1
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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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2
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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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3
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Cheung E, Xia Y, Caporini MA, Gilmore JL. Tools shaping drug discovery and development. BIOPHYSICS REVIEWS 2022; 3:031301. [PMID: 38505278 PMCID: PMC10903431 DOI: 10.1063/5.0087583] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 06/21/2022] [Indexed: 03/21/2024]
Abstract
Spectroscopic, scattering, and imaging methods play an important role in advancing the study of pharmaceutical and biopharmaceutical therapies. The tools more familiar to scientists within industry and beyond, such as nuclear magnetic resonance and fluorescence spectroscopy, serve two functions: as simple high-throughput techniques for identification and purity analysis, and as potential tools for measuring dynamics and structures of complex biological systems, from proteins and nucleic acids to membranes and nanoparticle delivery systems. With the expansion of commercial small-angle x-ray scattering instruments into the laboratory setting and the accessibility of industrial researchers to small-angle neutron scattering facilities, scattering methods are now used more frequently in the industrial research setting, and probe-less time-resolved small-angle scattering experiments are now able to be conducted to truly probe the mechanism of reactions and the location of individual components in complex model or biological systems. The availability of atomic force microscopes in the past several decades enables measurements that are, in some ways, complementary to the spectroscopic techniques, and wholly orthogonal in others, such as those related to nanomechanics. As therapies have advanced from small molecules to protein biologics and now messenger RNA vaccines, the depth of biophysical knowledge must continue to serve in drug discovery and development to ensure quality of the drug, and the characterization toolbox must be opened up to adapt traditional spectroscopic methods and adopt new techniques for unraveling the complexities of the new modalities. The overview of the biophysical methods in this review is meant to showcase the uses of multiple techniques for different modalities and present recent applications for tackling particularly challenging situations in drug development that can be solved with the aid of fluorescence spectroscopy, nuclear magnetic resonance spectroscopy, atomic force microscopy, and small-angle scattering.
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Affiliation(s)
- Eugene Cheung
- Moderna, 200 Technology Square, Cambridge, Massachusetts 02139, USA
| | - Yan Xia
- Moderna, 200 Technology Square, Cambridge, Massachusetts 02139, USA
| | - Marc A. Caporini
- Moderna, 200 Technology Square, Cambridge, Massachusetts 02139, USA
| | - Jamie L. Gilmore
- Moderna, 200 Technology Square, Cambridge, Massachusetts 02139, USA
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4
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O’Brien TE, Ioffe LB, Su Y, Fushman D, Neven H, Babbush R, Smelyanskiy V. Quantum computation of molecular structure using data from challenging-to-classically-simulate nuclear magnetic resonance experiments. PRX QUANTUM : A PHYSICAL REVIEW JOURNAL 2022; 3:030345. [PMID: 36624758 PMCID: PMC9825292 DOI: 10.1103/prxquantum.3.030345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
We propose a quantum algorithm for inferring the molecular nuclear spin Hamiltonian from time-resolved measurements of spin-spin correlators, which can be obtained via nuclear magnetic resonance (NMR). We focus on learning the anisotropic dipolar term of the Hamiltonian, which generates dynamics that are challenging to classically simulate in some contexts. We demonstrate the ability to directly estimate the Jacobian and Hessian of the corresponding learning problem on a quantum computer, allowing us to learn the Hamiltonian parameters. We develop algorithms for performing this computation on both noisy near-term and future fault-tolerant quantum computers. We argue that the former is promising as an early beyond-classical quantum application since it only requires evolution of a local spin Hamiltonian. We investigate the example of a protein (ubiquitin) confined on a membrane as a benchmark of our method. We isolate small spin clusters, demonstrate the convergence of our learning algorithm on one such example, and then investigate the learnability of these clusters as we cross the ergodic to non-ergodic phase transition by suppressing the dipolar interaction. We see a clear correspondence between a drop in the multifractal dimension measured across many-body eigenstates of these clusters, and a transition in the structure of the Hessian of the learning cost function (from degenerate to learnable). Our hope is that such quantum computations might enable the interpretation and development of new NMR techniques for analyzing molecular structure.
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Affiliation(s)
| | - Lev B. Ioffe
- Google Quantum AI, Venice, CA 90291, United States
| | - Yuan Su
- Google Quantum AI, Venice, CA 90291, United States
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, United States
| | | | - Ryan Babbush
- Google Quantum AI, Venice, CA 90291, United States
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5
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Ceccon A, Kubatova N, Louis JM, Clore GM, Tugarinov V. Global Dynamics of a Protein on the Surface of Anisotropic Lipid Nanoparticles Derived from Relaxation-Based NMR Spectroscopy. J Phys Chem B 2022; 126:5646-5654. [PMID: 35877206 DOI: 10.1021/acs.jpcb.2c03519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The global motions of ubiquitin, a model protein, on the surface of anisotropically tumbling 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (POPG):1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC) bicelles are described. The shapes of POPG:DHPC bicelles prepared with high molar ratios q of POPG to DHPC can be approximated by prolate ellipsoids, with the ratio of ellipsoid dimensions and dimensions themselves increasing with higher values of q. Adaptation of the nuclear magnetic resonance (NMR) relaxation-based approach that we previously developed for interactions of ubiquitin with spherical POPG liposomes (Ceccon, A. J. Am. Chem. Soc. 2016, 138, 5789-5792) allowed us to quantitatively analyze the variation in lifetime line broadening of NMR signals (ΔR2) measured for ubiquitin in the presence of q = 2 POPG:DHPC bicelles and the associated transverse spin relaxation rates (R2,B) of bicelle-bound ubiquitin. Ubiquitin, transiently bound to POPG:DHPC bicelles, undergoes internal rotation about an axis orthogonal to the surface of the bicelle and perpendicular to the principal axis of its rotational diffusion tensor on the low microsecond time scale (∼3 μs), while the rotation axis itself wobbles in a cone on a submicrosecond time scale (≤ 500 ns).
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Affiliation(s)
- Alberto Ceccon
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - Nina Kubatova
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - John M Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - G Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - Vitali Tugarinov
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
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6
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An Y, Sedinkin SL, Venditti V. Solution NMR methods for structural and thermodynamic investigation of nanoparticle adsorption equilibria. NANOSCALE ADVANCES 2022; 4:2583-2607. [PMID: 35769933 PMCID: PMC9195484 DOI: 10.1039/d2na00099g] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 05/07/2022] [Indexed: 05/09/2023]
Abstract
Characterization of dynamic processes occurring at the nanoparticle (NP) surface is crucial for developing new and more efficient NP catalysts and materials. Thus, a vast amount of research has been dedicated to developing techniques to characterize sorption equilibria. Over recent years, solution NMR spectroscopy has emerged as a preferred tool for investigating ligand-NP interactions. Indeed, due to its ability to probe exchange dynamics over a wide range of timescales with atomic resolution, solution NMR can provide structural, kinetic, and thermodynamic information on sorption equilibria involving multiple adsorbed species and intermediate states. In this contribution, we review solution NMR methods for characterizing ligand-NP interactions, and provide examples of practical applications using these methods as standalone techniques. In addition, we illustrate how the integrated analysis of several NMR datasets was employed to elucidate the role played by support-substrate interactions in mediating the phenol hydrogenation reaction catalyzed by ceria-supported Pd nanoparticles.
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Affiliation(s)
- Yeongseo An
- Department of Chemistry, Iowa State University Hach Hall, 2438 Pammel Drive Ames Iowa 50011 USA +1-515-294-7550 +1-515-294-1044
| | - Sergey L Sedinkin
- Department of Chemistry, Iowa State University Hach Hall, 2438 Pammel Drive Ames Iowa 50011 USA +1-515-294-7550 +1-515-294-1044
| | - Vincenzo Venditti
- Department of Chemistry, Iowa State University Hach Hall, 2438 Pammel Drive Ames Iowa 50011 USA +1-515-294-7550 +1-515-294-1044
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University Ames Iowa 50011 USA
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7
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Tugarinov V, Ceccon A, Clore GM. NMR methods for exploring 'dark' states in ligand binding and protein-protein interactions. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 128:1-24. [PMID: 35282867 PMCID: PMC8921508 DOI: 10.1016/j.pnmrs.2021.10.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/21/2021] [Accepted: 10/26/2021] [Indexed: 05/24/2023]
Abstract
A survey, primarily based on work in the authors' laboratory during the last 10 years, is provided of recent developments in NMR studies of exchange processes involving protein-ligand and protein-protein interactions. We start with a brief overview of the theoretical background of Dark state Exchange Saturation Transfer (DEST) and lifetime line-broadening (ΔR2) NMR methodology. Some limitations of the DEST/ΔR2 methodology in applications to molecular systems with intermediate molecular weights are discussed, along with the means of overcoming these limitations with the help of closely related exchange NMR techniques, such as the measurements of Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion, exchange-induced chemical shifts or rapidly-relaxing components of relaxation decays. Some theoretical underpinnings of the quantitative description of global dynamics of proteins on the surface of very high molecular weight particles (nanoparticles) are discussed. Subsequently, several applications of DEST/ΔR2 methodology are described from a methodological perspective with an emphasis on providing examples of how kinetic and relaxation parameters for exchanging systems can be reliably extracted from NMR data for each particular model of exchange. Among exchanging systems that are not associated with high molecular weight species, we describe several exchange NMR-based studies that focus on kinetic modelling of transient pre-nucleation oligomerization of huntingtin peptides that precedes aggregation and fibril formation.
