein corona concept breaks down for GNPs in the ultrasmall size regime (<3 nm), and, as a result, our understanding of ultrasmall GNP (usGNP)-protein interactions remains incomplete. Herein, we used anionic usGNPs and six different proteins as model systems to systematically investigate usGNP-protein interactions, with particular focus on the time evolution and long-term behavior of complex formation. The different proteins comprised chymotrypsin (Cht), trypsin (Try), thrombin (Thr), serum albumin (HSA), cytochrome c (Cyt c), and factor XII (FXII). We used a range of biochemical and biophysical methods to estimate binding affinities, determine the effects of usGNPs on protein structure and function, assess the reversibility of any protein structural and functional changes, and evaluate usGNP-protein complex stability. Among the main findings, we observed that prolonged (24 h)─but not short-term (10 min)─interactions between proteins and usGNPs permanently altered protein function, including enzyme activities (Try, Thr, and FXIIa), peroxidase-like activity (Cyt c), and ligand-binding properties (HSA). Remarkably, this occurred without any large-scale loss of the native global conformation, implying time-dependent effects of usGNPs on local protein conformation or dynamics. We also found that both short-(10 min) and long-term (24 h) interactions between proteins and usGNPs yielded short-lived complexes, i.e., there was no time-dependent "hardening" of the interactions at the binding interface as usually seen with large GNPs. The present study increases our fundamental understanding of nano-bio interactions in the ultrasmall size regime, which may assist the safe and effective translation of usGNPs into the clinic.
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Affiliation(s)
- André F Lima
- Department of Biochemistry, Federal University of São Paulo, São Paulo SP 04044-020, Brazil
| | - Vinicius S Guido
- Department of Biochemistry, Federal University of São Paulo, São Paulo SP 04044-020, Brazil
| | - Natasha Mina
- Department of Biochemistry, Federal University of São Paulo, São Paulo SP 04044-020, Brazil
| | - Ricardo J S Torquato
- Department of Biochemistry, Federal University of São Paulo, São Paulo SP 04044-020, Brazil
| | - Alioscka A Sousa
- Department of Biochemistry, Federal University of São Paulo, São Paulo SP 04044-020, Brazil
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3
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Viola G, Barracchia CG, Tira R, Parolini F, Leo G, Bellanda M, Munari F, Capaldi S, D’Onofrio M, Assfalg M. New Paradigm for Nano-Bio Interactions: Multimolecular Assembly of a Prototypical Disordered Protein with Ultrasmall Nanoparticles. NANO LETTERS 2022; 22:8875-8882. [PMID: 36346924 PMCID: PMC9706667 DOI: 10.1021/acs.nanolett.2c02902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 10/24/2022] [Indexed: 05/20/2023]
Abstract
Understanding the interactions between nanoparticles (NPs) and proteins is crucial for the successful application of NPs in biological contexts. Protein adsorption is dependent on particle size, and protein binding to ultrasmall (1-3 nm) NPs is considered to be generally weak. However, most studies have involved structured biomacromolecules, while the interactions of ultrasmall NPs with intrinsically disordered proteins (IDPs) have remained elusive. IDPs are abundant in eukaryotes and found to associate with NPs intracellularly. As a model system, we focused on ultrasmall gold nanoparticles (usGNPs) and tau, a cytosolic IDP associated with Alzheimer's disease. Using site-resolved NMR, steady-state fluorescence, calorimetry, and circular dichroism, we reveal that tau and usGNPs form stable multimolecular assemblies, representing a new type of nano-bio interaction. Specifically, the observed interaction hot spots explain the influence of usGNPs on tau conformational transitions, with implications for the intracellular targeting of aberrant IDP aggregation.
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Affiliation(s)
- Giovanna Viola
- Department
of Biotechnology, University of Verona, 37134 Verona, Italy
| | | | - Roberto Tira
- Department
of Biotechnology, University of Verona, 37134 Verona, Italy
| | | | - Giulia Leo
- Department
of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Massimo Bellanda
- Department
of Chemistry, University of Padova, 35131 Padova, Italy
| | - Francesca Munari
- Department
of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Stefano Capaldi
- Department
of Biotechnology, University of Verona, 37134 Verona, Italy
| | | | - Michael Assfalg
- Department
of Biotechnology, University of Verona, 37134 Verona, Italy
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4
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Jameson G, Xiang X, Brüschweiler R. Quantitative Multistate Binding Model of Silica Nanoparticle-Protein Interactions Obtained from Multinuclear Spin Relaxation. J Phys Chem B 2022; 126:9089-9094. [PMID: 36316009 PMCID: PMC9661470 DOI: 10.1021/acs.jpcb.2c05967] [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] [Indexed: 11/11/2022]
Abstract
Nanoparticle-assisted NMR spin relaxation (NASR), which makes internal protein dynamics in solution directly observable on nanosecond to microsecond time scales, has been applied to different nuclei and relaxation processes of the same protein system. A model is presented describing the transient interaction between ubiquitin and anionic silica nanoparticles for the unified interpretation of a wealth of experimental data including 2H, 13C, and 15N relaxation of methyl side chain and backbone moieties. The best model, implemented using a stochastic Liouville equation, describes the exchange process via an intermediary encounter state between free and fully nanoparticle-bound protein. The implication of the three-state binding model on the interpretation of NASR data is discussed.
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Affiliation(s)
- Gregory Jameson
- Department
of Chemistry and Biochemistry, The Ohio
State University, Columbus, Ohio43210, United States
| | - Xinyao Xiang
- Department
of Chemistry and Biochemistry, The Ohio
State University, Columbus, Ohio43210, United States
| | - Rafael Brüschweiler
- Department
of Chemistry and Biochemistry, The Ohio
State University, Columbus, Ohio43210, United States,Department
of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, Ohio43210, United States,
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5
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Gudhka RB, Vats M, Bilodeau CL, McCallum SA, McCoy MA, Roush DJ, Snyder MA, Cramer SM. Probing IgG1 F C-Multimodal Nanoparticle Interactions: A Combined Nuclear Magnetic Resonance and Molecular Dynamics Simulations Approach. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:12188-12203. [PMID: 34633195 DOI: 10.1021/acs.langmuir.1c02114] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
In this study, NMR and molecular dynamics simulations were employed to study IgG1 FC binding to multimodal surfaces. Gold nanoparticles functionalized with two multimodal cation-exchange ligands (Capto and Nuvia) were synthesized and employed to carry out solution-phase NMR experiments with the FC. Experiments with perdeuterated 15N-labeled FC and the multimodal surfaces revealed micromolar residue-level binding affinities as compared to millimolar binding affinities with these ligands in free solution, likely due to cooperativity and avidity effects. The binding of FC with the Capto ligand nanoparticles was concentrated near an aliphatic cluster in the CH2/CH3 interface, which corresponded to a focused hydrophobic region. In contrast, binding with the Nuvia ligand nanoparticles was more diffuse and corresponded to a large contiguous positive electrostatic potential region on the side face of the FC. Results with lower-ligand-density nanoparticles indicated a decrease in binding affinity for both systems. For the Capto ligand system, several aliphatic residues on the FC that were important for binding to the higher-density surface did not interact with the lower-density nanoparticles. In contrast, no significant difference was observed in the interacting residues on the FC to the high- and low-ligand density Nuvia surfaces. The binding affinities of FC to both multimodal-functionalized nanoparticles decreased in the presence of salt due to the screening of multiple weak interactions of polar and positively charged residues. For the Capto ligand nanoparticle system, this resulted in an even more focused hydrophobic binding region in the interface of the CH2 and CH3 domains. Interestingly, for the Nuvia ligand nanoparticles, the presence of salt resulted in a large transition from a diffuse binding region to the same focused binding region determined for Capto nanoparticles at 150 mM salt. Molecular dynamics simulations corroborated the NMR results and provided important insights into the molecular basis of FC binding to these different multimodal systems containing clustered (observed at high-ligand densities) and nonclustered ligand surfaces. This combined biophysical and simulation approach provided significant insights into the interactions of FC with multimodal surfaces and sets the stage for future analyses with even more complex biotherapeutics.
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Affiliation(s)
| | | | | | | | - Mark A McCoy
- Mass Spectrometry & Biophysics, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - David J Roush
- Biologics Process R&D, Downstream Purification Development and Engineering, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Mark A Snyder
- Process Chemistry Division, Bio-Rad Laboratories, Hercules, California 94547, United States
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6
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Sousa AA, Schuck P, Hassan SA. Biomolecular interactions of ultrasmall metallic nanoparticles and nanoclusters. NANOSCALE ADVANCES 2021; 3:2995-3027. [PMID: 34124577 PMCID: PMC8168927 DOI: 10.1039/d1na00086a] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/16/2021] [Indexed: 05/03/2023]
Abstract
The use of nanoparticles (NPs) in biomedicine has made a gradual transition from proof-of-concept to clinical applications, with several NP types meeting regulatory approval or undergoing clinical trials. A new type of metallic nanostructures called ultrasmall nanoparticles (usNPs) and nanoclusters (NCs), while retaining essential properties of the larger (classical) NPs, have features common to bioactive proteins. This combination expands the potential use of usNPs and NCs to areas of diagnosis and therapy traditionally reserved for small-molecule medicine. Their distinctive physicochemical properties can lead to unique in vivo behaviors, including improved renal clearance and tumor distribution. Both the beneficial and potentially deleterious outcomes (cytotoxicity, inflammation) can, in principle, be controlled through a judicious choice of the nanocore shape and size, as well as the chemical ligands attached to the surface. At present, the ability to control the behavior of usNPs is limited, partly because advances are still needed in nanoengineering and chemical synthesis to manufacture and characterize ultrasmall nanostructures and partly because our understanding of their interactions in biological environments is incomplete. This review addresses the second limitation. We review experimental and computational methods currently available to understand molecular mechanisms, with particular attention to usNP-protein complexation, and highlight areas where further progress is needed. We discuss approaches that we find most promising to provide relevant molecular-level insight for designing usNPs with specific behaviors and pave the way to translational applications.
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Affiliation(s)
- Alioscka A Sousa
- Department of Biochemistry, Federal University of São Paulo São Paulo SP 04044 Brazil
| | - Peter Schuck
- National Institute of Biomedical Imaging and Bioengineering, NIH Bethesda MD 20892 USA
| | - Sergio A Hassan
- BCBB, National Institute of Allergy and Infectious Diseases, NIH Bethesda MD 20892 USA
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7
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Perera YR, Hill RA, Fitzkee NC. Protein Interactions with Nanoparticle Surfaces: Highlighting Solution NMR Techniques. Isr J Chem 2019; 59:962-979. [PMID: 34045771 PMCID: PMC8152826 DOI: 10.1002/ijch.201900080] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 09/02/2019] [Indexed: 12/14/2022]
Abstract
In the last decade, nanoparticles (NPs) have become a key tool in medicine and biotechnology as drug delivery systems, biosensors and diagnostic devices. The composition and surface chemistry of NPs vary based on the materials used: typically organic polymers, inorganic materials, or lipids. Nanoparticle classes can be further divided into sub-categories depending on the surface modification and functionalization. These surface properties matter when NPs are introduced into a physiological environment, as they will influence how nucleic acids, lipids, and proteins will interact with the NP surface. While small-molecule interactions are easily probed using NMR spectroscopy, studying protein-NP interactions using NMR introduces several challenges. For example, globular proteins may have a perturbed conformation when attached to a foreign surface, and the size of NP-protein conjugates can lead to excessive line broadening. Many of these challenges have been addressed, and NMR spectroscopy is becoming a mature technique for in situ analysis of NP binding behavior. It is therefore not surprising that NMR has been applied to NP systems and has been used to study biomolecules on NP surfaces. Important considerations include corona composition, protein behavior, and ligand architecture. These features are difficult to resolve using classical surface and material characterization strategies, and NMR provides a complementary avenue of characterization. In this review, we examine how solution NMR can be combined with other analytical techniques to investigate protein behavior on NP surfaces.