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Affiliation(s)
- Vitali Tugarinov
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, United States.
| | - Alberto Ceccon
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, United States
| | - G Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, United States.
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8
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Oliyantakath Hassan MS, Somasundaran SM, Abdul Shukkoor MB, Ayyappan S, Abdul Vahid A, Vijayan V. Examining the Transient Dark State in Protein-Quantum Dot Interaction by Relaxation-Based Solution NMR. J Phys Chem B 2021; 125:10119-10125. [PMID: 34473517 DOI: 10.1021/acs.jpcb.1c04853] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We probed the "dark" state involved in the protein-quantum dot (QD) interaction using a relaxation-based solution nuclear magnetic resonance (NMR) approach. We examined the dynamics and exchange kinetics of the ubiquitin-CdTe model system, which undergoes a fast exchange in the transverse relaxation time scale. We applied the recently developed dark-state exchange saturation transfer (DEST), lifetime line broadening (ΔR2), and exchange-induced chemical shift (δex) solution NMR techniques to obtain a residue-specific binding behavior of the protein on the QD surface. The variation in the estimated 15N-R2bound values clearly shows the dynamic nature of bound Ub. Upon mapping the amino acid residues showing a faster relaxation rate on the electrostatic potential surface of the protein, we have determined that the interaction is preferably electrostatic, and the amino acid residues involved in binding lie on the positively charged surface of the protein. We believe that our experimental approach should provide more in-depth knowledge to engineer new hybrid protein-QD systems in the future.
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Affiliation(s)
| | - Sanoop Mambully Somasundaran
- School of Chemistry, IISER-Thiruvananthapuram, Maruthamala P.O, Vithura, Thiruvananthapuram, Kerala 695551, India
| | | | - Shine Ayyappan
- School of Chemistry, IISER-Thiruvananthapuram, Maruthamala P.O, Vithura, Thiruvananthapuram, Kerala 695551, India
| | - Arshad Abdul Vahid
- School of Chemistry, IISER-Thiruvananthapuram, Maruthamala P.O, Vithura, Thiruvananthapuram, Kerala 695551, India
| | - Vinesh Vijayan
- School of Chemistry, IISER-Thiruvananthapuram, Maruthamala P.O, Vithura, Thiruvananthapuram, Kerala 695551, India
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9
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Xu JX, Alom MS, Fitzkee NC. Quantitative Measurement of Multiprotein Nanoparticle Interactions Using NMR Spectroscopy. Anal Chem 2021; 93:11982-11990. [PMID: 34432422 DOI: 10.1021/acs.analchem.1c01911] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
An effective intensity-based reference is a cornerstone for quantitative nuclear magnetic resonance (NMR) studies, as the molecular concentration is encoded in its signal. In theory, NMR is well suited for the measurement of competitive protein adsorption onto nanoparticle (NP) surfaces, but current referencing systems are not optimized for multidimensional experiments. Presented herein is a simple and novel referencing system using 15N tryptophan (Trp) as an external reference for 1H-15N 2D NMR experiments. The referencing system is validated by the determination of the binding capacity of a single protein onto gold NPs. Then, the Trp reference is applied to protein mixtures, and signals from each protein are accurately quantified. All results are consistent with previous studies, but with substantially higher precision, indicating that the Trp reference can accurately calibrate the residue peak intensities and reduce systematic errors. Finally, the proposed Trp reference is used to kinetically monitor in situ and in real time the competitive adsorption of different proteins. As a challenging test case, we successfully apply our approach to a mixture of protein variants differing by only a single residue. Our results show that the binding of one protein will affect the binding of the other, leading to an altered NP corona composition. This work therefore highlights the importance of studying protein-NP interactions in protein mixtures in situ, and the referencing system developed here enables the quantification of binding kinetics and thermodynamics of multiple proteins using various 1H-15N 2D NMR techniques.
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Affiliation(s)
- Joanna Xiuzhu Xu
- Department of Chemistry, Mississippi State University, Starkville, Mississippi 39762, United States
| | - Md Siddik Alom
- Department of Chemistry, Mississippi State University, Starkville, Mississippi 39762, United States
| | - Nicholas C Fitzkee
- Department of Chemistry, Mississippi State University, Starkville, Mississippi 39762, United States
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10
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Holzinger J, Kotisch H, Richter KW, Konrat R. Binding Mode Characterization of Osteopontin on Hydroxyapatite by Solution NMR Spectroscopy. Chembiochem 2021; 22:2300-2305. [PMID: 33914399 PMCID: PMC8359842 DOI: 10.1002/cbic.202100139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/28/2021] [Indexed: 01/13/2023]
Abstract
Extracellular matrix glycoproteins play a major role in bone mineralization and modulation of osteogenesis. Among these, the intrinsically disordered protein osteopontin (OPN) is associated with the inhibition of formation, growth and proliferation of the bone mineral hydroxyapatite (HAP). Furthermore, post-translational modifications like phosphorylation can alter conformations and interaction properties of intrinsically disordered proteins (IDPs). Therefore, the actual interaction of OPN with a HAP surface on an atomic level and how this interaction is affected by phosphorylation is of great interest. Here, we study the interaction of full-length OPN on the surface of suspended HAP nanoparticles by solution NMR spectroscopy. We report the binding modes of this IDP and provide evidence for the influence of hyperphosphorylation on the binding character and an explanation for the differing roles in biomineralization. Our study moreover presents an easy and suitable option to measure interaction of nanoparticles in a stable suspension with full-length proteins.
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Affiliation(s)
- Julian Holzinger
- Department of Structural and Computational BiologyUniversity of Vienna, Max Perutz LabsVienna BioCenter Campus 51030ViennaAustria
| | - Harald Kotisch
- Vienna Biocenter Core Facilities GmbHDr. Bohr Gasse 31030ViennaAustria
| | - Klaus W. Richter
- Department of Inorganic Chemistry, Functional MaterialsUniversity of ViennaWähringer Str. 421090ViennaAustria
| | - Robert Konrat
- Department of Structural and Computational BiologyUniversity of Vienna, Max Perutz LabsVienna BioCenter Campus 51030ViennaAustria
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11
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Guyon L, Groo AC, Malzert-Fréon A. Relevant Physicochemical Methods to Functionalize, Purify, and Characterize Surface-Decorated Lipid-Based Nanocarriers. Mol Pharm 2020; 18:44-64. [PMID: 33244972 DOI: 10.1021/acs.molpharmaceut.0c00857] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Surface functionalization of lipid-based nanocarriers (LBNCs) with targeting ligands has attracted huge interest in the field of nanomedicines for their ability to overcome some physiological barriers and their potential to deliver an active molecule to a specific target without causing damage to healthy tissues. The principal objective of this review is to summarize the present knowledge on LBNC decoration used for biomedical applications, with an emphasis on the ligands used, the functionalization approaches, and the purification methods after ligand corona formation. The most potent experimental techniques for the LBNC surface characterization are described. The potential of promising methods such as nuclear magnetic resonance spectroscopy and isothermal titration calorimetry to characterize ligand surface corona is also outlined.