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Affiliation(s)
- Y Randika Perera
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762, USA
| | - Rebecca A Hill
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762, USA
| | - Nicholas C Fitzkee
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762, USA
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8
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Tollefson EJ, Allen CR, Chong G, Zhang X, Rozanov ND, Bautista A, Cerda JJ, Pedersen JA, Murphy CJ, Carlson EE, Hernandez R. Preferential Binding of Cytochrome c to Anionic Ligand-Coated Gold Nanoparticles: A Complementary Computational and Experimental Approach. ACS NANO 2019; 13:6856-6866. [PMID: 31082259 DOI: 10.1021/acsnano.9b01622] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Membrane-bound proteins can play a role in the binding of anionic gold nanoparticles (AuNPs) to model bilayers; however, the mechanism for this binding remains unresolved. In this work, we determine the relative orientation of the peripheral membrane protein cytochrome c in binding to a mercaptopropionic acid-functionalized AuNP (MPA-AuNP). As this is nonrigid binding, traditional methods involving crystallographic or rigid molecular docking techniques are ineffective at resolving the question. Instead, we have implemented a computational assay technique using a cross-correlation of a small ensemble of 200 ns long molecular dynamics trajectories to identify a preferred nonrigid binding orientation or pose of cytochrome c on MPA-AuNPs. We have also employed a mass spectrometry-based footprinting method that enables the characterization of the stable protein corona that forms at long time-scales in solution but remains in a dynamic state. Through the combination of these computational and experimental primary results, we have established a consensus result establishing the identity of the exposed regions of cytochrome c in proximity to MPA-AuNPs and its complementary pose(s) with amino-acid specificity. Moreover, the tandem use of the two methods can be applied broadly to determine the accessibility of membrane-binding sites for peripheral membrane proteins upon adsorption to AuNPs or to determine the exposed amino-acid residues of the hard corona that drive the acquisition of dynamic soft coronas. We anticipate that the combined use of simulation and experimental methods to characterize biomolecule-nanoparticle interactions, as demonstrated here, will become increasingly necessary as the complexity of such target systems grows.
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Affiliation(s)
- Emily J Tollefson
- Department of Chemistry , University of Minnesota-Twin Cities , Minneapolis , Minnesota 55455 , United States
| | - Caley R Allen
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Gene Chong
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Xi Zhang
- Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Nikita D Rozanov
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Anthony Bautista
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Jennifer J Cerda
- Department of Chemistry , University of Minnesota-Twin Cities , Minneapolis , Minnesota 55455 , United States
| | - Joel A Pedersen
- Environmental Chemistry and Technology Program , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Catherine J Murphy
- Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Erin E Carlson
- Department of Chemistry , University of Minnesota-Twin Cities , Minneapolis , Minnesota 55455 , United States
| | - Rigoberto Hernandez
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
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9
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Curvature-dependent effects of nanotopography on classical immune complement activation. Acta Biomater 2018; 74:112-120. [PMID: 29723704 DOI: 10.1016/j.actbio.2018.04.053] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 04/17/2018] [Accepted: 04/30/2018] [Indexed: 12/27/2022]
Abstract
The aim of this study was to investigate how the size of nanosized surface features affect classical immune complement activation through adsorption of IgG and the following binding of C1q. By using model surfaces with immobilized SiO2 nanoparticles of different sizes (8, 32 and 68 nm in diameter), three different curvatures with the same chemistry was systematically studied and analyzed using the acoustic sensing technique; Quartz Crystal Microbalance with Dissipation Monitoring (QCM-D). Circular Dichroism (CD) was employed to study any changes in the secondary structure of IgG using a methodology with stacked functionalized substrates. Our results show that the amount of IgG adsorption increased slightly with nanoparticle size, but also showed a strong size/curvature-dependent effect on the following C1q binding, with the highest binding to IgG adsorbed on the largest nanoparticles and a smooth control surface, indicating that classical immune complement activation possibly increase with decreasing curvature. We conclude that the difference in C1q binding was not due to changes in the secondary structure of IgG, suggesting that geometrical arrangement of adsorbed IgG is the determining factor. STATEMENT OF SIGNIFICANCE We have shown that small changes at the topographical nanoscale can give large effects on the initiation of the classical immune complement cascade, an important immunological reaction that take place when a foreign material is inserted in the body. By developing a methodology using silicon dioxide nanoparticles with three different sizes, to systematically study their impact on the secondary structure and binding of human immunoglobulin G (IgG) to the initiator protein C1q of the classical complement cascade, we have shown that the initiation of the classical immune complement is hampered by the sharp curvature of the smaller nanoparticles. We conclude that this is not mediated by changes in the secondary structure of the adsorbed proteins, but rather an effect of curvature-induced spatial mismatch. The results provide a possible mechanistic explanation on how nanotopography may effect protein adsorption and protein cascade events.
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10
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Bortot A, Zanzoni S, D'Onofrio M, Assfalg M. Specific Interaction Sites Determine Differential Adsorption of Protein Structural Isomers on Nanoparticle Surfaces. Chemistry 2018; 24:5911-5919. [PMID: 29446497 DOI: 10.1002/chem.201705994] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Indexed: 11/08/2022]
Abstract
In biological systems, nanoparticles (NPs) elicit bioactivity upon interaction with proteins. As a result of post-translational modification, proteins occur in a variety of alternative covalent forms, including structural isomers, which present unique molecular surfaces. We aimed at a detailed description of the recognition of protein isomeric species by NP surfaces. The transient adsorption of isomeric ubiquitin (Ub) dimers by NPs was investigated by solution NMR spectroscopy. Lys63- and Lys48-linked Ub2 were adsorbed by large anionic NPs with different affinities, whereas the binding strength was similar in the cases of smaller particles. After the incorporation of paramagnetic tags into NPs, the observed site-resolved paramagnetic footprints provided a high-resolution map of the different protein surfaces binding to NPs. The approach described could be extended to further protein isoforms and more specialized NP systems to allow better control of the interactions between NPs and protein targets.