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Affiliation(s)
- Léna Guyon
- CERMN, UNICAEN Université de Caen Normandie, F-14000 Caen, France
| | - Anne-Claire Groo
- CERMN, UNICAEN Université de Caen Normandie, F-14000 Caen, France
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12
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Pearce OM, Duncan JS, Lama B, Dukovic G, Damrauer NH. Binding Orientation of a Ruthenium-Based Water Oxidation Catalyst on a CdS QD Surface Revealed by NMR Spectroscopy. J Phys Chem Lett 2020; 11:9552-9556. [PMID: 33118823 DOI: 10.1021/acs.jpclett.0c02639] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We report on the binding of a Ru-based water oxidation catalyst (WOC) to CdS quantum dots (QDs) revealed by 1H NMR spectroscopy. Spin centers within the WOC exhibit correlated trends in chemical shift and T2 lifetime shortening upon QD binding. These effects are a highly directional function of proton position within the WOC, thus uncovering orientation information relative to the QD surface. The data suggest that the WOC interacts with the QD surface via the Ru terpyridine ligand, an unexpected orientation that has important implications for interfacial charge transfer and subsequent catalysis. This binding motif enables strong enough donor-acceptor electronic coupling for ultrafast photoinduced hole transfer while maintaining electronically distinct functional subunits.
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Affiliation(s)
- Orion M Pearce
- Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Jeremiah S Duncan
- Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Bimala Lama
- Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Gordana Dukovic
- Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Niels H Damrauer
- Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, Colorado 80309, United States
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13
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Insights into a Protein-Nanoparticle System by Paramagnetic Perturbation NMR Spectroscopy. MOLECULES (BASEL, SWITZERLAND) 2020; 25:molecules25215187. [PMID: 33171781 PMCID: PMC7664681 DOI: 10.3390/molecules25215187] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/12/2020] [Accepted: 10/22/2020] [Indexed: 11/18/2022]
Abstract
Background: The interaction between proteins and nanoparticles is a very relevant subject because of the potential applications in medicine and material science in general. Further interest derives from the amyloidogenic character of the considered protein, β2-microglobulin (β2m), which may be regarded as a paradigmatic system for possible therapeutic strategies. Previous evidence showed in fact that gold nanoparticles (AuNPs) are able to inhibit β2m fibril formation in vitro. Methods: NMR (Nuclear Magnetic Resonance) and ESR (Electron Spin Resonance) spectroscopy are employed to characterize the paramagnetic perturbation of the extrinsic nitroxide probe Tempol on β2m in the absence and presence of AuNPs to determine the surface accessibility properties and the occurrence of chemical or conformational exchange, based on measurements conducted under magnetization equilibrium and non-equilibrium conditions. Results: The nitroxide perturbation analysis successfully identifies the protein regions where protein-protein or protein-AuNPs interactions hinder accessibility or/and establish exchange contacts. These information give interesting clues to recognize the fibrillation interface of β2m and hypothesize a mechanism for AuNPs fibrillogenesis inhibition. Conclusions: The presented approach can be advantageously applied to the characterization of the interface in protein-protein and protein-nanoparticles interactions.
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14
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Egner TK, Naik P, An Y, Venkatesh A, Rossini AJ, Slowing II, Venditti V. ‘Surface Contrast’ NMR Reveals Non‐innocent Role of Support in Pd/CeO
2
Catalyzed Phenol Hydrogenation. ChemCatChem 2020. [DOI: 10.1002/cctc.202000608] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Timothy K. Egner
- Department of Chemistry Iowa State University 2438 Pammel Dr. Ames IA 50011 USA
| | - Pranjali Naik
- Department of Chemistry Iowa State University 2438 Pammel Dr. Ames IA 50011 USA
- U.S. Department of Energy Ames Laboratory 2756 Gilman Hall Ames IA 50011 USA
| | - Yeongseo An
- Department of Chemistry Iowa State University 2438 Pammel Dr. Ames IA 50011 USA
| | - Amrit Venkatesh
- Department of Chemistry Iowa State University 2438 Pammel Dr. Ames IA 50011 USA
| | - Aaron J. Rossini
- Department of Chemistry Iowa State University 2438 Pammel Dr. Ames IA 50011 USA
- U.S. Department of Energy Ames Laboratory 2756 Gilman Hall Ames IA 50011 USA
| | - Igor I. Slowing
- Department of Chemistry Iowa State University 2438 Pammel Dr. Ames IA 50011 USA
- U.S. Department of Energy Ames Laboratory 2756 Gilman Hall Ames IA 50011 USA
| | - Vincenzo Venditti
- Department of Chemistry Iowa State University 2438 Pammel Dr. Ames IA 50011 USA
- Roy J. Carver Department of Biochemistry Biophysics and Molecular Biology Iowa State University 2437 Pammel Drive Ames IA 50011 USA
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15
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Raj EN, Lin Y, Chen C, Liu K, Chao J. Selective Autophagy Pathway of Nanoparticles and Nanodrugs: Drug Delivery and Pathophysiological Effects. ADVANCED THERAPEUTICS 2020. [DOI: 10.1002/adtp.202000085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Emmanuel Naveen Raj
- Institute of Molecular Medicine and Bioengineering National Chiao Tung University Hsinchu 30068 Taiwan
- Department of Biological Science and Technology National Chiao Tung University Hsinchu 30068 Taiwan
| | - Yu‐Wei Lin
- Department of Biological Science and Technology National Chiao Tung University Hsinchu 30068 Taiwan
| | - Chien‐Hung Chen
- Department of Biological Science and Technology National Chiao Tung University Hsinchu 30068 Taiwan
| | - Kuang‐Kai Liu
- Department of Biological Science and Technology National Chiao Tung University Hsinchu 30068 Taiwan
| | - Jui‐I Chao
- Institute of Molecular Medicine and Bioengineering National Chiao Tung University Hsinchu 30068 Taiwan
- Department of Biological Science and Technology National Chiao Tung University Hsinchu 30068 Taiwan
- Center For Intelligent Drug Systems and Smart Bio‐devices National Chiao Tung University Hsinchu 30068 Taiwan
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16
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Malik SA, Mohanta Z, Srivastava C, Atreya HS. Modulation of protein-graphene oxide interactions with varying degrees of oxidation. NANOSCALE ADVANCES 2020; 2:1904-1912. [PMID: 36132498 PMCID: PMC9419239 DOI: 10.1039/c9na00807a] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 03/22/2020] [Indexed: 06/11/2023]
Abstract
The degree of oxidation of graphene oxide (GO) has been shown to be important for its toxicity and drug-loading efficiency. However, the effect of its variations on GO-protein interaction remains unclear. Here, we evaluate the effect of the different oxidation degrees of GO on its interaction with human ubiquitin (8.6 kDa) using solution state nuclear magnetic resonance (NMR) spectroscopy in combination with other biophysical techniques. Our findings show that the interaction between the protein and the different GO samples is weak and electrostatic in nature. It involves fast dynamic exchange of the protein molecules from the surface of the GO. As the oxidation degree of the GO increases, the extent of the interaction with the protein changes. The interaction of the protein with GO can thus be modulated by tuning the degree of oxidation. This study opens up new avenues to design appropriate graphenic materials for use in various biomedical fields such as drug delivery, biomedical devices and imaging.
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Affiliation(s)
- Shahid A Malik
- Department of Solid State and Structural Chemistry Unit, Indian Institute of Science Bangalore-560012 India
- Nuclear Magnetic Resonance Research Centre, Indian Institute of Science Bangalore-560012 India
| | - Zinia Mohanta
- Nuclear Magnetic Resonance Research Centre, Indian Institute of Science Bangalore-560012 India
- Centre for Bio Systems Science and Engineering, Indian Institute of Science Bangalore-560012 India
| | - Chandan Srivastava
- Department of Materials Engineering, Indian Institute of Science Bangalore-560012 India
| | - Hanudatta S Atreya
- Department of Solid State and Structural Chemistry Unit, Indian Institute of Science Bangalore-560012 India
- Nuclear Magnetic Resonance Research Centre, Indian Institute of Science Bangalore-560012 India
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17
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Preparation, characterization, physicochemical property and potential application of porous starch: A review. Int J Biol Macromol 2020; 148:1169-1181. [DOI: 10.1016/j.ijbiomac.2020.02.055] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 01/10/2020] [Accepted: 02/06/2020] [Indexed: 11/20/2022]
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18
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Munari F, D'Onofrio M, Assfalg M. Solution NMR insights into dynamic supramolecular assemblies of disordered amyloidogenic proteins. Arch Biochem Biophys 2020; 683:108304. [PMID: 32097611 DOI: 10.1016/j.abb.2020.108304] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 02/12/2020] [Accepted: 02/14/2020] [Indexed: 12/29/2022]
Abstract
The extraordinary flexibility and structural heterogeneity of intrinsically disordered proteins (IDP) make them functionally versatile molecules. We have now begun to better understand their fundamental role in biology, however many aspects of their behaviour remain difficult to grasp experimentally. This is especially true for the intermolecular interactions which lead to the formation of transient or highly dynamic supramolecular self-assemblies, such as oligomers, aggregation intermediates and biomolecular condensates. Both the emerging functions and pathogenicity of these structures have stimulated great efforts to develop methodologies capable of providing useful insights. Significant progress in solution NMR spectroscopy has made this technique one of the most powerful to describe structural and dynamic features of IDPs within such assemblies at atomic resolution. Here, we review the most recent works that have illuminated key aspects of IDP assemblies and contributed significant advancements towards our understanding of the complex conformational landscape of prototypical disease-associated proteins. We also include a primer on some of the fundamental and innovative NMR methods being used in the discussed studies.
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Affiliation(s)
- Francesca Munari
- 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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19
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Judge PT, Sesti EL, Price LE, Albert BJ, Alaniva N, Saliba EP, Halbritter T, Sigurdsson ST, Kyei GB, Barnes AB. Dynamic Nuclear Polarization with Electron Decoupling in Intact Human Cells and Cell Lysates. J Phys Chem B 2020; 124:2323-2330. [DOI: 10.1021/acs.jpcb.9b10494] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Patrick T. Judge
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
- Department of Biochemistry, Biophysics & Structural Biology, Washington University in St. Louis, St. Louis, Missouri 63110, United States
| | - Erika L. Sesti
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Lauren E. Price
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Brice J. Albert
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Nicholas Alaniva
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Edward P. Saliba
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Thomas Halbritter
- Department of Chemistry, Science Institute, University of Iceland, Dunhaga 3, 107 Reykjavik, Iceland
| | - Snorri Th. Sigurdsson
- Department of Chemistry, Science Institute, University of Iceland, Dunhaga 3, 107 Reykjavik, Iceland
| | - George B. Kyei
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63130, United States
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana,
Legon, Accra 02233, Ghana
| | - Alexander B. Barnes
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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20
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Alderson TR, Kay LE. Unveiling invisible protein states with NMR spectroscopy. Curr Opin Struct Biol 2020; 60:39-49. [DOI: 10.1016/j.sbi.2019.10.008] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 10/28/2019] [Indexed: 12/24/2022]
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21
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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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22
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Zeng L, Gao J, Liu Y, Gao J, Yao L, Yang X, Liu X, He B, Hu L, Shi J, Song M, Qu G, Jiang G. Role of protein corona in the biological effect of nanomaterials: Investigating methods. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.05.039] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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23
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Tugarinov V, Clore GM. Exchange saturation transfer and associated NMR techniques for studies of protein interactions involving high-molecular-weight systems. JOURNAL OF BIOMOLECULAR NMR 2019; 73:461-469. [PMID: 31407202 PMCID: PMC6819251 DOI: 10.1007/s10858-019-00244-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 03/27/2019] [Indexed: 05/15/2023]
Abstract
A brief overview of theoretical and experimental aspects of the Dark state Exchange Saturation Transfer (DEST) and lifetime line broadening ([Formula: see text]) NMR methodologies is presented from a physico-chemical perspective. We describe how the field-dependence of [Formula: see text] can be used for determining the exchange regime on the transverse spin relaxation time-scale. Some limitations of DEST/[Formula: see text] methodology in applications to molecular systems with intermediate molecular weights are discussed, and the means of overcoming these limitations via the use of closely related exchange NMR techniques is presented. Finally, several applications of DEST/[Formula: see text] methodology are described from a methodological viewpoint, with an emphasis on providing examples of how kinetic and relaxation parameters of exchange can be reliably extracted from the experimental data in each particular case.
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Affiliation(s)
- Vitali Tugarinov
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA.
| | - G Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA.
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24
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Ahmed R, Akcan M, Khondker A, Rheinstädter MC, Bozelli JC, Epand RM, Huynh V, Wylie RG, Boulton S, Huang J, Verschoor CP, Melacini G. Atomic resolution map of the soluble amyloid beta assembly toxic surfaces. Chem Sci 2019; 10:6072-6082. [PMID: 31360412 PMCID: PMC6585597 DOI: 10.1039/c9sc01331h] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 05/19/2019] [Indexed: 12/11/2022] Open
Abstract
Atomic resolution map of the soluble amyloid beta assembly (Aβn) “toxic surfaces” that facilitate the early pathogenic events in Alzheimer's disease (AD).
Soluble amyloid beta assemblies (Aβn) are neurotoxic and play a central role in the early phases of the pathogenesis cascade leading to Alzheimer's disease. However, the current knowledge about the molecular determinants of Aβn toxicity is at best scant. Here, we comparatively analyze Aβn prepared in the absence or presence of a catechin library that modulates cellular toxicity. By combining solution NMR with dynamic light scattering, fluorescence spectroscopy, electron microscopy, wide-angle X-ray diffraction and cell viability assays, we identify a cluster of unique molecular signatures that distinguish toxic vs. nontoxic Aβ assemblies. These include the exposure of a hydrophobic surface spanning residues 17–28 and the concurrent shielding of the highly charged N-terminus. We show that the combination of these two dichotomous structural transitions promotes the colocalization and insertion of β-sheet rich Aβn into the membrane, compromising membrane integrity. These previously elusive toxic surfaces mapped here provide an unprecedented foundation to establish structure-toxicity relationships of Aβ assemblies.
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Affiliation(s)
- Rashik Ahmed
- Department of Biochemistry and Biomedical Sciences , McMaster University , Hamilton , ON L8S 4M1 , Canada .
| | - Michael Akcan
- Department of Biochemistry and Biomedical Sciences , McMaster University , Hamilton , ON L8S 4M1 , Canada .
| | - Adree Khondker
- Department of Physics and Astronomy , McMaster University , Hamilton , ON L8S 4M1 , Canada
| | - Maikel C Rheinstädter
- Department of Physics and Astronomy , McMaster University , Hamilton , ON L8S 4M1 , Canada
| | - José C Bozelli
- Department of Biochemistry and Biomedical Sciences , McMaster University , Hamilton , ON L8S 4M1 , Canada .
| | - Richard M Epand
- Department of Biochemistry and Biomedical Sciences , McMaster University , Hamilton , ON L8S 4M1 , Canada .
| | - Vincent Huynh
- Department of Chemistry and Chemical Biology , McMaster University , Hamilton , ON L8S 4M1 , Canada
| | - Ryan G Wylie
- Department of Chemistry and Chemical Biology , McMaster University , Hamilton , ON L8S 4M1 , Canada
| | - Stephen Boulton
- Department of Biochemistry and Biomedical Sciences , McMaster University , Hamilton , ON L8S 4M1 , Canada .
| | - Jinfeng Huang
- Department of Chemistry and Chemical Biology , McMaster University , Hamilton , ON L8S 4M1 , Canada
| | - Chris P Verschoor
- Department of Health Research Methods, Evidence, and Impact (HEI) , McMaster University , Hamilton , ON L8S 4M1 , Canada
| | - Giuseppe Melacini
- Department of Biochemistry and Biomedical Sciences , McMaster University , Hamilton , ON L8S 4M1 , Canada . .,Department of Chemistry and Chemical Biology , McMaster University , Hamilton , ON L8S 4M1 , Canada
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25
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Falahati M, Attar F, Sharifi M, Haertlé T, Berret JF, Khan RH, Saboury AA. A health concern regarding the protein corona, aggregation and disaggregation. Biochim Biophys Acta Gen Subj 2019; 1863:971-991. [PMID: 30802594 PMCID: PMC7115795 DOI: 10.1016/j.bbagen.2019.02.012] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 12/23/2018] [Accepted: 02/19/2019] [Indexed: 01/03/2023]
Abstract
Nanoparticle (NP)-protein complexes exhibit the "correct identity" of NP in biological media. Therefore, protein-NP interactions should be closely explored to understand and modulate the nature of NPs in medical implementations. This review focuses mainly on the physicochemical parameters such as dimension, surface chemistry, morphology of NPs, and influence of pH on the formation of protein corona and conformational changes of adsorbed proteins by different kinds of techniques. Also, the impact of protein corona on the colloidal stability of NPs is discussed. Uncontrolled protein attachment on NPs may bring unwanted impacts such as protein denaturation and aggregation. In contrast, controlled protein adsorption by optimal concentration, size, pH, and surface modification of NPs may result in potential implementation of NPs as therapeutic agents especially for disaggregation of amyloid fibrils. Also, the effect of NPs-protein corona on reducing the cytotoxicity and clinical implications such as drug delivery, cancer therapy, imaging and diagnosis will be discussed. Validated correlative physicochemical parameters for NP-protein corona formation frequently derived from protein corona fingerprints of NPs which are more valid than the parameters obtained only on the base of NP features. This review may provide useful information regarding the potency as well as the adverse effects of NPs to predict their behavior in vivo.