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Affiliation(s)
- Andrea Bortot
- Department of Biotechnology, University of Verona, Strada Le Grazie, 15, 37134, Verona, Italy
| | - Serena Zanzoni
- Department of Biotechnology, University of Verona, Strada Le Grazie, 15, 37134, Verona, Italy
| | - Mariapina D'Onofrio
- Department of Biotechnology, University of Verona, Strada Le Grazie, 15, 37134, Verona, Italy
| | - Michael Assfalg
- Department of Biotechnology, University of Verona, Strada Le Grazie, 15, 37134, Verona, Italy
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11
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Dal Cortivo G, Wagner GE, Cortelletti P, Padmanabha Das KM, Zangger K, Speghini A, Dell'Orco D, Meyer NH. Luminescent and paramagnetic properties of nanoparticles shed light on their interactions with proteins. Sci Rep 2018; 8:3420. [PMID: 29467422 PMCID: PMC5821874 DOI: 10.1038/s41598-018-21571-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 02/06/2018] [Indexed: 12/14/2022] Open
Abstract
Nanoparticles have been recognized as promising tools for targeted drug-delivery and protein therapeutics. However, the mechanisms of protein-nanoparticle interaction and the dynamics underlying the binding process are poorly understood. Here, we present a general methodology for the characterization of protein-nanoparticle interaction on a molecular level. To this end we combined biophysical techniques including nuclear magnetic resonance (NMR), circular dichroism (CD), resonance energy transfer (RET) and surface plasmon resonance (SPR). Particularly, we analyzed molecular mechanisms and dynamics of the interaction of CaF2 nanoparticles with the prototypical calcium sensor calmodulin (CaM). We observed the transient formation of an intermediate encounter complex involving the structural region linking the two domains. Specific interaction of CaM with CaF2 NPs is driven by the N-terminal EF-hands, which seem to recognize Ca2+ on the surface of the nanoparticle. We conclude that CaF2 NP-CaM interaction is fully compatible with potential applications in nanomedicine. Overall, the methods presented in this work can be extended to other systems and may be useful to quantitatively characterize structural and dynamic features of protein-NP interactions with important implications for nanomedicine and nano-biotechnology.
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Affiliation(s)
- Giuditta Dal Cortivo
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, Strada le Grazie 8, Verona, Italy
| | - Gabriel E Wagner
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstraße 6, 8010, Graz, Austria
| | - Paolo Cortelletti
- Nanomaterials Research Group, Department of Biotechnology, University of Verona and INSTM, UdR Verona, Strada Le Grazie 15, Verona, Italy
| | | | - Klaus Zangger
- Institute of Chemistry, University of Graz, Heinrichstr. 28, 8010, Graz, Austria
| | - Adolfo Speghini
- Nanomaterials Research Group, Department of Biotechnology, University of Verona and INSTM, UdR Verona, Strada Le Grazie 15, Verona, Italy
| | - Daniele Dell'Orco
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, Strada le Grazie 8, Verona, Italy.
| | - N Helge Meyer
- Department of Human Medicine and Department of Neuroscience, University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26131, Oldenburg, Germany.
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12
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Yu G, Zhou J. Understanding the curvature effect of silica nanoparticles on lysozyme adsorption orientation and conformation: a mesoscopic coarse-grained simulation study. Phys Chem Chem Phys 2018; 18:23500-7. [PMID: 27465065 DOI: 10.1039/c6cp01478j] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In nanobiotechnology applications, curvature of nanoparticles has a significant effect on protein activities. In this work, lysozyme adsorption on different-sized silica nanoparticles (SNPs) was simulated at the microsecond timescale by using mesoscopic coarse-grained molecular dynamics simulations. It is found that, with the increase of nanoparticle size, which indicates a decrease of surface curvature, adsorbed lysozyme shows a narrower orientation distribution and a greater conformation change, as the electrostatic attraction dominates lysozyme adsorption, and this trend is more pronounced on larger SNPs. Interestingly, the effect induced by different SNP surface curvatures is not related to the direct contact area between lysozyme and SNPs, but to the interfacial hydration layer above the silica surface, since a smaller curvature can lead to a stronger interfacial hydration and make the distribution of interfacial water molecules more ordered. Besides, at higher ionic strength, lysozyme conformation is less affected by strongly negatively charged SNPs, especially for larger nanoparticles. This work might shed some light on how to prepare protein coronas with higher bioactivities in nanobiotechnology.
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Affiliation(s)
- Gaobo Yu
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology, Guangzhou, 510640, P. R. China.
| | - Jian Zhou
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology, Guangzhou, 510640, P. R. China.
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13
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Shi B, Shin YK, Hassanali AA, Singer SJ. Biomolecules at the amorphous silica/water interface: Binding and fluorescence anisotropy of peptides. Colloids Surf B Biointerfaces 2017; 157:83-92. [DOI: 10.1016/j.colsurfb.2017.05.048] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 05/15/2017] [Accepted: 05/17/2017] [Indexed: 01/19/2023]
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14
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Melby ES, Lohse SE, Park JE, Vartanian AM, Putans RA, Abbott HB, Hamers RJ, Murphy CJ, Pedersen JA. Cascading Effects of Nanoparticle Coatings: Surface Functionalization Dictates the Assemblage of Complexed Proteins and Subsequent Interaction with Model Cell Membranes. ACS NANO 2017; 11:5489-5499. [PMID: 28482159 DOI: 10.1021/acsnano.7b00231] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Interactions of functionalized nanomaterials with biological membranes are expected to be governed by not only nanoparticle physiochemical properties but also coatings or "coronas" of biomacromolecules acquired after immersion in biological fluids. Here we prepared a library of 4-5 nm gold nanoparticles (AuNPs) coated with either ω-functionalized thiols or polyelectrolyte wrappings to examine the influence of surface functional groups on the assemblage of proteins complexing the nanoparticles and its subsequent impact on attachment to model biological membranes. We find that the initial nanoparticle surface coating has a cascading effect on interactions with model cell membranes by determining the assemblage of complexing proteins, which in turn influences subsequent interaction with model biological membranes. Each type of functionalized AuNP investigated formed complexes with a unique ensemble of serum proteins that depended on the initial surface coating of the nanoparticles. Formation of protein-nanoparticle complexes altered the electrokinetic, hydrodynamic, and plasmonic properties of the AuNPs. Complexation of the nanoparticles with proteins reduced the attachment of cationic AuNPs and promoted attachment of anionic AuNPs to supported lipid bilayers; this trend is observed with both lipid bilayers comprising 100% zwitterionic phospholipids and those incorporating anionic phosphatidylinositol. Complexation with serum proteins led to attachment of otherwise noninteracting oligo(ethylene glycol)-functionalized AuNPs to bilayers containing phosphatidylinositol. These results demonstrate the importance of considering both facets of the nano-bio interface: functional groups displayed on the nanoparticle surface and proteins complexing the nanoparticles influence interaction with biological membranes as does the molecular makeup of the membranes themselves.