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Affiliation(s)
- Mojtaba Falahati
- Department of Nanotechnology, Faculty of Advanced Science and Technology, TehranMedical Sciences, Islamic Azad University, Tehran, Iran.
| | - Farnoosh Attar
- Department of Biology, Faculty of Food Industry & Agriculture, Standard Research Institute (SRI), Karaj, Iran
| | - Majid Sharifi
- Department of Nanotechnology, Faculty of Advanced Science and Technology, TehranMedical Sciences, Islamic Azad University, Tehran, Iran
| | - Thomas Haertlé
- UR1268, Biopolymers Interactions Assemblies, INRA, BP 71627, 44316 Nantes Cedex 3, France; Poznan University of Life Sciences, Department of Animal Nutrition and Feed Management, ul.Wołyńska 33, 60-637 Poznań, Poland; Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Jean-François Berret
- Matière etSystèmes Complexes, UMR 7057 CNRS Université Denis Diderot Paris-VII, Bâtiment Condorcet, 10 rue Alice Domon et LéonieDuquet, F-75205 Paris, France
| | - Rizwan Hasan Khan
- Molecular Biophysics and Biophysical Chemistry Group, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Ali Akbar Saboury
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
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26
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A Peptide-Nanoparticle System with Improved Efficacy against Multidrug Resistant Bacteria. Sci Rep 2019; 9:4485. [PMID: 30872680 PMCID: PMC6418133 DOI: 10.1038/s41598-019-41005-7] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 02/27/2019] [Indexed: 11/08/2022] Open
Abstract
The recent rise of multidrug resistant microbial strains requires development of new and novel therapeutic alternatives. In this study, we present a novel antibacterial system that comprises of modified naturally abundant antimicrobial peptides in conjugation with silver nanoparticles. Further, we propose a simple route to incorporate a cysteine residue either at the N- or C-terminal of the parent peptide. Tagging a cysteine residue at the terminals not only enhances the binding propensity of the resultant peptide with the silver nanoparticle, but also increases its antimicrobial property against several pathogenic bacterial strains including K. pneumoniae. The minimum inhibitory concentration (MIC) values of the cysteine tagged nanoconjugates were obtained in the range of 5-15 μM compared to 50 μM for peptides devoid of the cysteines. The origin and mechanism of such improved activity of the conjugates were investigated using NMR spectroscopy and molecular dynamics (MD) simulations. The application of 13C-isotope labelled media to track the metabolic lifecycle of E. coli cells provided further insights into the system. MD simulations showed that pore formation in membrane bilayer is mediated through a hydrophobic collapse mechanism. The design strategy described herein opens up new-avenues for using biocompatible nanomedicines as a potential alternative to conventional antibiotics.
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27
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Cao S, Chung S, Kim S, Li Z, Manor D, Buck M. K-Ras G-domain binding with signaling lipid phosphatidylinositol (4,5)-phosphate (PIP2): membrane association, protein orientation, and function. J Biol Chem 2019; 294:7068-7084. [PMID: 30792310 DOI: 10.1074/jbc.ra118.004021] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 12/12/2018] [Indexed: 12/14/2022] Open
Abstract
Ras genes potently drive human cancers, with mutated proto-oncogene GTPase KRAS4B (K-Ras4B) being the most abundant isoform. Targeted inhibition of oncogenic gene products is considered the "holy grail" of present-day cancer therapy, and recent discoveries of small-molecule KRas4B inhibitors were made thanks to a deeper understanding of the structure and dynamics of this GTPase. Because interactions with biological membranes are key for Ras function, Ras-lipid interactions have become a major focus, especially because such interactions evidently involve both the Ras C terminus for lipid anchoring and its G-protein domain. Here, using NMR spectroscopy and molecular dynamics simulations complemented by biophysical- and cell-biology assays, we investigated the interaction between K-Ras4B with the signaling lipid phosphatidylinositol (4,5)-phosphate (PIP2). We discovered that the β2 and β3 strands as well as helices 4 and 5 of the GTPase G-domain bind to PIP2 and identified the specific residues in these structural elements employed in these interactions, likely occurring in two K-Ras4B orientation states relative to the membrane. Importantly, we found that some of these residues known to be oncogenic when mutated (D47K, D92N, K104M, and D126N) are critical for K-Ras-mediated transformation of fibroblast cells, but do not substantially affect basal and assisted nucleotide hydrolysis and exchange. Moreover, the K104M substitution abolished localization of K-Ras to the plasma membrane. The findings suggest that specific G-domain residues can critically regulate Ras function by mediating interactions with membrane-associated PIP2 lipids; these insights that may inform the future design of therapeutic reagents targeting Ras activity.
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Affiliation(s)
- Shufen Cao
- From the Departments of Physiology and Biophysics
| | | | | | - Zhenlu Li
- From the Departments of Physiology and Biophysics
| | - Danny Manor
- Nutrition, .,Pharmacology, and.,the Case Comprehensive Cancer Center and
| | - Matthias Buck
- From the Departments of Physiology and Biophysics, .,the Case Comprehensive Cancer Center and.,Neurosciences, Case Western Reserve University, School of Medicine, Cleveland, Ohio 44106 and.,Center for Proteomics and Bioinformatics, Case Western Reserve University, School of Medicine, Cleveland, Ohio 44106
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28
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Ceccon A, Tugarinov V, Clore GM. TiO 2 Nanoparticles Catalyze Oxidation of Huntingtin Exon 1-Derived Peptides Impeding Aggregation: A Quantitative NMR Study of Binding and Kinetics. J Am Chem Soc 2018; 141:94-97. [PMID: 30540190 DOI: 10.1021/jacs.8b11441] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Polyglutamine expansion within the N-terminal region of the huntingtin protein results in the formation of intracellular aggregates responsible for Huntington's disease, a fatal neurodegenerative condition. The interaction between TiO2 nanoparticles and huntingtin peptides comprising the N-terminal amphiphilic domain without (httNT) or with (httNTQ10) a ten-residue C-terminal polyglutamine tract, is investigated by NMR spectroscopy. TiO2 nanoparticles decrease aggregation of httNTQ10 by catalyzing the oxidation of Met7 to a sulfoxide, resulting in an aggregation-incompetent peptide. The oxidation agent is hydrogen peroxide generated on the surface of the TiO2 nanoparticles either by UV irradiation or at low steady-state levels in the dark. The binding kinetics of nonaggregating httNT to TiO2 nanoparticles is characterized by quantitative analysis of 15N dark state exchange saturation transfer and lifetime line broadening NMR data. Binding involves a sparsely populated intermediate that experiences hindered rotational diffusion relative to the free state. Catalysis of methionine oxidation within the N-terminal domain of the huntingtin protein may potentially provide a strategy for delaying the onset of Huntington's disease.
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Affiliation(s)
- Alberto Ceccon
- Laboratory of Chemical Physics , National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda , Maryland 20892-0520 , United States
| | - Vitali Tugarinov
- Laboratory of Chemical Physics , National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda , Maryland 20892-0520 , United States
| | - G Marius Clore
- Laboratory of Chemical Physics , National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda , Maryland 20892-0520 , United States
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29
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Zhang Y, Xu H, Casabianca LB. Interaction between cyanine dye IR-783 and polystyrene nanoparticles in solution. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2018; 56:1054-1060. [PMID: 29771468 DOI: 10.1002/mrc.4751] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 05/04/2018] [Accepted: 05/08/2018] [Indexed: 06/08/2023]
Abstract
The interactions between small molecule drugs or dyes and nanoparticles are important to the use of nanoparticles in medicine. Noncovalent adsorption of dyes on nanoparticle surfaces is also important to the development of nanoparticle dual-use imaging contrast agents. In this work, solution-state NMR is used to examine the noncovalent interaction between a near-infrared cyanine dye and the surface of polystyrene nanoparticles in solution. Using 1D proton NMR, we can approximate the number of dye molecules that associate with each nanoparticle for different sized nanoparticles. Saturation-Transfer Difference NMR was also used to show that protons near the positively charged nitrogen in the dye are more strongly associated with the negatively charged nanoparticle surface than protons near the negatively charged sulfate groups of the dye. The methods described here can be used to study similar drug or dye molecules interacting with the surface of organic nanoparticles.