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Affiliation(s)
- Eric S Melby
- Environmental Chemistry and Technology Program, University of Wisconsin-Madison , 1525 Observatory Drive, Madison, Wisconsin 53706, United States
| | - Samuel E Lohse
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Ji Eun Park
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Ariane M Vartanian
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Rebecca A Putans
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Hannah B Abbott
- Environmental Chemistry and Technology Program, University of Wisconsin-Madison , 1525 Observatory Drive, Madison, Wisconsin 53706, United States
| | - Robert J Hamers
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Catherine J Murphy
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Joel A Pedersen
- Environmental Chemistry and Technology Program, University of Wisconsin-Madison , 1525 Observatory Drive, Madison, Wisconsin 53706, United States
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
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15
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Frost R, Langhammer C, Cedervall T. Real-time in situ analysis of biocorona formation and evolution on silica nanoparticles in defined and complex biological environments. NANOSCALE 2017; 9:3620-3628. [PMID: 28247891 DOI: 10.1039/c6nr06399c] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Biomolecules such as proteins immediately adsorb on the surface of nanoparticles upon their exposure to a biological environment. The formed adlayer is commonly referred to as biomolecule corona (biocorona) and defines the biological activity and toxicity of the nanoparticle. Therefore, it is essential to understand in detail the biocorona formation process, and how it is governed by parameters like composition of the biological environment, and nanoparticle size, shape and faceting. Here we present a detailed equilibrium and real time in situ study of biocorona formation at SiO2-nanoparticle surfaces upon exposure to defined (BSA, IgG) and complex (bovine serum, IgG depleted bovine serum) biological samples. We use both nanofabricated surface-associated Au core-SiO2 shell nanoparticles (faceted, d = 92-167 nm) with integrated nanoplasmonic sensing function and dispersed SiO2 nanoparticles (using DLS and SDS-PAGE). The results show that preadsorbed BSA or IgG are exchanged for other proteins when exposed to bovine serum. In addition, the results show that IgG forms a biocorona with different properties at curved (edge) and flat (facet) SiO2-nanoparticle surfaces. Our study paves the way for further real time in situ investigations of the biocorona formation and evolution kinetics, as well as the role of molecular orientation in biocorona formation, on nanoparticles with surface faceting.
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Affiliation(s)
- Rickard Frost
- Department of Energy and Environment, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden. and Department of Physics, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Christoph Langhammer
- Department of Physics, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Tommy Cedervall
- Biochemistry and Structural Biology and NanoLund, Lund University, Box 124, SE-221 00 Lund, Sweden
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16
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Xie M, Hansen AL, Yuan J, Brüschweiler R. Residue-Specific Interactions of an Intrinsically Disordered Protein with Silica Nanoparticles and their Quantitative Prediction. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2016; 120:24463-24468. [PMID: 28337243 PMCID: PMC5358802 DOI: 10.1021/acs.jpcc.6b08213] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Elucidation of the driving forces that govern interactions between nanoparticles and intrinsically disordered proteins (IDP) is important for the understanding of the effect of nanoparticles in living systems and for the design of new nanoparticle-based assays to monitor health and combat disease. The quantitative interaction profile of the intrinsically disordered transactivation domain of p53 and its mutants with anionic silica nanoparticles is reported at atomic resolution using nuclear magnetic spin relaxation experiments. These profiles are analyzed with a novel interaction model that is based on a quantitative nanoparticle affinity scale separately derived for the 20 natural amino acids. The results demonstrate how the interplay of attractive and repulsive Coulomb interactions with hydrophobic effects is responsible for the sequence-dependent binding of a disordered protein to nanoparticles.
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Affiliation(s)
- Mouzhe Xie
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Alexandar L. Hansen
- Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jiaqi Yuan
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Rafael Brüschweiler
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, Ohio 43210, United States
- To whom correspondence should be addressed: Rafael Brüschweiler, Ph.D., Department of Chemistry and Biochemistry, CBEC building, The Ohio State University, Columbus, Ohio 43210, , Tel. 614-688-2083
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17
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Wang A, Perera YR, Davidson MB, Fitzkee NC. Electrostatic Interactions and Protein Competition Reveal a Dynamic Surface in Gold Nanoparticle-Protein Adsorption. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2016; 120:24231-24239. [PMID: 27822335 PMCID: PMC5096844 DOI: 10.1021/acs.jpcc.6b08469] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Gold nanoparticle- (AuNP-) protein conjugates are potentially useful in a broad array of diagnostic and therapeutic applications, but the physical basis of the simultaneous adsorption of multiple proteins onto AuNP surfaces remains poorly understood. Here, we investigate the contribution of electrostatic interactions to protein-AuNP binding by studying the pH-dependent binding behavior of two proteins, GB3 and ubiquitin. For both proteins, binding to 15-nm citrate-coated AuNPs closely tracks with the predicted net charge using standard pKa values, and a dramatic reduction in binding is observed when lysine residues are chemically methylated. This suggests that clusters of basic residues are involved in binding, and using this hypothesis, we model the pKa shifts induced by AuNP binding. Then, we employ a novel NMR-based approach to monitor the binding competition between GB3 and ubiquitin in situ at different pH values. In light of our model, the NMR measurements reveal that the net charge, binding association constant, and size of each protein play distinct roles at different stages of protein adsorption. When citrate-coated AuNPs and proteins first interact, net charge appears to dominate. However, as citrate molecules are displaced by protein, the surface chemistry changes, and the energetics of binding becomes far more complex. In this case, we observed that GB3 is able to displace ubiquitin at intermediate time scales, even though it has a lower net charge. The thermodynamic model for binding developed here could be the first step toward predicting the binding behavior in biological fluids, such as blood plasma.
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18
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Zanzoni S, Pedroni M, D'Onofrio M, Speghini A, Assfalg M. Paramagnetic Nanoparticles Leave Their Mark on Nuclear Spins of Transiently Adsorbed Proteins. J Am Chem Soc 2015; 138:72-5. [PMID: 26683352 DOI: 10.1021/jacs.5b11582] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The successful application of nanomaterials in biosciences necessitates an in-depth understanding of how they interface with biomolecules. Transient associations of proteins with nanoparticles (NPs) are accessible by solution NMR spectroscopy, albeit with some limitations. The incorporation of paramagnetic centers into NPs offers new opportunities to explore bio-nano interfaces. We propose NMR paramagnetic relaxation enhancement as a new tool to detect NP-binding surfaces on proteins with increased sensitivity, also extending the applicability of NMR investigations to heterogeneous biomolecular mixtures. The adsorption of ubiquitin on gadolinium-doped fluoride-based NPs produced residue-specific NMR line-broadening effects mapping to a contiguous area on the surface of the protein. Importantly, an identical paramagnetic fingerprint was observed in the presence of a competing protein-protein association equilibrium, exemplifying possible interactions taking place in crowded biological media. The interaction was further characterized using isothermal titration calorimetry and upconversion emission measurements. The data indicate that the used fluoride-based NPs are not biologically inert but rather are capable of biomolecular recognition.
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Affiliation(s)
- Serena Zanzoni
- Biomolecular NMR Laboratory, Department of Biotechnology, University of Verona , 37134 Verona, Italy
| | - Marco Pedroni
- Nanomaterials Research Group, Department of Biotechnology, University of Verona and INSTM , 37134 Verona, Italy
| | - Mariapina D'Onofrio
- Biomolecular NMR Laboratory, Department of Biotechnology, University of Verona , 37134 Verona, Italy
| | - Adolfo Speghini
- Nanomaterials Research Group, Department of Biotechnology, University of Verona and INSTM , 37134 Verona, Italy
| | - Michael Assfalg
- Biomolecular NMR Laboratory, Department of Biotechnology, University of Verona , 37134 Verona, Italy
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19
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Qian X, Rameshbabu U, Dordick JS, Siegel RW. Selective characterization of proteins on nanoscale concave surfaces. Biomaterials 2015; 75:305-312. [PMID: 26513422 DOI: 10.1016/j.biomaterials.2015.10.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 10/03/2015] [Accepted: 10/10/2015] [Indexed: 01/03/2023]
Abstract
Nanoscale curvature plays a critical role in nanostructure-biomolecule interactions, yet the understanding of such effects in concave nanostructures is still very limited. Because concave nanostructures usually possess convex surface curvatures as well, it is challenging to selectively study the proteins on concave surfaces alone. In this work, we have developed a novel and facile method to address this issue by desorbing proteins on the external surfaces of hollow gold nanocages (AuNG), allowing the selective characterization of retained proteins immobilized on their internal concave surfaces. The selective desorption of proteins was achieved via varying the solution ionic strength, and was demonstrated by both calculation and experimental comparison with non-hollow nanoparticles. This method has created a new platform for the discrete observation of proteins adsorbed inside AuNG hollow cores, and this work suggests an expanded biomedical application space for hollow nanomaterials.
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Affiliation(s)
- Xi Qian
- Department of Materials Science and Engineering, Rensselaer Polytechnic Institute, Troy NY 12180, USA; Rensselaer Nanotechnology Center, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy NY 12180, USA
| | - Utthara Rameshbabu
- Department of Materials Science and Engineering, Rensselaer Polytechnic Institute, Troy NY 12180, USA; Rensselaer Nanotechnology Center, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Jonathan S Dordick
- Department of Materials Science and Engineering, Rensselaer Polytechnic Institute, Troy NY 12180, USA; Rensselaer Nanotechnology Center, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy NY 12180, USA; Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy NY 12180, USA.
| | - Richard W Siegel
- Department of Materials Science and Engineering, Rensselaer Polytechnic Institute, Troy NY 12180, USA; Rensselaer Nanotechnology Center, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy NY 12180, USA.
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20
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Lin W, insley T, Tuttle MD, Zhu L, Berthold DA, Král P, Rienstra CM, Murphy CJ. Control of protein orientation on gold nanoparticles. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2015; 119:21035-21043. [PMID: 28626495 PMCID: PMC5472360 DOI: 10.1021/acs.jpcc.5b07701] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Gold nanoparticles (Au NPs) have attracted much attention due to their potential applications in nano-medicine. While numerous studies have quantified biomolecular adsorption to Au NPs in terms of equilibrium binding constants, far less is known about biomolecular orientation on nanoparticle surfaces. In this study, the binding of the protein α-synuclein to citrate and (16-mercaptohexadecyl) trimethylammonium bromide (MTAB) coated 12 nm Au NPs is examined by heteronuclear single quantum coherence NMR spectroscopy to provide site-specific measurements of protein-nanoparticle binding. Molecular dynamics simulations support the orientation assignments, which show N-terminus binding to the Au NP for citrate-capped NPs, and C-terminus binding for the MTAB-capped NPs.