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Affiliation(s)
- Yunzhi Zhang
- Department of Chemistry, Clemson University, Clemson, SC, USA
| | - Hui Xu
- Department of Chemistry, Clemson University, Clemson, SC, USA
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30
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Xie M, Li DW, Yuan J, Hansen AL, Brüschweiler R. Quantitative Binding Behavior of Intrinsically Disordered Proteins to Nanoparticle Surfaces at Individual Residue Level. Chemistry 2018; 24:16997-17001. [PMID: 30240067 DOI: 10.1002/chem.201804556] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Indexed: 11/11/2022]
Abstract
The quantitative and predictive understanding how intrinsically disordered proteins (IDPs) interact with engineered nanoparticles has potentially important implications for new therapeutics as well as nanotoxicology. Based on a recently developed solution 15 N NMR relaxation approach, the interactions between four representative IDPs with silica nanoparticles are reported at atomic detail. Each IDP possesses distinct binding modes, which can be quantitatively explained by the local amino-acid residue composition using a "free residue interaction model". The model was parameterized using the binding affinities of free proteinogenic amino acids along with long-range effects, derived by site-specific mutagenesis, that exponentially scale with distance along the primary sequence. The model, which is accessible through a web server, can be applied to predict the residue-specific binding affinities of a large number of IDPs.
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Affiliation(s)
- Mouzhe Xie
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA
| | - Da-Wei Li
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Jiaqi Yuan
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA
| | - Alexandar L Hansen
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Rafael Brüschweiler
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA.,Campus Chemical Instrument Center, The Ohio State University, Columbus, OH, 43210, USA.,Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, 43210, USA
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31
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Ceccon A, Clore GM, Tugarinov V. Decorrelating Kinetic and Relaxation Parameters in Exchange Saturation Transfer NMR: A Case Study of N-Terminal Huntingtin Peptides Binding to Unilamellar Lipid Vesicles. J Phys Chem B 2018; 122:11271-11278. [PMID: 30156416 DOI: 10.1021/acs.jpcb.8b07112] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dark state exchange saturation transfer (DEST) and lifetime line-broadening (Δ R2, the difference in the measured transverse relaxation rates for the observable species in the presence and absence of exchange with a species characterized by very large intrinsic transverse relaxation rates) have proven to be powerful NMR tools for studying exchange phenomena between a NMR visible species and a high-molecular weight, "dark", NMR invisible state. However, in the exchange regime, where the transverse spin relaxation rates in the bound state ( R2bound) are smaller than the strength of the DEST saturation radio frequency field, typically corresponding to systems below ∼6 MDa, the combination of DEST and Δ R2 data, while sufficient to define the apparent association rate constant, cannot unambiguously determine the population of the bound state pB and R2bound values independently. We show that the latter exchange and relaxation parameters can be decorrelated by the measurement of the maximal value of the contribution of the fast-relaxing magnetization component to the total NMR signal, Cfastmax, an observable that is directly proportional to pB. When integrated into the analysis of DEST/Δ R2 data, Cfastmax provides an indispensable source of information for quantitative studies of exchange involving high-molecular-weight dark states. We demonstrate the utility of this approach by investigating the binding kinetics of two huntingtin exon-1-derived peptides to small unilamellar lipid vesicles (SUV), ∼ 31 nm in diameter and 4.3 MDa in molecular weight. The interaction of the N-terminal amphiphilic domain of huntingtin exon-1 with membrane surfaces promotes polyglutamine-mediated aggregation and, as such, is thought to play a role in the etiology of Huntington's disease, an autosomal dominant fatal neurodegenerative condition. The first peptide comprises the 16-residue N-terminal amphiphilic domain (httNT) alone, while the second contains an additional seven residue polyglutamine tract at the C-terminus (httNTQ7). At a peptide-to-lipid molar ratio of 1:4, the population of peptide bound to the SUV surface is substantial, ∼ 7-8%, while exchange between the free and SUV-bound peptide is slow on the relaxation time-scale ( kex ∼ 200 s-1). The last two C-terminal residues of httNT and the last 9 of httNTQ7 remain flexible in the SUV-bound form due to transient detachment from the lipid surface that occurs on a time-scale several-fold faster than binding.
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Affiliation(s)
- Alberto Ceccon
- Laboratory of Chemical Physics , National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda , Maryland 20892-0520 , United States
| | - G Marius Clore
- Laboratory of Chemical Physics , National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda , Maryland 20892-0520 , United States
| | - Vitali Tugarinov
- Laboratory of Chemical Physics , National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda , Maryland 20892-0520 , United States
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Ajdary M, Moosavi MA, Rahmati M, Falahati M, Mahboubi M, Mandegary A, Jangjoo S, Mohammadinejad R, Varma RS. Health Concerns of Various Nanoparticles: A Review of Their in Vitro and in Vivo Toxicity. NANOMATERIALS 2018; 8:nano8090634. [PMID: 30134524 PMCID: PMC6164883 DOI: 10.3390/nano8090634] [Citation(s) in RCA: 137] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 08/13/2018] [Accepted: 08/15/2018] [Indexed: 01/01/2023]
Abstract
Nanoparticles (NPs) are currently used in diagnosis and treatment of many human diseases, including autoimmune diseases and cancer. However, cytotoxic effects of NPs on normal cells and living organs is a severe limiting factor that hinders their use in clinic. In addition, diversity of NPs and their physico-chemical properties, including particle size, shape, surface area, dispersity and protein corona effects are considered as key factors that have a crucial impact on their safe or toxicological behaviors. Current studies on toxic effects of NPs are aimed to identify the targets and mechanisms of their side effects, with a focus on elucidating the patterns of NP transport, accumulation, degradation, and elimination, in both in vitro and in vitro models. NPs can enter the body through inhalation, skin and digestive routes. Consequently, there is a need for reliable information about effects of NPs on various organs in order to reveal their efficacy and impact on health. This review covers the existing knowledge base on the subject that hopefully prepares us better to address these challenges.
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Affiliation(s)
- Marziyeh Ajdary
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran P.O. Box 1449614525, Iran.
| | - Mohammad Amin Moosavi
- Department of Molecular Medicine, National Institute of Genetic Engineering and Biotechnology, Tehran P.O Box 14965/161, Iran.
| | - Marveh Rahmati
- Cancer Biology Research Center, Cancer Institute of Iran, Tehran University of Medical Sciences, Tehran P.O. Box 13145-158, Iran.
| | - Mojtaba Falahati
- Department of Nanotechnology, Faculty of Advance Science and Technology, Pharmaceutical Sciences Branches, Islamic Azad University of Tehran, Tehran P.O. Box 1916893813, Iran.
| | - Mohammad Mahboubi
- Department of Midwifery and Reproductive Health, Faculty of Nursing and Midwifery, Abadan School of Medical Sciences, Abadan P.O. Box 517, Iran.
| | - Ali Mandegary
- Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman P.O. Box 1355576169, Iran.
- Neuroscience Research Center, Institute of Neuropharmacology, and Department of Pharmacology & Toxicology, School of Pharmacy, Kerman University of Medical Sciences, Kerman P.O. Box 7616911319, Iran.
| | - Saranaz Jangjoo
- School of Medicine, International Branch, Shiraz University of Medical Sciences, Shiraz 7134845794, Iran.
| | - Reza Mohammadinejad
- Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman P.O. Box 1355576169, Iran.
| | - Rajender S Varma
- Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University in Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic.
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Robson T, Shah DSH, Solovyova AS, Lakey JH. Modular Protein Engineering Approach to the Functionalization of Gold Nanoparticles for Use in Clinical Diagnostics. ACS APPLIED NANO MATERIALS 2018; 1:3590-3599. [PMID: 30101217 PMCID: PMC6083416 DOI: 10.1021/acsanm.8b00737] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 06/28/2018] [Indexed: 05/21/2023]
Abstract
Functional protein-gold nanoparticle (AuNP) conjugates have a wide variety of applications including biosensing and drug delivery. Correct protein orientation, which is important to maintain functionality on the nanoparticle surface, can be difficult to achieve in practice, and dedicated protein scaffolds have been used on planar gold surfaces to drive the self-assembly of oriented protein arrays. Here we use the transmembrane domain of Escherichia coli outer membrane protein A (OmpATM) to create protein-AuNP conjugates. The addition of a single cysteine residue into a periplasmic loop, to create cysOmpATM, drives oriented assembly and increased equilibrium binding. As the protein surface concentration increases, the sulfur-gold bond in cysOmpATM creates a more densely populated AuNP surface than the poorly organized wtOmpATM layer. The functionalization of AuNP improved both their stability and homogeneity. This was further exploited using multidomain protein chimeras, based on cysOmpATM, which were shown to form ordered protein arrays with their functional domains displayed away from the AuNP surface. A fusion with protein G was shown to specifically bind antibodies via their Fc region. Next, an in vitro selected single chain antibody (scFv)-cysOmpATM fusion protein, bound to AuNP, detected influenza A nucleoprotein, a widely used antigen in diagnostic assays. Finally, using the same scFv-cysOmpATM-AuNP conjugates, a prototype lateral flow assay for influenza demonstrated the utility of fully recombinant self-assembling sensor layers. By simultaneously removing the need for both animal antibodies and a separate immobilization procedure, this technology could greatly simplify the development of a range of in vitro diagnostics.