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Affiliation(s)
- Wayne Lin
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Matthews Avenue, Urbana, Illinois, 61801, USA
| | - Thomas insley
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois, 60607, USA
| | - Marcus D. Tuttle
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Matthews Avenue, Urbana, Illinois, 61801, USA
| | - Lingyang Zhu
- School of Chemical Sciences, University of Illinois at Urbana-Champaign, 505 South Matthews Avenue, Urbana, Illinois, 61801, USA
| | - Deborah A. Berthold
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Matthews Avenue, Urbana, Illinois, 61801, USA
| | - Petr Král
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois, 60607, USA
- Department of Physics, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois, 60607, USA
| | - Chad M. Rienstra
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Matthews Avenue, Urbana, Illinois, 61801, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Matthews Avenue, Urbana, Illinois, 61801, USA
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 607 South Matthews Avenue, Urbana, Illinois, 61801, USA
| | - Catherine J. Murphy
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Matthews Avenue, Urbana, Illinois, 61801, USA
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21
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Chhoden T, Clausen PA, Larsen ST, Nørgaard AW, Lauritsen FR. Interactions between nanoparticles and lung surfactant investigated by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:1080-1086. [PMID: 26044276 DOI: 10.1002/rcm.7199] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Revised: 03/12/2015] [Accepted: 03/16/2015] [Indexed: 06/04/2023]
Abstract
RATIONALE Inhaled nanoparticles may cause adverse effects due to inactivation of lung surfactants. We have studied how three different nanoparticles interact with dipalmitoyl-phosphatidylcholine (DPPC), the main component in lung surfactant. METHODS DPPC in solution was mixed with a suspension of nanoparticles, both in organic solvent, and allowed to interact for 40 min under conditions partly resembling the alveolar lining. Nanoparticles were isolated by centrifugation, washed, and re-suspended in ethanol/water 1:1 (v/v). The resulting solution was analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) using dihydroxybenzoic acid as matrix. RESULTS The developed methodology was successfully applied for quantitative detection of phospholipid lung surfactant bound to three different types of nanoparticles. Titanium dioxide nanoparticles had a strong affinity for binding of lipid lung surfactant in contrast to pristine and methylated silica nanoparticles. When the concentration of lipid surfactant was raised in the reaction mixture, the titanium dioxide nanoparticles showed an apparently non-linear binding process. CONCLUSIONS This work demonstrates that MALDI-TOFMS can be used for direct determination of the binding of surfactant lipids to nanoparticles and represents an important initial step towards a simple and quantitative in vitro method for assessment of interactions of nanoparticles with lung surfactants.
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Affiliation(s)
- Tashi Chhoden
- National Research Centre for the Working Environment, Copenhagen, Denmark
- University of Southern Denmark, 5230, Odense, M, Denmark
| | - Per Axel Clausen
- National Research Centre for the Working Environment, Copenhagen, Denmark
| | - Søren T Larsen
- National Research Centre for the Working Environment, Copenhagen, Denmark
| | - Asger W Nørgaard
- National Research Centre for the Working Environment, Copenhagen, Denmark
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22
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Ogorzalek TL, Wei S, Liu Y, Wang Q, Brooks CL, Chen Z, Marsh ENG. Molecular-Level Insights into Orientation-Dependent Changes in the Thermal Stability of Enzymes Covalently Immobilized on Surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:6145-53. [PMID: 25973638 DOI: 10.1021/acs.langmuir.5b01735] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Surface-immobilized enzymes are important for a wide range of technological applications, including industrial catalysis, drug delivery, medical diagnosis, and biosensors; however, our understanding of how enzymes and proteins interact with abiological surfaces on the molecular level remains extremely limited. We have compared the structure, activity, and thermal stability of two variants of a β-galactosidase attached to a chemically well-defined maleimide-terminated self-assembled monolayer surface through a unique cysteinyl residue. In one case the enzyme is attached through an α helix and in the other case through an adjacent loop. Both enzymes exhibit similar specific activities and adopt similar orientations with respect to the surface normal, as determined by sum-frequency generation and attenuated total reflectance FT-IR spectroscopies. Surprisingly, however, the loop-tethered enzyme exhibits a thermal stability 10 °C lower than the helix-tethered enzyme and 13 °C lower than the enzyme in free solution. Using coarse-grain models, molecular dynamics simulations of the thermal unfolding of the surface-tethered enzymes were able to reproduce these differences in stability. Thus, revealing that tethering through the more flexible loop position provides more opportunity for surface residues on the protein to interact with the surface and undergo surface-induced unfolding. These observations point to the importance of the location of the attachment point in determining the performance of surface-supported biocatalysts and suggest strategies for optimizing their activity and thermal stability through molecular simulations.
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Affiliation(s)
- Tadeusz L Ogorzalek
- †Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Shuai Wei
- †Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Yuwei Liu
- †Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Quiming Wang
- †Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Charles L Brooks
- †Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
- §Department of Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Zhan Chen
- †Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
- ‡Department of Macromolecular Science and Engineering, University of Michigan, 2300 Hayward Street, Ann Arbor, Michigan 48109, United States
| | - E Neil G Marsh
- †Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
- ∥Department of Biological Chemistry, University of Michigan, 1150 West Medical Center Drive, Ann Arbor, Michigan 48109, United States
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23
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The study of transient protein-nanoparticle interactions by solution NMR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1864:102-14. [PMID: 25936778 DOI: 10.1016/j.bbapap.2015.04.024] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 04/20/2015] [Accepted: 04/21/2015] [Indexed: 12/30/2022]
Abstract
The rapid development of novel nanoscale materials for applications in biomedicine urges an improved characterization of the nanobio interfaces. Nanoparticles exhibit unique structures and properties, often different from the corresponding bulk materials, and the nature of their interactions with biological systems remains poorly characterized. Solution NMR spectroscopy is a mature technique for the investigation of biomolecular structure, dynamics, and intermolecular associations, however its use in protein-nanoparticle interaction studies remains scarce and highly challenging, particularly due to unfavorable hydrodynamic properties of most nanoscale assemblies. Nonetheless, recent efforts demonstrated that a number of NMR observables, such as chemical shifts, signal intensities, amide exchange rates and relaxation parameters, together with newly designed saturation transfer experiments, could be successfully employed to characterize the orientation, structure and dynamics of proteins adsorbed onto nanoparticle surfaces. This review provides the first survey and critical assessment of the contributions from solution NMR spectroscopy to the study of transient interactions between proteins and both inorganic (gold, silver, and silica) and organic (polymer, carbon and lipid based) nanoparticles. This article is part of a Special Issue entitled: Physiological Enzymology and Protein Functions.