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Affiliation(s)
- Timothy Robson
- Institute
for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle
upon Tyne NE2 4HH, U.K.
| | - Deepan S. H. Shah
- Orla
Protein Technologies Ltd., Biosciences Centre, International Centre for Life, Times Square, Newcastle upon Tyne NE1 4EP, U.K.
| | - Alexandra S. Solovyova
- Institute
for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle
upon Tyne NE2 4HH, U.K.
| | - Jeremy H. Lakey
- Institute
for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle
upon Tyne NE2 4HH, U.K.
- E-mail:
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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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Qiu TA, Clement PL, Haynes CL. Linking nanomaterial properties to biological outcomes: analytical chemistry challenges in nanotoxicology for the next decade. Chem Commun (Camb) 2018; 54:12787-12803. [DOI: 10.1039/c8cc06473c] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This article provides our perspective on the analytical challenges in nanotoxicology as the field is entering its third decade.
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Affiliation(s)
- Tian A. Qiu
- Department of Chemistry
- University of Minnesota
- Minneapolis
- USA
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Munari F, Bortot A, Assfalg M, D'Onofrio M. Alzheimer's disease-associated ubiquitin mutant Ubb +1: Properties of the carboxy-terminal domain and its influence on biomolecular interactions. Int J Biol Macromol 2017; 108:24-31. [PMID: 29175520 DOI: 10.1016/j.ijbiomac.2017.11.121] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 11/17/2017] [Accepted: 11/19/2017] [Indexed: 12/19/2022]
Abstract
Ubb+1, a ubiquitin (Ub) mutant protein originating from misreading of the Ub B gene, is found accumulated in brain tissues of Alzheimer's disease patients. The mutant attracts strong interest due to its possible participation in the molecular events leading to neurodegeneration. Ubb+1 is composed of the globular domain of Ub, linked to a 19-residue C-terminal peptide. Based on NMR relaxation and solvent accessibility measurements we obtained new insight into the molecular properties of Ubb+1. We further determined the thermal stability of Ubb+1 in the monomeric form, and in Lys48- and Lys63-linked dimers. Finally, we explored the influence of the C-terminal fragment on the interactions of Ubb+1 with an isolated UBA2 domain and with membrane mimics. Our data indicate that the C-terminal fragment of Ubb+1 is overall highly flexible, except for a short stretch which appears less solvent-exposed. While influencing the hydrodynamic properties of the globular domain, the fragment does not establish long-lived interactions with the globular domain. It results that the structure and stability of Ub are minimally perturbed by the peptide extension. However, binding to UBA2 and to membrane mimics are both affected, exemplifying possible changes in biomolecular recognition experienced by the disease-associated Ubb+1 compared to the wild-type protein.
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Affiliation(s)
- Francesca Munari
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Andrea Bortot
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Michael Assfalg
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
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37
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Chen D, Ganesh S, Wang W, Amiji M. Plasma protein adsorption and biological identity of systemically administered nanoparticles. Nanomedicine (Lond) 2017; 12:2113-2135. [DOI: 10.2217/nnm-2017-0178] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Although a variety of nanoparticles (NPs) have been used for drug delivery applications, their surfaces are immediately covered by plasma protein corona upon systemic administration. As a result, the adsorbed proteins create a unique biological identity of the NPs that lead to unpredictable performance. The protein corona on NPs could also impede active targeting, induce off-target effects, trigger particle clearance and even provoke toxicity. This article reviews the fundamentals of NP–plasma protein interaction, the consequences of the interactions, and provides insights into the correlations of protein corona with biodistribution and cellular delivery. We hope that this review will trigger additional questions and possible solutions that lead to more favorable developments in NP-based targeted delivery systems.
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Affiliation(s)
- Dongyu Chen
- Department of Pharmaceutical Sciences, School of Pharmacy, Northeastern University, Boston, MA 02115, USA
| | - Shanthi Ganesh
- Department of Pre-Clinical Oncology, Dicerna Pharmaceuticals, Inc., Cambridge, MA 02140, USA
| | - Weimin Wang
- Department of Chemistry and Formulation, Dicerna Pharmaceuticals, Inc., Cambridge, MA 02140, USA
| | - Mansoor Amiji
- Department of Pharmaceutical Sciences, School of Pharmacy, Northeastern University, Boston, MA 02115, USA
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Abstract
We present a novel method that breaks the resolution barrier in nuclear magnetic resonance (NMR) spectroscopy, allowing one to accurately estimate the chemical shift values of highly overlapping or broadened peaks. This problem is routinely encountered in NMR when peaks have large linewidths due to rapidly decaying signals, hindering its application. We address this problem based on the notion of finite-rate-of-innovation (FRI) sampling, which is based on the premise that signals such as the NMR signal, can be accurately reconstructed using fewer measurements than that required by existing approaches. The FRI approach leads to super-resolution, beyond the limits of contemporary NMR techniques. Using this method, we could measure for the first time small changes in chemical shifts during the formation of a Gold nanorod-protein complex, facilitating the quantification of the strength of such interactions. The method thus opens up new possibilities for the application and acceleration of multidimensional NMR spectroscopy across a wide range of systems.
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39
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Ahmed R, VanSchouwen B, Jafari N, Ni X, Ortega J, Melacini G. Molecular Mechanism for the (-)-Epigallocatechin Gallate-Induced Toxic to Nontoxic Remodeling of Aβ Oligomers. J Am Chem Soc 2017; 139:13720-13734. [PMID: 28841302 DOI: 10.1021/jacs.7b05012] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
(-)-Epigallocatechin gallate (EGCG) effectively reduces the cytotoxicity of the Alzheimer's disease β-amyloid peptide (Aβ) by remodeling seeding-competent Aβ oligomers into off-pathway seeding-incompetent Aβ assemblies. However, the mechanism of EGCG-induced remodeling is not fully understood. Here we combine 15N and 1H dark-state exchange saturation transfer (DEST), relaxation, and chemical shift projection NMR analyses with fluorescence, dynamic light scattering, and electron microscopy to elucidate how EGCG remodels Aβ oligomers. We show that the remodeling adheres to a Hill-Scatchard model whereby the Aβ(1-40) self-association occurs cooperatively and generates Aβ(1-40) oligomers with multiple independent binding sites for EGCG with a Kd ∼10-fold lower than that for the Aβ(1-40) monomers. Upon binding to EGCG, the Aβ(1-40) oligomers become less solvent exposed, and the β-regions, which are involved in direct monomer-protofibril contacts in the absence of EGCG, undergo a direct-to-tethered contact shift. This switch toward less engaged monomer-protofibril contacts explains the seeding incompetency observed upon EGCG remodeling and suggests that EGCG interferes with secondary nucleation events known to generate toxic Aβ assemblies. Unexpectedly, the N-terminal residues experience an opposite EGCG-induced shift from tethered to direct contacts, explaining why EGCG remodeling occurs without release of Aβ(1-40) monomers. We also show that upon binding Aβ(1-40) oligomers the relative positions of the EGCG B and D rings change with respect to that of ring A. These distinct structural changes occurring in both Aβ(1-40) oligomers and EGCG during remodeling offer a foundation for understanding the molecular mechanism of EGCG as a neurotoxicity inhibitor. Furthermore, the results reported here illustrate the effectiveness of DEST-based NMR approaches in investigating the mechanism of low-molecular-weight amyloid inhibitors.
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Affiliation(s)
- Rashik Ahmed
- Department of Biochemistry and Biomedical Sciences and ‡Department of Chemistry and Chemical Biology, McMaster University , 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
| | - Bryan VanSchouwen
- Department of Biochemistry and Biomedical Sciences and ‡Department of Chemistry and Chemical Biology, McMaster University , 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
| | - Naeimeh Jafari
- Department of Biochemistry and Biomedical Sciences and ‡Department of Chemistry and Chemical Biology, McMaster University , 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
| | - Xiaodan Ni
- Department of Biochemistry and Biomedical Sciences and ‡Department of Chemistry and Chemical Biology, McMaster University , 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
| | - Joaquin Ortega
- Department of Biochemistry and Biomedical Sciences and ‡Department of Chemistry and Chemical Biology, McMaster University , 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
| | - Giuseppe Melacini
- Department of Biochemistry and Biomedical Sciences and ‡Department of Chemistry and Chemical Biology, McMaster University , 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
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40
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Egner TK, Naik P, Nelson NC, Slowing II, Venditti V. Mechanistic Insight into Nanoparticle Surface Adsorption by Solution NMR Spectroscopy in an Aqueous Gel. Angew Chem Int Ed Engl 2017. [PMID: 28640513 DOI: 10.1002/anie.201704471] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Engineering nanoparticle (NP) functions at the molecular level requires a detailed understanding of the dynamic processes occurring at the NP surface. Herein we show that a combination of dark-state exchange saturation transfer (DEST) and relaxation dispersion (RD) NMR experiments on gel-stabilized NP samples enables the accurate determination of the kinetics and thermodynamics of adsorption. We used the former approach to describe the interaction of cholic acid (CA) and phenol (PhOH) with ceria NPs with a diameter of approximately 200 nm. Whereas CA formed weak interactions with the NPs, PhOH was tightly bound to the NP surface. Interestingly, we found that the adsorption of PhOH proceeds via an intermediate, weakly bound state in which the small molecule has residual degrees of rotational diffusion. We believe the use of aqueous gels for stabilizing NP samples will increase the applicability of solution NMR methods to the characterization of nanomaterials.
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Affiliation(s)
- Timothy K Egner
- Department of Chemistry, Iowa State University, 2438 Pammel Drive, Ames, IA, 50011, USA
| | - Pranjali Naik
- Department of Chemistry, Iowa State University, 2438 Pammel Drive, Ames, IA, 50011, USA.,US Department of Energy, Ames Laboratory, 2756 Gilman Hall, Ames, IA, 50011, USA
| | - Nicholas C Nelson
- Department of Chemistry, Iowa State University, 2438 Pammel Drive, Ames, IA, 50011, USA.,US Department of Energy, Ames Laboratory, 2756 Gilman Hall, Ames, IA, 50011, USA
| | - Igor I Slowing
- Department of Chemistry, Iowa State University, 2438 Pammel Drive, Ames, IA, 50011, USA.,US Department of Energy, Ames Laboratory, 2756 Gilman Hall, Ames, IA, 50011, USA
| | - Vincenzo Venditti
- Department of Chemistry, Iowa State University, 2438 Pammel Drive, Ames, IA, 50011, USA
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41
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Egner TK, Naik P, Nelson NC, Slowing II, Venditti V. Mechanistic Insight into Nanoparticle Surface Adsorption by Solution NMR Spectroscopy in an Aqueous Gel. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201704471] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Timothy K. Egner
- Department of Chemistry Iowa State University 2438 Pammel Drive Ames IA 50011 USA
| | - Pranjali Naik
- Department of Chemistry Iowa State University 2438 Pammel Drive Ames IA 50011 USA
- US Department of Energy Ames Laboratory 2756 Gilman Hall Ames IA 50011 USA
| | - Nicholas C. Nelson
- Department of Chemistry Iowa State University 2438 Pammel Drive Ames IA 50011 USA
- US Department of Energy Ames Laboratory 2756 Gilman Hall Ames IA 50011 USA
| | - Igor I. Slowing
- Department of Chemistry Iowa State University 2438 Pammel Drive Ames IA 50011 USA
- US Department of Energy Ames Laboratory 2756 Gilman Hall Ames IA 50011 USA
| | - Vincenzo Venditti
- Department of Chemistry Iowa State University 2438 Pammel Drive Ames IA 50011 USA
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42
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Ceccon A, Tugarinov V, Boughton AJ, Fushman D, Clore GM. Probing the Binding Modes of a Multidomain Protein to Lipid-based Nanoparticles by Relaxation-based NMR. J Phys Chem Lett 2017; 8:2535-2540. [PMID: 28530812 PMCID: PMC5576874 DOI: 10.1021/acs.jpclett.7b01019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The interactions of two model multidomain proteins-covalently linked diubiquitins, Ub2-with lipid-based nanoparticles have been quantitatively probed by the measurements of NMR lifetime line broadening, ΔR2. By combined analysis of ΔR2 profiles arising from interactions with liposomes of varying sizes, an approach recently developed for the characterization of interactions of monoubiquitin with liposomes, we determine how the parameters of exchange (liposome binding) and dynamics of each individual domain of Ub2 on the surface of liposomes change when the domains are covalently attached to one another by a flexible linker. Two different covalent linkages were used: K63-linked and K48-linked Ub2. The possibility of three distinct modes of binding of Ub2 to liposomes requires the introduction of simple but important modifications to the strategy of analysis originally developed for monoubiquitin.
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Affiliation(s)
- Alberto Ceccon
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - Vitali Tugarinov
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
- Corresponding Authors: G.M.C.: ., V.T.:
| | - Andrew J. Boughton
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, Maryland 20742-4454, United States
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, Maryland 20742-4454, United States
| | - G. Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
- Corresponding Authors: G.M.C.: ., V.T.:
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43
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Pal I, Brahmkhatri VP, Bera S, Bhattacharyya D, Quirishi Y, Bhunia A, Atreya HS. Enhanced stability and activity of an antimicrobial peptide in conjugation with silver nanoparticle. J Colloid Interface Sci 2016; 483:385-393. [DOI: 10.1016/j.jcis.2016.08.043] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/18/2016] [Accepted: 08/18/2016] [Indexed: 11/27/2022]
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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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45
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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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Ceccon A, Marius Clore G, Tugarinov V. Towards interpretation of intermolecular paramagnetic relaxation enhancement outside the fast exchange limit. JOURNAL OF BIOMOLECULAR NMR 2016; 66:1-7. [PMID: 27558624 DOI: 10.1007/s10858-016-0053-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 08/12/2016] [Indexed: 06/06/2023]
Abstract
In an exchanging system between major and minor species, the transverse paramagnetic relaxation enhancement rate observed on the resonances of the major species (Γ 2 (app) ) is dependent upon the exchange regime between the species. Quantitative analysis of PRE data in such systems typically assumes that the overall exchange rate k ex between the species is fast on the PRE time scale (k ex ≫ Γ2). Recently, we have characterized the kinetics of binding of the model protein ubiquitin to large (LUV) and small (SUV) unilamellar lipid-based nanoparticles or liposomes (Ceccon A, Tugarinov V, Bax A, Clore GM (2016). J Am Chem Soc 138:5789-5792). Building upon these results and taking advantage of a strong paramagnetic agent with an isotropic g-tensor, Gd(3+), we were able to measure intermolecular methyl carbon and proton PREs between paramagnetically-tagged liposomes and ubiquitin. In the limit of fast exchange (k ex ≫ Γ2) the ratio of the apparent proton to carbon methyl PREs, ((1)Hm-Γ 2 (app) )/((13)Cm-Γ 2 (app) ), is equal to the square of the ratio of the gyromagnetic ratios of the two nuclei, (γΗ/γC)(2). However, outside the fast exchange regime, under intermediate exchange conditions (e.g. when Γ2 is comparable in magnitude to k ex) the ((1)Hm-Γ 2 (app) )/((13)Cm-Γ 2 (app) ) ratio provides a reliable measure of the 'true' methyl PREs.
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Affiliation(s)
- Alberto Ceccon
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA
| | - G Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA.
| | - Vitali Tugarinov
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA.
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Mondal S, Thirupathi R, Rao LP, Atreya HS. Unraveling the dynamic nature of protein–graphene oxide interactions. RSC Adv 2016. [DOI: 10.1039/c6ra03759c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The globular protein ubiquitin interacts with graphene oxide and undergoes dynamic and reversible association–dissociation as revealed by NMR spectroscopy.
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Affiliation(s)
- Somnath Mondal
- NMR Research Centre
- Indian Institute of Science
- Bangalore-560012
- India
- Solid State and Structural Chemistry Unit
| | - Ravula Thirupathi
- NMR Research Centre
- Indian Institute of Science
- Bangalore-560012
- India
- Solid State and Structural Chemistry Unit
| | - Lokeswara P. Rao
- NMR Research Centre
- Indian Institute of Science
- Bangalore-560012
- India
- Department of Physics
| | - Hanudatta S. Atreya
- NMR Research Centre
- Indian Institute of Science
- Bangalore-560012
- India
- Solid State and Structural Chemistry Unit
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