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24
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Zanzoni S, Ceccon A, Assfalg M, Singh RK, Fushman D, D'Onofrio M. Polyhydroxylated [60]fullerene binds specifically to functional recognition sites on a monomeric and a dimeric ubiquitin. NANOSCALE 2015; 7:7197-205. [PMID: 25811293 PMCID: PMC4443925 DOI: 10.1039/c5nr00539f] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The use of nanoparticles (NPs) in biomedical applications requires an in-depth understanding of the mechanisms by which NPs interact with biomolecules. NPs associating with proteins may interfere with protein-protein interactions and affect cellular communication pathways, however the impact of NPs on biomolecular recognition remains poorly characterized. In this respect, particularly relevant is the study of NP-induced functional perturbations of proteins implicated in the regulation of key biochemical pathways. Ubiquitin (Ub) is a prototypical protein post-translational modifier playing a central role in numerous essential biological processes. To contribute to the understanding of the interactions between this universally distributed biomacromolecule and NPs, we investigated the adsorption of polyhydroxylated [60]fullerene on monomeric Ub and on a minimal polyubiquitin chain in vitro at atomic resolution. Site-resolved chemical shift and intensity perturbations of Ub's NMR signals, together with (15)N spin relaxation rate changes, exchange saturation transfer effects, and fluorescence quenching data were consistent with the reversible formation of soluble aggregates incorporating fullerenol clusters. The specific interaction epitopes were identified, coincident with functional recognition sites in a monomeric and lysine48-linked dimeric Ub. Fullerenol appeared to target the open state of the dynamic structure of a dimeric Ub according to a conformational selection mechanism. Importantly, the protein-NP association prevented the enzyme-catalyzed synthesis of polyubiquitin chains. Our findings provide an experiment-based insight into protein/fullerenol recognition, with implications in functional biomolecular communication, including regulatory protein turnover, and for the opportunity of therapeutic intervention in Ub-dependent cellular pathways.
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Affiliation(s)
- Serena Zanzoni
- Department of Biotechnology, University of Verona, 37134 Verona, Italy.
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25
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Shim KH, Hulme J, Maeng EH, Kim MK, An SSA. Analysis of SiO2 nanoparticles binding proteins in rat blood and brain homogenate. Int J Nanomedicine 2014; 9 Suppl 2:207-15. [PMID: 25565838 PMCID: PMC4279766 DOI: 10.2147/ijn.s58203] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
A multitude of nanoparticles, such as titanium oxide (TiO2), zinc oxide, aluminum oxide, gold oxide, silver oxide, iron oxide, and silica oxide, are found in many chemical, cosmetic, pharmaceutical, and electronic products. Recently, SiO2 nanoparticles were shown to have an inert toxicity profile and no association with an irreversible toxicological change in animal models. Hence, exposure to SiO2 nanoparticles is on the increase. SiO2 nanoparticles are routinely used in numerous materials, from strengthening filler for concrete and other construction composites, to nontoxic platforms for biomedical application, such as drug delivery and theragnostics. On the other hand, recent in vitro experiments indicated that SiO2 nanoparticles were cytotoxic. Therefore, we investigated these nanoparticles to identify potentially toxic pathways by analyzing the adsorbed protein corona on the surface of SiO2 nanoparticles in the blood and brain of the rat. Four types of SiO2 nanoparticles were chosen for investigation, and the protein corona of each type was analyzed using liquid chromatography-tandem mass spectrometry technology. In total, 115 and 48 plasma proteins from the rat were identified as being bound to negatively charged 20 nm and 100 nm SiO2 nanoparticles, respectively, and 50 and 36 proteins were found for 20 nm and 100 nm arginine-coated SiO2 nanoparticles, respectively. Higher numbers of proteins were adsorbed onto the 20 nm sized SiO2 nanoparticles than onto the 100 nm sized nanoparticles regardless of charge. When proteins were compared between the two charges, higher numbers of proteins were found for arginine-coated positively charged SiO2 nanoparticles than for the negatively charged nanoparticles. The proteins identified as bound in the corona from SiO2 nanoparticles were further analyzed with ClueGO, a Cytoscape plugin used in protein ontology and for identifying biological interaction pathways. Proteins bound on the surface of nanoparticles may affect functional and conformational properties and distributions in complicated biological processes.
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Affiliation(s)
- Kyu Hwan Shim
- Department of Bionano Technology, Gachon Medical Research Institute, Gachon University, Sungnam-si, South Korea
| | - John Hulme
- Department of Bionano Technology, Gachon Medical Research Institute, Gachon University, Sungnam-si, South Korea
| | - Eun Ho Maeng
- Department of Analysis, KTR, Kimpo, Gyeonggi-do, South Korea
| | - Meyoung-Kon Kim
- Department of Biochemistry and Molecular Biology, Korea University Medical School and College, Seoul, South Korea
| | - Seong Soo A An
- Department of Bionano Technology, Gachon Medical Research Institute, Gachon University, Sungnam-si, South Korea
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26
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Mudunkotuwa IA, Grassian VH. Histidine adsorption on TiO2 nanoparticles: an integrated spectroscopic, thermodynamic, and molecular-based approach toward understanding nano-bio interactions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:8751-8760. [PMID: 24978817 DOI: 10.1021/la500722n] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Nanoparticles in biological media form dynamic entities as a result of competitive adsorption of proteins on nanoparticle surfaces called protein coronas. The protein affinity toward nanoparticle surfaces potentially depends on the constituent amino acid side chains which are on the protein exterior and thus exposed to the solution and available for interaction. Therefore, studying the adsorption of individual amino acids on nanoparticle surfaces can provide valuable insights into the overall evolution of nanoparticles in solution and the protein corona that forms. In the current study, the surface adsorption of l-histidine on TiO2 nanoparticles with a diameter of 5 nm at pH 7.4 (physiological pH) is studied from both macroscopic and molecular perspectives. Quantitative adsorption measurements of l-histidine on 5 nm TiO2 particles yield maximum adsorption coverage of 6.2 ± 0.3 × 10(13) molecules cm(-2) at 293 K and pH 7.4. These quantitative adsorption measurements also yield values for the equilibrium constant and free energy of adsorption of K = 4.3 ± 0.5 × 10(2) L mol(-1) and ΔG = -14.8 ± 0.3 kJ mol(-1), respectively. Detailed analysis of the adsorption between histidine and 5 nm TiO2 nanoparticle surfaces with attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy indicates both the imidazole side chain and the amine group interacting with the nanoparticle surface and the adsorption to be reversible. The adsorption results in no change in surface charge and therefore does not change nanoparticle-nanoparticle interactions and thus aggregation behavior of these 5 nm TiO2 nanoparticles in aqueous solution.
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Affiliation(s)
- Imali A Mudunkotuwa
- Department of Chemistry, University of Iowa , Iowa City, Iowa 52242, United States
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